gebhart/patrepeval huggingface dataset:
Consistency Penalized Graph Matching for Image-Based Identification of Dendritic Patterns (2020)

Recently, physically unclonable functions (PUFs) have received considerable attention from the research community due to their potential use in security mechanisms for applications such as the Internet of things (IoT). The concept generally employs the fabrication variability and naturally embedded randomness of device characteristics for secure identification. This approach complements and improves upon the conventional cryptographic security algorithms by covering their vulnerability against counterfeiting, cloning attacks, and physical hijacking. In this work, we propose a new identification/authentication mechanism based on a specific implementation of optical PUFs based on electrochemically formed dendritic patterns. Dendritic tags are built by growing unique, complex, and unclonable nano-scaled metallic patterns on highly nonreactive substrates using electrolyte solutions. Dendritic patterns with 3D surfaces are technically impossible to reproduce, hence they can be used as the fingerprints of objects. Current optical PUF-based identification mechanisms rely on image processing methods that require high-complexity computations and massive storage and communication capacity to store and exchange high-resolution image databases in large-scale networks. To address these issues, we propose a light-weight identification algorithm that converts the images of dendritic patterns into representative graphs and uses a graph-matching approach for device identification. More specifically, we develop a probabilistic graph matching algorithm that makes linkages between the similar feature points in the test and reference graphs while considering the consistency of their local subgraphs. The proposed method demonstrates a high level of accuracy in the presence of imaging artifacts, noise, and skew compared to existing image-based algorithms. The computational complexity of the algorithm grows linearly with the number of extracted feature points and is therefore suitable for large-scale networks.
Effect of N-doping on Performance and Durability of Supported PtRu Direct Methanol Fuel Cell Catalyst (2012)

Abstract not Available.
Separation Logic Verification of C Programs with an SMT Solver (2009)

This paper presents a methodology for automated modular verification of C programs against specifications written in separation logic. The distinguishing features of the approach are representation of the C memory model in separation logic by means of rewrite rules suitable for automation and the careful integration of an SMT solver behind the separation logic prover to guide the proof search.
Cell biology as the centuries change (2007)

It was in an article at the turn of the millennium that former Editor of JCS Rick Horwitz first cautioned about the short memories of modern cell biologists ([Horwitz, 2000][1]). Indeed it is all too easy to dismiss early hypotheses of cell function as naive and assume that, without the arsenal of
Abstracts from Proceedings of the Society of Hematologic Oncology 2015 Annual Meeting (2015)

Context: Identification of prognostic factors in ALL patients is most important for stratifying patients into risk groups and “tailoring” treatment accordingly. Molecular and cytogenetic abnormalities are the most important prognostic factors. Minimal residual disease (MRD) is also an important predictor of relapse in ALL. However, correlation of both prognostic variables has not been thoroughly studied. Objective: In this study we investigated the correlation between defined cytogenetic abnormalities and selected new MRD markers (CD79b, CD123 and CD200). Design: The expression profile of a selected group of CDs (CD123, CD79b and CD200) was combined with cytogenetic profiling to define and characterize the underlying genetic changes in B-ALL patients. Follow up of patients by MRD monitoring was continued for 6 months to validate CDs expression profile. Patients and Settings: 40 newly diagnosed Egyptian pediatric B-ALL patients, presented to NCI’ pediatric oncology outpatient clinic, were included in this study. Interventions: CDs expression and MRD monitoring were studied using 4 colors flowcytometry analyzer, while cytogenetic methods included Karyotyping, DNA index, FISH and PCR. Results: CD123 found to be expressed in 45% of patients and CD200 was expressed in 82.5% of them, while CD79b was negative in 32.5% of patients. MRD analysis during treatment showed stable expression patterns of CD200. There was significant association of CD123 expression with hyperdiploid-ALL group (P¼0.039). Another association (P¼0.031) was found between CD79b negativity and t(12;21) group. CD200 was widely expressed inallgroups.Conclusions: There is a significant correlation between some markers and certain ALL’ recurrent cytogenetic subgroups (CD123 and hyperdiploidy, CD79b negativity and ETV-RUNX1 group) denotes good prognostic value. CD200 can be used as MRD markers in ALL patients and also can serve as therapy targets.
Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies (2005)

These results present a detailed characterization of a unique set of genes, which can be used to assess the hESC differentiation.
Abstract 1397: Collagen COL26A1 promotes papillary thyroid cancer invasion and metastasis and correlates with poor survival and clinical outcomes (2023)

Abstract Papillary thyroid cancer (PTC) is the most common cancer in women under 25 years of age and is increasing in incidence. While PTC is often slow-growing and surgically resectable, recurrence years to decades after initial surgery occurs in ~20% of patients (now only in their 40s/50s), with mortality of 38-69%. The identification of both prognostic biomarkers and actionable therapeutic targets for high-risk PTC at diagnosis is critically important and an unmet need. RNASeq analysis of 45 PTC and matched normal patient tissues from our biobank identified collagen 26A1 (COL26A1) as significantly upregulated in patients with higher risk extrathyroidal extension, lymph node metastasis, and multifocal tumors, compared to those with localized disease. Kaplan Meier survival curves of The Cancer Genome Atlas (TCGA) data confirmed that increased COL26A1 expression significantly decreases survival probability by 25% (p=0.0086). Further analyses of TCGA data indicated that COL26A1 expression significantly correlated with clinical attributes including MACIS score (q=0.001), differentiation score (q=0.025), and tumor stage (q=0.025). Data from our in vitro culture PTC model system indicated that COL26A1 expression was increased 3X in PTC cell line K1, compared to immortalized “normal” thyroid epithelial cells, NThy-ori-3-1. Two CRISPR guides designed to target COL26A1 introduced into K1 resulted in repression of COL26A1 RNA and protein levels by 50% and 70%, respectively. COL26A1 repression decreased critical tumor phenotypes of aggressiveness and metastasis including proliferation (30%), clonogenicity (33%), anchorage-independent growth (37%), cell motility (43%), invasion (30%) and migration (33%). Cell-to-cell adhesion and cell-matrix adhesion also decreased (36% and 25%, respectively). Thus, COL26A1 may have use as a prognostic marker and actionable target for small molecule inhibitors in PTC. Citation Format: Michelle Carnazza, Danielle Quaranto, Nicole DeSouza, Sina Dadafarin, Augustine Moscatello, Jan Geliebter, Raj K. Tiwari. Collagen COL26A1 promotes papillary thyroid cancer invasion and metastasis and correlates with poor survival and clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1397.
The effect of intracrystalline chain dynamics on melting and reorganization during heating in semicrystalline polymers (2020)

Using Fast Scanning Calorimetry we investigate the effect of intracrystalline chain dynamics on melting, recrystallization and crystal reorganization during heating, whereby we employ polyethyleneoxide (PEO) and polycaprolactone (PCL) as model polymers with and without such dynamics. We show that in PCL marginally stable crystallites form during isothermal crystallization, which melt immediately upon heating. During further heating continuous melting and recrystallization occurs. At low crystallization temperatures PEO shows a similar behavior, as the intracrystalline dynamics is strongly slowed down. However, during heating the intracrystalline chain dynamics becomes faster leading to fast lamellar thickening and increased thermal stability, until final melting occurs at some high temperature. Our observations demonstrate that melting, recrystallization, and reorganization are competing kinetic processes occurring during heating in semicrystalline polymers. These characteristics cannot be observed by conventional DSC due to low scanning rates and low accessible supercooling. The consequences for the Hoffman–Weeks analysis of polymer melting temperatures are discussed.
Sensemaking (2008)

When confronted with a large or complex amount of information, how DO people come to understand it? This workshop will focus on the most recent work in sensemaking, the activities, technologies and behaviors that people do when making sense of their complex information spaces.
Cambiarenes: Single-Step Synthesis and Anion Binding of a Clip- Shaped Macrocycle with a Redox-Active Core (2019)

We report the synthesis of a novel macrocyclic host molecule that forms in a single step from commercially available starting materials. The core of the macrocycle backbone possesses two quinone rings and, thus, is redox-active. Host-guest binding involving the clip-shaped cavity indicates selective binding of pyridine N-oxides based of the electron density of and steric bulk of the anionic oxygen.
Effect of Surface Properties on Boiling Heat Transfer Characteristics in Micro-Channel Vapor Generator (2004)

The reformer fuel cell vehicle requires high heat exchange efficiency and low heat capacity to meet powertrain requirements for quick response and compactness. The use of a micro-channel type of vapor generator for the reformer is one possible approach to meeting these requirements. However, as reported in previous studies, the characteristics of evaporation in the micro-channel are completely different from those of poll boiling. The effects of wettability of heating surface on heat transfer characteristics in the micro channel were experimentally evaluated and an attempt was made to deduce the mechanism that would explain how differences in surface properties influence heat transfer characteristics. Under the experimental conditions used in this study, it was confirmed that wettability has an effect on heat transfer characteristics in the micro channel and that an improvement in wettability leads to more efficient heat transfer characteristics.
Hybrid achromatic microlenses with high numerical apertures and focusing efficiencies across the visible (2023)

Compact visible wavelength achromats are essential for miniaturized and lightweight optics. However, fabrication of such achromats has proved to be exceptionally challenging. Here, using subsurface 3D printing inside mesoporous hosts we densely integrate aligned refractive and diffractive elements, forming thin high performance hybrid achromatic imaging micro-optics. Focusing efficiencies of 51-70% are achieved for 15μm thick, 90μm diameter, 0.3 numerical aperture microlenses. Chromatic focal length errors of less than 3% allow these microlenses to form high-quality images under broadband illumination (400-700 nm). Numerical apertures upwards of 0.47 are also achieved at the cost of some focusing efficiency, demonstrating the flexibility of this approach. Furthermore, larger area images are reconstructed from an array of hybrid achromatic microlenses, laying the groundwork for achromatic light-field imagers and displays. The presented approach precisely combines optical components within 3D space to achieve thin lens systems with high focusing efficiencies, high numerical apertures, and low chromatic focusing errors, providing a pathway towards achromatic micro-optical systems.
Experimental Infections of Oryzomys couesi with Sympatric Arboviruses from Mexico (2010)

Coues rice rat (Oryzomys couesi), a species abundant throughout Central America, was evaluated experimentally for the ability to serve as an amplifying host for three arboviruses: Patois (Bunyaviridae, Orthobunyavirus), Nepuyo (Orthobunyavirus), and Venezuelan equine encephalitis virus subtype ID (Togaviridae, Alphavirus). These three viruses have similar ecologies and are known to co-circulate in nature. Animals from all three cohorts survived infection and developed viremia with no apparent signs of illness and long-lasting antibodies. Thus, O. couesi may play a role in the general maintenance of these viruses in nature.
Preparation and application of antibodies to phosphoamino acid sequences (2001)

In this review, we describe methods to generate and characterize sequence-specific phosphoamino acid antibodies. Several of the early contributions regarding the utility of such antibodies are summarized. Three antiphosphopeptide antibodies derived from sequences of the Bcr protein are described. They are anti-Bcr pSer-354, anti-Bcr pTyr-328, and anti-Bcr pTyr-360. These anti-Bcr phosphopeptide antibodies are directed toward phosphorylated sequences encoded by the first exon of the BCR gene, which is the critical portion of the Bcr sequence present in the Bcr-Abl oncoprotein. Using these antibodies, we established/confirmed the in vivo phosphorylation of Ser-354, Tyr-328, and Tyr-360 in Bcr and Bcr-Abl proteins. The cross-reactivity of these antibodies, which is a common problem with antipeptide antibodies, was also investigated and discussed.
70 GEFITINIB RESPONSE OF ERLOTINIB-REFRACTORY LUNG CANCER WITH LEPTOMENINGEAL METASTASIS. (2006)

<h3></h3> Although various mutations of the epidermal growth factor receptor (<i>EGFR</i>) gene, most commonly L858R (exon 21) and short exon 19 deletions, have been identified to confer sensitivity toward EGFR tyrosine kinase inhibitors (TKIs), gefitinib and erlotinib, it is not known if there are mutations that may result in differential activities of the two inhibitors. We describe a 70-year-old Japanese American woman diagnosed with stage IV non-small-cell lung cancer (NSCLC) with rib metastasis. While receiving treatment with the EGFR small molecule TKI erlotinib, she progressed and developed new brain metastases. She failed further chemotherapy treatments and subsequently developed symptomatic extensive leptomeningeal carcinomatosis associated with diplopia, hemiparesis, weight loss, and incontinence. Monotherapy gefitinib 250 mg daily was initiated, and she showed striking response both clinically and radiographically within the first few weeks. Using laser microdissection (LMD), we performed genomic DNA extraction and <i>EGFR</i> gene sequencing from the enriched tumor cells in her pretreatment tumor biopsy specimen and tumor cells found in her cerebrospinal fluid. Two heterozygous somatic <i>EGFR</i> mutations, L858R (exon 21) and E884K (exon 22), were identified in both specimens. In vitro transfection and biochemical studies revealed that the novel E884K mutation confers opposite effects in sensitivity to the two EGFR inhibitors. EGFR<sup>E884K</sup> and EGFR<sup>L858R+E884K</sup> enhanced the sensitivity of the mutated receptor to gefitinib inhibition. Conversely, the E884K mutation resulted in decreased responsiveness of the receptor to erlotinib, and it significantly abrogated the drug sensitivity conferred by L858R (EGFR<sup>L858R+E884K</sup>). This study demonstrates that it is possible to have differential response to alternative EGFR TKIs. This also represents the first report of a response of leptomeningeal metastases to EGFR inhibition by small molecule inhibitor gefitinib alone in NSCLC. Further structural studies of the mutant EGFR are warranted to improve individualized targeted therapy and small molecule inhibitors9 design in lung cancer in the future.
Automating Binding Procedures: Using INNOVACQ vs. An In-House Database (2020)

In this chapter, the authors begin with the workshop by discussing their experiences as the University of Toledo implemented the INNOVACQ binding preparation module. Prior to 1989, they had used a manual system for binding preparation. In 1989, the authors begin using INNOVACQ to produce pull-slips and to display binding status in the OPAC. The main tasks required to get the INNOVACQ binding module up were the creation of the binding database and the design of an acceptable binding slip format that met both the library’s and the binder’s needs. Binding information keyed into the INNOVACQ check-in records included: bind information, bind title and bind note. Once the system was implemented, the binding database is kept up to date by sending to the binder a paper copy of records to be added or changed before the INNOVACQ system is modified.
Basics of Biology (2003)

Chapter 3 focuses on building a molecular understanding of biological structures and their relation to biological functions. It provides the basics of biology and introduces the necessary terminology and concepts of biology used in this book. The chapter is written primarily for those unfamiliar with biological concepts, or those wishing to refresh their background in this subject. The chapter describes the chemical make up of a biological cell and the different organelles. The various cellular functions are also discussed. Then, assembling of cells to form a tissue structure is described, along with the nature of extra cellular components in a tissue. The chapter ends with a brief description of tumors and cancers.
Structure-activity relationships of 2-pyrimidinecarbohydrazides as utrophin modulators for the potential treatment of Duchenne muscular dystrophy (2022)

A therapeutic approach that holds the potential to treat all Duchenne muscular dystrophy (DMD) patient populations is utrophin modulation. Ezutromid, a first generation utrophin modulator which was later found to act via antagonism of the arylhydrocarbon receptor, progressed to Phase 2 clinical trials. Although interim data showed target engagement and functional improvements, ezutromid ultimately failed to meet its clinical endpoints. We recently described the identification of a new class of hydrazide utrophin modulators which has a different mechanism of action to ezutromid. In this study we report our early optimisation studies on this hydrazide series. The new analogues had significantly improved potency in cell-based assays, increased sp<sup>3</sup> character and reduced lipophilicity, which also improved their physicochemical properties. A representative new analogue combining these attributes increased utrophin protein in dystrophic mouse cells showing it can be used as a chemical tool to reveal new insights regarding utrophin upregulation as a strategy for DMD therapeutic intervention.
Model of forebrain regionalization based on spatiotemporal patterns of POU‐III homeobox gene expression, birthdates, and morphological features (1995)

In situ hybridization was used to map spatiotemporal expression patterns of the four known intronless POU-III transcription factor genes Brn-1, Brn-2, Brn-4, and Tst-1 in the developing rat forebrain vesicle, beginning on embryonic day 10. The results indicate that the proliferation layers (ventricular and subventricular) and mantle layer of the forebrain neural tube each display a strikingly unique pattern of regionalized POU-III expression. Within a particular region, or layer within a region, none to all four of the mRNAs may be detected, and during development a particular mRNA in a particular region displays one of five expression patterns, or a combination of these patterns, which may be described as conserved, lost, transient, acquired, or redeployed expression. In the developing brain as a whole, Brn-1 and Brn-2 early on display somewhat different spatial expression patterns that converge to essential identity in the adult, whereas Brn-4 expression is initially broad and becomes much more restricted in the adult, and Tst-1 expression expands greatly through development. Usually, though not always, expression patterns tend to correlate with major histological features in the forebrain (often internal or external sulci associated with proliferation zones), and little evidence for waves of expression moving through the whole forebrain over time was obtained. Thus, clear differences in hybridization intensity often are observed between the cerebral cortex, basal telencephalic nuclei, hypothalamus, ventral thalamus, dorsal thalamus, and pretectal region. In contrast, transverse bands of hybridization extending from the roof to the floor of the forebrain, corresponding to proposed neuromeres, were not observed with these probes. The results suggest that POU-III transcription factors help define specific regions in the early neuroepithelium as well as different cellular phenotypes in the ventricular, subventricular, and mantle layers of specific regions later in development. Thus, the functions of these regulatory proteins may be different in proliferating neuroepithelial cells, young neurons, and mature neurons and appear to be region-specific.