gebhart/patrepeval huggingface dataset:
Encapsulation of a Rhodamine Dye within a Bile Acid Binding Protein: Toward Water Processable Functional Bio Host–Guest Materials (2013)

New strategies are requested for the preparation of bioinspired host-guest complexes to be employed in technologically relevant applications, as sensors and optoelectronic devices. We report here a new approach employing a single monomeric protein as host for the strongly fluorescent rhodamine dye. The selected protein, belonging to the intracellular lipid binding protein family, fully encapsulates one rhodamine molecule inside its cavity forming a host-guest complex stabilized by H and π-hydrogen bonds, a salt bridge, and favorable hydrophobic contacts, as revealed by the NMR derived structural model. The protein-dye solutions are easily processable and form homogeneous thin films exhibiting excellent photophysical and morphological properties, as derived from photoluminescence and AFM data. The obtained results represent the proof of concept of the viability of this bio host-guest system for the development of bioinspired optoelectronic devices.
Counterfeit Electronics Detection Using Image Processing and Machine Learning (2017)

Counterfeiting is an increasing concern for businesses and governments as greater numbers of counterfeit integrated circuits (IC) infiltrate the global market. There is an ongoing effort in experimental and national labs inside the United States to detect and prevent such counterfeits in the most efficient time period. However, there is still a missing piece to automatically detect and properly keep record of detected counterfeit ICs. Here, we introduce a web application database that allows users to share previous examples of counterfeits through an online database and to obtain statistics regarding the prevalence of known defects. We also investigate automated techniques based on image processing and machine learning to detect different physical defects and to determine whether or not an IC is counterfeit.
An experimental digital VCR with new DCT-based bit-rate reduction system (1991)

A high-picture-quality digital VCR was experimentally developed, using the triple Reed-Solomon product code, a novel block-coding technique with extensive lower frequency level suppression and a DCT (discrete cosine transform)-based bit-rate reduction system. It is suggested that this experimental system can reproduce HDTV (high-definition television) signal records by simulation, and a system to prevent picture quality deterioration by duplication is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
[Treatment of type 2 diabetes. Early detection of secondary oral treatment failure is important]. (1999)

As type II diabetes is caused by decreased insulin secretion and increased insulin resistance, treatment must be aimed at the correction of these abnormalities. To this end, oral hypoglycaemic agents (OHAs) are used once adverse lifestyle factors have been suitably modified. New OHAs are being developed, or have already been approved. Subsequent treatment failure, after an initially satisfactory response, occurs in 5-10 per cent of patients on OHAs, and is currently treated with a combination of an OHA for daytime use and NPH insulin (isophane insulin) for use at bedtime. This yields metabolic control at least as good as that obtained with intensive insulin treatment, and at less risk of weight gain.
Algorithm of Sand Painting Simulation Based on Kinect (2016)

How to combine the human-and-computer interaction and painting art is a hot topic in the fields of computer graphics, virtual reality, film-television advertisements and games. This paper presents an algorithm for interactive simulation of realistic sand painting based on Kinect in real-time, which consists of three sub-systems: the preprocessing system, the user interaction information capture system, and the real-time processing-and-rendering sand painting system. The experimental results reveal that our sand painting simulation is suitable for realistic, interactive and real-time artistic sand painting.
Neighborhood-Level Disadvantage Impacts Mortality and Lung Transplantation in Patients with Idiopathic Pulmonary Fibrosis (2021)

Background: Social determinants of health impact the outcome of many chronic diseases. Environmental and occupational factors contribute to the development and progression of idiopathic pulmonary fibrosis (IPF); however, the impacts of neighborhood-level socioeconomic factors have not been clearly defined. Neighborhood-level disadvantage, as measured by the Area Deprivation Index (ADI), is a surrogate measure of socioeconomic status that is implicated with health outcomes. Methods: Consecutive patients with IPF were enrolled into the prospective University of Pittsburgh Simmons Center for Interstitial Lung Disease (ILD) Registry at UPMC beginning in March 2000, with data collection through to January 2020. Geocoded residential address was used to determine individual ADI. We used multivariable Cox hazards models to test the association of ADI and mortality (considering time to death or lung transplant as a composite outcome). Binary and multinomial logistic regression were used to evaluate the impact of ADI on odds of receiving a lung transplant and location of death, respectively. Models were adjusted for age, sex, smoking status, race, and baseline lung function (forced vital capacity, FVC; and diffusion capacity for carbon monoxide, D L CO). Results: 410 patients with IPF were evaluated for the primary outcome. The highest ADI quartile (indicating the greatest level of neighborhood-level disadvantage) was associated with a hazard ratio (HR) of 2.10 (95% CI 1.25-3.52; p-value = 0.005) compared to the first quartile (Figure There was no association between continuous ADI or ADI quartile and baseline FVC or D L CO. Highest ADI quartile was associated with lower odds of receiving a lung transplant (odds ratio, OR = 0.57; 95% CI 0.32-0.98; p-value = 0.045). Of 110 patients for whom location of death information was available (17%, 32%, 35%, and 15% died at home, in hospice, on a hospital floor, and in the ICU respectively), there was no association between ADI and this outcome. Conclusions: Patients with IPF living in neighborhoods with the highest disadvantage level experience increased risk of mortality and are less likely to receive a lung transplant. These findings suggest that the ADI is a practical indicator of socioeconomic status that can be used in the future to explore health disparities in the IPF patient population. Figure
Vascular burden and cognition: Mediating roles of neurodegeneration and amyloid PET (2022)

It remains unclear to what extent cerebrovascular burden relates to amyloid beta (Aβ) deposition, neurodegeneration, and cognitive dysfunction in mixed disease populations with small vessel disease and Alzheimer's disease (AD) pathology. In 120 subjects, we investigated the association of vascular burden (white matter hyperintensity [WMH] volumes) with cognition. Using mediation analyses, we tested the indirect effects of WMH on cognition via Aβ deposition (<sup>18</sup> F-AV45 positron emission tomography [PET]) and neurodegeneration (cortical thickness or <sup>18</sup> F fluorodeoxyglucose PET) in AD signature regions. We observed that increased total WMH volume was associated with poorer performance in all tested cognitive domains, with the strongest effects observed for semantic fluency. These relationships were mediated mainly via cortical thinning, particularly of the temporal lobe, and to a lesser extent serially mediated via Aβ and cortical thinning of AD signature regions. WMH volumes differentially impacted cognition depending on lobar location and Aβ status. In summary, our study suggests mainly an amyloid-independent pathway in which vascular burden affects cognitive function via localized neurodegeneration. HIGHLIGHTS: Alzheimer's disease often co-exists with vascular pathology. We studied a unique cohort enriched for high white matter hyperintensities (WMH). High WMH related to cognitive impairment of semantic fluency and executive function. This relationship was mediated via temporo-parietal atrophy rather than metabolism. This relationship was, to lesser extent, serially mediated via amyloid beta and atrophy.
Topology and irregularity in cellular networks (2015)

The analysis of cellular systems has been carried out modeling the access network by means of deterministic and stochastic methods. Deterministic models include hexagonal geometries or real-world data. Stochastic methods, given their nature, capture (in a statistical manner) the inhomogeneities found in realistic deployments. Beyond pros and cons of each approach, the notion of ‘topology’ associated to these models is either geometric (regular or non-regular) or architectonic (heterogeneous or not), but it is not enough to describe many aspects of real-world deployments. Despite the term is widely used in the context of cellular communications, there is no precise (mathematical) definition for it. In the light of this situation, this paper presents a set of proper definitions to describe network topology and its compatibility with service demand distribution in a way that is useful from the planning and optimization perspective. In addition, a novel view of ‘irregularity’ is also introduced. Due to its generality, this statistical framework is timely for 5G where 1) hyper-dense and hierarchical deployments are foreseen, and 2) more complex performance indicators such as energy, spectral, and deployment efficiency per area unit need to be accurately estimated. In addition, operator-specific criteria such as QoS can be taken into account in the model presented herein.
Inhibition of uridine phosphorylase: synthesis and structure-activity relationships of aryl-substituted 5-benzyluracils and 1-[(2-hydroxyethoxy)methyl]-5-benzyluracils. (1995)

A series of 1-[(2-hydroxyethoxy)methyl]-5-benzyluracils were synthesized and tested for inhibition of murine liver uridine phosphorylase (UrdPase). Inhibitors of UrdPase are reported to enhance the chemotherapeutic utility of 5-fluoro-2'-deoxyuridine and 5-fluorouracil and to ameliorate zidovudine-induced anemia in animal models. We prepared a series of 5-aryl-substituted analogues of 5-benzylacyclouridine (BAU), a good inhibitor of UrdPase (IC50 of 0.46 microM), to develop a compound with enhanced potency and improved pharmacokinetics. The first phase of structure-activity relationship studies on a series of 32 aryl-substituted 5-benzyluracils found several 5-(3-alkoxybenzyl) analogues of 5-benzyluracil with enhanced potency. The acyclovir side chain, the (2-hydroxyethoxy)methyl group, was substituted on the more potent aryl-substituted 5-benzyluracils. The two most potent compounds, 10y (3-propoxy) and 10dd (3-sec-butoxy), were inhibitors of UrdPase with IC50s of 0.047 and 0.027 microM, respectively. Six compounds were tested in vivo for effects on steady-state concentrations of circulating uridine in rats. Plasma uridine levels were elevated 3-9-fold by compound levels that ranged from 8 to 50 microM.
The adaptive cross-approximation technique for the 3D boundary-element method (2002)

It is well known that the classical boundary-element method (BEM) yields fully populated matrices. Their manipulation is cumbersome with respect to memory consumption and computational costs. This paper describes a novel approach where the matrices are split into collections of blocks of various sizes. Those blocks which describe remote interactions are adaptively approximated by low rank submatrices. This procedure reduces the algorithmic complexity for matrix setup and matrix-by-vector products to approximately O(N). The proposed method has been examined in a testing environment and implemented into an existing BEM-finite-element method (FEM) code for electromagnetic and electromechanical problems. The advantages of the new method are demonstrated by means of several examples.
Correspondence and Affine Shape from Two Orthographic Views: Motion and Recognition (1991)

The paper presents a simple model for recovering affine shape and correspondence from two orthographic views of a three--dimensional object. The paper has two parts. In the first part it is shown that four corresponding points along two orthographic views, taken under similar illumination conditions, determine affine shape and correspondence for all other points. In the second part it is shown that the scheme is useful for purposes of visual recognition by generating novel views of an object given two model views in full correspondence and four corresponding points between the model views and the novel view. It is also shown that the scheme can handle objects with smooth boundaries, to a good approximation, without introducing any modifications or additional model views. Copyright c fl Massachusetts Institute of Technology, 1991 This report describes research done at the Artificial Intelligence Laboratory of the Massachusetts Institute of Technology. Support for the laboratory&amp;apos;s artifi...
Data from Scatter Spectroscopic Imaging Distinguishes between Breast Pathologies in Tissues Relevant to Surgical Margin Assessment (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; A new approach to spectroscopic imaging was developed to detect and discriminate microscopic pathologies in resected breast tissues; diagnostic performance of the prototype system was tested in 27 tissues procured during breast conservative surgery.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; A custom-built, scanning &lt;i&gt;in situ&lt;/i&gt; spectroscopy platform sampled broadband reflectance from a 150-μm-diameter spot over a 1 × 1 cm&lt;sup&gt;2&lt;/sup&gt; field using a dark field geometry and telecentric lens; the system was designed to balance sensitivity to cellular morphology and imaging the inherent diversity within tissue subtypes. Nearly 300,000 broadband spectra were parameterized using light scattering models and spatially dependent spectral signatures were interpreted using a cooccurrence matrix representation of image texture.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Local scattering changes distinguished benign from malignant pathologies with 94% accuracy, 93% sensitivity, 95% specificity, and 93% positive and 95% negative predictive values using a threshold-based classifier. Texture and shape features were important to optimally discriminate benign from malignant tissues, including pixel-to-pixel correlation, contrast and homogeneity, and the shape features of fractal dimension and Euler number. Analysis of the region-based diagnostic performance showed that spectroscopic image features from 1 × 1 mm&lt;sup&gt;2&lt;/sup&gt; areas were diagnostically discriminant and enabled quantification of within-class tissue heterogeneities.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Localized scatter-imaging signatures detected by the scanning spectroscopy platform readily distinguished benign from malignant pathologies in surgical tissues and showed new spectral-spatial signatures of clinical breast pathologies. &lt;i&gt;Clin Cancer Res; 18(22); 6315–25. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Covalent Rpn13-Binding Inhibitors for the Treatment of Ovarian Cancer (2018)

Substitution of the <i>m</i>,<i>p</i>-chloro groups of bis-benzylidinepiperidone RA190 for <i>p</i>-nitro, generating RA183, enhanced covalent drug binding to Cys88 of RPN13. Treatment of cancer cell lines with RA183 inhibited ubiquitin-mediated protein degradation, resulting in rapid accumulation of high-molecular-weight polyubiquitinated proteins, blockade of NFκB signaling, endoplasmic reticulum stress, an unfolded protein response, production of reactive oxygen species, and apoptotic cell death. High-grade ovarian cancer, triple-negative breast cancer, and multiple myeloma cell lines were particularly vulnerable to RA183. RA183 stabilized a tetraubiquitin-linked firefly luciferase reporter protein in cancer cell lines and mice, demonstrating in vitro and in vivo proteasomal inhibition, respectively. However, RA183 was rapidly cleared from plasma, likely reflecting its rapid degradation to the active compound RA9, as seen in human liver microsomes. Intraperitoneal administration of RA183 inhibited proteasome function and orthotopic tumor growth in mice bearing human ovarian cancer model ES2-luc ascites or syngeneic ID8-luc tumor.
Dose-Dependent Metabolic Alterations in Human Cells Exposed to Gamma Irradiation (2014)

Radiation exposure is a threat to public health because it causes many diseases, such as cancers and birth defects, due to genetic modification of cells. Compared with the past, a greater number of people are more frequently exposed to higher levels of radioactivity today, not least due to the increased use of diagnostic and therapeutic radiation-emitting devices. In this study, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS)-based metabolic profiling was used to investigate radiation- induced metabolic changes in human fibroblasts. After exposure to 1 and 5 Gy of γ-radiation, the irradiated fibroblasts were harvested at 24, 48, and 72 h and subjected to global metabolite profiling analysis. Mass spectral peaks of cell extracts were analyzed by pattern recognition using principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). The results showed that the cells irradiated with 1 Gy returned to control levels at 72 h post radiation, whereas cells irradiated with 5 Gy were quite unlike the controls; therefore, cells irradiated with 1 Gy had recovered, whereas those irradiated with 5 Gy had not. Lipid and amino acid levels increased after the higher-level radiation, indicating degradation of membranes and proteins. These results suggest that MS-based metabolite profiling of γ-radiation-exposed human cells provides insight into the global metabolic alterations in these cells.
Linaclotide Significantly Improved Abdominal Pain, Constipation and Global Assessments in Adults with Irritable Bowel Syndrome with Constipation (2008)

Purpose: Linaclotide, a first-in-class, minimally absorbed peptide agonist of human intestinal guanylate cyclase type-C receptors, is a novel treatment for irritable bowel syndrome with constipation (IBS-C). Linaclotide significantly relieved visceral hyperalgesia in several animal pain models and, in a large Phase 2 study in patients with chronic constipation, significantly improved bowel function and abdominal symptoms. A Phase 2 study was conducted to evaluate the safety and efficacy of a range of linaclotide doses in adults with IBS-C. Methods: This randomized, multicenter, double-blind, placebo-controlled, dose-range-finding, parallel-group study evaluated the effects of 75, 150, 300 or 600 μg linaclotide or placebo administered orally once daily to adults meeting modified Rome II criteria for IBS-C. Participants underwent 2-week-baseline, 12-week-treatment, and 2-week-post-treatment evaluations with daily assessments of bowel habits and symptom severity, and weekly global assessments using an interactive voice response system. During the baseline period patients had to demonstrate < 3 complete spontaneous bowel movements (CSBM)/week and mean daily abdominal pain of at least mild severity. Treatment effects in the intent-to-treat (ITT) population were estimated using an analysis of covariance and the Cochran-Mantel Haenszel test. Results: Of the 420 patients randomized, 419 were in the ITT population and 337 completed the study. Abdominal pain was clinically and statistically significantly improved in all linaclotide treatment groups compared to placebo and, in the 26% of patients with severe/very severe baseline abdominal pain, improvement was even more pronounced (see Table). The change from baseline vs placebo for CSBM frequency (primary endpoint) was significant at all linaclotide dose levels. Results for other abdominal symptoms and bowel habits, and for 3 global assessments (binary adequate relief, 7-point balanced degree of relief, and 5-point IBS symptom severity) were highly statistically significant for the 300 μg and 600 μg dose groups. Treatment effects of linaclotide were rapid in onset (within the first week of treatment) and were maintained throughout the entire 12-week treatment period; there was no indication of rebound clinical effects following cessation of treatment. The most common adverse event was diarrhea; however, there were no associated dehydration or electrolyte abnormalities and discontinuations for diarrhea were infrequent (see Table).TableConclusion: Once daily oral linaclotide across a wide dose range improved all measured bowel habits, abdominal symptoms and global assessments in patients with IBS-C with a safety and tolerability profile that supports advancing this novel compound into Phase 3 clinical trials.
Safe configuration of TLS connections (2013)

Transport Layer Security (TLS) and its precursor Secure Sockets Layer (SSL) are the most widely deployed protocol to establish secure communication over insecure Internet Protocol (IP) networks. Providing a secure session layer on top of TCP, TLS is frequently the first defense layer encountered by adversaries who try to cause loss of confidentiality by sniffing live traffic or loss of integrity using man-in-the-middle attacks. Despite its wide deployment and evolution over the last 18 years, TLS remains vulnerable to a number of threats at the protocol layer and therefore does not provide strong security out-of-the-box, requiring tweaks to its configuration in order to provide the expected security benefits. This paper provides a summary of the current TLS threat surface together with a validated approach for minimizing the risk of TLS-compromise. The main contributions of this paper include 1) identification of configuration options that together maximize security guarantees in the context of recent TLS exploits and 2) specification of expected flows and automated comparison with observed flows to flag inconsistencies.
Extending the field of view by a scattering window in an I-COACH system (2018)

Interferenceless coded aperture correlation holography (I-COACH) is an incoherent digital holography technique developed to record and reconstruct 3D images of objects without two-wave interference. Herein, we introduce a novel technique to extend the field of view (FOV) of I-COACH beyond the limit imposed by the ratio between the finite area of the image sensor and the magnification of the optical system. Light diffracted from a point object located on the optical axis is modulated by a pseudorandom coded phase mask, and the central part of the point spread hologram (PSH) on the image sensor is recorded. The point object is shifted laterally to predetermined lateral locations in order to collect the exterior parts of the PSH. The recorded PSHs are stitched together to produce a synthetic PSH (SPSH) with an area nine times that of any individual PSH recorded by the image sensor. An object with a lateral extent beyond the FOV limit of the image sensor is placed at the same axial location as the point object, and the object hologram is recorded. The object is reconstructed by a cross-correlation between the zero-padded object hologram and the SPSH. Hence, the object parts beyond the FOV limit of the image sensor are recovered. An SPSH library is created for different axial planes, and the corresponding axial planes of the object are reconstructed.