gebhart/patrepeval huggingface dataset:
Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors (2016)

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.
Functional MRI detection of pharmacologically induced memory impairment (2001)

To examine alterations in brain activation associated with pharmacologically induced memory impairment, we used functional MRI (fMRI) to study the effects of lorazepam and scopolamine on a face-name associative encoding paradigm. Ten healthy young subjects were scanned on four occasions, 2 weeks apart; they were administered i.v. saline during two placebo-scanning sessions and then alternately administered i.v. lorazepam (1 mg) or scopolamine (0.4 mg) in a double-blind, randomized, cross-over design. Both the extent and magnitude of activation within anatomic regions of interest (ROIs) were examined to determine the reproducibility of activation in the placebo sessions and the regional specificity of the pharmacologic effects. Activation within all ROIs was consistent across the two placebo scans during the encoding of novel face-name pairs (compared with visual fixation). With the administration of either lorazepam or scopolamine, significant decreases were observed in both the extent and magnitude of activation within the hippocampal, fusiform, and inferior prefrontal ROIs, but no significant alterations in activation in the striate cortex were found. Both medications impaired performance on postscan memory measures, and significant correlations between memory performance and extent of activation were found in hippocampal and fusiform ROIs. These findings suggest that pharmacologic effects can be detected with fMRI by using a reproducible experimental paradigm and that medications that impair memory also diminish activation in specific brain regions thought to subserve complex memory processes.
Gene Therapy Approaches to Sensitization of Human Prostate Carcinoma to Cisplatin by Adenoviral Expression of p53 and by Antisense Jun Kinase Oligonucleotide Methods (2003)

One of the challenges of medical research today is to find ways of bringing our genetic knowledge of cancer to clinical application and to develop improved therapies by exploiting gene-based strategies. By offering increased specificity and reduced toxicity, gene-based approaches promise alternatives when conventional treatments fail. Gene therapy also offers improved responses to conventional treatments when used in combination with gene therapy. Chief among the cancers in urgent need of improved treatment options is prostate cancer—the most commonly diagnosed cancer in men.
Synthesis of 1,2,4-Trisubstituted Imidazoles and 1,3,5-Trisubstituted 1,2,4-Triazoles (2008)

We report synthetic strategies to easily access 1,2,4-trisubstituted imidazoles by introduction of different residues at C(2) and C(4) followed by substitution at N(1). Furthermore, a synthesis of trisubstituted 1,2,4-triazoles via a cyclization of hydrazonamides is described.
AntMonitor: System and Applications. (2016)

Author(s): Shuba, Anastasia; Le, Anh; Alimpertis, Emmanouil; Gjoka, Minas; Markopoulou, Athina
Supplementary Figure Legends 1-6, Table Legends 1-2 from ICOS-Ligand Expression on Plasmacytoid Dendritic Cells Supports Breast Cancer Progression by Promoting the Accumulation of Immunosuppressive CD4<sup>+</sup> T Cells (2023)

&lt;p&gt;PDF file - 68K&lt;/p&gt;
A novel carbon fiber based porous carbon monolith (1995)

A novel porous carbon material based on carbon fibers has been developed. The material, when activated, develops a significant micro- or mesopore volume dependent upon the carbon fiber type utilized (isotropic pitch or polyacrylonitrile). The materials will find applications in the field of fluid separations or as a catalyst support. Here, the manufacture and characterization of our porous carbon monoliths are described.
Abstract 17556: The Symptom Limited Up-titration of VNS May Result in Neural Damage, Thus Too Strong to Benefit Chronic Heart Failure (2014)

Background: Vagal nerve stimulation (VNS) improves chronic heart failure (CHF) in animals and in human. Although the stimulus intensity was up-titrated to the symptomatic threshold such as twitching and cough, whether such symptom-limited threshold exerts maximum benefits for CHF remains unknown. In this study we investigated the dose response of VNS for CHF after large myocardial infarction (MI) in rats. Methods: In 8 weeks Sprague-Dawley rats, we created large MI. We implanted a device for VNS and started stimulation from 2 weeks after MI (Sham: n=21, C-VNS: n=15, H-VNS: n=16). In the conventional stimulation group (C-VNS), we up-titrated VNS until it reached the symptom limits. In the second group, we halved VNS intensity (H-VNS). To evaluate the early impact of VNS on inflammatory responses, we compared the macrophage invasion and plasma inflammatory cytokines at 3 days after VNS. 4 weeks after VNS, we evaluated its chronic effects on hemodynamics and CHF parameters. Results: At 3 days after VNS, both...
Investigation of Downstream Signals of the Soybean Autoregulation of Nodulation Receptor Kinase GmNARK (2008)

The Glycine max nodule autoregulation receptor kinase (GmNARK) plays a central role in the systemic signal transduction pathway controlling nodulation in soybean. We used transcriptional profiling to identify potential downstream signals of this receptor kinase. These studies revealed that GmNARK-mediated signaling controls the expression of genes involved in the jasmonic acid (JA) pathway. Genes encoding the key enzymes controlling JA biosynthesis as well as JA-response genes were regulated systemically but not locally by root inoculation with Bradyrhizobium japonicum. This systemic regulation was abolished in Gmnark mutant plants, indicating that their expression was specifically controlled by signaling events associated with this receptor kinase. Foliar application of a JA biosynthesis inhibitor significantly reduced nodulation specifically in supernodulating mutant plants. These results indicate that the receptor-mediated regulation of JA signaling plays an important role in the AON signal transduction pathway. A second class of genes was identified that were controlled by GmNARK in a rhizobia-independent manner. These candidates provide insight on additional, nonsymbiotic signaling pathways that are likely regulated by GmNARK, such as those involved in root growth and defense. The discovery of downstream components of the GmNARK receptor kinase advances our understanding of the systemic control of nodule development and its association with other signaling networks.
Enabling Privacy for the Paranoids (2004)

P3P is a set of standards that allow corporations to declare their privacy policies. Hippocratic Databases have been proposed to implement such policies within a corporation's datastore. From an end-user individual's point of view, both of these rest on an uncomfortable philosophy of trusting corporations to protect his/her privacy. Recent history chronicles several episodes when such trust has been willingly or accidentally violated by corporations facing bankruptcy courts, civil subpoenas or lucrative mergers. We contend that data management solutions for information privacy must restore controls in the individual's hands. We suggest that enabling such control will require a radical re-think on modeling, release/acquisition, and management of personal data.
Data from Computationally Derived Image Signature of Stromal Morphology Is Prognostic of Prostate Cancer Recurrence Following Prostatectomy in African American Patients (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Between 30%–40% of patients with prostate cancer experience disease recurrence following radical prostatectomy. Existing clinical models for recurrence risk prediction do not account for population-based variation in the tumor phenotype, despite recent evidence suggesting the presence of a unique, more aggressive prostate cancer phenotype in African American (AA) patients. We investigated the capacity of digitally measured, population-specific phenotypes of the intratumoral stroma to create improved models for prediction of recurrence following radical prostatectomy.&lt;/p&gt;Experimental Design:&lt;p&gt;This study included 334 radical prostatectomy patients subdivided into training (V&lt;sub&gt;T&lt;/sub&gt;, &lt;i&gt;n&lt;/i&gt; = 127), validation 1 (V&lt;sub&gt;1&lt;/sub&gt;, &lt;i&gt;n&lt;/i&gt; = 62), and validation 2 (V&lt;sub&gt;2&lt;/sub&gt;, &lt;i&gt;n&lt;/i&gt; = 145). Hematoxylin and eosin–stained slides from resected prostates were digitized, and 242 quantitative descriptors of the intratumoral stroma were calculated using a computational algorithm. Machine learning and elastic net Cox regression models were constructed using V&lt;sub&gt;T&lt;/sub&gt; to predict biochemical recurrence-free survival based on these features. Performance of these models was assessed using V&lt;sub&gt;1&lt;/sub&gt; and V&lt;sub&gt;2&lt;/sub&gt;, both overall and in population-specific cohorts.&lt;/p&gt;Results:&lt;p&gt;An AA-specific, automated stromal signature, AAstro, was prognostic of recurrence risk in both independent validation datasets [V&lt;sub&gt;1,AA&lt;/sub&gt;: AUC = 0.87, HR = 4.71 (95% confidence interval (CI), 1.65–13.4), &lt;i&gt;P&lt;/i&gt; = 0.003; V&lt;sub&gt;2,AA&lt;/sub&gt;: AUC = 0.77, HR = 5.7 (95% CI, 1.48–21.90), &lt;i&gt;P&lt;/i&gt; = 0.01]. AAstro outperformed clinical standard Kattan and CAPRA-S nomograms, and the underlying stromal descriptors were strongly associated with IHC measurements of specific tumor biomarker expression levels.&lt;/p&gt;Conclusions:&lt;p&gt;Our results suggest that considering population-specific information and stromal morphology has the potential to substantially improve accuracy of prognosis and risk stratification in AA patients with prostate cancer.&lt;/p&gt;&lt;/div&gt;
Characterization of SNARE Proteins in Human Pituitary Adenomas: Targeted Secretion Inhibitors as a New Strategy for the Treatment of Acromegaly? (2013)

SNARE proteins are present in human pituitary somatotroph adenomas that can be targeted by TSIs to inhibit GH secretion. qGHRH-LH(N)/D was unable to inhibit GH secretion from human somatotroph adenoma cells. Further studies are required to understand how the SNARE proteins drive GH secretion in human somatotrophs to allow the development of novel TSIs with a potential therapeutic benefit.
Selection Bias Tracking and Detailed Subset Comparison for High-Dimensional Data (2019)

The collection of large, complex datasets has become common across a wide variety of domains. Visual analytics tools increasingly play a key role in exploring and answering complex questions about these large datasets. However, many visualizations are not designed to concurrently visualize the large number of dimensions present in complex datasets (e.g. tens of thousands of distinct codes in an electronic health record system). This fact, combined with the ability of many visual analytics systems to enable rapid, ad-hoc specification of groups, or cohorts, of individuals based on a small subset of visualized dimensions, leads to the possibility of introducing selection bias-when the user creates a cohort based on a specified set of dimensions, differences across many other unseen dimensions may also be introduced. These unintended side effects may result in the cohort no longer being representative of the larger population intended to be studied, which can negatively affect the validity of subsequent analyses. We present techniques for selection bias tracking and visualization that can be incorporated into high-dimensional exploratory visual analytics systems, with a focus on medical data with existing data hierarchies. These techniques include: (1) tree-based cohort provenance and visualization, including a user-specified baseline cohort that all other cohorts are compared against, and visual encoding of cohort “drift”, which indicates where selection bias may have occurred, and (2) a set of visualizations, including a novel icicle-plot based visualization, to compare in detail the per-dimension differences between the baseline and a user-specified focus cohort. These techniques are integrated into a medical temporal event sequence visual analytics tool. We present example use cases and report findings from domain expert user interviews.
A Highly Efficient Domain Decomposition Method Applied to 3-D Finite-Element Analysis of Electromechanical and Electric Machine Problems (2012)

A highly efficient domain decomposition method, called the dual-primal finite-element tearing and interconnecting (FETI-DP) method, is applied to improve the efficiency of three-dimensional (3-D) finite-element analysis of electromechanical and electric machine problems. The FETI-DP method decomposes an original large-scale 3-D problem into many subdomain problems and then treats the subdomain problems concurrently using parallel computing schemes to reduce the total computation time. Higher order hierarchical basis functions are implemented to improve the accuracy of the simulation and also to facilitate the treatment of the low-frequency breakdown problem, which is encountered by the traditional finite-element method with vector basis functions when solving electromechanical problems. With the separation of higher order basis functions from the lowest order ones offered by hierarchical basis functions, the low-frequency breakdown problem can be handled by applying the tree-cotree splitting method to the lowest order basis functions. The resulting accurate finite-element computation of the magnetic field is then used to calculate force and torque by using the Maxwell stress tensor method.
Changing Paradigms in Biopreservation (2009)

The field of cryopreservation has a long and successful history of in-depth study and progress. Advances in our knowledge base and our ability to cryopreserve cells have been consequential and have led to its widespread integration into academic, clinical, and agricultural settings. While many cell systems are successfully cryopreserved today, there remains significant cell loss associated with cryopreservation. Moreover, even today some cell systems remain uncryopreservable from a practical perspective. This is due to the diversity of post-freeze responses of individual cells to the various stressors experienced during the freeze-thaw process. In 1998, several independent groups reported on the direct involvement of apoptotic and necrotic cell death following cryopreservation (Baust, et al., 1998 and Borderie, et al., 1998). In addition to those reports, a substantial literature base describing the modulation of cell death through the use of various protease inhibitors, free radical scavengers, media formulations, and other novel compounds exist. These studies have identified diverse molecular-based, cellular responses to cryopreservation and have further demonstrated the significant improvements in cell survival through the modulation of molecular events. Numerous studies have reported on the molecular-based phenomena of cryopreservation-induced delayed onset cell death, yet our understanding of the pathway activation, progression, control, and the downstream effect on cell function remains in its infancy. To this end, modulation studies, such as targeted apoptotic control (TAC), have shown promise in furthering our understanding of the activation pathways and are proving to be a critical next step in the evolution of the cryopreservation sciences. This review provides an overview of the current literature on the mechanisms of cell death associated with cryopreservation failure.
Design of Via Structure for High-speed Signal Transmission in Multilayer Circuit Board (2015)

Via structures are unavoidable to connect signal paths when a multilayer circuit board is used to increase the signal density. It however becomes clear recently that high-speed via transmission causes not only impedance discontinuities but also the undesirable leak of signal power as the emission with the parallel plate transmission mode between the solid ground planes. In order to solve above problems, the suppression method for them is proposed in this paper. The proposed method is expanding a part of the clearance around the signal via as a fan shape. As a result of the 3D electromagnetic simulation, we confirmed that it could improve the levels of the signal power emissions from signal via from 57% to 30%. This method might be available to low-cost production of the multilayer circuit board in the next generation, in the point that it is applicable to conventional low-cost substrate manufacturing methods.
Computed Tomographic Liver Enhancement with Poly(d,1-Lactide)-Microencapsulated Contrast Media (1994)

Yang DJ, Kuang L-R, Li C, Kan Z, Wallace S. Computed tomographic liver enhancement with poly(d,1-lactide) mi-croencapsulated contrast media. Invest Radiol 1994;29:S267–S270.
Antimicrobial/Antifouling Polycarbonate Coatings: Role of Block Copolymer Architecture (2015)

The high prevalence of catheter-associated infections accounts for more than 3 billion dollars annually in hospitals, and antimicrobial polymer coatings on catheter surface may serve as an attractive weapon to mitigate infections. Triblock polycarbonate polymers consisting of three critical components including antifouling poly(ethylene glycol) (PEG), antimicrobial cationic polycarbonate, and a tethering or adhesive functional block were synthesized. In this study, the block topology or placement of the distinctive blocks was varied and their efficacy as antimicrobial and antifouling agents investigated on coated surfaces. The individual blocks were designed to have comparable lengths that were subsequently grafted onto a prefunctionalized catheter surface through covalent bonding under mild conditions. The anchoring/adhesive functional moiety based on a maleimide functional carbonate was positioned at either the center or end of the polymer block and subsequently tethered to the surface via Michael addition chemistry. The placement of the adhesive block was investigated in terms of its effect on antimicrobial and antifouling properties. The surface coated with the polymer containing the center-positioned tethering block (2.4k-V) was unable to prevent bacteria fouling, even though demonstrated higher bacteria killing efficacy in solution as compared to the surface coated with the polymer containing the end-positioned tethering block (2.4k-S). In contrast, the 2.4k-S coating resisted fouling of both Gram-positive S. aureus and Gram-negative E. coli effectively under conditions that simulate the device lifetime (1 week). Moreover, the coating prevented protein fouling and platelet adhesion without inducing significant hemolysis. Consequently, this antibacterial and antifouling polymer coating is an interesting candidate to prevent catheter-associated bloodstream infections.
Scholarly productivity and professional advancement of junior researchers receiving KL2, K23, or K08 awards at a large public research institution (2017)

At our institution, scholarly productivity and professional advancement did not differ by type of K-award.
Autoregressive Tree Models for Time-Series Analysis (2002)

1 Introduction The analysis and modeling of time-series data is an important area of research for many communities. In this paper, our goal is to identify models for continuousvalued time-series data that are useful for data mining in that they (1) can be learned eficiently from data, (2) support accurate predictions, and (3) are easy to interpret. To these ends, we describe an interpretable class of models that we call AutoRegressive Tree models, or ART models, that are a generalization of standard autoregressive (AR) models. We describe learning methods for ART models and compare these methods to those for alternative models. Our experiments, performed on 2,494 time-series data sets from the International Institute of Forecasters, demonstrate that ART models provide superior predictive accuracy. We concentrate on the problem of modeling the evolution of values of a continuous variable over time; that is, we model a univariate time series. The generalization to multivariate time-series analysis is straightforward and is discussed in Section 6.
Osteoclast precursor differentiation by MCPIP via oxidative stress, endoplasmic reticulum stress, and autophagy (2011)

Osteoclasts (OCs) are responsible for bone resorption in inflammatory joint diseases. Monocyte chemotactic protein-1 (MCP-1) has been shown to induce differentiation of monocytes to OC precursors, but nothing is known about the underlying mechanisms. Here, we elucidate how MCPIP, induced by MCP-1, mediates this differentiation. Knockdown of MCPIP abolished MCP-1-mediated expression of OC markers, tartrate-resistant acid phosphatase, and serine protease cathepsin K. Expression of MCPIP induced p47(PHOX) and its membrane translocation, reactive oxygen species formation, and induction of endoplasmic reticulum (ER) stress chaperones, up-regulation of autophagy marker, Beclin-1, and lipidation of LC3, and induction of OC markers. Inhibition of oxidative stress attenuated ER stress and autophagy, and suppressed expression of OC markers. Inhibition of ER stress by a specific inhibitor or by knockdown of IRE1 blocked autophagy and induction of OC markers. ER stress inducers, tunicamycin and thapsigargin, induced expression of OC markers. Autophagy inhibition by 3'-methyladenine, LY294002, wortmannin or by knockdown of Beclin-1 or Atg 7 inhibited MCPIP-induced expression of OC markers. These results strongly suggest that MCP-1-induced differentiation of OC precursor cells is mediated via MCPIP-induced oxidative stress that causes ER stress leading to autophagy, revealing a novel mechanistic insight into the role of MCP-1 in OCs differentiation.
Inversion gate capacitance of undoped single-gate and double-gate field-effect transistor geometries in the extreme quantum limit (2015)

We present first-principle analytical derivations and numerically modeled data to show that the gate capacitance per unit gate area CG of extremely thin undoped-channel single-gate and double-gate field-effect transistor geometries in the extreme quantum limit with single-subband occupancy can be written as 1/CG = 1/COX + NG/CDOS + NG/ηCWF, where NG is the number of gates, COX is the oxide capacitance per unit area, CDOS is the density-of-states capacitance per unit area, CWF is the wave function spreading capacitance per unit area, and η is a constant on the order of 1.