gebhart/patrepeval huggingface dataset:
Systemic Lupus Erythematosus and Osteonecrosis: A Comparison of Patients with Single versus Multiple Joint Involvement (2010)

Objective: The purpose of this study was to determine the clinical and laboratory features associated with osteonecrosis of multiple (>/= 3) joints in systemic lupus erythematosus (SLE).
Hedgehog signaling is required at multiple stages of zebrafish tooth development (2010)

We have identified previously unknown requirements for hedgehog signaling for early tooth initiation and later morphogenesis. The similarity of our results with data from mouse and other vertebrates suggests that despite gene duplication and changes in the location of where teeth form, the roles of hedgehog signaling in tooth development have been largely conserved during evolution.
Abstract 2992: The landscape of long non-coding RNAs in cancer (2015)

Abstract Long non-coding RNAs (lncRNAs) are emerging as important players in cancer. The emergence of high-throughput RNA sequencing (RNA-Seq) technology provides a revolutionary means for systematic discovery of transcribed elements. However, efforts to catalog lncRNAs have thus far failed to appreciate the transcriptional robustness and complexity in the human genome because they were confined to select cell lines or small numbers of mostly normal tissue. In order to delineate genome-wide lncRNA expression, we curated 7,256 RNA-Seq libraries comprising over 43 terabases of sequence from 25 independent studies including tumors, normal tissues, and cell lines. The data were processed using ab initio transcriptome meta-assembly methodologies to develop a consensus of 91,013 expressed genes. Over 68% (58,648) of genes were classified as lncRNAs, of which 79% (48,952) were previously unannotated. About 1% (597) of the lncRNAs harbor ultraconserved elements and 7% (3,900) overlap disease-associated single nucleotide polymorphisms (SNPs). To prioritize lineage-specific, disease-associated lncRNA expression, we developed a non-parametric method for differential expression testing called Sample Set Enrichment Analysis (SSEA), and nominated 7,942 lineage- or cancer-associated lncRNA genes. In order to interrogate potential functionality for these lncRNAs, gene set enrichment testing was performed on genes correlated with each lncRNA. By uncovering this expansive landscape of cancer-associated lncRNAs, we provide the scientific community a powerful starting point to begin investigating their biological relevance. We anticipate that the lncRNAs identified by this study, as well as the computational tools developed herein, will provide a foundation for lncRNA genomics, biomarker development, and the delineation of cancer disease mechanisms. Citation Format: Yashar S. Niknafs, Matthew K. Iyer, Arul M. Chinnaiyan. The landscape of long non-coding RNAs in cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2992. doi:10.1158/1538-7445.AM2015-2992
Motion Capture from Pan-Tilt Cameras with Unknown Orientation (2019)

In sports, such as alpine skiing, coaches would like to know the speed and various biomechanical variables of their athletes and competitors. Existing methods use either body-worn sensors, which are cumbersome to setup, or manual image annotation, which is time consuming. We propose a method for estimating an athlete's global 3D position and articulated pose using multiple cameras. By contrast to classical markerless motion capture solutions, we allow cameras to rotate freely so that large capture volumes can be covered. In a first step, tight crops around the skier are predicted and fed to a 2D pose estimator network. The 3D pose is then reconstructed using a bundle adjustment method. Key to our solution is the rotation estimation of Pan-Tilt cameras in a joint optimization with the athlete pose and conditioning on relative background motion computed with feature tracking. Furthermore, we created a new alpine skiing dataset and annotated it with 2D pose labels, to overcome shortcomings of existing ones. Our method estimates accurate global 3D poses from images only and provides coaches with an automatic and fast tool for measuring and improving an athlete's performance.
Structure-Dependent Hydrostatic Deformation Potentials of Individual Single-Walled Carbon Nanotubes (2004)

The hydrostatic pressure coefficients of interband transition energies of a number of single-walled carbon nanotubes with different chiralities were measured. Optical experiments were performed on debundled, single-walled carbon nanotube suspensions with hydrostatic pressure applied by diamond anvil cells. The pressure coefficients of the band-gap energies are negative and dependent on the nanotube structure, while the second van Hove transitions are much less sensitive to hydrostatic pressure. An empirical equation that relates the pressure coefficients to nanotube structure is presented and discussed.
Supplemental Figure S2 from Endothelial ALK1 Is a Therapeutic Target to Block Metastatic Dissemination of Breast Cancer (2023)

&lt;p&gt;The therapeutic benefit of ALK1-Fc is due to on-target effects on ALK1 signaling.&lt;/p&gt;
BactoSpin: Novel Technology for Rapid Bacteria Detection and Antibiotic Susceptibility Testing (2021)

Inappropriate use of antibiotics is one of the leading causes of the increasing numbers of resistant bacteria strains, resulting in 700,000 deaths worldwide each year. Reducing unnecessary use of antibiotics and choosing the most effective antibiotics instead of broad-spectrum drugs will slow the arms race between germs and humans. Urinary tract infections (UTIs) are among the most common bacterial infections. Currently, accurate diagnosis of UTI requires approximately 48 h from the time of urine sample collection until antibiotic susceptibility test (AST) results. This work presents a rapid bacterial detection device that integrates a centrifuge, microscope, and incubator. Two disposable microfluidic chips were developed. The first chip was designed for bacteria concentration, detection, and medium exchange. A second multi-channel chip was developed for AST. This chip contains superhydrophobic and hydrophilic coatings to ensure liquid separation between the channels without the need for valves. The designed chips supported the detection of <i>E. coli</i> at a concentration as low as 5 × 10<sup>3</sup> cells/mL within 5 min and AST in under 2 h. AST was also successfully performed with <i>Klebsiella pneumonia</i> isolated from a human urine sample. In addition, machine-learning-based image recognition was shown to reduce the required time for AST and to provide results within 1 h for <i>E. coli</i> cells. Thus, the BactoSpin device can serve as an efficient and rapid platform for UTI diagnostics and AST.
Keeping an Eye on Bardet-Biedl Syndrome: A Comprehensive Review of the Role of Bardet-Biedl Syndrome Genes in the Eye. (2017)

Upwards of 90% of individuals with Bardet-Biedl syndrome (BBS) display rod-cone dystrophy with early macular involvement. BBS is an autosomal recessive, genetically heterogeneous, pleiotropic ciliopathy for which 21 causative genes have been discovered to date. In addition to retinal degeneration, the cardinal features of BBS include obesity, cognitive impairment, renal anomalies, polydactyly, and hypogonadism. Here, we review the genes, proteins, and protein complexes involved in BBS and the BBS model organisms available for the study of retinal degeneration. We include comprehensive lists for all known BBS genes, their known phenotypes, and the model organisms available. We also review the molecular mechanisms believed to lead to retinal degeneration. We provide an overview of the mode of inheritance and describe the relationships between BBS genes and Joubert syndrome, Leber Congenital Amaurosis, Senior-Løken syndrome, and non-syndromic retinitis pigmentosa. Finally, we propose ways that new advances in technology will allow us to better understand the role of different BBS genes in retinal formation and function.
Crystallization of Silver Carboxylates from Sodium Carboxylate Mixtures (2007)

Silver carboxylates can be made by the reaction of silver nitrate and the corresponding sodium carboxylates. The length of the alkyl chain has a significant impact on the product behavior. In this study, 18, 20, and 22 carbon chains (stearate, arachidate, and behenate, respectively) have been selected. All three sodium carboxylates are very insoluble in water at room temperature. Solutions are obtained above the Krafft temperature, which precipitates lamellar crystals if cooled at the proper cooling rate. Depending on the chain length, metastable morphologies, such as vesicles and tiny fibers, can be seen consecutively before hexagonal plates form. The carboxylate with the shorter chain length reaches equilibrium more quickly. All three silver carboxylates also take on a lamellar structure. Small-angle X-ray scattering (SAXS) shows that the d spacing of the crystals increases as the chain length increases. Cryo-TEM illustrates that the crystallites are the result of micelle nucleation and micelle aggregation. In addition, the crystallization process in the presence of silver bromide nanocrystals has been investigated. In the initial stage, an epitaxial interface is formed between the silver carboxylate crystallites and the cubic silver bromide grains. Budlike and strandlike structures grow because of it. The consequent strand enclosure restrains the crystal growth, which reduces the size and changes the morphology of the crystals.
Quantitative analysis of hyperpolarized 3He ventilation changes in mice challenged with methacholine (2010)

The capability to use high-resolution (3)He MRI to depict regional ventilation changes and airway narrowing in mice challenged with methacholine (MCh) offers the opportunity to gain new insights into the study of asthma. However, to fully exploit the value of this novel technique, it is important to move beyond visual inspection of the images toward automated and quantitative analysis. To address this gap, we describe a postprocessing approach to create ventilation difference maps to better visualize and quantify regional ventilation changes before and after MCh challenge. We show that difference maps reveal subtle changes in airway caliber, and highlight both focal and diffuse regional alterations in ventilation. Ventilation changes include both hypoventilation and compensatory areas of hyperventilation. The difference maps can be quantified by a histogram plot of the ventilation changes, in which the standard deviation increases with MCh dose (R(2) = 0.89). This method of analysis is shown to be more sensitive than simple threshold-based detection of gross ventilation defects.
Isolation and structure elucidation of twelve new prenylated flavonoids from Onobrychis spp. (Leguminosae) employing LC-HRMS, HSCCC and NMR techniques (2016)

Onobrychis spp. (Leguminosae), mostly known as tanniferous forage legumes, bear great economic impact on agricultural and livestock fields. In our previous reports, the phytochemical and pharmacological evaluation of Onobrychis ebenoides, a Greek endemic plant, yielded novel prenylated compounds with remarkable cytotoxic and estrogenic activities [1]. The continuation of our studies suggested the prenyl moiety position, as the decisive component of the cytotoxicity and/or estrogenicity in a cell-dependent manner [2, 3]. Therefore, the present study was aimed firstly at a comparative phytochemical investigation between Onobrychis ebenoides and Onobrychis alba subsp. laconica, another endemic species of Greece without scientific reports. Among these lines, LC-HRMS-based dereplication approaches were employed for targeted isolation purposes. Secondly, both extracts subjected to isolation and purification of putative new compounds using High Speed Countercurrent Chromatography (HSCCC) technique. The profiling of methanol extracts from both plants was performed on a UHPLC-ESI (-)-LTQ-Orbitrap system. Chromatographic and spectrometric features were incorporated for the identification procedure [4]. Both extracts revealed a rich content in prenylated derivatives of isoflavonoids, coumestans and benzofurans. Consequent targeted fractionation with step-gradient HSCCC afforded 5 new isoflavonoids namely albalacone I-II, ebenosin I-III, 4 new coumestans albalacol, onobenol I-III, 1 new pterocarpan onopterol and 2 new benzofurans ebenfuran IV and bis-ebenfuran II, as indicated in the figure below, along with 10 known compounds belonging to the respective chemical classes. Conclusively, both Onobrychis ebenoides and Onobrychis alba subsp. laconica, found to be significantly rich in at least three different classes of phytoestrogens, known for their estrogenic as well as their cytotoxic properties.
Phylogeny and primary structure analysis of fiber shafts of all human adenovirus types for rational design of adenoviral gene-therapy vectors (2009)

The fiber shaft of human adenoviruses (HAdVs) is essential for bringing the penton base into proximity to the secondary cellular receptor. Fiber shaft sequences of all 53 HAdV types were studied. Phylogeny of the fiber shaft revealed clustering corresponding to the HAdV species concept. An intraspecies recombination hot spot was found at the shaft/knob boundary, a highly conserved sequence stretch. For example, HAdV-D20 clustered with HAdV-D23 in the fiber shaft, but with HAdV-D47 in the fiber knob. Although all shafts exhibited the typical pseudorepeats, amino acid sequence identity was found to be as high as 92 % (interspecies) and 54 % (intraspecies). In contrast to a previous study, a flexibility motif (KXGGLXFD/N) was found in eight HAdV-D types, whereas the putative heparan sulfate-binding site (KKTK) was only found in species HAdV-C. Our results suggest that pseudotyping of gene-therapy vectors at the shaft/knob boundary is feasible, but that flexibility data of shafts should be considered.
On the Discrete Time MRACS for System with Input Saturation (1992)

In this paper, the discrete time MRAC is considered for systems with input saturation. We propose a method which modifies the reference input so that the control input stay inside the saturation limit and assures the convergence.
Abstract 976: FOXA1 promotes a luminal growth program in prostate cancer (2018)

Abstract FOXA1 is an important pioneering transcription factor for androgen receptor (AR), a key driver of prostate cancer. FOXA1 has emerged as one of the most recurrently mutated genes in primary and metastatic castrate resistant prostate cancer, with alterations frequencies ranging from 4-15% in various cohorts. Given the well-established role of FOXA1 in modulating AR function, we hypothesize that FOXA1 mutations contribute to prostate oncogenesis by altering the chromatin landscape, resulting in changes in the AR cistrome and AR transcriptional output. Here we use prostate organoids to show that acute FOXA1WT overexpression promotes lumen formation and drives luminal differentiation. Consistent with this, CRISPR/Cas9-mediated deletion of FOXA1 slows proliferation and organoids lacking FOXA1 fail to form lumens. Assays to evaluate the functionality of recurrent FOXA1 mutations (measured by cell viability, lumen formation, and lumen size) along with RNA-sequencing suggest there are distinct classes of FOXA1 mutations. The first are the gain-of-function mutations (such as FOXA1FE254-255del), which promote growth and lumen formation to a larger extent than wild-type FOXA1. Interestingly, a FOXA1 luciferase reporter assay we developed in HEK293 cells indicates that the majority of mutants tested behave as gain of function. The only mutant to score as loss of function, FOXA1R219S, is found nearly exclusively in prostate cancer, and is enriched in neuroendocrine prostate cancer cohorts. Expression of FOXA1R219S suppresses lumen formation and promotes both basal and epithelial-mesenchymal transition transcriptional programs. However, this mutant also provides a growth advantage beyond what is conferred by FOXA1WT. Taken together, these data suggest that FOXA1R219S is not simply a loss of function allele and instead may drive disease progression through a different set of signaling pathways than the FOXA1 alleles that promote luminal differentiation. Further study of these classes of mutations and how they relate to patient outcome, along with analysis of the FOXA1mut/AR cistromes, is ongoing to determine the genome-wide implications of FOXA1 alterations and how they promote prostate cancer progression. Citation Format: Elizabeth J. Adams, Elizabeth Hoover, Wouter R. Karthaus, Charles L. Sawyers. FOXA1 promotes a luminal growth program in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 976.
Application of High-Frequency Leakage Current Model for Characterizing Failure Modes in Digital Logic Gates (2021)

In this paper, a predictive model is developed to characterize the impact of high-frequency electromagnetic interference (EMI) on the leakage current of CMOS integrated circuits. It is shown that the frequency dependence can be easily described by a transfer function that depends only on a few dominant parasitic elements. The developed analytical model is successfully compared against measurement data from devices fabricated using 180 nm, 130 nm, and 65 nm standard CMOS processes through TSMC. Based on the predictive model, the impact of EMI on leakage current in a CMOS inverter is reduced by increasing the frequency from 10 MHz to 4 GHz.
Generalized geometry-based optimal power control in wireless networks (2012)

Geometry-based optimal power control was proposed in [14] to transform the power-control problem to a new geometrical problem on the position relationship between a line and some points. This scheme provides a novel visual perspective and lowers the complexity of optimization. We generalize this scheme to a larger class of power-control optimization problems so as to maximize the network utility with multiple average and peak power constraints in wireless networks. To facilitate the handling of the geometrical model, we define a subset of geometrical models with specified characteristics, called a regular geometrical model, and derive the type of power-control problems eligible for the regular geometrical model. For such a type of problems, two strategies are proposed for the construction of the regular geometrical model. Utilizing geometrical properties, we propose a novel geometry-based optimization scheme for the general power-control problem. Its computational complexity is significantly lower than the conventional algorithms. We also provide a further discussion on irregular geometrical model cases. Finally, we provide two examples of deploying the proposed geometry-based power-control scheme.
PICOntrol (2012)

Today's environments are populated with a growing number of electric devices which come in diverse form factors and provide a plethora of functions. However, rich interaction with these devices can become challenging if they need be controlled from a distance, or are too small to accommodate user interfaces on their own. In this work, we explore PICOntrol, a new approach using an off-the-shelf handheld pico projector for direct control of physical devices through visible light. The projected image serves a dual purpose by simultaneously presenting a visible interface to the user, and transmitting embedded control information to inexpensive sensor units integrated with the devices. To use PICOntrol, the user points the handheld projector at a target device, overlays a projected user interface on its sensor unit, and performs various GUI-style or gestural interactions. PICOntrol enables direct, visible, and rich interactions with various physical devices without requiring central infrastructure. We present our prototype implementation as well as explorations of its interaction space through various application examples.
TO TISSUE ENGINEER HEART MUSCLE (2003)

A challenging goal of this program is to tissue engineer (or regenerate) heart muscle that might be useful for in vivo reparative surgery. The unique muscle cells populating the heart, cardiomyocytes, have lost the ability to replicate. The heart muscle itself is highly vascularized. Muscle tissue is also aligned, organized with a mechanically appropriate extracellular matrix and innervated. Surgical considerations must be addressed. An interdisciplinary team funded through the NIH Bioengineering Research Partnership (BRP) program is exploring the feasibility of engineering heart muscle by addressing many of these challenges in a coordinated research effort. Individual investigator projects, coordinated through a strategic plan, are studying: (1) unique porous gels to stimulate angiogenesis, (2) three-dimensional muscle structures generated on 3-D scaffold arrays (3) the release of drugs, growth factors, angiogenic factors etc (4) a gene transfer system to improve the infarct bed for surgical transplantation (5 to investigate the conversion of embryonic myocardiocytes to conductive Purkinje fiber cells (6) the optimized culture conditions for production of functional basement membrane by myocytes in scaffolds, (7) the development of a bioengineered microvessel capable of sprouting capillaries with a supportive outer wall for the microvessel. (8) development of a perfusion system for oxygenating tissue during in vitro growth.
Helicobacter pylori Virulence and Genetic Geography (1999)

Isolated for the first time in 1982 from human gastric biopsy, Helicobacter pylori is responsible for gastritis, peptic ulcer, and gastric cancer. A pathogenicity island acquired by horizontal transfer, coding for a type IV secretion system, is a major determinant of virulence. The infection is now treated with antibiotics, and vaccines are in preparation. The geographic distribution suggests coevolution of man and Helicobacter pylori.
Lipase-Catalyzed Epoxy–Acid Addition and Transesterification: from Model Molecule Studies to Network Build-Up (2021)

Commercially available lipase from <i>Pseudomonas stutzeri</i> (lipase TL) is investigated as a biocatalyst for the formation of an acid-epoxy chemical network. Molecular model reactions are performed by reacting 2-phenyl glycidyl ether and hexanoic acid in bulk, varying two parameters: temperature and water content. Characterizations of the formed products by <sup>1</sup>H NMR spectroscopy and gas chromatography-mass spectrometry combined with enzymatic assays confirm that lipase TL is able to simultaneously promote acid-epoxy addition and transesterification reactions below 100 °C and solely the acid-epoxy addition after denaturation at <i>T</i> > 100 °C. A prototype bio-based chemical network with β-hydroxyester links was obtained using resorcinol diglycidyl ether and sebacic acid as monomers with lipase TL as catalyst. Differential scanning calorimetry, attenuated total reflection, and swelling analysis confirm gelation of the network.