gebhart/patrepeval huggingface dataset:
Families of retinoid dehydrogenases regulating vitamin A function (2000)

Vitamin A (retinol) and provitamin A (beta-carotene) are metabolized to specific retinoid derivatives which function in either vision or growth and development. The metabolite 11-cis-retinal functions in light absorption for vision in chordate and nonchordate animals, whereas all-trans-retinoic acid and 9-cis-retinoic acid function as ligands for nuclear retinoic acid receptors that regulate gene expression only in chordate animals. Investigation of retinoid metabolic pathways has resulted in the identification of numerous retinoid dehydrogenases that potentially contribute to metabolism of various retinoid isomers to produce active forms. These enzymes fall into three major families. Dehydrogenases catalyzing the reversible oxidation/reduction of retinol and retinal are members of either the alcohol dehydrogenase (ADH) or short-chain dehydrogenase/reductase (SDR) enzyme families, whereas dehydrogenases catalyzing the oxidation of retinal to retinoic acid are members of the aldehyde dehydrogenase (ALDH) family. Compilation of the known retinoid dehydrogenases indicates the existence of 17 nonorthologous forms: five ADHs, eight SDRs, and four ALDHs, eight of which are conserved in both mouse and human. Genetic studies indicate in vivo roles for two ADHs (ADH1 and ADH4), one SDR (RDH5), and two ALDHs (ALDH1 and RALDH2) all of which are conserved between humans and rodents. For several SDRs (RoDH1, RoDH4, CRAD1, and CRAD2) androgens rather than retinoids are the predominant substrates suggesting a function in androgen metabolism as well as retinoid metabolism.
Exploring the therapeutic space around NAD+ (2012)

NAD(+) is a central metabolite in the cell. Changes in NAD(+) abundance and the activity of NAD(+)-dependent enzymes, such as the sirtuins, are at the core of metabolic/mitochondrial diseases, such as obesity and diabetes, and of cancer and neurodegeneration. Here, we discuss how maintaining or raising NAD(+) levels can improve metabolism and prevent age-related functional decline and associated disease, and how basic scientific discoveries in the NAD(+) signaling pathway are being translated to the clinic.
Controllable Self-Assembly of Nanoparticles for Specific Delivery of Multiple Therapeutic Molecules to Cancer Cells Using RNA Nanotechnology (2005)

By utilizing RNA nanotechnology, we engineered both therapeutic siRNA and a receptor-binding RNA aptamer into individual pRNAs of phi29's motor. The RNA building block harboring siRNA or other therapeutic molecules was fabricated subsequently into a trimer through the interaction of engineered right and left interlocking RNA loops. The incubation of the protein-free nanoscale particles containing the receptor-binding aptamer or other ligands resulted in the binding and co-entry of the trivalent therapeutic particles into cells, subsequently modulating the apoptosis of cancer cells and leukemia model lymphocytes in cell culture and animal trials. The use of such antigenicity-free 20-40 nm particles holds promise for the repeated long-term treatment of chronic diseases.
Analysis of VH Genes in Follicular and Diffuse Lymphoma Shows Ongoing Somatic Mutation and Multiple Isotype Transcripts in Early Disease With Changes During Disease Progression (1998)

Investigations of VH gene mutational patterns in B-cell tumors are often performed at an arbitrary time point of disease. To assess the effects of disease progression, tumor-derived VHgenes have been monitored from presentation through treatment and relapse in one patient with follicle center lymphoma (FCL), and two patients with primary diffuse large B-cell lymphoma (DLCL). The patient with FCL and one patient with DLCL both achieved clinical remission, although this was only partial in the FCL. However, both subsequently relapsed, and the second patient with DLCL was refractory to radiotherapy and chemotherapy. In each case, the tumor-derived VH sequence was identified, and the CDR3 “clonal signature” was used to track tumor cell sequences in subsequent biopsies. All cases showed somatic mutations, with intraclonal heterogeneity evident at presentation, and some sequences were aberrant. The VH sequences of the DLCL which responded to treatment became homogeneous at relapse. The sequences of both the FCL and the refractory DLCL remained heterogeneous. In all cases, transcripts of multiple Ig isotypes could be identified, and there was immunophenotypic evidence for expression of several Ig isotypes. The case of refractory DLCL had identifiable transcripts from IgM, IgD, IgA, IgG, and IgE, but appeared to lose the ability to produce alternative isotype transcripts and protein at the late stage of disease. These cases indicate that VH gene analysis can be used to probe tumor cell behavior in cases of lymphoma and that perturbations caused by therapy and disease progression can occur.
Declining Plasma Fibrinogen Alpha Fragment Identifies HER2-Positive Breast Cancer Patients and Reverts to Normal Levels after Surgery (2006)

Breast cancer is the most common nonskin malignancy affecting women. Currently, no simple, blood-based diagnostic test exists to complement radiological screening and increase sensitivity of detection. To screen plasma specimens and identify biomarkers that detect HER2-positive breast cancer, automated robotic sample processing followed by surface-enhanced laser desorption ionization time-of-flight (SELDI-TOF) mass spectroscopy was used. Multiple statistical algorithms were used to select biomarkers that segregate cancer patients versus controls and produced average CV rates ranging from 20% to 29%. A set of seven biomarkers were validated on an independent test data set and achieved the best error rate of 19.1%. A permutation test indicated a p-value for CV error less than 0.002. Moreover, a ROC curve using these biomarkers achieved an area-under-the-curve value of 0.95 on an independent test data set. The marker responsible for most of the resolving power was identified as a fragment of Fibrinogen Alpha (FGA) encompassing residues 605-629. This marker was present at lower levels in cancer patients as compared to controls. The importance of this biomarker was validated in a longitudinal study comparing pre- and post-operative levels and was shown to revert to normal levels after surgery. This fragment may serve as a useful diagnostic and treatment-monitoring marker.
In Vivo Tracking of Human Hematopoiesis Reveals Patterns of Clonal Dynamics during Early and Steady-State Reconstitution Phases (2016)

Hematopoietic stem/progenitor cells (HSPCs) are capable of supporting the lifelong production of blood cells exerting a wide spectrum of functions. Lentiviral vector HSPC gene therapy generates a human hematopoietic system stably marked at the clonal level by vector integration sites (ISs). Using IS analysis, we longitudinally tracked >89,000 clones from 15 distinct bone marrow and peripheral blood lineages purified up to 4 years after transplant in four Wiskott-Aldrich syndrome patients treated with HSPC gene therapy. We measured at the clonal level repopulating waves, populations' sizes and dynamics, activity of distinct HSPC subtypes, contribution of various progenitor classes during the early and late post-transplant phases, and hierarchical relationships among lineages. We discovered that in-vitro-manipulated HSPCs retain the ability to return to latency after transplant and can be physiologically reactivated, sustaining a stable hematopoietic output. This study constitutes in vivo comprehensive tracking in humans of hematopoietic clonal dynamics during the early and late post-transplant phases.
Purification of the mRNA for chicken very low density lipoproteirtIIand molecular cloning of its full-length double-stranded cDNA (1979)

The mRNA coding for the small apo-Very Low Density Lipoprotein (apo-VLDLII) from chicken serum was highly enriched by oligo(dT) chromatography and preparative gel electrophoresis of estrogenised liver RNA. Double-stranded cDNA was synthesised by the subsequent actions of reverse transcriptase and DNA polymerase, and used for a preliminary characterisation of the structural gene. Molecular cloning of dC-tailed ds-cDNA into the Pst I site of plasmid pBR 322 yielded several recombinant clones. Five chimeric DNAs were selected and characterised by restriction enzyme mapping and electron microscopy of R-loops. At least two of them (pVLDLII 3.33 and pVLDLII 4.82) contain an almost full-length ds-transcript of VLDLII mRNA in which no more than 10-20 bases at the 5'- end are missing.
Epidemiology of Uterine Fibroids (2016)

Uterine leiomyomata (UL) have a substantial impact on women's health, but relatively few studies have identified opportunities for primary prevention of these neoplasms. Most established risk factors are not modifiable, including premenopausal age, African ancestry, age at menarche, and childbearing history. The main challenge in studying UL is that a large proportion of tumors are asymptomatic. Herein, we review the epidemiology of UL from published studies to date. We highlight the advantages of ultrasound screening studies and the ways in which their innovative methods have helped clarify the etiology of disease. We conclude with a discussion of promising new hypotheses.
Overcoming deception in evolution of cognitive behaviors (2014)

When scaling neuroevolution to complex behaviors, cognitive capabilities such as learning, communication, and memory become increasingly important. However, successfully evolving such cognitive abilities remains difficult. This paper argues that a main cause for such difficulty is deception, i.e. evolution converges to a behavior unrelated to the desired solution. More specifically, cognitive behaviors often require accumulating neural structure that provides no immediate fitness benefit, and evolution often thus converges to non-cognitive solutions. To investigate this hypothesis, a common evolutionary robotics T-Maze domain is adapted in three separate ways to require agents to communicate, remember, and learn. Indicative of deception, evolution driven by objective-based fitness often converges upon simple non-cognitive behaviors. In contrast, evolution driven to explore novel behaviors, i.e. novelty search, often evolves the desired cognitive behaviors. The conclusion is that open-ended methods of evolution may better recognize and reward the stepping stones that are necessary for cognitive behavior to emerge.
Accounting for All Costs in the Total Cost of Chimeric Antigen Receptor T-Cell Immunotherapy (2018)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
All are not equal: A benchmark of different homology modeling programs (2005)

Modeling a protein structure based on a homologous structure is a standard method in structural biology today. In this process an alignment of a target protein sequence onto the structure of a template(s) is used as input to a program that constructs a 3D model. It has been shown that the most important factor in this process is the correctness of the alignment and the choice of the best template structure(s), while it is generally believed that there are no major differences between the best modeling programs. Therefore, a large number of studies to benchmark the alignment qualities and the selection process have been performed. However, to our knowledge no large-scale benchmark has been performed to evaluate the programs used to transform the alignment to a 3D model. In this study, a benchmark of six different homology modeling programs- Modeller, SegMod/ENCAD, SWISS-MODEL, 3D-JIGSAW, nest, and Builder-is presented. The performance of these programs is evaluated using physiochemical correctness and structural similarity to the correct structure. From our analysis it can be concluded that no single modeling program outperform the others in all tests. However, it is quite clear that three modeling programs, Modeller, nest, and SegMod/ ENCAD, perform better than the others. Interestingly, the fastest and oldest modeling program, SegMod/ ENCAD, performs very well, although it was written more than 10 years ago and has not undergone any development since. It can also be observed that none of the homology modeling programs builds side chains as well as a specialized program (SCWRL), and therefore there should be room for improvement.
VHL Inactivation Induces HEF1 and Aurora Kinase A (2010)

The ciliary hypothesis for cystic renal diseases postulates that most of these conditions result from abnormalities in the primary cilium, a microtubule-based structure that acts as a sensor for extracellular cues. Inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene predisposes to renal cysts and clear cell renal cell carcinoma. VHL plays a critical role in the formation of primary cilia in kidney epithelium, but the underlying mechanisms are poorly understood. Here, we demonstrate that VHL inactivation induces HEF1/Cas-L/NEDD9 and Aurora kinase A via the stabilization of hypoxia-inducible factors 1 and 2. Aurora kinase A is a mitotic kinase commonly upregulated in cancer that causes regression of the primary cilium by promoting histone deacetylase-dependent tubulin depolymerization of the ciliary axoneme. HEF1/Cas-L/NEDD9 is a component of focal adhesions that has a prominent role in inducing metastasis and that colocalizes with Aurora kinase A at the centrosome, thereby enhancing the harmful effect of Aurora kinase A on the cilium. Suppression of this pathway improved the formation of primary cilia and reduced cell motility in VHL-defective renal cancer cells. Our results highlight the gatekeeper role of VHL in the kidney epithelium.
Thymidylate Synthase Expression in Colorectal Cancer: A Prognostic and Predictive Marker of Benefit From Adjuvant Fluorouracil-Based Chemotherapy (2002)

TS expression predicts for survival independent of Dukes' stage in patients with CRC treated with surgery alone. The study indicates that patients with high TS levels may benefit from adjuvant 5-FU-based chemotherapy. However, patients with low TS levels seem to have a worse outcome when treated with adjuvant chemotherapy.
Isopoly-L-ornithine Derivatives of Thymine and Thymidine (1998)

Abstract L-Ornithine derivatives of thymine, and thymidine gave oligomers by solid phase elongation reactions. These oligomers 2 and 3, however, hardly interact with the complementary polynucleotide. Conformational studies of the oligomers with CD and NMR revealed that stable intramolecular hydrogen bonding was formed between thymine base and ornithine unit.
Volumetric Capture of Humans With a Single RGBD Camera via Semi-Parametric Learning (2019)

Volumetric (4D) performance capture is fundamental for AR/VR content generation. Whereas previous work in 4D performance capture has shown impressive results in studio settings, the technology is still far from being accessible to a typical consumer who, at best, might own a single RGBD sensor. Thus, in this work, we propose a method to synthesize free viewpoint renderings using a single RGBD camera. The key insight is to leverage previously seen “calibration” images of a given user to extrapolate what should be rendered in a novel viewpoint from the data available in the sensor. Given these past observations from multiple viewpoints, and the current RGBD image from a fixed view, we propose an end-to-end framework that fuses both these data sources to generate novel renderings of the performer. We demonstrate that the method can produce high fidelity images, and handle extreme changes in subject pose and camera viewpoints. We also show that the system generalizes to performers not seen in the training data. We run exhaustive experiments demonstrating the effectiveness of the proposed semi-parametric model (i.e. calibration images available to the neural network) compared to other state of the art machine learned solutions. Further, we compare the method with more traditional pipelines that employ multi-view capture. We show that our framework is able to achieve compelling results, with substantially less infrastructure than previously required.
Selective loss of sarcolemmal nitric oxide synthase in Becker muscular dystrophy. (1996)

Becker muscular dystrophy is an X-linked disease due to mutations of the dystrophin gene. We now show that neuronal-type nitric oxide synthase (nNOS), an identified enzyme in the dystrophin complex, is uniquely absent from skeletal muscle plasma membrane in many human Becker patients and in mouse models of dystrophinopathy. An NH2-terminal domain of nNOS directly interacts with alpha 1-syntrophin but not with other proteins in the dystrophin complex analyzed. However, nNOS does not associate with alpha 1-syntrophin on the sarcolemma in transgenic mdx mice expressing truncated dystrophin proteins. This suggests a ternary interaction of nNOS, alpha 1-syntrophin, and the central domain of dystrophin in vivo, a conclusion supported by developmental studies in muscle. These data indicate that proper assembly of the dystrophin complex is dependent upon the structure of the central rodlike domain and have implications for the design of dystrophin-containing vectors for gene therapy.
Docosahexaenoic Acid Therapy of Experimental Ischemic Stroke (2010)

We examined the neuroprotective efficacy of docosahexaenoic acid (DHA), an omega-3 essential fatty acid family member, in acute ischemic stroke; studied the therapeutic window; and investigated whether DHA administration after an ischemic stroke is able to salvage the penumbra. In each series described below, SD rats underwent 2 h of middle cerebral artery occlusion (MCAo). In series 1, DHA or saline was administered i.v. at 3, 4, 5, or 6 h after stroke. In series 2, MRI was conducted on days 1, 3 and 7. In series 3, DHA or saline was administered at 3 h, and lipidomic analysis was conducted on day 3. Treatment with DHA significantly improved behavior and reduced total infarct volume by a mean of 40% when administered at 3 h, by 66% at 4 h, and by 59% at 5 h. Total lesion volumes computed from T2-weighted images were reduced in the DHA group at all time points. Lipidomic analysis showed that DHA treatment potentiates neuroprotectin D1 (NPD1) synthesis in the penumbra 3 days after MCAo. DHA administration provides neurobehavioral recovery, reduces brain infarction and edema, and activates NPD1 synthesis in the penumbra when administered up to 5 h after focal cerebral ischemia in rats.
Changing paradigms in management of metastatic Castration Resistant Prostate Cancer (mCRPC) (2014)

Recently, the standard of care for metastatic Castration Resistant Prostate Cancer (mCRPC) has changed considerably. Persistent androgen receptor (AR) signaling has been identified as a target for novel therapies and reengages the fact that AR continues to be the primary target responsible for metastatic prostate cancer. Androgen receptor gene amplification and over expression have been found to result in a higher concentration of androgen receptors on tumor cells, making them extremely sensitive to low levels of circulating androgens. Additionally, prostate cancer cells are able to maintain dihydrotestosterone (DHT) concentration in excess of serum concentrations to support tumor growth. For many years ketoconazole was the only CYP17 inhibitor that was used to treat mCRPC. However, significant toxicities limit its use. Newly approved chemotherapeutic agents such as Abiraterone (an oral selective inhibitor of CYP17A), which blocks androgen biosynthesis both within and outside the prostate cancer cells), and enzalutamide (blocks AR signaling) have improved overall survival. There are also ongoing phase III trials for Orteronel (TAK- 700), ARN- 509 and Galeterone (TOK-001), which targets androgen signaling. In this review, we will present the rationale for the newly approved hormonal treatments, their indications and complications, and we will discuss ongoing trials that are being done to improve the efficacy of the approved agents. Finally, we will talk about the potential upcoming hormonal treatments for mCRPC.
Imaging in scattering media by use of laser speckle (1997)

We present a method for the detection and localization of inhomogeneities embedded within highly scattering media that employs speckle statistics with a partially coherent light source. Variations in speckle contrast as a function of position are used to interrogate inhomogeneities deeply embedded within scattering media. A numerical model based on photon diffusion theory is introduced to predict speckle contrast as a function of scan position. This model uses measured speckle data to determine scattering and absorption parameters.
Electronic Transport in 8 Mole Percent  Y 2 O 3 ‐ ZrO2 (1989)

By means of a gas‐tight electrochemical cell, oxygen permeation measurements have been performed on the oxygen ion conductor 8 mole percent (m/o) yttria‐stabilized zirconia, as a function of (800°–1050°C) and (0.21–10−17 atm). Ionic conductivity was measured by the conventional four‐probe method. The following empirical equations were derived for the ion, electron, and hole conductivities, in ohm−1 cm−1
Subband-domain filtering of MPEG audio signals (1999)

The cosine modulated filter bank is commonly used for the time-frequency decomposition of audio signals. For example, it is a basic element of the MPEG-1 and MPEG-2 audio coding standards. While this filter bank is not perfectly-reconstructing, it does provide for the cancelation of aliasing components that are introduced during the analysis decomposition. If the subband signals are to be processed, care must be taken to preserve the properties of the subband signals such that the aliased terms will be canceled successfully in the synthesis filter bank despite the modification of the subband signals. In this paper, a framework is provided for the generation and application of arbitrary FIR filters to signals that have been decomposed using the MPEG filter bank.
Targeting the Angiopoietin/Tie2 Pathway: Cutting Tumor Vessels With a Double-Edged Sword? (2011)

Article Tools UNDERSTANDING THE PATHWAY Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.2011.38.7621 Journal of Clinical Oncology - published online before print December 19, 2011 PMID: 22184396 Targeting the Angiopoietin/Tie2 Pathway: Cutting Tumor Vessels With a Double-Edged Sword? Tina CasconexTina CasconeSearch for articles by this author , John V. HeymachxJohn V. HeymachSearch for articles by this author Show More The University of Texas MD Anderson Cancer Center, Houston, TX https://doi.org/10.1200/JCO.2011.38.7621 First Page Full Text PDF Figures and Tables Supplements © 2011 by American Society of Clinical Oncology