gebhart/patrepeval huggingface dataset:
Tissue-specific promoters regulate aromatase cytochrome P450 expression (1993)

In humans, estrogen biosynthesis occurs in several tissue sites, including ovary, placenta, adipose, and brain. Recent work from our laboratory indicates that tissue-specific expression of aromatase cytochrome P450 (P450arom), the enzyme responsible for estrogen biosynthesis, is determined, in part, by the use of tissue-specific promoters. Thus, the expression of P450arom in human ovary appears to utilize a promoter proximal to the translation start site. This promoter is not utilized in placenta; instead, the promoter used to drive aromatase expression in placenta is > or = 40 kb upstream from the translational start site. In addition, a minor promoter used in the expression of a small proportion of placental transcripts is 9 kb upstream from the start of translation. Transcripts from these promoters are also expressed in other fetal tissues, including placenta-related cells such as JEG-3 choriocarcinoma cells and hydatidiform moles and other fetal tissues such as fetal liver. In adipose tissue, on the other hand, expression of P450arom may be achieved by yet another, adipose-specific promoter. The various 5'-untranslated exons unique for expression driven by each of these promoters are spliced into a common intron/exon boundary upstream from the translational start site. This means that the protein expressed in each of the various tissue-specific sites of estrogen biosynthesis is identical.
Inhibition Of Call-Cell Binding By Kipid Assemblies (2003)

This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.
Predicting escalations of medical queries based on web page structure and content (2010)

Logs of users' searches on Web health topics can exhibit signs of escalation of medical concerns, where initial queries about common symptoms are followed by queries about serious, rare illnesses. We present an effort to predict such escalations based on the structure and content of pages encountered during medical search sessions. We construct and then characterize the performance of classifiers that predict whether an escalation will occur after the access of a page. Our findings have implications for ranking algorithms and the design of search interfaces.
Lack of Toll-like receptor 4 or myeloid differentiation factor 88 reduces atherosclerosis and alters plaque phenotype in mice deficient in apolipoprotein E (2004)

Toll-like receptors (TLRs) and the downstream adaptor molecule myeloid differentiation factor 88 (MyD88) play an essential role in the innate immune responses. Here, we demonstrate that genetic deficiency of TLR4 or MyD88 is associated with a significant reduction of aortic plaque areas in atherosclerosis-prone apolipoprotein E-deficient mice, despite persistent hypercholesterolemia, implying an important role for the innate immune system in atherogenesis. Apolipoprotein E-deficient mice that also lacked TLR4 or MyD88 demonstrated reduced aortic atherosclerosis that was associated with reductions in circulating levels of proinflammatory cytokines IL-12 or monocyte chemoattractant protein 1, plaque lipid content, numbers of macrophage, and cyclooxygenase 2 immunoreactivity in their plaques. Endothelial-leukocyte adhesion in response to minimally modified low-density lipoprotein was reduced in aortic endothelial cells derived from MyD88-deficient mice. Taken together, our results suggest an important role for TLR4 and MyD88 signaling in atherosclerosis in a hypercholesterolemic mouse model, providing a pathophysiologic link between innate immunity, inflammation, and atherogenesis.
CueTIP (2006)

With advances in pen-based computing devices, handwriting has become an increasingly popular input modality. Researchers have put considerable effort into building intelligent recognition systems that can translate handwriting to text with increasing accuracy. However, handwritten input is inherently ambiguous, and these systems will always make errors. Unfortunately, work on error recovery mechanisms has mainly focused on interface innovations that allow users to manually transform the erroneous recognition result into the intended one. In our work, we propose a mixed-initiative approach to error correction. We describe CueTIP, a novel correction interface that takes advantage of the recognizer to continually evolve its results using the additional information from user corrections. This significantly reduces the number of actions required to reach the intended result. We present a user study showing that CueTIP is more efficient and better preferred for correcting handwriting recognition errors. Grounded in the discussion of CueTIP, we also present design principles that may be applied to mixed-initiative correction interfaces in other domains.
Understanding transportation modes based on GPS data for web applications (2010)

User mobility has given rise to a variety of Web applications, in which the global positioning system (GPS) plays many important roles in bridging between these applications and end users. As a kind of human behavior, transportation modes, such as walking and driving, can provide pervasive computing systems with more contextual information and enrich a user's mobility with informative knowledge. In this article, we report on an approach based on supervised learning to automatically infer users' transportation modes, including driving, walking, taking a bus and riding a bike, from raw GPS logs. Our approach consists of three parts: a change point-based segmentation method, an inference model and a graph-based post-processing algorithm. First, we propose a change point-based segmentation method to partition each GPS trajectory into separate segments of different transportation modes. Second, from each segment, we identify a set of sophisticated features, which are not affected by differing traffic conditions (e.g., a person's direction when in a car is constrained more by the road than any change in traffic conditions). Later, these features are fed to a generative inference model to classify the segments of different modes. Third, we conduct graph-based postprocessing to further improve the inference performance. This postprocessing algorithm considers both the commonsense constraints of the real world and typical user behaviors based on locations in a probabilistic manner. The advantages of our method over the related works include three aspects. (1) Our approach can effectively segment trajectories containing multiple transportation modes. (2) Our work mined the location constraints from user-generated GPS logs, while being independent of additional sensor data and map information like road networks and bus stops. (3) The model learned from the dataset of some users can be applied to infer GPS data from others. Using the GPS logs collected by 65 people over a period of 10 months, we evaluated our approach via a set of experiments. As a result, based on the change-point-based segmentation method and Decision Tree-based inference model, we achieved prediction accuracy greater than 71 percent. Further, using the graph-based post-processing algorithm, the performance attained a 4-percent enhancement.
Raman spectroscopy for cancer detection: instrument development and tissue diagnosis (1994)

Raman spectroscopy can provide quantitative molecular information about the biochemical composition of human tissues exhibiting various stages of disease. Fluorescence interference is ubiquitous in Raman spectra of biological samples excited with visible light. However, it can be avoided by using near-infrared (NIR) or ultraviolet (UV) excitation. We are exploring the potential of these methods for detecting precancerous/cancerous changes in human tissues. The NIR studies use 830 nm excitation from a Ti:sapphire laser. Raman signals are collected by an imaging spectrograph/deep-depletion CCD detection system. High quality tissue spectra can be obtained in a few seconds or less. The UV resonance Raman studies employ wavelengths below 300 nm for selective excitation of nucleic acids, proteins and lipids. Excitation is provided by a frequency tripled/quadrupled mode-locked Ti:sapphire laser, and Raman light is collected by a one meter spectrograph/UV-enhanced CCD detector. The two systems can be coupled to appropriate microscopes for extracting morphological and biochemical information at the cellular level, which is important for understanding the origin of the Raman spectra of bulk tissue. The results of the initial studies for cancer detection in various human tissues are reported here.
Trihydroxamate Siderophore–Fluoroquinolone Conjugates Are Selective Sideromycin Antibiotics that Target Staphylococcus aureus (2013)

Siderophores are multidentate iron(III) chelators used by bacteria for iron assimilation. Sideromycins, also called siderophore–antibiotic conjugates, are a unique subset of siderophores that enter bacterial cells via siderophore uptake pathways and deliver the toxic antibiotic in a “Trojan horse” fashion. Sideromycins represent a novel antibiotic delivery technology with untapped potential for developing sophisticated microbe-selective antibacterial agents that limit the emergence of bacterial resistance. The chemical synthesis of a series of mono-, bis-, and trihydroxamate sideromycins are described here along with their biological evaluation in antibacterial susceptibility assays. The linear hydroxamate siderophores used for the sideromycins in this study were derived from the ferrioxamine family and inspired by the naturally occurring salmycin sideromycins. The antibacterial agents used were a β-lactam carbacepholosporin, Lorabid, and a fluoroquinolone, ciprofloxacin, chosen for the different locations of their biological targets, the periplasm (extracellular) and the cytoplasm (intracellular). The linear hydroxamate-based sideromycins were selectively toxic toward Gram-positive bacteria, especially Staphylococcus aureus SG511 (MIC = 1.0 μM for the trihydroxamate–fluoroquinolone sideromycin). Siderophore–sideromycin competition assays demonstrated that only the fluoroquinolone sideromycins required membrane transport to reach their cytoplasmic biological target and that a trihydroxamate siderophore backbone was required for protein-mediated active transport of the sideromycins into S. aureus cells via siderophore uptake pathways. This work represents a comprehensive study of linear hydroxamate sideromycins and teaches how to build effective hydroxamate-based sideromycins as Gram-positive selective antibiotic agents.
A Monoclonal Antibody Against the Oncogenic Mucin 1 Cytoplasmic Domain (2011)

Mucin 1 (MUC1) is a heterodimeric protein that is aberrantly overexpressed in diverse human carcinomas and certain hematologic malignancies. The transmembrane MUC1-C subunit confers tumorigenicity and is a target for anti-cancer drug development. In this regard, the MUC1-C cytoplasmic domain interacts with multiple effectors that have been linked to transformation. Here we report on the generation of a mouse monoclonal antibody (MAb) against the human MUC1-C cytoplasmic domain (MUC1-CD). This IgG1 MAb, designated anti-MUC1-CD, reacts with the NYGQLDIFP epitope. We show that anti-MUC1-CD is useful in immunoblotting and immunoprecipitation experiments. In addition, anti-MUC1-CD can be used to detect expression of the MUC1-C subunit in formalin-fixed, paraffin-embedded tissues. The MUC1-C inhibitor has entered Phase I evaluation for patients with refractory solid tumors. The present results indicate that the anti-MUC1-CD antibody could be useful as a biomarker to identify patients with tumors that may be responsive to MUC1-C inhibitors.
Bipyramid-templated synthesis of monodisperse anisotropic gold nanocrystals (2015)

Much of the interest in noble metal nanoparticles is due to their plasmonic resonance responses and local field enhancement, both of which can be tuned through the size and shape of the particles. However, both properties suffer from the loss of monodispersity that is frequently associated with various morphologies of nanoparticles. Here we show a method to generate diverse and monodisperse anisotropic gold nanoparticle shapes with various tip geometries as well as highly tunable size augmentations through either oxidative etching or seed-mediated growth of purified, monodisperse gold bipyramids. The conditions employed in the etching and growth processes also offer valuable insights into the growth mechanism difficult to realize with other gold nanostructures. The high-index facets and more complicated structure of the bipyramid lead to a wider variety of intriguing regrowth structures than in previously studied nanoparticles. Our results introduce a class of gold bipyramid-based nanoparticles with interesting and potentially useful features to the toolbox of gold nanoparticles.
CMOS Photonics Using Germanium Photodetectors (2006)

Today, CMOS Photonics technology has matured so that most waveguide based optical functions are available inside a CMOS die. While an integrated light source is still an outstanding problem, photodetection can be accomplished by the addition of pure germanium photodetectors to the CMOS process. These components have the potential to enable outstanding sensitivity levels when integrated monolithically with CMOS circuitry.
Biotemplated Synthesis of Perovskite Nanomaterials for Solar Energy Conversion (2012)

A synthetic method of using genetically engineered M13 virus to mineralize perovskite nanomaterials, particularly strontium titanate (STO) and bismuth ferrite (BFO), is presented. Genetically engineered viruses provide effective templates for perovskite nanomaterials. The virus-templated nanocrystals are small in size, highly crystalline, and show photocatalytic and photovoltaic properties.
Grating acoustic scanner using bulk acoustic waves (1981)

A new type of electronically scanned and focused acoustic beam scanner, based on coherent scattering of a grazing incident bulk wave with chirped frequencies by an array of surface grooves, is discussed. Experimental results of a 40 MHz bulk wave grating acoustic scanner with 1" field of view and 300 μm lateral resolution will be presented as a feasibility demonstration.
An advanced multipurpose dental adhesive system (1995)

An advanced dental adhesive system, composed of acrylic monomers and coupling agents, characterized by high tensile bond strength, enhanced durability, and biocompatibility was developed. The adhesive composition is curable chemically (self curing) or by visible light. This adhesive composition can be used for bonding to various substrates such as dentin, enamel, precious and nonprecious alloys, 'fresh' and 'set' amalgam, porcelain, and dental composite. Thus, the developed liquid adhesive composition could be considered as a universal dental adhesive.
Engineered Cell Penetrating Peptides (2017)

Cell penetrating peptides (CPPs) have shown promise in delivery of therapeutics into cells. CPPs can be described as short amino acid sequences, typically <40-mer, that is able to readily translocate across the cell membranes. The properties and uptake mechanism depend largely on the amino acid sequence, which dictates the CPP secondary structure and overall interactions with the phospholipid bilayer. This book chapter aims to give a general overview on the various classes of CPPs, the cell-entry mechanisms, and published pre-clinical and clinical trials using CPPs.
PAR reduction for DMT systems with unloaded subchannels (2003)

The inverse discrete Fourier transform used by discrete multitone modulation produces transmitted signals with a large peak-to-average ratio. Peak-to-average ratio reduction methods allow the transmitter to reduce the probability of clipping, or maintain the same probability of clipping while reducing the dynamic range requirements of the analog front end. In this paper we propose a method of peak-to-average ratio reduction that uses unloaded subchannels to prevent clipping in the transmitted signal. Considerations such as efficient adaptation methods and extensions to compensate for upsampling and filtering are addressed.
High-Q, over-coupled tuning for near-field RFID systems (2016)

Commonly, near field RFID is used in situations where a tag is brought close to some device that is to read the identity of the tag thereby enabling some action: unlocking a door, reading payment information at a merchant's register, or sharing social information between enabled devices. In all these cases, the ergonomics of the physical reading process can be hindered if read range requires a user to awkwardly maneuver the tag near the reader until a read is achieved. One way to facilitate an extended and reliable read range borrows on knowledge from the wireless power transfer community where it is known that increasing the Quality factor of the reader or tag coil will increase power transfer. However, RFID engineers have typically limited maximum coil Q factor to about 10-20 due to the need for maintaining a system bandwidth that is broad enough to support the necessary communication data rates. To meet this challenge, this paper introduces a method of impedance matching high Q reader coils to the source known as "over-coupling" the source to the system input. On one hand, the use of high Q coils extends the range where the tag receives sufficient power to turn on, while it is over-coupling that slightly damps the system resonance, producing an effective system Q factor that simultaneously supports a bandwidth wide enough to accommodate necessary data rates. This work will show both theoretically and through experimentation that using high Q coils in the over-coupled regime supports extension of read range in near field RFID systems by 81% or more compared to the next best impedance matching strategies.
Fast and Accurate Estimation of Typed Graphlets (2020)

Typed graphlets are small typed (labeled, colored) induced subgraphs and were recently shown to be the fundamental building blocks of rich complex heterogeneous networks. In many applications, speed is more important than accuracy, and it is sufficient to trade-off a tiny amount of accuracy for a significantly faster method. In this work, we propose fast and accurate estimators for typed graphlets. The typed graphlet estimation techniques naturally support general heterogeneous graphs with any arbitrary number of types, which include bipartite, k-partite, k-star, labeled graphs, and attributed networks as special cases. The experiments demonstrate the effectiveness of the typed graphlet estimation techniques.
A Novel E3 Ubiquitin Ligase Substrate Screen Identifies Rho Guanine Dissociation Inhibitor as a Substrate of Gene Related to Anergy in Lymphocytes (2006)

Ubiquitination of eukaryotic proteins regulates a broad range of cellular processes, including regulation of T cell activation and tolerance. We have previously demonstrated that gene related to anergy in lymphocytes (GRAIL), a ring finger ubiquitin E3 ligase, is required for the induction of T cell anergy; however, the substrate(s) for GRAIL E3 ligase activity is/are unknown. In this study, we report a novel prokaryotic system developed to screen for substrates of E3 ligases. Using this screen, Rho guanine dissociation inhibitor (RhoGDI) was identified as a potential substrate of GRAIL. GRAIL was subsequently demonstrated to bind and ubiquitinate RhoGDI, although GRAIL-mediated ubiquitination of RhoGDI did not result in proteosomal degradation. Expression of GRAIL in T cells resulted in specific inhibition of RhoA GTPase activation; activation of Rac1, cdc42, and Ras GTPases were not affected. Interestingly, stable T cell lines expressing dominant-negative RhoA mimicked the GRAIL-mediated IL-2 inhibition phenotype, and T cells expressing constitutively active RhoA were able to overcome GRAIL-mediated inhibition of IL-2 expression. These findings validate our prokaryotic screen as a method of identifying substrates for ubiquitin E3 ligases and suggest a role for Rho effector molecules in T cell anergy.
A Fragment of Prosaposin (SGP‐1) from Rooster Sperm Promotes Sperm‐Egg Binding and Improves Fertility in Chickens (2001)

A protein isolated from the supernatant of cryopreserved rooster sperm was found to increase the capability of cryopreserved rooster sperm to bind in vitro to the perivitelline membrane of a chicken egg and substantially raise fertility after artificial insemination (AI). That activity was partially purified and termed universal primary sperm-egg binding protein (UPSEBP). Insufficient protein remained from 6 x 10(11) sperm, despite retention of bioactivity, to allow sequencing. We deduced that the protein may be related to prosaposin (also termed SGP-1, for sulfated glycoprotein-1), and we used published amino acid sequences of prosaposin as a guide for synthesis of peptides. Certain peptides were found to increase in vitro sperm-egg binding and increase fertility of frozen-thawed or fresh rooster sperm, in a manner similar to semipurified UPSEBP. Active epitopes were in a 60 amino acid sequence, reflecting the intervening sequence between saposins A and B, plus short extensions into saposins A and B. Highest activity was found when this synthetic peptide was oxidized to form a disulfide bond between terminal cysteines. Antibody against a synthetic peptide consisting of 58 of these 60 amino acids bound to a 7-9 kilodalton protein in UPSEBP. Collectively, the data support the conclusion that UPSEBP is a fragment of prosaposin. Because prosaposin is in semen in humans and animals, these observations have broad implications for possible cause and therapy of one type of subfertility.
Photochemical Ablation of Intestinal Mucosa for Bladder Augmentation (1994)

Complications associated with enterocystoplasty include mucus production, electrolyte abnormalities, infections, stones and cancer at the vesicoenteric anastomosis. Removal of the intestinal mucosa with subsequent urothelialization may obviate these problems. We describe a unique approach whereby photodynamic therapy is used to de-epithelialize an ileal segment before augmentation. Enterocystoplasty was performed in 32 female Fischer 344 rats using a 1.5 cm. patch of terminal ileum. Of the 32 rats 24 survived at least 6 weeks before euthanasia. The experimental group (10 rats) received hematoporphyrin derivative intravenously 24 hours before surgery. The ileal patch was treated with red light for 20 minutes and then used for augmentation. There were 3 control groups, including 1 group of 5 rats that underwent augmentation alone, while the other 2 groups were augmented but received either light treatment (4 rats) or hematoporphyrin derivative (5 rats). Histological analysis revealed urothelialization of the augments treated with hematoporphyrin derivative and light, which did not occur in the controls. The preoperative and postoperative bladder capacities increased substantially in all groups. Mucus production and bacterial colonization were reduced while stone formation increased in the treated animals.