gebhart/patrepeval huggingface dataset:
Data from Activator Protein-1 Activity Regulates Epithelial Tumor Cell Identity (2023)

&lt;div&gt;Abstract&lt;p&gt;To examine the consequences of inhibiting activator protein-1 (AP-1) transcription factors in skin, transgenic mice were generated, which use the tetracycline system to conditionally express A-FOS, a dominant negative that inhibits AP-1 DNA binding. Older mice develop mild alopecia and hyperplasia of sebaceous glands, particularly around the eyes. When A-FOS was expressed during chemical-induced skin carcinogenesis, mice do not develop characteristic benign and malignant squamous lesions but instead develop benign sebaceous adenomas containing a signature mutation in the &lt;i&gt;H-ras&lt;/i&gt; proto-oncogene. Inhibiting AP-1 activity after tumor formation caused squamous tumors to transdifferentiate into sebaceous tumors. Furthermore, reactivating AP-1 in sebaceous tumors results in a reciprocal transdifferentiation into squamous tumors. In both cases of transdifferentiation, individual cells express molecular markers for both cell types, indicating individual tumor cells have the capacity to express multiple lineages. Molecular characterization of cultured keratinocytes and tumor material indicates that AP-1 regulates the balance between the wnt/β-catenin and hedgehog signaling pathways that determine squamous and sebaceous lineages, respectively. Chromatin immunoprecipitation analysis indicates that c-Jun binds several wnt promoters, which are misregulated by A-FOS expression, suggesting that members of the wnt pathway can be a primary targets of AP-1 transcriptional regulation. Thus, AP-1 activity regulates tumor cell lineage and is essential to maintain the squamous tumor cell identity. (Cancer Res 2006; 66(15): 7578-88)&lt;/p&gt;&lt;/div&gt;
A Readily Scalable, Clinically Demonstrated, Antibiofouling Zwitterionic Surface Treatment for Implantable Medical Devices (2022)

Unlike growth on tissue, microbes can grow freely on implantable devices with minimal immune system intervention and often form resilient biofilms that continuously pump out pathogenic cells. The efficacy of antibiotics used to treat infection is declining due to increased rates of pathogenic resistance. A simple, one-step zwitterionic surface modification is developed to significantly reduce protein and microbial adhesion to synthetic materials and demonstrate the successful modification of several clinically relevant materials, including recalcitrant materials such as elastomeric polydimethylsiloxane. The treated surfaces exhibit robust adhesion resistance against proteins and microorganisms in both static and flow conditions. Furthermore, the surface treatment prevents the adhesion of mammalian fibroblast cells while displaying no cytotoxicity. To demonstrate the clinical efficacy of the novel technology in the real-world, a surface-treated, commercial silicone foley catheter is developed that is cleared for use by the U.S. Food and Drug Administration (K192034). 16 long-term catheterized patients received surface-treated catheters and completed a Patient Global Impression of Improvement (PGI-I) questionnaire. 10 out of 16 patients described their urinary tract condition post implantation as "much better" or "very much better" and 72% (n = 13) of patients desire to continue using the surface-treated catheter over conventional latex or silicone catheters.
Purification and characterization of Haemophilus influenzae pili, and their structural and serological relatedness to Escherichia coli P and mannose-sensitive pili. (1985)

Haemophilus influenzae pili were purified, and their physical and serological properties were examined. The solution properties of the pili were determined, and then a purification scheme involving repeated cycles of precipitation and solubilization was developed. The purified pili from one type b isolate (A02) were found to consist of multiple copies of a 25,000 mol wt subunit. Amino-terminal sequence analysis of A02 pili was carried out to 40 amino acid residues, and a remarkable degree of sequence homology was found with E. coli P and mannose-sensitive (MS) pili (27.5 and 25% homology, respectively). Purified A02 pili were found to be highly immunogenic, and serological analysis by enzyme-linked immunosorbent assay and whole piliated cell agglutination revealed significant cross-reactivity between A02 pilus antiserum and the pili of seven other H. influenzae strains tested (heterologous titers = 2-100% of the homologous titer). Cross-reactivity was also observed between the H. influenzae pili (five of eight strains tested) and the P pili from E. coli strains HU849 and 3669; no cross-reactivity was detected with MS pili from E. coli strain H10407 and C94. The structural similarities between H. influenzae and E. coli P and MS pili suggest a common gene ancestry.
Expression of homeobox gene‐GBX2 in human prostatic cancer cells (1996)

BACKGROUND Homeobox genes encode transcription factors involved in the genetic control of normal development and differentiation, as well as in malignant transformation. To begin to assess the possible role of homeobox genes in prostatic cell carcinogenesis, we surveyed initially for expression of homeobox-containing genes in the TSU-PR1 cell line. METHODS This was performed by RT-PCR using degenerate oligodeoxyribonucleotide primers to the homeobox-binding sequence to generate partial cDNAs which were cloned and sequenced. RESULTS Using this method, expression of 14 members of homeobox-containing genes were detected in TSU-PR1 cells. All of these expressed genes correspond to previously identified homeobox genes located within the HOXA, B, C, and D clusters. We further examined the expression of these homeobox genes in different human prostatic cell lines by using whole cDNA slot blot and Northern blot analysis. One of the sequences corresponding to the human GBX2 homeobox gene is overexpressed in TSU-PR1, LNCaP, PC-3, and DU145 metastatic prostate cell lines relative to the normal prostate. CONCLUSIONS Our results suggest that the homeobox gene GBX2 may participate in metastatic progression in prostatic cancer. © 1996 Wiley-Liss, Inc.
Hydroxocobalamin dose escalation improves metabolic control in cblC (2009)

Cobalamin C (cblC), a combined form of methylmalonic acidaemia and hyperhomocysteinaemia, is recognized as the most frequent inborn error of intracellular cobalamin metabolism. This condition can be detected by expanded newborn screening and can have an acute neonatal presentation that is life-threatening if not suspected and promptly treated. Intramuscular (IM) hydroxocobalamin (OHCbl) is the main treatment for patients with cblC, but formal dosing guidelines do not exist. A clinical improvement and a decrease of plasma methylmalonic acid (MMA) and total homocysteine (tHcy) levels, and an increase in methionine are typically observed after its initiation. It is well recognized that despite treatment, long-term complications such as developmental delay and progressive visual loss, may still develop. We describe the biochemical response of a 13-year-old boy with worsening metabolic parameters despite strict adherence to a conventional treatment regimen. We progressively increased the OHCbl dose from 1 to 20 mg IM per day and observed a dose-dependent response with an 80% reduction of plasma MMA (25 to 5.14 micromol/L; normal range <0.27 micromol/L), a 55% reduction of tHcy (112 to 50 micromol/L; normal range: 0-13 micromol/L) and a greater than twofold increase in methionine (17 to 36 micromol/L; normal range: 7-47 micromol/L). This suggests that higher OHCbl doses might be required to achieve an optimal biochemical response in cblC patients, but it is unknown whether it may slow or eliminate other complications. Future clinical trials to determine the benefits of higher-dose OHCbl therapy in patients with cblC and other disorders of intracellular cobalamin metabolism should be planned.
Metal-Amplified Density Assays, (MADAs), including a Density-Linked Immunosorbent Assay (DeLISA) (2014)

This paper reports the development of Metal-amplified Density Assays, or MADAs - a method of conducting quantitative or multiplexed assays, including immunoassays, by using Magnetic Levitation (MagLev) to measure metal-amplified changes in the density of beads labeled with biomolecules. The binding of target analytes (i.e. proteins, antibodies, antigens) to complementary ligands immobilized on the surface of the beads, followed by a chemical amplification of the binding in a form that results in a change in the density of the beads (achieved by using gold nanoparticle-labeled biomolecules, and electroless deposition of gold or silver), translates analyte binding events into changes in density measureable using MagLev. A minimal model based on diffusion-limited growth of hemispherical nuclei on a surface reproduces the dynamics of the assay. A MADA - when performed with antigens and antibodies - is called a Density-Linked Immunosorbent Assay, or DeLISA. Two immunoassays provided a proof of principle: a competitive quantification of the concentration of neomycin in whole milk, and a multiplexed detection of antibodies against Hepatitis C virus NS3 protein and syphilis T. pallidum p47 protein in serum. MADAs, including DeLISAs, require, besides the requisite biomolecules and amplification reagents, minimal specialized equipment (two permanent magnets, a ruler or a capillary with calibrated length markings) and no electrical power to obtain a quantitative readout of analyte concentration. With further development, the method may be useful in resource-limited or point-of-care settings.
A Sequential Detector for Biochemical Release in Realistic Environments (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We develop a sequential detector for the release of a biochemical substance, with potential applications in environmental security. The proposed detector provides online detection of the appearance of a biochemical source in realistic complex environments. To obtain optimal performance, we use an integrated approach combining statistical analysis of measurements given by an array of biochemical sensors with a physical model of the dispersion, amenable to arbitrary geometries and wind turbulence. We first focus on formulating a detector that is applicable in the presence of unknown source parameters (e.g., release time, intensity, and location). We then derive a bound on the expected delay before a false detection in order to select the threshold of the test. For a fixed false-alarm rate, we obtain the detection probability of a release as a function of its location and initial concentration. Numerical examples illustrate the applicability of our methods to real-world scenarios of an urban area and indoor ventilation duct. </para>
Dual oxidase 2 is essential for house dust mite‐induced pro‐inflammatory cytokine production in human keratinocytes (2015)

House dust mites (HDMs) are known to trigger chronic inflammation through Toll-like receptors (TLRs) and their signalling cascades. In this study, we found that TLR2 ligation by HDMs induced the activation of dual oxidase 2 (Duox2) and nuclear factor-κB (NF-κB), leading to the production of pro-inflammatory cytokines in human keratinocytes. Stimulation of human keratinocytes with HDMs resulted in increases in interleukin-8 (IL-8) and chemokine (C-C motif) ligand 20 (CCL20) levels. However, pro-inflammatory cytokine production was abolished in keratinocytes transfected with TLR2 siRNA, indicating that HDM-induced cytokine production was mediated via TLR2 signalling. We also examined the function of Duox1/2 isozymes, which are primarily expressed in keratinocytes, in HDM-mediated pro-inflammatory cytokine production. Human keratinocytes transfected with control siRNA or Duox1 siRNA showed no inhibition of IL-8 or CCL20 production in response to HDMs, whereas the silencing of Duox2 expression resulted in a failure to induce cytokine production. Moreover, the phosphorylation and nuclear localization of RelA/p65, a component of NF-κB, were induced by HDMs in human keratinocytes. Transfection of human keratinocytes with TLR2 siRNA or Duox2 siRNA resulted in the complete abolishment of RelA/p65 nuclear localization in response to HDMs. Taken together, these results indicate that the HDM-dependent TLR2-Duox2 signalling axis indeed promotes NF-κB activation, which induces IL-8 and CCL20 production and mediates epidermal keratinocyte inflammation.
Power Law as a Method for Ultrasound Detection of Internal Bleeding: In Vivo Rabbit Validation (2010)

New detection methods for vascular injuries can augment the usability of an ultrasound (US) imager in trauma settings. The goal of this study was to evaluate a potential-detection strategy for internal bleeding that employs a well-established theoretical biofluid model, the power law. This law characterizes normal blood-flow rates through an arterial tree by its bifurcation geometry. By detecting flows that deviate from the model, we hypothesized that vascular abnormalities could be localized. We devised a bleed metric, flow-split deviation (FSD), that quantified the difference between patient and model blood flows at vessel bifurcations. Femoral bleeds were introduced into ten rabbits (∼5 kg) using a cannula attached to a variable pump. Different bleed rates (0% as control, 5%, 10%, 15%, 20%, 25%, and 30% of descending aortic flow) were created at two physiological states (rest and elevated state with epinephrine). FSDs were found by US imaging the iliac arteries. Our bleed metric demonstrated good sensitivity and specificity at moderate bleed rates; area under receiver-operating characteristic curves were greater than 0.95 for bleed rates 20% and higher. Thus, FSD was a good indicator of bleed severity and may serve as an additional tool in the US bleed detection.
ChemInform Abstract: Novel Methods to Functionalize Thiazolo[4,5‐c]pyridines. (2010)

Abstract Functionalization of the parent compound (III) as an interesting biological core structure at the 4‐ and 6‐position via the corresponding pyrido N‐oxides [cf.
HepaRG Self-Assembled Spheroids in Alginate Beads Meet the Clinical Needs for Bioartificial Liver (2020)

In liver tissue engineering, cell culture in spheroids is now well recognized to promote the maintenance of hepatic functions. However, the process leading to spheroids formation is time consuming, costly, and not easy to scale-up for further use in human bioartificial liver (BAL) applications. In this study, we encapsulated HepaRG cells (precursors of hepatocyte-like cells) in 1.5% alginate beads without preforming spheroids. Starting from a given hepatic biomass, we analyzed cell differentiation and metabolic performance for further use in a fluidized-bed BAL. We observed that cells self-rearranged as aggregates within the beads and adequately differentiated over time, in the absence of any differentiating factors classically used. On day 14 postencapsulation, cells displayed a wide range of hepatic features necessary for the treatment of a patient in acute liver failure. These activities include albumin synthesis, ammonia and lactate detoxification, and the efficacy of the enzymes involved in the xenobiotic metabolism (such as CYP1A1/2). Impact statement It has been recognized that culturing cells in spheroids (SPHs) is advantageous as they better reproduce the three-dimensional physiological microenvironment. This approach can be exploited in bioartificial liver applications, where obtaining a functional hepatic biomass is the major challenge. Our study describes an original method for culturing hepatic cells in alginate beads that makes possible the autonomous formation of SPHs after 3 days of culture. In turn, the cells differentiate adequately and display a wide range of hepatic features. They are also capable of treating a pathological plasma model. Finally, this setup can easily be scaled-up to treat acute liver failure.
Oxidative Desulfurization of Jet and Diesel Fuels Using Hydroperoxide Generated in Situ by Catalytic Air Oxidation (2010)

The objective of this work is to explore the potential of carrying out oxidative desulfurization using air as an oxidant. The liquid fuels to be desulfurized were first contacted with air to produce hydroperoxides in situ, which were then used as selective oxidants to oxidize the sulfur compounds. Unsupported CuO was tested as a catalyst for producing hydroperoxides in the fuel at 120 °C in the presence of air. Air oxidation was also carried out in the presence of Al2O3-supported CuO and also noncatalytically. Unsupported CuO was substantially more active than the other two cases. The yield of the hydroperoxides depends strongly on the catalyst and the reaction temperature; the yield decreased in the order of 120 °C > 140 °C ≫ 100 °C but the rate of oxidation to produce hydroperoxides decreased in the order of 140 °C > 120 °C ≫ 100 °C. It was found that more hydroperoxides could be generated in diesel fuel than in jet fuel, which might be related to the higher concentration of alkyl aromatics in diesel fuel when compared to JP-8 jet fuel. The hydroperoxides generated in situ were then used to oxidize the sulfur compounds in the fuel in the presence of SiO2-supported MoO3 catalyst. Hydroperoxides generated in situ were effective in oxidizing the alkyl-substituted benzothiophene and dibenzothiophene present in jet and diesel fuels to their corresponding sulfones which were then removed by adsorption on beta zeolite. On the other hand, the amount of cumene hydroperoxide required per mole of S for oxidation to sulfone was 1.5 and 10 times higher than the stoichiometric amounts for JP-8 jet fuel and diesel fuel, respectively. This study demonstrates that oxidative desulfurization can be effectively carried out by using air as an oxidant for generating hydroperoxides in situ, which can then be used to selectively oxidize the sulfur compounds to sulfones, thereby eliminating the need for use, storage, and handling of expensive liquid-phase peroxide oxidants.
Structure and function of A 1 adenosine receptors 1 (1991)

The A1 adenosine receptor is the best characterized of the widely distributed purinergic receptor family. The purified brain A1 receptor is a monomeric 35- to 36-kDa glycoprotein. A1 receptors can be clearly distinguished from A2 adenosine receptors on the basis of structure activity relationships with selective ligands. Recent structure activity data suggest that subtypes of A1 (A1a, A1b, and A3) and A2 (A2a and A2b) receptors may exist. A1 receptor-mediated responses are coupled via multiple pertussis toxin-sensitive GTP binding proteins (G proteins) to many different effectors in various tissues: adenylate cyclase, phospholipase C, Na+- Ca2+ exchange, Ca2+ channels, Cl- channels, and K+ channels. The formation of calcium-mobilizing inositol phosphates can either be enhanced or inhibited. In general, adenosine has been found to act in concert with other hormones or neurotransmitters in either an inhibitory or a stimulatory way. The myriad modulatory actions of adenosine suggest that: 1) adenosine may simultaneously produce multiple effects within the same cell; and 2) activation of A1 receptors may lead to either a decrease or an increase in the coupling of other receptors to their G proteins.
Transcellular Targeting of Fiber- and Hexon-Modified Adenovirus Vectors across the Brain Microvascular Endothelial Cells In Vitro (2012)

In central nervous system (CNS)-directed gene therapy, efficient targeting of brain parenchyma through the vascular route is prevented by the endothelium and the epithelium of the blood-brain and the blood-cerebrospinal fluid barriers, respectively. In this study, we evaluated the feasibility of the combined genetic and chemical adenovirus capsid modification technology to enable transcellular delivery of targeted adenovirus (Ad) vectors across the blood-brain barrier (BBB) in vitro models. As a proof-of-principle ligand, maleimide-activated full-length human transferrin (hTf) was covalently attached to cysteine-modified Ad serotype 5 vectors either to its fiber or hexon protein. In transcytosis experiments, hTf-coupled vectors were shown to be redirected across the BBB models, the transcytosis activity of the vectors being dependent on the location of the capsid modification and the in vitro model used. The transduction efficiency of hTf-targeted vectors decreased significantly in confluent, polarized cells, indicating that the intracellular route of the vectors differed between unpolarized and polarized cells. After transcellular delivery the majority of the hTf-modified vectors remained intact and partly capable of gene transfer. Altogether, our results demonstrate that i) covalent attachment of a ligand to Ad capsid can mediate transcellular targeting across the cerebral endothelium in vitro, ii) the attachment site of the ligand influences its transcytosis efficiency and iii) combined genetic/chemical modification of Ad vector can be used as a versatile platform for the development of Ad vectors for transcellular targeting.
Design Review Of A Complete Angle Scatter Instrument (1989)

An instrument has been designed and built to measure plane of incidence scatter at multiple wavelengths including .6328&mu;m, from reflective, transmissive, specular, diffuse, flat and curved optics. An extensive software package accompanies the instrument and is used both to control the measurement process and to analyze the measurement data. Techniques employed in the design and development of this instrument are described. An error analysis for the measured BSDF is provided and calibration of the instrument is discussed.
Safe and Sustained Expression of Human Iduronidase After Intrathecal Administration of Adeno-Associated Virus Serotype 9 in Infant Rhesus Monkeys (2019)

Many neuropathic diseases cause early, irreversible neurologic deterioration, which warrants therapeutic intervention during the first months of life. In the case of mucopolysaccharidosis type I, a recessive lysosomal storage disorder that results from a deficiency of the lysosomal enzyme α-l-iduronidase (IDUA), one of the most promising treatment approaches is to restore enzyme expression through gene therapy. Specifically, administering pantropic adeno-associated virus (AAV) encoding IDUA into the cerebrospinal fluid (CSF) via suboccipital administration has demonstrated remarkable efficacy in large animals. Preclinical safety studies conducted in adult nonhuman primates supported a positive risk-benefit profile of the procedure while highlighting potential subclinical toxicity to primary sensory neurons located in the dorsal root ganglia (DRG). This study investigated the long-term performance of intrathecal cervical AAV serotype 9 gene transfer of human IDUA administered to 1-month-old rhesus monkeys (<i>N</i> = 4) with half of the animals tolerized to the human transgene at birth via systemic administration of an AAV serotype 8 vector expressing human IDUA from the liver. Sustained expression of the transgene for almost 4 years is reported in all animals. Transduced cells were primarily pyramidal neurons in the cortex and hippocampus, Purkinje cells in the cerebellum, lower motor neurons, and DRG neurons. Both tolerized and non-tolerized animals were robust and maintained transgene expression as measured by immunohistochemical analysis of brain tissue. However, the presence of antibodies in the non-tolerized animals led to a loss of measurable levels of secreted enzyme in the CSF. These results support the safety and efficiency of treating neonatal rhesus monkeys with AAV serotype 9 gene therapy delivered into the CSF.