gebhart/patrepeval huggingface dataset:
Nanotube–antibody biosensor arrays for the detection of circulating breast cancer cells (2008)

Recent reports have shown that nanoscale electronic devices can be used to detect a change in electrical properties when receptor proteins bind to their corresponding antibodies functionalized on the surface of the device, in extracts from as few as ten lysed tumor cells. We hypothesized that nanotube-antibody devices could sensitively and specifically detect entire live cancer cells. We report for the first time a single nanotube field effect transistor array, functionalized with IGF1R-specific and Her2-specific antibodies, which exhibits highly sensitive and selective sensing of live, intact MCF7 and BT474 human breast cancer cells in human blood. Those two cell lines both overexpress IGF1R and Her2, at different levels. Single or small bundle of nanotube devices that were functionalized with IGF1R-specific or Her2-specific antibodies showed 60% decreases in conductivity upon interaction with BT474 or MCF7 breast cancer cells in two µl drops of blood. Control experiments with non-specific antibodies or with MCF10A control breast cells produced a less than 5% decrease in electrical conductivity, illustrating the high sensitivity for whole cell binding by these single nanotube-antibody devices. We postulate that the free energy change due to multiple simultaneous cell-antibody binding events exerted stress along the nanotube surface, decreasing its electrical conductivity due to an increase in band gap. Because the free energy change upon cell-antibody binding, the stress exerted on the nanotube, and the change in conductivity are specific to a specific antigen-antibody interaction; these properties might be used as a fingerprint for the molecular sensing of circulating cancer cells. From optical microscopy observations during sensing, it appears that the binding of a single cell to a single nanotube field effect transistor produced the change in electrical conductivity. Thus we report a nanoscale oncometer with single cell sensitivity with a diameter 1000 times smaller than a cancer cell that functions in a drop of fresh blood.
Laser Photocoagulation Induces Transduction of Retinal Pigment Epithelial Cells by Intravitreally Administered Adeno-Associated Viral Vectors (2015)

Retinal transduction by intravitreally administered adeno-associated viral (AAV) vector is previously known to be extremely limited to the neural retina except AAV2 capsid type. Recently, we showed that prior laser photocoagulation enhances retinal transduction of intravitreally administered AAV vectors, including the outer retina and retinal pigment epithelium (RPE). Here, by performing short-pulse laser pretreatment on the mouse retina, we demonstrate RPE cells transduced by three different capsid types of AAV vectors, AAV2, AAV5, and AAV8, using RPE wholemounts. For all capsid types, laser pretreatment effectively induced the transduction of RPE cells in and around the laser site.
Infection Control Practices in Gastrointestinal Endoscopy in the United States: A National Survey (1991)

We conclude that cleaning, disinfection, and sterilization procedures for gastrointestinal endoscopic instruments vary, that appropriate protective apparel is not always worn, and that some practices may lead to preventable endoscopy-related infection in patients.
Toxicity of ligand-dependent Cre recombinases and generation of a conditional Cre deleter mouse allowing mosaic recombination in peripheral tissues (2007)

Ligand-activated Cre recombinases are widely used for studying gene function in vitro and in conditional mouse models. To compare ligand-dependent Cre recombinases, different Cre estrogen receptor fusions were introduced into the ROSA26 locus of embryonic stem (ES) cells and assayed for genotoxicity and recombination efficiency. Of the tested recombinases, the CreERT2 variant showed no toxicity and was highly responsive to ligand induction. To constitutively express CreERT2 in mice and also to clarify whether the CreERT2 system displays background activity, we generated a knock-in mouse line harboring the CreERT2 coding region under the control of the ROSA26 locus. Analysis of this ROSA26-CreERT2 deleter mouse with different reporter strains revealed ubiquitous recombination in the embryo and partial recombination in peripheral and hematopoietic tissues but no effective CreERT2 expression in the brain. Furthermore, using flow cytometry, we found low-level background recombination in noninduced bitransgenic ROSA26-CreERT2/EGFP reporter mice. To determine whether background activity poses a general problem for conducting conditional in vivo experiments with the ROSA26-CreERT2 deleter, we used a sensitive conditional skin cancer model. In this assay, cancer induction was completely restricted to induced bitransgenic CreERT2/K-Ras(V12) mice, whereas noninduced control animals did not show any sign of cancer, indicating the usefulness of the ROSA-CreERT2 system for regulating conditional gene expression in vivo. The ROSA26-CreERT2 deleter strain will be a convenient experimental tool for studying gene function under circumstances requiring partial induction of recombination in peripheral tissues and will be useful for uncovering previously unknown or unsuspected phenotypes.
GrainGenes, the genome database for small-grain crops (2003)

GrainGenes, http://www.graingenes.org, is the international database for the wheat, barley, rye and oat genomes. For these species it is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with the help of many members of the research community, are integrated with sequence and bibliographic records selected from external databases and results of BLAST searches of the ESTs. Records are linked to corresponding records in other important databases, e.g. Gramene's EST homologies to rice BAC/PACs, TIGR's Gene Indices and GenBank. In addition to this information within the GrainGenes database itself, the GrainGenes homepage at http://wheat.pw.usda.gov provides many other community resources including publications (the annual newsletters for wheat, barley and oat, monographs and articles), individual datasets (mapping and QTL studies, polymorphism surveys, variety performance evaluations), specialized databases (Triticeae repeat sequences, EST unigene sets) and pages to facilitate coordination of cooperative research efforts in specific areas such as SNP development, EST-SSRs and taxonomy. The goal is to serve as a central point for obtaining and contributing information about the genetics and biology of these cereal crops.
Naturalness of Natural Language Artifacts in Software (2015)

We present a study on the naturalness of the natural language artifacts in software. Naturalness is essentially repetitiveness or predictability. By natural language artifacts, we mean source code comments, revision history messages, bug reports and so on. We measure "naturalness" using a standard measure, cross-entropy or perplexity from the widely used N-Gram models. Previously, Hindle et al. demonstrated empirically that source code was comparatively more repetitive or regular (i.e., more natural) when compared with traditional English text. A question that logically follows from their work is the naturalness of other artifacts associated with software. We present our findings on source code comments, commit logs, bug reports, string messages and content present in the popular question and answer forum, StackOverflow. Each of the artifact that we examine is a natural language artifact that is associated with software. However, they do not exhibit the same amount of regularity (naturalness). Commit logs were the most regular, followed by string literal messages and source code comments. Content from StackOverflow (viz., title, question and answers) showed a behavior similar to traditional English text i.e., comparatively lesser regularity. Bug reports from industrial projects exhibited more regularity than bug reports from open source projects, whose naturalness resembled that of typical English text. Our findings have implications for feasibility of building tools such as comment and bug report completion engines. We describe a next-word prediction tool that we built using the N-Gram language model. This tool achieved an accuracy ranging from 70 to 90% on commit messages in different projects. It also achieved an accuracy ranging from 56 to 78% on source comments. We also present a part of speech based analysis of words that are easy to predict and difficult to predict.
MiR-196a Promotes Pancreatic Cancer Progression by Targeting Nuclear Factor Kappa-B-Inhibitor Alpha (2014)

Aberrant expression of miR-196a has been frequently reported in different cancers including pancreatic cancer. However, its function in pancreatic cancer has not been fully elucidated. Here, we investigated the expression pattern and the biological role of miR-196a in pancreatic cancer cell lines, as well as its interaction with a metastasis-related gene, nuclear factor-kappa-B-inhibitor alpha (NFKBIA). We demonstrated that miR-196a was up-regulated in human pancreatic cancer cell lines compared with immortalized pancreatic ductal epithelial cells by means of microRNAs microarray and qRT-PCR. Furthermore, down-regulation of miR-196a in PANC-1 suppressed its proliferation and migration with an increase in G0/G1 transition and decreased expression of Cyclin D1 and CDK4/6. Meanwhile, an increased expression in E-cadherin and decreased expression in N-cadherin and Vimentin were also observed. We identified a novel miR-196a target, NFKBIA, and down-regulation of miR-196a enhanced the expression of NFKBIA protein. Luciferase assay confirmed that NFKBIA was a direct and specific target of miR-196a. Silencing NFKBIA in PANC-1 cells enhanced its proliferation and migration. Taken together, our findings indicate that miR-196a is highly expressed in pancreatic cancer cell lines, and may play a crucial role in pancreatic cancer proliferation and migration, possibly through its downstream target, NFKBIA. Thus, miR-196a may serve as a potential therapeutic target for pancreatic cancer.
Chemistry of thienopyridines. XV. Syntheses of thieno [3,4‐<i>b</i>] ‐ and thieno[3,4‐<i>c</i>] pyridines (1972)

Abstract Thieno [3,4‐ b ] pyridine (5) was synthesized by means of the successive steps of (a) photochlorination of 2,3‐dimethylpyridine to the bis(chloromethyl) compound, (b) condensation with sodium sulfide, (c) oxidation to the sulfoxide, and (d) catalytic dehydration by means of alumina. Thieno[3,4‐ c ]pyridine (6) was obtained in an analogous manner. Spectral properties indicate that 5 and 6 have aromatic character.
<i>KCNK9</i> imprinting syndrome—further delineation of a possible treatable disorder (2016)

Patients with KCNK9 imprinting syndrome demonstrate congenital hypotonia, variable cleft palate, normal MRIs and EEGs, delayed development, and feeding problems. Associated facial dysmorphic features include dolichocephaly with bitemporal narrowing, short philtrum, tented upper lip, palatal abnormalities, and small mandible. This disorder maps to chromosomal region 8q24, and it is caused by a specific missense mutation 770G>A in exon 2, replacing glycine at position 236 by arginine (G236R) in the maternal copy of KCNK9 within this locus. KCNK9 (also called TASK3) encodes a member of the two pore- domain potassium channel (K2P) subfamily. This gene is normally imprinted with paternal silencing, thus a mutation in the maternal copy of the gene will result in disease, whereas a mutation in the paternal copy will have no effect. Exome sequencing in four new patients with developmental delay and central hypotonia revealed de novo G236R mutations. Older members of a previously reported Arab-Israeli family have intellectual disability of variable severity, persistent feeding difficulties in infancy with dysphagia of liquids and dysphonia with a muffled voice in early adulthood, generalized hypotonia, weakness of proximal muscles, elongated face with narrow bitemporal diameter, and reduced facial movements. We describe the clinical features in four recently recognized younger patients and compare them with those found in members of the originally reported Arab-Israeli family and suggest this may be a treatable disorder. © 2016 Wiley Periodicals, Inc.
Prognostic value of pulmonary artery pressure in chronic obstructive pulmonary disease. (1981)

In 175 patients with chronic obstructive lung disease (157 chronic bronchitic and 18 emphysematous patients) exhibiting moderate to severe airway obstruction (mean FEV1/vital capacity = 40.2 +/- 11.1%), cumulative survival rates calculated by the actuarial method were compared in subgroups according to the initial level of mean pulmonary artery pressure, pulmonary volumes, and arterial blood gases. Patients were catheterised between 1968 and 1972 and were followed for at least five years. The results emphasise the high prognostic value of PAP since survival rates after four and seven years were significantly lower in the subgroup with PAP greater than 20 mmHg (2.7 kPa). Certain other parameters ("driving" pressure across the pulmonary circulation, FEV1 and Paco2) appear to be equally good at predicting survival as PAP in these obstructed patients. The effect of age should be taken into account in prognostic studies such as ours since survival rates were significantly lower in patients over 60 years of age. In 64 patients who underwent a second right heart catheterisation at least three years after the first (average delay: 5.5 +/- 2 years), the prognostic value of changes in PAP, arterial blood gases, and pulmonary volumes was studied but with the exception of Pao2 was unremarkable. Further studies are needed in this field.
Home networking at 60 GHz: challenges and research issues (2008)

The recent developments in CMOS technology are about opening a new exciting door to affordable 60-GHz radio applications. One promising application area for 60-GHz radio is home networks in which there is an increasing demand for multi-gigabit wireless networking. The research efforts so far have generally focused on utilizing the 60-GHz band for point-to-point communication by addressing its physical aspects like propagation characteristics and channel models. The issues of 60-GHz networking at the system level have not been adequately considered. In this paper, the challenges and the research issues of 60-GHz networking are reviewed from the system-level perspective. We present them in the context of wireless local area networks for future home networks with discussions on some possible solutions for the introduced challenges.
Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression (2006)

These data suggest a role for SSAT, the rate-limiting enzyme in the catabolism of polyamines, in suicide and depression and a role for the SSAT342 locus in the regulation of SSAT gene expression.
On optimal coding of visual information for Rate-Controlled communication (2008)

A new approach to rate-control of visual communication is presented. This method is based on a recently introduced rate-distortion function for image compression. We show that this rate-distortion approach can be used to develop an efficient coding algorithm, suitable for wireless and Internet transmission. We demonstrate this approach for subband transform coding using the discrete cosine transform (DCT). We show how rate-control is performed both for still images and for video streams. Simulation results are presented to support the efficiency of our algorithm, which outperforms presently available compression methods.
Separating nucleation and growth in protein crystallization using dynamic light scattering (2002)

A means of controlling crystallization is to separate the phases of nucleation and growth. Methods to achieve this, other than seeding, involve lowering the supersaturation by changing the temperature or diluting drops after incubating them for a given time at nucleation conditions. However, by the time nuclei or crystals are visible under the microscope too many nuclei will have formed. Dynamic Light Scattering was applied practically, to determine the most likely time for nucleation-growth decoupling to be performed successfully. The time at which DLS showed a significant change in the size-distribution of species in solution, corresponded to that optimal time.
Control and tracking of longitudinal dynamics of UAVs in synchronized motion (2013)

Study of multi UAVs in synchronized motion has drawn attention of late. The study is demonstrated for two UAVs and can be easily generalized for multi UAVs.This paper aims to maintain the relative motion between two UAVs with a fixed distance in forward and vertical direction and with tracking pitch orientation in a longitudinal plane.The longitudinal dynamics control of leader UAV and its tracking by a follower UAV are performed by tuned conventional PIT) controllers and H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> controllers for each state separately under nominal and perturbed conditions.The well designed robust H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> controllers performed the given MIMO system tracking even in perturbed state very efficiently as compared to the conventional PID techniques with the simplified plant dynamics.
High temperature superconducting multilayer multichip module: fabrication and high speed characterization (1999)

Superconductivity is attractive for high performance multichip modules (MCMs) for increasing wiring density while eliminating attenuation and dispersion caused by wiring resistance. However, multilayer HTS structures have been difficult to fabricate. A methodology and materials set was developed to fabricate a multilayer structure with superconducting traces in the X-Y planes and normal metal interconnects in the Z-plane. A simple, multilayer circuit was designed to characterize the high-speed digital waveform characteristics and pulse integrity. Design guidelines were employed to maintain constant impedance through multiple transmission lines. The circuit was modeled on a 3D simulator with a one nanosecond rise-time pulse. The goal was to correlate the modeled and measured data with respect to the pulse integrity and impedance. Eye-diagrams were produced using a one-gigahertz pulse train. In addition, thermal cycling was performed on the structures to identify if any thermal expansion mismatches occurred. Electrical tests were performed before and after the cycling to verify circuit integrity. The data from the thermal cycling will be discussed.
A Simplified Direct Lipid Mixing Lipoplex Preparation: Comparison of Liposomal-, Dimethylsulfoxide-, and Ethanol-Based Methods (2016)

Established transfection methodology often uses commercial reagents, which must be formed into liposomes in a sequence of about half a dozen steps. The simplified method reported here is a direct lipid mixing approach that requires fewer steps, less manipulation, and is less time-consuming. Results are comparable to those obtained with more commonly used methods, as judged by a variety of analytical techniques and by comparisons of transfection results. The method reported here may be applied to non-liposome-forming compounds, thereby greatly expanding the range of structures that can be tested for transfection ability.
Ciprofloxacin Dry Powder for Inhalation (ciprofloxacin DPI): Technical design and features of an efficient drug–device combination (2018)

Bronchiectasis is a chronic respiratory disease with heterogeneous etiology, characterized by a cycle of bacterial infection and inflammation, resulting in increasing airway damage. Exacerbations are an important cause of morbidity and are strongly associated with disease progression. Many patients with bronchiectasis suffer from two or more exacerbations per year. However, there are no approved therapies to reduce or delay exacerbations in this patient population. Ciprofloxacin DPI is in development as a long-term, intermittent therapy to reduce exacerbations in patients with non-cystic fibrosis (CF) bronchiectasis and evidence of respiratory pathogens. Ciprofloxacin DPI combines drug substance, dry powder manufacturing technology, and an efficient, pocket-sized, dry powder inhaler to deliver an effective antibiotic directly to the site of infection, with minimal systemic exposure and treatment burden. Here we review the drug substance and particle engineering (PulmoSphere™) technology used, and key physical properties of Ciprofloxacin Inhalation Powder, including deposition, delivered dose uniformity, consistency, and stability. Design features of the T-326 Inhaler are described in relation to lung targeting, safety and tolerability of inhalation powders, as well as treatment burden and adherence. If approved, Ciprofloxacin DPI may provide a valuable treatment option for those with frequent exacerbations and respiratory pathogens.
Antisera to scrapie-associated fibril protein and prion protein decorate scrapie-associated fibrils (1987)

Scrapie-associated fibrils (SAF) are an infection-specific structure observed in the unconventional-agent diseases. Polyclonal antisera raised to scrapie proteins were used to test the antigenic relationship between purified fibrils and SAF isolated from non-protease-treated synaptosomal-mitochondrial preparations. The experimental design utilized fibrils from scrapie strain 263K-infected hamsters, scrapie strain 139A-infected mice, and scrapie strain ME7-infected mice. Preparations were examined by negative-stain immune electron microscopy and Western blot analysis of the polypeptides. Fibrils and polypeptides from each preparation reacted with a rabbit antiserum raised to each of the following: hamster 263K prion protein (PrP 27-30), hamster 263K SAF protein, and mouse ME7 SAF protein. Immune electron microscopy and Western blot analysis revealed similar antigenic relationships among the three scrapie antisera. Thus, fibrils and polypeptides can be considered to be the same in each preparation. No reactivity of the fibrils was observed with antisera raised to Alzheimer neurofibrillary tangles or a synthetic peptide of cerebrovascular amyloid. Thus, the fibrils observed in purified preparations share structural and antigenic similarities plus biochemically related peptides with SAF present in non-protease-treated preparations.
Lymphocytes bearing the gamma delta T-cell receptor in acute toxoplasmosis. (1992)

Although the relative and absolute numbers of CD3+ cells (T lymphocytes) were similar in eight children with acquired Toxoplasma gondii infection and 10 uninfected age- and sex-matched healthy controls, the proportion of cells bearing the gamma delta T-cell receptor was significantly higher in the subjects with acute toxoplasmosis. The great majority of gamma delta T cells from the infected patients expressed covalently bound gamma delta chains on their surface, i.e. were BB3+ lymphocytes. Since the gamma delta T-cell subsets exert both restricted and unrestricted major histocompatibility complex cytotoxicity, further research is needed to elucidate the role of gamma delta T cells in the control of this coccidian protozoan infection.