gebhart/patrepeval huggingface dataset:
Arrayed Profiling of Multiple Glycans on Whole Living Cell Surfaces (2013)

An array-based method for profiling and quantification of multiple glycans on whole living cell surfaces was developed through combining DNA encoding technology with DNA microarray. Using four kinds of lectins as the model to recognize four types of cell surface glycans, the specific barcode-lectin probes that contained the endonuclease cutting site were designed. The barcode-lectin probes had the DNA sequences complementary to four sequences immobilized on a DNA microarray, respectively. After the living cells were incubated with the mixture of four barcode-lectin probes, these probes could bind to cell surface through the specific interaction between the lectins and corresponding glycans. Thus, the glycans and their amounts could be profiled by releasing the barcodes from cell surface with endonuclease cleaving, binding the barcodes to DNA microarray with specific hybridization, and then producing the amplified fluorescence signal with hybridization chain reaction (HCR). The HCR was performed with two kinds of Cy5 labeled hairpins. The average amount of mannose, N-acetylgalactosamine, N-acetylglucosamine, and N-acetylneuraminic acid on BGC cell was obtained to be 6.8 × 10(7), 3.8 × 10(7), 2.1 × 10(8), and 1.1 × 10(7) moieties per cell, respectively. The proposed method possessed whole cell surface accessibility, powerful distinguishing capability, fast recognition kinetics, easy miniaturization, and high throughput without need of cell pretreatment or labeling. It could become a powerful tool for elucidation of the complex glycan-related biological processes.
Formation of defined microporous 3D structures starting from cross‐linked hydrogels (2003)

A new and simple technique was developed to obtain polysaccharide (hyaluronane, alginate and carboxymethylcellulose) -based hydrogels with a defined porous morphology. The technique consists of stratifying a cross-linked hydrogel on a filter with known pore diameter. CO(2) bubbles, produced by the addition of HCl to a porogen salt NaHCO(3), are forced to pass through the filter, and they induce the hydrogel to assume a porous morphology. The presence and distribution of pores was confirmed by scanning-electron microscopy (SEM). A strict correspondence was found between the porosity of the filter and the pore diameter in the hydrogels. Water uptake measurements showed a decreased amount of water taken up by the porous hydrogels compared with the native hydrogels, due to a compacting of the material. An explanation of the porous material properties of Hyal hydrogel was given on the basis of FTIR spectra.
Convertible manganese contrast for molecular and cellular MRI (2008)

We describe here the use of inorganic manganese based particles as convertible MRI agents. As has been demonstrated with iron oxide particles, manganese oxide and manganese carbonate particles can be internalized within phagocytotic cells, being subsequently shuttled to endosomes and/or lysosomes. As intact particles, only susceptibility-induced MRI contrast is exhibited, most often seen as dark contrast in susceptibility-weighted images. Modulation of MRI contrast is accomplished by the selective degradation of these particles within the endosomal and lysosomal compartments of cells. Upon particle deconstruction in the endosomes and lysosomes, the dissolved Mn(2+) acts as a T(1) agent, eliciting bright contrast in T(1)-weighted images. This modulation of MRI contrast is demonstrated both in vitro in cells in culture, and also in vivo, in rat brain. These particles are the potential building blocks for an entire class of new environmentally responsive MRI contrast agents.
Protein Stability During Freezing: Separation of Stresses and Mechanisms of Protein Stabilization (2007)

Although proteins are often frozen during processing or freeze-dried after formulation to improve their stability, they can undergo degradation leading to losses in biological activity during the process. During freezing, the physical environment of a protein changes dramatically leading to the development of stresses that impact protein stability. Low temperature, freeze-concentration, and ice formation are the three chief stresses resulting during cooling and freezing. Because of the increase in solute concentrations, freeze-concentration could also facilitate second order reactions, crystallization of buffer or non-buffer components, phase separation, and redistribution of solutes. An understanding of these stresses is critical to the determination of when during freezing a protein suffers degradation and therefore important in the design of stabilizer systems. With the exception of a few studies, the relative contribution of various stresses to the instability of frozen proteins has not been addressed in the freeze-drying literature. The purpose of this review is to describe the various stages of freezing and examine the consequences of the various stresses developing during freezing on protein stability and to assess their relative contribution to the destabilization process. The ongoing debate on thermodynamic versus kinetic mechanisms of stabilization in frozen environments and the current state of knowledge concerning those mechanisms are also reviewed in this publication. An understanding of the relative contributions of freezing stresses coupled with the knowledge of cryoprotection mechanisms is central to the development of more rational formulation and process design of stable lyophilized proteins.
Reliability and Validity of Imaging Diagnosis of Temporomandibular Joint Disorder (1993)

The purpose of this article is to review reliability and validity of imaging diagnosis of temporomandibular joint disorders. Plain-film and tomography are basic imaging techniques for assessment of the temporomandibular joint. These can be used for evaluation of osseous disease and as a baseline for follow-up. In patients with symptoms from the joint, plain-film and tomography are rarely definitive, and evaluation of the soft tissues is frequently necessary. Arthrography, computed tomography, and magnetic resonance imaging have all been used for evaluation of the soft-tissue components of the joints. Accuracy studies of these techniques have demonstrated the highest diagnostic accuracy for magnetic resonance imaging. Arthrography is relatively insensitive for detection of medial and lateral displacements. Magnetic resonance imaging accurately depicts both hard and soft tissues, and this technique is emerging as the prime diagnostic imaging technique in patients presenting with clinical signs and symptoms of a disorder of the temporomandibular joint. The most frequent findings when patients with clinical symptoms of temporomandibular joint disorders are "imaged" are different forms of disc displacement and degenerative joint disease. Studies have demonstrated a high prevalence of different forms of disc displacement in patients, although these abnormalities are also seen in some asymptomatic volunteers. Future research should further refine imaging techniques to come closer to an understanding of the association between morphologic alterations and patient symptoms.
Application of Subset Autoregressive Integrated Moving Average Model for Short-Term Freeway Traffic Volume Forecasting (1999)

Traffic volume is one of the fundamental types of data that have been used for the traffic control and planning process. Forecasting needs and efforts for various applications will be increased with the deployment of advanced traffic management systems. With the importance of the short-term traffic forecasting task, numerous techniques have been utilized to improve its accuracy. The use of the subset autoregressive integrated moving average (ARIMA) model for short-term traffic volume forecasting is investigated. A typical time-series modeling procedure was employed for this study. Model identification was carried out with Akaike’s information criterion. The conditional maximum likelihood method was used for the parameter estimation process. Two white noise tests were applied for model verification. From the analysis results, four time-series models in different categories were identified and used for the one-step-ahead forecasting task. The performance of each model was evaluated using two statistical error estimates. Results showed that all time-series models performed well with reasonable accuracy. However, it was observed that the subset ARIMA model gave more stable and accurate results than other time-series models, especially a full ARIMA model. It is believed that the use of a subset ARIMA model could increase the accuracy of the short-term forecasting task within time-series models.
Sequential Operation Droplet Array: An Automated Microfluidic Platform for Picoliter-Scale Liquid Handling, Analysis, and Screening (2013)

This contribution describes a sequential operation droplet array (SODA) system, a fully automated droplet-based microfluidic system capable of performing picoliter-scale liquid manipulation, analysis, and screening. The SODA system was built using a tapered capillary-syringe pump module and a two-dimensional (2D) oil-covered droplet array installed on an x-y-z translation stage. With the system, we developed a novel picoliter-scale droplet depositing technique for forming a 2D picoliter-droplet array. On this basis, an automated droplet manipulation method with picoliter precision was established using the programmable combination of the capillary-based liquid aspirating-depositing and the moving of the oil-covered droplet array, the so-called "aspirating-depositing-moving" (ADM) method. Differing from the previously reported droplet systems based on microchips, microcapillaries, or digital microfluidics, this method can achieve complete and flexible droplet manipulations, including droplet assembling, generation, indexing, transferring, splitting, and fusion in the picoliter range, endowing the present system with ultralow sample/reagent consumptions and substantial versatility in analysis and screening for multiple different samples. To demonstrate its feasibility and versatility, we applied the SODA system in multiple experiments required in drug screening, including the screening of inhibitors for capases-1 from a chemical library, the measurement of IC50 values for the identified inhibitors, and the screening of the synergistic effect of multiple inhibitors. In the experiments, the consumptions of samples and reagents are only 60-180 pL for each droplet microreactor, which are commonly 3-5 orders of magnitude lower than those of conventional multiwell plate systems, and 1-2 orders of magnitude lower than other droplet-based microfluidic systems for multiple sample screening. The ability of the SODA system in performing complicated and multistep droplet manipulations was further demonstrated in the serial dilution of nanoliter-scale inhibitor droplets with concentrations spanning 6 orders of magnitude for IC50 profiling, which includes droplet generation, indexing, splitting, transferring, and fusion with picoliter precision.
Corneal Abrasion During Induction (1987)

Senior Instructor of Anesthesiology University of Rochester Medical Center Strong Memorial Hospital 601 Elmwood Avenue Rochester, NY 14642Associate Resident in Anesthesiology University of Rochester Medical Center Strong Memorial Hospital 601 Elmwood Avenue Rochester, NY 14642
A bridged nucleic acid, 2′,4′-BNA COC : synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2′,4′-BNA COC monomers and RNA-selective nucleic-acid recognition (2009)

Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNA(COC)) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNA(COC) monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNA(COC)/BNA(COC) duplex possessed excellent thermal stability and that the BNA(COC) increased thermal stability with a complementary RNA strand. On the other hand, BNA(COC)/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.
Klotho, a Gene Related to a Syndrome Resembling Human Premature Aging, Functions in a Negative Regulatory Circuit of Vitamin D Endocrine System (2003)

The klotho gene encodes a novel type I membrane protein of beta-glycosidase family and is expressed principally in distal tubule cells of the kidney and choroid plexus in the brain. These mutants displayed abnormal calcium and phosphorus homeostasis together with increased serum 1,25-(OH)2D. In kl-/- mice at the age of 3 wk, elevated levels of serum calcium (10.9 +/- 0.31 mg/dl vs. 10.0 +/- 0.048 mg/dl in wild-type mice), phosphorus (14.7 +/- 1.1 mg/dl vs. 9.7 +/- 1.5 mg/dl in wild type) and most notably, 1,25-(OH)2D (403 +/- 99.7 mg/dl vs. 88.0 +/- 34.0 mg/dl in wild type) were observed. Reduction of serum 1,25-(OH)2D concentrations by dietary restriction resulted in alleviation of most of the phenotypes, suggesting that they are downstream events resulting from elevated 1,25-(OH)2D. We searched for the signals that lead to up-regulation of vitamin D activating enzymes. We examined the response of 1alpha-hydroxylase gene expression to calcium regulating hormones, such as PTH, calcitonin, and 1,25-(OH)2D3. These pathways were intact in klotho null mutant mice, suggesting the existence of alternate regulatory circuits. We also found that the administration of 1,25-(OH)2D3 induced the expression of klotho in the kidney. These observations suggest that klotho may participate in a negative regulatory circuit of the vitamin D endocrine system, through the regulation of 1alpha-hydroxylase gene expression.
A Method to Attenuate Pneumoperitoneum-Induced Reductions in Splanchnic Blood Flow (2005)

The data indicate that ENO can effectively attenuate pneumoperitoneum-induced blood flow decreases within the peritoneal cavity. The result suggests a novel therapeutic method of regulating hemodynamic changes during laparoscopic procedures.
Online Coupling of Electrochemical Reactions with Liquid Sample Desorption Electrospray Ionization-Mass Spectrometry (2009)

The combination of electrochemistry (EC) and mass spectrometry (MS) is a powerful analytical tool to study redox reactions. This work reports the online coupling of a thin-layer electrochemical flow cell with liquid sample desorption electrospray ionization mass spectrometry (DESI-MS) and its applications in investigating various electrochemical reactions of biological molecules such as oxidative formation and reductive cleavage of disulfide bonds and online derivatization of peptides/proteins. As a result of the direct sampling nature of DESI, several useful features of such a coupling have been found, including simple instrumentation, fast response time (e.g., 3.6 s in the case of dopamine oxidation), freedom to choose a favorable ionization mode of DESI or traditional electrolysis solvent systems, and the absence of background signal possibly resulting from ionization when the cell is off (e.g., in the case of dopamine oxidation). More importantly, with the use of this new coupling apparatus, three disulfide bonds of insulin were fully cleaved by electrolytic reduction and both the A and B chains of the protein were successfully detected online by DESI-MS. In addition, online tagging of free cysteine residues of peptides/proteins employing electrogenerated dopamine o-quinone can be performed. These revealed characteristics of the coupling along with examined electrochemical reactions suggest that EC/DESI-MS has good potential in bioanalysis.
Farnesoid X receptor inhibits gankyrin in mouse livers and prevents development of liver cancer (2012)

FXR prevents liver cancer by inhibiting the gankyrin promoter via C/EBPβ-HDAC1 complexes, leading to subsequent protection of tumor suppressor proteins from degradation.
Heyd-Scuseria-Ernzerhof hybrid functional for calculating the lattice dynamics of semiconductors (2009)

We present an ab initio study of the lattice dynamics of group-IV elemental semiconductors and insulators using a finite differences approach. The investigated solids include cubic diamond (C), silicon (Si), germanium (Ge), and the zero-gap semiconductor gray tin $(\ensuremath{\alpha}\text{-Sn})$. The main objective of this work is to examine the performance of the screened hybrid functional (HSE) proposed by Heyd, Scuseria, and Ernzerhof [J. Chem. Phys. 118, 8207 (2003); J. Chem. Phys. 124, 219906(E) (2006)] for calculating phonon-dispersion relations. We find that all local and semilocal functionals tend to underestimate the phonon frequencies, with the errors increasing with increasing atomic mass. For $\ensuremath{\alpha}\text{-Sn}$, semilocal functionals even qualitatively fail to describe the dispersion of the highest optical phonon mode. We show that this is related to semilocal functionals predicting $\ensuremath{\alpha}\text{-Sn}$ to be a metal, whereas experimentally it is a zero-gap semiconductor. The HSE functional yields the correct electronic band structure resulting in qualitatively correct phonon-dispersion relations for all four solids. Quantitatively, the phonon frequencies are slightly overestimated using HSE, in particular for the lighter elements C and Si. Our results are compared to previously reported theoretical findings.
Local Perception for Mobile Robot Navigation in Natural Terrain: Two Approaches (2018)

Robotics Institute
Outer Membranec-Type Cytochromes Required for Fe(III) and Mn(IV) Oxide Reduction inGeobacter sulfurreducens (2005)

The potential role of outer membrane proteins in electron transfer to insoluble Fe(III) oxides by Geobacter sulfurreducens was investigated because this organism is closely related to the Fe(III) oxide-reducing organisms that are predominant in many Fe(III)-reducing environments. Two of the most abundant proteins that were easily sheared from the outer surfaces of intact cells were c-type cytochromes. One, designated OmcS, has a molecular mass of ca. 50 kDa and is predicted to be an outer membrane hexaheme c-type cytochrome. Transcripts for omcS could be detected during growth on Fe(III) oxide, but not on soluble Fe(III) citrate. The omcS mRNA consisted primarily of a monocistronic transcript, and to a lesser extent, a longer transcript that also contained the downstream gene omcT, which is predicted to encode a second hexaheme outer membrane cytochrome with 62.6% amino acid sequence identity to OmcS. The other abundant c-type cytochrome sheared from the outer surface of G. sulfurreducens, designated OmcE, has a molecular mass of ca. 30 kDa and is predicted to be an outer membrane tetraheme c-type cytochrome. When either omcS or omcE was deleted, G. sulfurreducens could no longer reduce Fe(III) oxide but could still reduce soluble electron acceptors, including Fe(III) citrate. The mutants could reduce Fe(III) in Fe(III) oxide medium only if the Fe(III) chelator, nitrilotriacetic acid, or the electron shuttle, anthraquinone 2,6-disulfonate, was added. Expressing omcS or omcE in trans restored the capacity for Fe(III) oxide reduction. OmcT was not detected among the sheared proteins, and genetic studies indicated that G. sulfurreducens could not reduce Fe(III) oxide when omcT was expressed but OmcS was absent. In contrast, Fe(III) oxide was reduced when omcS was expressed in the absence of OmcT. These results suggest that OmcS and OmcE are involved in electron transfer to Fe(III) oxides in G. sulfurreducens. They also emphasize the importance of evaluating mechanisms for Fe(III) reduction with environmentally relevant Fe(III) oxide, rather than the more commonly utilized Fe(III) citrate, because additional electron transfer components are required for Fe(III) oxide reduction that are not required for Fe(III) citrate reduction.
Interplay of Insulin-Like Growth Factor-II, Insulin-Like Growth Factor-I, Insulin-Like Growth Factor-I Receptor, COX-2, and Matrix Metalloproteinase-7, Play Key Roles in the Early Stage of Colorectal Carcinogenesis (2004)

IGF-II, in conjunction with IGF-IR, IGF-I, COX-2, and MMP-7, seems to play a key role in the early stage of colorectal carcinogenesis.
Somatic EGFR Mutation and Gene Copy Gain as Predictive Biomarkers for Response to Tyrosine Kinase Inhibitors in Non–Small Cell Lung Cancer (2009)

This analysis provides empirical evidence that EGFR mutations are sensitive and specific predictors of response to single-agent epidermal growth factor receptor TKIs in advanced NSCLC. The diagnostic performance of mutations seems better than that of EGFR gene gain.
Biodiversity, chemical diversity and drug discovery (2007)

Drugs developed from microbial natural products are in the fundaments of modern pharmaceutical companies. Despite decades of research, all evidences suggest that there must remain many interesting natural molecules with potential therapeutic application yet to be discovered. Any efforts to successfully exploit the chemical diversity of microbial secondary metabolites need to rely heavily on a good understanding of microbial diversity, being the working hypothesis that maximizing biological diversity is the key strategy to maximizing chemical diversity. This chapter presents an overview of diverse topics related with this basic principle, always in relation with the discovery of novel secondary metabolites. The types of microorganisms more frequently used for natural products discovery are briefly reviewed, as well as the differences between terrestrial and marine habitats as sources of bioactive secondary metabolite producers. The concepts about microbial diversity as applied to prokaryotes have evolved in the last years, but recent data suggest the existence of true biogeographic patterns of bacterial diversity, which are also discussed. Special attention is dedicated to the existing strategies to exploit the microbial diversity that is not easy to tackle by conventional approaches. This refers explicitly to the current attempts to isolate and cultivate the previously uncultured bacteria, including the application of high throughput techniques. Likewise, the advances of microbial molecular biology has allowed the development of metagenomic approaches, i.e., the expression of biosynthetic pathways directly obtained from environmental DNA and cloned in a suitable host, as another way of accessing microbial genetic resources. Also, approaches relying on the genomics of metabolite producers are reviewed.