gebhart/patrepeval huggingface dataset:
Development of bioadhesives from marine mussels (2008)

Mussel adhesive proteins have received increased attention as potential biomedical and environmentally friendly underwater adhesives thanks to their fascinating properties, including strong and flexible adhesion, adhesion to various material substrates, water displacement, that they are harmless to human body, and controlled biodegradability. Several mussel adhesive proteins have been identified and characterized from mussels, and profound biochemical knowledge for mussel adhesions has been accumulated. In addition, a lot of effort has been put into realizing the promise of these bioadhesive materials from marine mussels. Here, progress in the diverse developmental approaches, with particular emphasis on functional production of mussel adhesive proteins, are reviewed.
Solving ptychography with a convex relaxation (2015)

Ptychography is a powerful computational imaging technique that transforms a collection of low-resolution images into a high-resolution sample reconstruction. Unfortunately, algorithms that currently solve this reconstruction problem lack stability, robustness, and theoretical guarantees. Recently, convex optimization algorithms have improved the accuracy and reliability of several related reconstruction efforts. This paper proposes a convex formulation of the ptychography problem. This formulation has no local minima, it can be solved using a wide range of algorithms, it can incorporate appropriate noise models, and it can include multiple a priori constraints. The paper considers a specific algorithm, based on low-rank factorization, whose runtime and memory usage are near-linear in the size of the output image. Experiments demonstrate that this approach offers a 25% lower background variance on average than alternating projections, the ptychographic reconstruction algorithm that is currently in widespread use.
High-Frequency Variation of Purine Biosynthesis Genes Is a Mechanism of Success in Campylobacter jejuni (2015)

C. jejuni is an important cause of bacterial diarrheal illness. Bacterial populations have many strategies for stress survival, but phenotypic variation due to genetic diversity has a powerful advantage: no matter how swift the change in environment, a fraction of the population already expresses the survival trait. Nonclonality is thus increasingly viewed as a mechanism of population success. Our previous work identified prominent resistant/sensitive colonial variation in C. jejuni bacteria in response to hyperosmotic stress; in the work presented here, we attribute that to high-frequency genetic variation in two purine biosynthesis genes, purF and apt. We demonstrated selective pressure for nonlethal mutant alleles of both genes, showed that single-cell variants had the capacity to give rise to diverse purF and apt populations, and determined that stress exposure selected for desirable alleles. Thus, a novel C. jejuni adaptive strategy was identified, which was, unusually, reliant on prevalent genetic variation in two housekeeping genes.
ECG signal smoothing based on combining wavelet denoising levels (2006)

We present in this study an algorithm of smoothing real noisy ECG signal based on the classical wavelet denoising theory. The key idea of our proposed algorithm consists on generating a constructed denoised ECG signal by extracting and combining the delimited QRS complexes from the 2nd level wavelet denoising and the P and T waves from the 4th or 5th level wavelet denoising outputs. The used classical denoising algorithm utilizes the `VisuShrink` calculus rule and the `soft` thresholding strategy. On the other hand, the best suitable wavelet function and decomposition DWT level, for the denoising process, are determined by the means of the mean square error value. Two synthesis parameters have been utilized: the output SNR and the MSE values. We have applied our proposed algorithm to a set of MIT-BIH Arrhythmia Database ECG records added to a simulated 5dB and 0 dB SNR white Gaussian noise where it has been noticed an improvement of the input SNR (5 dB) to an output value of, generally, around 10 dB. To evaluate our algorithm, a comparative study was carried out referred to the low pass Butterworth filter and the 4th and 5th level classical wavelet denoising process. The obtained results demonstrate the superior performance of our proposed algorithm regarded to the tested filtering techniques where the output SNR remains in the most of cases less than 7 dB in the case of the input 5 dB WGN.
Carbon Monoxide Protects Pancreatic β-Cells From Apoptosis and Improves Islet Function/Survival After Transplantation (2002)

Pancreatic islets transplanted to treat autoimmune type 1 diabetes often fail to function (primary nonfunction), likely because of islet beta-cell apoptosis. We show that carbon monoxide (CO), a product of heme oxygenase activity, protects beta-cells from apoptosis. Protection is mediated through guanylate cyclase activation, generation of cyclic GMP (cGMP), and activation of cGMP-dependent protein kinases. This antiapoptotic effect is still observed when beta-cells are exposed to CO for 1 h before the apoptotic stimulus. In a similar manner, mouse islets exposed to CO for just 2 h function significantly better after transplantation than islets not exposed to CO. These findings suggest a potential therapeutic application for CO in improving islet function/survival after transplantation in humans.
Human estrogen receptor forms multiple protein-DNA complexes. (1990)

A baculovirus expression system was used to overproduce the human estrogen receptor in insect cells. The estrogen receptor made in this system is full-length, binds estrogen specifically, and is recognized by a monoclonal antibody to the human estrogen receptor. The recombinant estrogen receptor binds the estrogen response element (ERE) in both the absence and presence of estrogen if the binding is carried out in the absence of Mg2+. In the presence of Mg2+, the estrogen receptor binds the ERE in a hormone-dependent fashion. This effect is more pronounced at higher temperatures. Tamoxifen, a nonsteroidal anti-estrogen, is able to stimulate ERE binding to the same extent and under the same conditions as estradiol. Estradiol stimulates formation of an estrogen receptor-ERE complex with an increased mobility in native gels as compared with the complex formed without hormone or with tamoxifen. These results demonstrate that specific DNA binding of the estrogen receptor is not absolutely dependent on the presence of hormone and that estradiol but not tamoxifen is able to induce a change in the estrogen receptor. This differential effect of estradiol and tamoxifen may be important in understanding the role of the receptor to activate target genes differentially.
Beyond crystallography: the study of disorder, nanocrystallinity and crystallographically challenged materials with pair distribution functions (2004)

Studying the structure of disordered and partially ordered materials is notoriously difficult. Recently, significant advances have been made using the atomic pair distribution function (PDF) analysis of powder diffraction data coupled with the use of advanced X-ray and neutron sources and fast computers. Here we summarize some of the more spectacular successes of this technique in studying the structure of complex materials and compounds. Our purpose is to make the PDF analysis technique familiar to the chemical community by describing its methodologies and highlighting its potential in solving structural characterization problems that are intractable by any other technique available to this community e.g. single crystal diffraction, Rietveld refinement of powder diffraction data and extended X-ray absorption fine structure analysis (EXAFS).
Androgen receptors in endocrine‐therapy‐resistant human prostate cancer (1991)

Despite the initial androgen-dependent growth of most human prostate cancers, eventually all prostate cancers become androgen-independent at varying intervals after androgen ablation or anti-androgen therapy. In order to gain more insight into the role of the androgen receptor (AR) in this process, AR and prostate-specific antigen (PA) expression was evaluated immunohistochemically in prostatic tumour tissues from patients who developed urinary flow obstruction between 4 and 107 months after onset of treatment. AR expression was evaluated with a monoclonal antibody (MAb) specific for the N-terminal domain of the human AR. To substantiate the progressive tumour growth, proliferative activity was assessed immunohistochemically by staining with MAb Ki-67. Ki-67-defined tumour-growth fractions varied from 0.8-64.7%. In 13 of the 17 examined tumours over 80% of the tumour cells were AR-positive, 3 tumours showed a considerable heterogeneity in AR expression and in 1 tumour almost all tumour cells seemed to be AR-negative. Two-thirds of the examined tumours contained variable proportions of PA-positive tumour areas. These observations contrast with the view that androgen ablation induces a preferential outgrowth of receptor-negative tumour cells.
Immunosurveillance of Alglucerase Enzyme Therapy for Gaucher Patients: Induction of Humoral Tolerance in Seroconverted Patients After Repeat Administration (1999)

Alglucerase, a macrophage-targeted enzyme replacement therapy for Gaucher disease, has been successfully used for several years to improve clinical symptoms and reverse disease progression. As part of an immunosurveillance program, 1,122 Gaucher patients were monitored for antibody response to glucocerebrosidase, the active component of alglucerase. Seroconversion was detected in 142 patients (12.8%) by enzyme-linked immunosorbent assay (ELISA) and confirmed by radioimmunoprecipitation. The majority (75%) of the seroconverted population had no detectable levels of circulating inhibitory antibody as assessed by in vitro inhibition of enzymatic activity of the therapeutic molecule. Of the remaining patients with putative inhibitory antibodies, the majority had only low levels of serum inhibitory activity, which was transient. A very small number of patients were identified as developing true neutralizing antibodies, as defined by the development of antibodies that impacted clinical efficacy. Many of the patient antibody responses were also diminished with time. Eighty-two of the 142 seroconverted patients have stopped producing antibody to the molecule and appear tolerized. The mean time for humoral tolerization was 28 months from initiation of therapy. Of 64 seroconverted patients followed for at least 30 months of therapy, the tolerization rate was 93%. These results show that although 12.8% of the patients on therapy developed antibodies to the molecule, 90% of these patients became tolerized over time.
Immunogenicity of therapeutic proteins: Influence of aggregation (2013)

The elicitation of anti-drug antibodies (ADA) against biotherapeutics can have detrimental effects on drug safety, efficacy, and pharmacokinetics. The immunogenicity of biotherapeutics is, therefore, an important issue. There is evidence that protein aggregation can result in enhanced immunogenicity; however, the precise immunological and biochemical mechanisms responsible are poorly defined. In the context of biotherapeutic drug development and safety assessment, understanding the mechanisms underlying aggregate immunogenicity is of considerable interest. This review provides an overview of the phenomenon of protein aggregation, the production of unwanted aggregates during bioprocessing, and how the immune response to aggregated protein differs from that provoked by non-aggregated protein. Of particular interest is the nature of the interaction of aggregates with the immune system and how subsequent ADA responses are induced. Pathways considered here include 'classical' activation of the immune system involving antigen presenting cells and, alternatively, the breakdown of B-cell tolerance. Additionally, methods available to screen for aggregation and immunogenicity will be described. With an increased understanding of aggregation-enhanced immune responses, it may be possible to develop improved manufacturing and screening processes to avoid, or at least reduce, the problems associated with ADA.
MEKK3 Regulates IFN-γ Production in T Cells through the Rac1/2-Dependent MAPK Cascades (2011)

MEKK3 is a conserved Ser/Thr protein kinase belonging to the MAPK kinase kinase (MAP3K) family. MEKK3 is constitutively expressed in T cells, but its function in T cell immunity has not been fully elucidated. Using Mekk3 T cell conditional knockout (T-cKO) mice, we show that MEKK3 is required for T cell immunity in vivo. Mekk3 T-cKO mice had reduced T cell response to bacterial infection and were defective in clearing bacterial infections. The Ag-induced cytokine production, especially IFN-γ production, was impaired in Mekk3-deficient CD4 T cells. The TCR-induced ERK1/2, JNK, and p38 MAPKs activation was also defective in Mekk3-deficient CD4 T cells. In vitro, MEKK3 is not required for Th1 and Th2 cell differentiation. Notably, under a nonpolarizing condition (Th0), Mekk3 deficiency led to a significant reduction of IFN-γ production in CD4 T cells. Furthermore, the IL-12/IL-18-driven IFN-γ production and MAPK activation in Mekk3-deficient T cells was not affected suggesting that MEKK3 may selectively mediate the TCR-induced MAPK signals for IFN-γ production. Finally, we found that MEKK3 activation by TCR stimulation requires Rac1/2. Taken together, our study reveals a specific role of MEKK3 in mediating the TCR signals for IFN-γ production.
GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer (2016)

Epigenetic control of gene expression is a major determinant of tumor phenotype and has been found to influence sensitivity to individual chemotherapeutic agents. Glutathione peroxidase 3 (GPX3, plasma glutathione peroxidase) is a key component of cellular antioxidant regulation and its gene has been reported to be methylated in specific tumor types. GPX3 role in oxidative damage has been associated with sensitivity to platinums in other tumors but its importance in colorectal cancer (CRC) has not been determined. We examined the role of GPX3 methylation in colorectal carcinoma in determining sensitivity to platinum drugs using primary tumor specimens, cell lines, knockdown cell lines, and tumor cell line xenografts. We find GPX3 promoter region methylation in approximately one third of CRC samples and GPX3 methylation leads to reduced GPX3 expression and increased oxaliplatin and cisplatin sensitivity. In contrast, in cell lines with high baseline levels of GPX3 expression or with the ability to increase GPX3 expression, platinum resistance is increased. The cisplatin IC<sub>50</sub> in GPX3-methylated cell lines is approximately 6-fold lower than that in GPX3-unmethylated lines. Additionally, knockdown cell lines with essentially no GPX3 expression require N-acetylcysteine to survive in culture underscoring the importance of GPX3 in redox biology. In vivo, GPX3 methylation predicts tumor xenograft sensitivity to platinum with regression of GPX3 knockdown xenografts with platinum treatment but continued growth of GPX3 wild type xenografts in the presence of platinum. These studies demonstrate the importance of GPX3 for CRC cells resistance to platinums and the potential utility of GPX3 methylation status as a predictive biomarker for platinum sensitivity in CRC.
Demonstration of an optimal polarization scrambler for long-haul optical amplifier systems (1994)

Polarization scrambling of the input signal in a long-haul erbium-doped fiber amplifier (EDFA) system is studied both experimentally and theoretically. Demonstration of an optimal polarization scrambler is achieved ensuring complete suppression of the signal decay caused by polarization dependent gain (PDG) in EDFAs. Best performance of the system is attained without imposing severe requirements on the polarization scrambler in terms of residual degree of polarization. Close agreement between measurements and calculations provides a valuable validation of the assumed linear dependency of the PDG differential gain with the degree of polarization of the light.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrophysiological Studies of Face Perception in Humans (1996)

Event-related potentials (ERPs) associated with face perception were recorded with scalp electrodes from normal volunteers. Subjects performed a visual target detection task in which they mentally counted the number of occurrences of pictorial stimuli from a designated category such us butterflies. In separate experiments, target stimuli were embedded within a series of other stimuli including unfamiliar human faces and isolated face components, inverted faces, distorted faces, animal faces, and other nonface stimuli. Unman faces evoked a negative potential at 172 msec (N170), which was absent from the ERPs elicited by other animate and inanimate nonface stimuli. N170 was largest over the posterior temporal scalp and was larger over the right than the left hemisphere. N170 was delayed when faces were presented upside-down, but its amplitude did not change. When presented in isolation, eyes elicited an N170 that was significantly larger than that elicited by whole faces, while noses and lips elicited small negative ERPs about 50 msec later than N170. Distorted human faces, in which the locations of inner face components were altered, elicited an N170 similar in amplitude to that elicited by normal faces. However, faces of animals, human hands, cars, and items of furniture did not evoke N170. N170 may reflect the operation of a neural mechanism tuned to detect (as opposed to identify) human faces, similar to the "structural encoder" suggested by Bruce and Young (1986). A similar function has been proposed for the face-selective N200 ERP recorded from the middle fusiform and posterior inferior temporal gyri using subdural electrodes in humans (Allison, McCarthy, Nobre, Puce, & Belger, 1994c). However, the differential sensitivity of N170 to eyes in isolation suggests that N170 may reflect the activation of an eye-sensitive region of cortex. The voltage distribution of N170 over the scalp is consistent with a neural generator located in the occipitotemporal sulcus lateral to the fusiform/inferior temporal region that generates N200.
Gene expression profiling in clinically localized prostate cancer: a four-gene expression model predicts clinical behavior. (2003)

Some dysregulated genes are good candidates for use as molecular markers and/or therapeutic targets. Furthermore, differential gene expression profiling of clinically localized prostate tumors from relapsing and nonrelapsing patients identified a set of four genes with a pattern of expression that defines a molecular signature that could predict the clinical behavior of this disease.
Alterations in cyst fluid genetics following endoscopic ultrasound-guided pancreatic cyst ablation with ethanol and paclitaxel (2014)

ClinicalTrials.gov (NCT01643460).
Kinetics and mechanism of angiotensin phosphorylation by the transforming gene product of Rous sarcoma virus. (1984)

We have studied steady state kinetics of phosphorylation of [Val5]angiotensin II by pp60src, the transforming gene product of Rous sarcoma virus. Results of initial rate studies at varying substrate concentrations indicated that the mechanism was sequential; Michaelis constants for ATP and peptide were 7 microM and 0.24 mM, respectively, and Vmax was 1.0 nmol/min/mg. The end product ADP and the ATP analog AMP-PNP were competitive inhibitors at varying ATP concentrations and noncompetitive inhibitors at varying peptide concentrations. A dead-end analog of angiotensin II, [delta Phe4]angiotensin II, was a noncompetitive inhibitor at varying ATP concentrations, but induced substrate inhibition at varying peptide concentrations. The kinetic data allowed us to conclude that the reaction proceeded via an Ordered Bi Bi mechanism with ATP as the first binding substrate. We also presented evidence that, while pp60src contained essential histidine and/or lysine residues in its active site, the mechanism does not involve a phosphoryl enzyme intermediate.
Multifunctional Materials in High-Performance OLEDs: Challenges for Solid-State Lighting (2010)

Recent advances in material chemistry have enabled white organic light-emitting device (OLED) efficacy beyond fluorescent tube efficacy up to 100 lm W−1. In this short review, we explore recent developments of small molecule-based multifunctional materials in high-performance OLEDs, especially blue phosphorescent emitters, host materials, and electron-transporting materials.
Multipotency of purified, transplanted globose basal cells in olfactory epithelium (2004)

By comparison with the rest of the nervous system, the olfactory epithelium has an unparalleled ability to renew and repair itself throughout life. However, the identity and capacity of the various types of progenitor cells that underlie that ability are not well established. We used selective isolation, transplantation, and engraftment of various types of marker-labeled cells into the epithelium of methyl bromide-lesioned, unmarked host mice to dissect progenitor cell capacity. Globose basal cells were purified from other potential progenitors using the monoclonal antibody GBC-2 (GBC, globose basal cell) and fluorescence activated cell sorting. Transplanted globose basal cells engraft and, in aggregate, give rise to globose basal cells, neurons, sustentacular cells, and several other kinds of non-neuronal cells. Individual clones, derived from single engrafted globose basal cells, can consist of a mixture of neurons and non-neuronal cells, only neurons, or only non-neuronal cells. Neurons that arise after transplantation mature to the point of expressing odorant receptors and olfactory marker protein and of projecting axons to the olfactory bulb. In contrast, other kinds of epithelial cells are neither neurogenic nor multipotent. For example, sustentacular and duct cells give rise only to themselves after transplantation. Furthermore, horizontal basal cells do not engraft in mice, in which the endogenous population is spared after lesion. Thus, some subtype(s) of GBC is a multipotent progenitor cell, whose multipotency is activated after destruction of both neurons and non-neuronal cells. The results suggest that progenitor cell transplantation may prove useful as a therapeutic modality as well as an analytical tool.