gebhart/patrepeval huggingface dataset:
alpha A-crystallin is expressed in non-ocular tissues (1992)

alpha-Crystallin, the predominant structural protein of the ocular lens, has been considered to be composed of two subunits, alpha A-crystallin and alpha B-crystallin. Of these two, alpha B-crystallin has been previously shown to be an extralenticular protein while alpha A-crystallin has been considered to be a lens-specific polypeptide. Using an antiserum directed against an N-terminal peptide of alpha-crystallin, we have detected a 20-kDa protein in various rat tissues including the brain, liver, lung, spleen, skin, and small intestine and in a number of established epithelial and fibroblast cell lines. PCR analysis of poly(A)-enriched RNA and Southern blot analysis indicated the presence of alpha A-crystallin mRNA sequences in different non-lenticular tissues. Among the non-ocular tissues examined, spleen showed the highest levels of alpha A-crystallin protein and mRNA. The identity of alpha A-crystallin sequences in the spleen was established by cloning and sequencing a polymerase chain reaction-amplified region of alpha A-crystallin mRNA. Sequences derived from spleen and eye revealed almost 100% identity at the nucleotide level. Interestingly, alpha A-crystallin and alpha B-crystallin seem to exist in an inverse quantitative relationship in the spleen and the heart, the two non-ocular tissues where they show highest concentrations, respectively. The known conserved evolution of alpha A-crystallin and the definitive demonstration of the non-ocular expression of this polypeptide suggest important non-crystallin functions for this protein.
Mast Cells At Mucosal Frontiers (2005)

Mast cells (MC) are major effector cells of IgE-mediated allergic inflammation. However, it has become increasingly clear that they also play important roles in a diversity of physiological and pathological processes. Recent advances have focused on the importance of MC in both innate and adaptive immune responses and have fostered studies of MC beyond the myopic focus on allergic reactions. MC possess a great variety of surface receptors and may be activated by inflammatory mediators, immunoglobulins, proteases, hormones, neuropeptides and bacterial products. Following activation they produce a plethora of pro-inflammatory mediators and may participate in inflammatory reactions in many organs. This review focuses on the role of MC in inflammatory reactions in mucosal surfaces with particular emphasis on their role in asthma and gastrointestinal inflammatory conditions.
Higher order filter response in coupled microring resonators (2000)

Second- and third-order filter response is experimentally shown in filters constructed using mutually coupled microring resonators. The higher order filters have passbands with sharper rolloff and flatter tops, and greater out-of-band rejection than previously demonstrated microring filters, which were first order. The effect of varying interesonator coupling on filter passband shape was studied.
Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice (2019)

Cytosine and adenine base editors (CBEs and ABEs) are promising new tools for achieving the precise genetic changes required for disease treatment and trait improvement. However, genome-wide and unbiased analyses of their off-target effects in vivo are still lacking. Our whole-genome sequencing analysis of rice plants treated with the third-generation base editor (BE3), high-fidelity BE3 (HF1-BE3), or ABE revealed that BE3 and HF1-BE3, but not ABE, induce substantial genome-wide off-target mutations, which are mostly the C→T type of single-nucleotide variants (SNVs) and appear to be enriched in genic regions. Notably, treatment of rice with BE3 or HF1-BE3 in the absence of single-guide RNA also results in the rise of genome-wide SNVs. Thus, the base-editing unit of BE3 or HF1-BE3 needs to be optimized in order to attain high fidelity.
The Propeptide Mediates Formation of Stromal Stores of PROMIC-1: Role in Determining Prostate Cancer Outcome (2005)

The extracellular matrix (ECM) is a reservoir of cellular binding proteins and growth factors that are critical for normal cell behavior, and aberrations in the ECM invariably accompany malignancies such as prostate cancer. Carcinomas commonly overexpress macrophage inhibitory cytokine 1 (MIC-1), a proapoptotic and antitumorigenic transforming growth factor-beta superfamily cytokine. Here we show that MIC-1 is often secreted in an unprocessed propeptide containing form. It is variably processed intracellularly, with unprocessed forms being secreted from several tumor lines, including prostate carcinoma lines, PC-3 and LNCaP. Once secreted, only unprocessed proMIC-1 binds ECM, demonstrating for the first time the occurrence of extracellular stores of MIC-1. The propeptide mediates this association via its COOH-terminal 89 amino acids. Xenograft models bearing tumors secreting various engineered forms of MIC-1 show that the propeptide regulates the balance between ECM stores and circulating serum levels of mature MIC-1 in vivo. The absence of propeptide results in approximately 20-fold increase in serum MIC-1 levels. The significance of stromal MIC-1 stores was evaluated in prostate cancer tissue cores, which show major variation in stromal levels of MIC-1. Stromal MIC-1 levels are linked to prostate cancer outcome following radical prostatectomy, with decreasing stromal levels providing an important independent predictor of disease relapse. In low-grade localized prostate cancer (Gleason sum score < or = 6), the level of MIC-1 stromal stores was the best predictor of future relapse when compared with all other clinicopathologic variables. The secretion and ECM association of unprocessed proMIC-1 is likely to play a central role in modulating local bioavailability of MIC-1 which can affect patient outcome in prostate cancer and other epithelial tumors.
Hydrogen Peroxide Triggers Nuclear Export of Telomerase Reverse Transcriptase via Src Kinase Family-Dependent Phosphorylation of Tyrosine 707 (2003)

The regulation of telomerase reverse transcriptase (TERT) plays an important role in the proliferative capacity and survival of cells. Here, we report that exogenously as well as endogenously induced oxidative stress leads to translocation of endogenous as well as overexpressed human TERT from the nucleus into the cytosol. TERT is transported through the nuclear pores in a leptomycin-sensitive and Ran GTPase-dependent process. H(2)O(2)-induced nuclear export of TERT is preceded by TERT tyrosine phosphorylation at position 707 and prevented by the Src kinase family inhibitor PP1. Oxidative stress-induced nuclear export of TERT depends on association with the Ran GTPase. In contrast, mutation of tyrosine 707 inhibits phosphorylation induced by oxidative stress and prevents association with Ran and nuclear export of TERT. Moreover, inhibition of tyrosine phosphorylation at 707 increases the antiapoptotic capacity of TERT. Taken together, depletion of nuclear TERT by tyrosine phosphorylation-dependent nuclear export of TERT is a novel mechanism for regulation of TERT localization, which reduces the antiapoptotic activity of TERT.
Ascorbic acid sulfate sulfohydrolase (C2 sulfatase): the modulator of cellular levels of L-ascorbic acid in rainbow trout. (1982)

The enzyme L-ascorbic acid 2-sulfate sulfohydrolase (C2 sulfatase) was purified from rainbow trout liver. The enzyme catalyzes the hydrolysis of L-ascorbic acid 2-sulfate and has a pH optimum at 6.0. It has a molecular weight of about 117,500 at pH 5.0 and is inhibited by a number of sulfhydryl blocking agents including L-ascorbic acid. C2 sulfatase activity was observed in most metabolic organs of rainbow trout. These findings suggest that the physiologic role of the enzyme is to maintain adequate cellular concentrations of L-ascorbic acid in the fish. The activity of the enzyme is controlled by L-ascorbic acid through feedback inhibition. Comparison of kinetic constants and inhibition patterns suggests that C2 sulfatase is structurally identical to human arylsulfatase A. However, unlike C2 sulfatase, human arylsulfatase A may not be involved in ascorbate metabolism. Its physiologic substrate is reported to be cerebroside-3-sulfate, not L-ascorbic acid 2-sulfate. A scheme is proposed to account for the functional divergence of these two structurally identical enzymes.
Electrical and Contractile Remodeling During the First Days of Atrial Fibrillation Go Hand in Hand (2003)

Depending on the duration of AF, different mechanisms contribute to the AF-induced atrial hypocontractility. Atrial contractile remodeling during several days of AF goes hand in hand with electrical remodeling and might be caused by a reduction of the L-type Ca2+-current.
The effect of Rho kinase inhibition on long-term keratinocyte proliferation is rapid and conditional (2014)

ROCK inhibition rapidly and conditionally induces indefinite proliferation of keratinocytes. This method has far-reaching applications for basic research, as well as for regenerative and personalized medicine.
Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids (2007)

Airway inflammation and epithelial remodeling are two key features of asthma. IL-13 and other cytokines produced during T helper type 2 cell-driven allergic inflammation contribute to airway epithelial goblet cell metaplasia and may alter epithelial-mesenchymal signaling, leading to increased subepithelial fibrosis or hyperplasia of smooth muscle. The beneficial effects of corticosteroids in asthma could relate to their ability to directly or indirectly decrease epithelial cell activation by inflammatory cells and cytokines. To identify markers of epithelial cell dysfunction and the effects of corticosteroids on epithelial cells in asthma, we studied airway epithelial cells collected from asthmatic subjects enrolled in a randomized controlled trial of inhaled corticosteroids, from healthy subjects and from smokers (disease control). By using gene expression microarrays, we found that chloride channel, calcium-activated, family member 1 (CLCA1), periostin, and serine peptidase inhibitor, clade B (ovalbumin), member 2 (serpinB2) were up-regulated in asthma but not in smokers. Corticosteroid treatment down-regulated expression of these three genes and markedly up-regulated expression of FK506-binding protein 51 (FKBP51). Whereas high baseline expression of CLCA1, periostin, and serpinB2 was associated with a good clinical response to corticosteroids, high expression of FKBP51 was associated with a poor response. By using airway epithelial cells in culture, we found that IL-13 increased expression of CLCA1, periostin, and serpinB2, an effect that was suppressed by corticosteroids. Corticosteroids also induced expression of FKBP51. Taken together, our findings show that airway epithelial cells in asthma have a distinct activation profile and identify direct and cell-autonomous effects of corticosteroid treatment on airway epithelial cells that relate to treatment responses and can now be the focus of specific mechanistic studies.
Ridge expansion and immediate implant placement in the esthetic zone. (2010)

Implant placement and tooth restoration in the maxillary esthetic zone is challenging. In the case reported here, the treatment site was tooth # 8, which had been extracted one year previously. Available bone in three dimensions was evaluated by computerized tomography. The bucco-lingual bone width at the crest was 3 mm to 4 mm wide, an inadequate width for implant placement. Ridge expansion was accomplished with hand osteotomes, followed by tapered drills. A 4.3 x 13 mm Nobel Biocare implant was placed. Following osseointegration, a PFM crown, supported by an esthetic abutment, was placed. A very pleasing esthetic result was achieved.
Photolithographic Immobilization of Biopolymers on Solid Supports (1992)

The new technique of site-specific immobilization of biomolecules, for example antibodies, may contribute to the development of biosensors and ligand-binding assays. (The key step is shown schematically here.) A benzophenone-derivatized surface is treated with a solution of the antibody (Ig) and then irradiated through a mask with a checkerboard pattern of transparent and opaque fields. The Ig molecules are bound covalently only in areas which were exposed to light. This was proved by epifluorescence microscopy after the surface was washed free of unbound Ig.
Parameters influencing the attachment of hepatitis A virus to a variety of continuous cell lines (1991)

We have investigated the interactions of purified radiolabelled hepatitis A virus (HAV) with a variety of continuous cell lines. Virus labelled either in vitro with radiolabelled iodine or in vivo with radiolabelled uridine bound to cells with similar efficiency. Attachment to BS-C-1 cells was calcium ion-dependent and this correlated with infectivity assay results. The cell tropism of HAV attachment was examined using cell suspensions and confluent cell monolayers at both 4 degrees C and 37 degrees C. The maximum level of attachment was observed at 4 degrees C with cells in suspension, but was severely inhibited by 2% foetal calf serum; these results again correlated with infectivity assays. The components of serum which inhibit attachment have been characterized by gel filtration chromatography, sucrose density gradient analysis, immunoprecipitation and Western blotting. The data show that such components are of high Mr and that the serum glycoprotein, alpha 2-macroglobulin, can partly mimic the inhibitory effect of whole serum.
Birth Weight and Adult Hypertension, Diabetes Mellitus, and Obesity in US Men (1996)

These findings support the hypothesis that early life exposures, for which birth weight is a marker, are associated with several chronic diseases in adulthood.
POLYAMINES (1984)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Ribozymes that cleave potato leafroll virus RNA within the coat protein and polymerase genes (1990)

Two ribozymes were synthesized which were designed to cleave potato leafroll virus (PLRV) positive strand RNA within the regions known to encode the viral coat protein and the predicted RNA polymerase gene. DNA sequences encoding the ribozymes were inserted into the Escherichia coli plasmids pTz18R and pTz19R under the control of the bacteriophage T7 promoter and enzymically active RNA molecules generated by transcription by T7 RNA polymerase in vitro. Each ribozyme cleaved its cognate site in RNA derived from either cDNA or PLRV particles. Ribozyme cleavage sites within the polymerase gene and coat protein gene were determined and shown to be at the predicted sequence immediately downstream from a GUC motif. An altered version of the ribozyme which recognized the sequence in the coat protein gene was isolated in which a single adenosine residue in the enzymic loop of the ribozyme was deleted. This mutated ribozyme was unable to cleave RNA molecules containing the coat protein ribozyme target site.
Overall Neutralization of Complement Factor H by Autoantibodies in the Acute Phase of the Autoimmune Form of Atypical Hemolytic Uremic Syndrome (2012)

Complement is a major innate immune surveillance system. One of its most important regulators is the plasma protein factor H (FH). FH inactivation by mutations or by autoantibodies is associated with a thrombotic microangiopathy disease, atypical hemolytic uremic syndrome. In this study, we report the characterization of blood samples from 19 anti-FH Ab-positive atypical hemolytic uremic syndrome patients collected at the acute phase of the disease. Analyses of the functional consequences and epitope mapping, using both fluid phase and solid phase approaches, were performed. The anti-FH Abs perturbed FH-mediated cell protection (100%), inhibited FH interaction with C3 (46%), and caused C3 consumption (47%). The Abs were directed against multiple FH epitopes located at the N and C termini. In all tested patients, high titers of FH-containing circulating immune complexes were detected. The circulating immune complex titers correlated with the disease stage better than did the Ab titers. Our results show that anti-FH autoantibodies induce neutralization of FH at acute phase of the disease, leading to an overall impairment of several functions of FH, extending the role of autoantibodies beyond the impairment of the direct cell surface protection.
Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides. (1995)

The tendency of a polypeptide chain to form alpha-helical or beta-strand secondary structure depends upon local and nonlocal effects. Local effects reflect the intrinsic propensities of the amino acid residues for particular secondary structures, while nonlocal effects reflect the positioning of the individual residues in the context of the entire amino acid sequence. In particular, the periodicity of polar and nonpolar residues specifies whether a given sequence is consistent with amphiphilic alpha-helices or beta-strands. The importance of intrinsic propensities was compared to that of polar/nonpolar periodicity by a direct competition. Synthetic peptides were designed using residues with intrinsic propensities that favored one or the other type of secondary structure. The polar/nonpolar periodicities of the peptides were designed either to be consistent with the secondary structure favored by the intrinsic propensities of the component residues or in other cases to oppose these intrinsic propensities. Characterization of the synthetic peptides demonstrated that in all cases the observed secondary structure correlates with the periodicity of the peptide sequence--even when this secondary structure differs from that predicted from the intrinsic propensities of the component amino acids. The observed secondary structures are concentration dependent, indicating that oligomerization of the amphiphilic peptides is responsible for the observed secondary structures. Thus, for self-assembling oligomeric peptides, the polar/nonpolar periodicity can overwhelm the intrinsic propensities of the amino acid residues and serves as the major determinant of peptide secondary structure.
Attention and Autonomic Self-Regulation (1983)

To examine how various aspects of attentional functioning are affected by autonomic self-regulation procedures, this study compared the effect of two treatment programs (EMG and thermal biofeedback used in conjunction with various somatic and cognitive relaxation/self-regulation strategies, and Benson's Relaxation Response procedure) and a Waiting List control group for essential hypertensive adults on three, perhaps overlapping, attentional dimensions: the capacity to disembed figure from ground (Embedded Figures Test, Block Design, and Picture Completion WAIS subtests); the capacity to voluntarily deploy attention (Digit Span subtest of the WAIS), and capacity to sustain attention or become absorbed (as measured by the Tellegen Absorption Scale). Thirty essential hypertensive men and women were randomly placed in one of the three groups. Attentional dimensions were assessed before and after the 10-week treatment program (or waiting period) and the relationship between blood pressure and attentional changes were assessed. The only group to evidence significant blood pressure reduction, the "Biofeedback Group," became significantly more Field Independent as measured by the EFT (p less than 0.001) and the Block Design measure (p less than 0.01) and evidenced a strong trend in the same direction on the Picture Completion measure (p less than 0.052, NS). No other significant pre-post attentional changes were found. A Pearson product correlation revealed that changes in diastolic blood pressure were significantly correlated with changes in EFT (r = 0.54, p less than 0.0001) and the Picture Completion measure (r = 0.32, p less than 0.05). The cognitive effect of autonomic self-regulation is discussed. In addition, the possible role of attention in autonomic self-regulation is examined.
Real-time profiling of respiratory motion: baseline drift, frequency variation and fundamental pattern change (2009)

To precisely ablate tumor in radiation therapy, it is important to locate the tumor position in real time during treatment. However, respiration-induced tumor motions are difficult to track. They are semi-periodic and exhibit variations in baseline, frequency and fundamental pattern (oscillatory amplitude and shape). In this study, we try to decompose the above-mentioned components from discrete observations in real time. Baseline drift, frequency (equivalently phase) variation and fundamental pattern change characterize different aspects of respiratory motion and have distinctive clinical indications. Furthermore, smoothness is a valid assumption for each one of these components in their own spaces, and facilitates effective extrapolation for the purpose of estimation and prediction. We call this process 'profiling' to reflect the integration of information extraction, decomposition, processing and recovery. The proposed method has three major ingredients: (1) real-time baseline and phase estimation based on elliptical shape tracking in augmented state space and Poincaré sectioning principle; (2) estimation of the fundamental pattern by unwarping the observation with phase estimate from the previous step; (3) filtering of individual components and assembly in the original temporal-displacement signal space. We tested the proposed method with both simulated and clinical data. For the purpose of prediction, the results are comparable to what one would expect from a human operator. The proposed approach is fully unsupervised and data driven, making it ideal for applications requiring economy, efficiency and flexibility.