gebhart/patrepeval huggingface dataset:
Fluid Transport by Gallbladder Epithelium (1983)

The absorption of fluid by epithelial tissues is thought to be due to the existence of hypertonic regions within the epithelium. The magnitude of the required hypertonicity as well as its localization have been the subject of considerable experimental and theoretical effort. Model calculations demonstrated the need for knowledge of the water permeability of the membranes of epithelial cells for the purpose of estimation of the osmotic gradients required for fluid absorption. We measured the hydraulic water permeability of the individual cell membranes of Necturus gallbladder by quantitative light microscopy. The water permeabilities were sufficiently high so that small osmotic gradients were required to achieve normal rates of fluid transport. The cell osmolality was calculated to exceed that of the mucosal bathing solution by about 2 mosmol kg-1, and the basolateral interstitial osmolality was calculated to be about 1 mosmol kg-1 greater than that of the cell. The fluid absorbed by the epithelium must be slightly hypertonic to the bathing solutions. Knowledge of the apical cell membrane water permeability and the relative area of the cell and tight junction allow a calculation of the relative flow of fluid across both pathways. It can be readily shown that osmotically induced flow across the epithelium occurs predominantly transcellularly because of the small area of the junctional pathway and the high water permeability of the cell membranes.
Physicochemical Stability of Crystalline Sugars and Their Spray-Dried Forms: Dependence upon Relative Humidity and Suitability for Use in Powder Inhalers (1998)

Lactose, trehalose, sucrose, and mannitol were purchased in crystalline form and fractionated by sieving. Coarse (125-212 microns) and fine (44-74 microns) free-flowing fractions were selected as typical of drug carriers in dry-powder inhalers. In addition, one batch of each sugar was spray-dried to form a respirable powder (> 50% [w/w], < 5 microns). Both fractions and the spray-dried powders were characterized before and after storage for 30 days at < 23%, 23%, 52%, 75% and 93% relative humidity (RH) at 25 degrees C. Moisture uptake was determined by thermogravimetric analysis (TGA) validated by Karl Fischer titration. Sieve fractions (before storage at different RHs) and spray-dried materials (before and after storage) were further characterized by differential scanning calorimetry (DSC) and x-ray powder diffraction (XRPD). All crystalline sieve fractions (except sucrose at 93% RH) were stable at 25 degrees C and showed insignificant moisture uptake when exposed to each relative humidity for 30 days. Sucrose dissolved in sorbed moisture at 93% RH. Spray-dried lactose, sucrose, and trehalose, which were collected in the amorphous form, showed moisture uptake, without recrystallization, when held for 30 days at 23% RH. These sugars recrystallized as sintered masses and became undispersible at > or = 52% RH. Spray-dried mannitol was apparently 100% crystalline when collected directly from the spray-dryer; it did not show humidity-induced changes. The physicochemical behavior of each sugar form is discussed as it relates to the sugar's suitability as a powder-inhaler excipient, with both conventional and protein drugs.
Recombinant vaccinia viruses expressing the F, G or N, but not the M2, protein of bovine respiratory syncytial virus (BRSV) induce resistance to BRSV challenge in the calf and protect against the development of pneumonic lesions. (1997)

The immunogenicity and protective efficacy of recombinant vaccinia viruses (rVV) encoding the F, G, N or M2 (22K) proteins of bovine respiratory syncytial virus (BRSV) were evaluated in calves, the natural host for BRSV. Calves were vaccinated either by scarification or intratracheally with rVV and challenged 6 to 7 weeks later with BRSV. Although replication of rVV expressing the F protein in the respiratory tract was limited after intratracheal vaccination, the levels of serum and pulmonary antibody were similar to those induced following scarification. The serum antibody response induced by the F protein was biased in favour of IgG1 antibody, whereas the G and the N proteins induced similar levels of IgG1:IgG2, and antibody was undetectable in calves primed with the M2 protein. The F protein induced neutralizing antibodies, but only low levels of complement-dependent neutralizing antibodies were induced by the G protein, and antibody induced by the N protein was not neutralizing. The F and N proteins primed calves for BRSV-specific lymphocyte proliferative responses, whereas proliferative responses were detected in calves primed with the G protein only after BRSV challenge. The M2 protein primed lymphocytes in only one out of five calves. Although there were differences in the immune responses induced by the rVVs, the F, G and N, but not the M2, proteins induced significant protection against BRSV infection and, in contrast with the enhanced lung pathology seen in mice vaccinated with rVV expressing individual proteins of human (H)RSV, there was a reduction in lung pathology in calves.
Trigramin. A low molecular weight peptide inhibiting fibrinogen interaction with platelet receptors expressed on glycoprotein IIb-IIIa complex. (1987)

Trigramin, a highly specific inhibitor of fibrinogen binding to platelet receptors, was purified to homogeneity from Trimeresurus gramineus snake venom. Trigramin is a single chain (approximately 9 kDa) cysteine-rich peptide with the Glu-Ala-Gly-Glu-Asp-Cys-Asp-Cys-Gly-Ser-Pro-Ala NH2-terminal sequence. Chymotryptic fragmentation showed the Arg-Gly-Asp sequence in trigramin. Trigramin inhibited fibrinogen-induced aggregation of platelets stimulated by ADP (IC50 = 1.3 X 10(-7)M) and aggregation of chymotrypsin-treated platelets. It did not affect the platelet secretion. Trigramin was a competitive inhibitor of the 125I-fibrinogen binding to ADP-stimulated platelets (Ki = 2 X 10(-8) M). 125I-Trigramin bound to resting platelets (Kd = 1.7 X 10(-7) M; n = 16,500), to ADP-stimulated platelets (Kd = 2.1 X 10(-8) M; n = 17,600), and to chymotrypsin-treated platelets (Kd = 8.8 X 10(-8) M; n = 13,800) in a saturable manner. The number of 125I-trigramin binding sites on thrombasthenic platelets amounted to 2.7-5.4% of control values obtained for normal platelets and correlated with the reduced number of GPIIb-GPIIIa molecules on the platelet surface. EDTA, monoclonal antibodies directed against the GPIIb-GPIIIa complex, and synthetic peptides (Arg-Gly-Asp-Ser and Tyr-Gly-Gln-Gln-His-His-Leu-Gly-Gly-Ala-Lys-Gln-Ala-Gly-Asp-Val) blocked both 125I-fibrinogen binding and 125I-trigramin binding to platelets. Fibrinogen binding was more readily inhibited by these compounds than was trigramin binding. Monoclonal antibodies directed either against GPIIb or GPIIIa molecules did not block the interaction of either ligand with platelets. Reduced, S-pyridylethyl, trigramin did not inhibit platelet aggregation and fibrinogen binding to platelets and it did not bind to platelets, suggesting that the secondary structure of this molecule is critical for expression of its biological activity.
High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems (2012)

Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.
Protective Effects Of An N-Terminal Fragment Of Bactericidal/Permeability-Increasing Protein In Rodent Models Of Gram-Negative Sepsis: Role Of Bactericidal Properties (1994)

Effects of an N-terminal fragment of bactericidal/permeability increasing protein (rBPI21) on bacterial infections were determined. Intravenous (i.v.) rBPI21 increased survival and reduced bacteremia in rats after an iv injection of Escherichia coli O7:K1 bacteria. rBPI21 inhibited the rise in tumor necrosis factor-alpha resulting from challenge with 2 strains of E. coli. Intraperitoneal (ip) injection of rBPI21 increased survival of mice after ip injection of E. coli O7:K1 and Pseudomonas aeruginosa and reduced bacteria in peritoneal lavage fluid and blood and inhibited cytokine production in response to E. coli. rBPI21 alone did not protect mice challenged with E. coli O111:B4 but was protective and reduced bacterial counts when administered in combination with the antibiotic cefamandole. The data show that protection with rBPI21 is associated with reductions in bacterial counts and is enhanced by antibiotics. Bactericidal activity, in addition to antiendotoxin activity, is involved in the efficacy of rBPI21 in models of gram-negative infection.
Asymmetric LSH (ALSH) for Sublinear Time Maximum Inner Product Search (MIPS) (2014)

We present the first provably sublinear time algorithm for approximate \emph{Maximum Inner Product Search} (MIPS). Our proposal is also the first hashing algorithm for searching with (un-normalized) inner product as the underlying similarity measure. Finding hashing schemes for MIPS was considered hard. We formally show that the existing Locality Sensitive Hashing (LSH) framework is insufficient for solving MIPS, and then we extend the existing LSH framework to allow asymmetric hashing schemes. Our proposal is based on an interesting mathematical phenomenon in which inner products, after independent asymmetric transformations, can be converted into the problem of approximate near neighbor search. This key observation makes efficient sublinear hashing scheme for MIPS possible. In the extended asymmetric LSH (ALSH) framework, we provide an explicit construction of provably fast hashing scheme for MIPS. The proposed construction and the extended LSH framework could be of independent theoretical interest. Our proposed algorithm is simple and easy to implement. We evaluate the method, for retrieving inner products, in the collaborative filtering task of item recommendations on Netflix and Movielens datasets.
Crystallization of Pentasil Zeolite in the Absence of Organic Templates (1989)

As- synthesized Na-ZSM- 5, which possesses an isostructure with TPA-ZSM- 5, exhibits a hexagonal-lath-shaped morphology. Liquid phase SiO2/Al2O3 ratio is important in controlling the formation of Na-ZSM- 5 and mordenite, and the silica source influences the liquid phase composition. High yield of Na-ZSM- 5 is obtained only when a small-sized silica sol is employed. A linear relationship between Na/Al starting atomic ratio and the nucleation rate indicates that charge neutralization of SBU is required for zeolite crystallization.
Comparison of partial malolactic enzyme gene sequences for phylogenetic analysis of some lactic acid bacteria species and relationships with the malic enzyme (1999)

DNA sequences covering 36% of the mle gene that encodes the malolactic enzyme were determined for 13 strains of lactic acid bacteria, representing Pediococcus, Leuconostoc, Lactobacillus and Oenococcus genera. The sequences were aligned with the corresponding region of mleS in Lactococcus lactis. The phylogenetic distance matrix tree of all mle sequences was compared with the 16S rRNA phylogenetic tree. The analysis showed that the mle fragment evolved more rapidly than the 16S gene and differently. Pediococcus and Lactobacillus species were intermixed in the 16S rRNA tree whereas they were separated in the mle tree. Leuconostoc mesenteroides and Oenococcus oeni were distinct from other species in the 16S rRNA tree, whereas they were intermixed with Lactobacillus species and Lactococcus lactis in the mle tree. The amino acid sequences deduced from partial mle genes were aligned with 22 malic enzyme sequences and the corresponding phylogenetic tree was constructed. Malic and malolactic enzymes were distinct at the phylogenetic level, except for malic enzymes of yeast and Escherichia coli which were nearer the malolactic enzymes than the other malic enzymes. The analysis of conserved sites showed several interesting amino acids specific to either malic enzyme or malolactic enzyme.
Nutrition in Chronic Disease Management in the Elderly (2003)

Older Americans experience chronic disease at rates well above other segments of our society. Rates of health services use are also 2 to 3 times that of younger age groups. The most rapidly growing segments of America's aging population are also its most nutritionally vulnerable-women, minorities, and those 85 years of age and older. The routine incorporation of nutrition screening and intervention into chronic disease management protocols will lower healthcare services usage, decrease healthcare costs, help relieve the burden of human suffering experienced by older Americans with chronic disease, and improve quality of life for our nation's elders.
Mitochondrial dysfunction and psychiatric disorders. (2009)

Mitochondria are intracellular organelles crucial in the production of cellular energy. Mitochondrial diseases may result from malfunctions in this biochemical cascade. Several investigators have proposed that mitochondrial dysfunction is related to the pathophysiology of bipolar disorder (BD), major depressive disorder (MDD) and schizophrenia (SZ). The authors reviewed recent study findings and tried to delineate the current understanding of the correlation between mitochondrial dysfunction and psychiatric disorders. A growing body of evidence suggests that mitochondrial dysfunction is important in patients with psychiatric disorders. The evidence include impaired energy metabolism in the brain detected using results of magnetic resonance spectroscopy, electron microscopy, co-morbidity with mitochondrial diseases, the effects of psychotropics on mitochondria, increased mitochondrial DNA (mtDNA) deletion in the brain, and association with mtDNA mutations/polymorphisms or nuclear-encoded mitochondrial genes. It is possible that the new information will lead to a focus on psychiatric disorder as a metabolic disease. Treatment with psychotropics might ultimately enhance energy metabolism and reduce the damage of oxidative stress. The next step in the study of mitochondrial dysfunction in patients with psychiatric disorders should be clarification of how mitochondrial dysfunction, a nonspecific risk factor, causes specific symptoms. Further study of mitochondrial dysfunction in patients with psychiatric disorder is expected to be useful for the development of cellular disease markers and new psychotropics.
T Cells and Thyroid Autoimmunity (1994)

Autoimmune thyroid disease is the archetype of organ-specific autoimmune disorders and shares with them T cell dependence. The observation that thyroid cells in autoimmune thyroid disease express the major histocompatibility complex molecule HLA-DR led to the hypothesis that they could present antigen and initiate or maintain the autoimmune process. However, functional experiments, and recent evidence indicating that provision of a co-stimulatory signal is also essential for efficient antigen presentation, argue against such a role. The analysis of T cell responses to two major thyroid antigens, thyroid peroxidase and the thyroid stimulating hormone receptor, reveals a heterogeneity both within and between patients, and intrathyroidal T cells show diverse usage of T cell receptor genes. Therefore, any strategy that uses modified peptides, monoclonal antibodies against specific T cell receptor molecules, or T cell vaccination for the purpose of treating thyroid autoimmunity is unlikely to succeed.
Ultra‐deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas (2013)

The recognition of cancer cells by T cells can impact upon prognosis and be exploited for immunotherapeutic approaches. This recognition depends on the specific interaction between antigens displayed on the surface of cancer cells and the T cell receptor (TCR), which is generated by somatic rearrangements of TCR α- and β-chains (TCRb). Our aim was to assess whether ultra-deep sequencing of the rearranged TCRb in DNA extracted from unfractionated clear cell renal cell carcinoma (ccRCC) samples can provide insights into the clonality and heterogeneity of intratumoural T cells in ccRCCs, a tumour type that can display extensive genetic intratumour heterogeneity (ITH). For this purpose, DNA was extracted from two to four tumour regions from each of four primary ccRCCs and was analysed by ultra-deep TCR sequencing. In parallel, tumour infiltration by CD4, CD8 and Foxp3 regulatory T cells was evaluated by immunohistochemistry and correlated with TCR-sequencing data. A polyclonal T cell repertoire with 367-16 289 (median 2394) unique TCRb sequences was identified per tumour region. The frequencies of the 100 most abundant T cell clones/tumour were poorly correlated between most regions (Pearson correlation coefficient, -0.218 to 0.465). 3-93% of these T cell clones were not detectable across all regions. Thus, the clonal composition of T cell populations can be heterogeneous across different regions of the same ccRCC. T cell ITH was higher in tumours pretreated with an mTOR inhibitor, which could suggest that therapy can influence adaptive tumour immunity. These data show that ultra-deep TCR-sequencing technology can be applied directly to DNA extracted from unfractionated tumour samples, allowing novel insights into the clonality of T cell populations in cancers. These were polyclonal and displayed ITH in ccRCC. TCRb sequencing may shed light on mechanisms of cancer immunity and the efficacy of immunotherapy approaches.
Oryzacystatin Exogenously Introduced into Protoplasts and Regeneration of Transgenic Rice (1994)

Oryzacystatin (OC) is a proteinaceous cysteine proteinase inhibitor involved in the biodefense of rice seeds. To create transgenic rice plants with increased OC activity, we introduced an OC expressing vector into rice protoplasts and obtained transformed calli. The expression vector contained a bacterial inaA DNA fragment in the 3'-noncoding region as a tag to distinguish the introduced DNA from the intrinsic OC gene. The OC vector and a selection marker gene conferring hygromycin resistance were used together to transfect into rice protoplasts. A number of hygromycin-resistant calli were obtained and studied by polymerase chain reaction and genomic Southern blotting to find if the exogenous OC gene had been integrated. The calli were studied by northern blotting as well to examine mRNA expression. The results showed that integration and expression of the introduced OC gene occurred in 51% and 27%, respectively, of 156 subcultures from 15 hygromycin-resistant calli. As a final step, transgenic rice plants were regenerated from the calli expressing OC. Leaves and seeds from the plants had higher OC activities than those from nontransgenic plants.
Metabolic Engineering of Synechocystis sp. PCC 6803 for Production of the Plant Diterpenoid Manoyl Oxide (2015)

Forskolin is a high value diterpenoid with a broad range of pharmaceutical applications, naturally found in root bark of the plant Coleus forskohlii. Because of its complex molecular structure, chemical synthesis of forskolin is not commercially attractive. Hence, the labor and resource intensive extraction and purification from C. forskohlii plants remains the current source of the compound. We have engineered the unicellular cyanobacterium Synechocystis sp. PCC 6803 to produce the forskolin precursor 13R-manoyl oxide (13R-MO), paving the way for light driven biotechnological production of this high value compound. In the course of this work, a new series of integrative vectors for use in Synechocystis was developed and used to create stable lines expressing chromosomally integrated CfTPS2 and CfTPS3, the enzymes responsible for the formation of 13R-MO in C. forskohlii. The engineered strains yielded production titers of up to 0.24 mg g(-1) DCW 13R-MO. To increase the yield, 13R-MO producing strains were further engineered by introduction of selected enzymes from C. forskohlii, improving the titer to 0.45 mg g(-1) DCW. This work forms a basis for further development of production of complex plant diterpenoids in cyanobacteria.
Translational Repression Mediates Activation of Nuclear Factor Kappa B by Phosphorylated Translation Initiation Factor 2 (2004)

Numerous stressful conditions activate kinases that phosphorylate the alpha subunit of translation initiation factor 2 (eIF2alpha), thus attenuating mRNA translation and activating a gene expression program known as the integrated stress response. It has been noted that conditions associated with eIF2alpha phosphorylation, notably accumulation of unfolded proteins in the endoplasmic reticulum (ER), or ER stress, are also associated with activation of nuclear factor kappa B (NF-kappaB) and that eIF2alpha phosphorylation is required for NF-kappaB activation by ER stress. We have used a pharmacologically activable version of pancreatic ER kinase (PERK, an ER stress-responsive eIF2alpha kinase) to uncouple eIF2alpha phosphorylation from stress and found that phosphorylation of eIF2alpha is both necessary and sufficient to activate both NF-kappaB DNA binding and an NF-kappaB reporter gene. eIF2alpha phosphorylation-dependent NF-kappaB activation correlated with decreased levels of the inhibitor IkappaBalpha protein. Unlike canonical signaling pathways that promote IkappaBalpha phosphorylation and degradation, eIF2alpha phosphorylation did not increase phosphorylated IkappaBalpha levels or affect the stability of the protein. Pulse-chase labeling experiments indicate instead that repression of IkappaBalpha translation plays an important role in NF-kappaB activation in cells experiencing high levels of eIF2alpha phosphorylation. These studies suggest a direct role for eIF2alpha phosphorylation-dependent translational control in activating NF-kappaB during ER stress.
CRISPR-SKIP: programmable gene splicing with single base editors (2018)

CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes through targeted double-strand breaks in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for off-target mutations, technologies capable of introducing targeted changes with increased precision, such as single-base editors, are preferred. We present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.
Inositol trisphosphate and diacylglycerol as second messengers (1984)

Research Article| June 01 1984 Inositol trisphosphate and diacylglycerol as second messengers M J Berridge M J Berridge Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1984) 220 (2): 345–360. https://doi.org/10.1042/bj2200345 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation M J Berridge; Inositol trisphosphate and diacylglycerol as second messengers. Biochem J 1 June 1984; 220 (2): 345–360. doi: https://doi.org/10.1042/bj2200345 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1984 London: The Biochemical Society1984 Article PDF first page preview Close Modal You do not currently have access to this content.