gebhart/patrepeval huggingface dataset:
Septin ring assembly involves cycles of GTP loading and hydrolysis by Cdc42p (2002)

At the beginning of the budding yeast cell cycle, the GTPase Cdc42p promotes the assembly of a ring of septins at the site of future bud emergence. Here, we present an analysis of cdc42 mutants that display specific defects in septin organization, which identifies an important role for GTP hydrolysis by Cdc42p in the assembly of the septin ring. The mutants show defects in basal or stimulated GTP hydrolysis, and the septin misorganization is suppressed by overexpression of a Cdc42p GTPase-activating protein (GAP). Other mutants known to affect GTP hydrolysis by Cdc42p also caused septin misorganization, as did deletion of Cdc42p GAPs. In performing its roles in actin polarization and transcriptional activation, GTP-Cdc42p is thought to function by activating and/or recruiting effectors to the site of polarization. Excess accumulation of GTP-Cdc42p due to a defect in GTP hydrolysis by the septin-specific alleles might cause unphysiological activation of effectors, interfering with septin assembly. However, the recessive and dose-sensitive genetic behavior of the septin-specific cdc42 mutants is inconsistent with the septin defect stemming from a dominant interference of this type. Instead, we suggest that assembly of the septin ring involves repeated cycles of GTP loading and GTP hydrolysis by Cdc42p. These results suggest that a single GTPase, Cdc42p, can act either as a ras-like GTP-dependent "switch" to turn on effectors or as an EF-Tu-like "assembly factor" using the GTPase cycle to assemble a macromolecular structure.
New biodegradable oligoesters for pharmaceutical application (1996)

Tartaric acid, malic acid, and glyceric acid were copolycondensed with glycolic acid at various molar ratios in feed to quickly synthesize biodegradable oligoesters. They were likely to have a moderately cross-linked structure with relatively low molecular weights and hydrophilic groups on the chains. In addition to macroscopic gels which were insoluble in any solvents, we could obtain the oligoesters which were insoluble in water but soluble in N,N-dimethylformamide. The degradation rate of the oligoesters was higher than that of lactic acid (LA) oligomers having molecular weights of a few thousands. On the contrary, their glass transition and flow temperatures were much higher than those of LA oligomers, indicating that their handling during the preparation of drug delivery dosage forms was much improved. The formulation of microspheres containing drugs from the oligoesters revealed that they were useful as biodegradable matrices having high degradation rates.
Unique mechanistic insights into the beneficial effects of soluble epoxide hydrolase inhibitors in the prevention of cardiac fibrosis (2013)

Tissue fibrosis represents one of the largest groups of diseases for which there are very few effective therapies. In the heart, myocardial infarction (MI) resulting in the loss of cardiac myocytes can culminate in adverse cardiac remodeling leading to eventual heart failure. Adverse cardiac remodeling includes myocyte hypertrophy, fibrosis, and electrical remodeling. We have previously demonstrated the beneficial effects of several potent soluble epoxide hydrolase inhibitors (sEHIs) in different models of cardiac hypertrophy and failure. Here, we directly determine the molecular mechanisms underlying the beneficial effects of sEHIs in cardiac remodeling post-MI. Treatment with a potent sEHI, 1-trifluoromethoxyphenyl-3-(1-propionylpiperidine-4-yl)urea (TPPU), which was started 1 wk post-MI in a murine model, results in a significant improvement in cardiac function. Importantly, treatment with TPPU results in a decrease in cardiac fibrosis as quantified using histological and immunostaining techniques. Moreover, single-cell-based assays demonstrate that treatment with TPPU results in a significant decrease not only in the percentages but also the proliferative capacity of different populations of cardiac fibroblasts as well as a reduction in the migration of fibroblasts into the heart from the bone marrow. Our study provides evidence for a possible unique therapeutic strategy to reduce cardiac fibrosis and improve cardiac function post-MI.
Inhibition of growth hormone action improves insulin sensitivity in liver IGF-1–deficient mice (2004)

Liver IGF-1–deficient (LID) mice have a 75% reduction in circulating IGF-1 levels and, as a result, a fourfold increase in growth hormone (GH) secretion. To block GH action, LID mice were crossed with GH antagonist (GHa) transgenic mice. Inactivation of GH action in the resulting LID + GHa mice led to decreased blood glucose and insulin levels and improved peripheral insulin sensitivity. Hyperinsulinemic-euglycemic clamp studies showed that LID mice exhibit severe insulin resistance. In contrast, expression of the GH antagonist transgene in LID + GHa mice led to enhanced insulin sensitivity and increased insulin-stimulated glucose uptake in muscle and white adipose tissue. Interestingly, LID + GHa mice exhibit a twofold increase in white adipose tissue mass, as well as increased levels of serum-free fatty acids and triglycerides, but no increase in the triglyceride content of liver and muscle. In conclusion, these results show that despite low levels of circulating IGF-1, insulin sensitivity in LID mice could be improved by inactivating GH action, suggesting that chronic elevation of GH levels plays a major role in insulin resistance. These results suggest that IGF-1 plays a role in maintaining a fine balance between GH and insulin to promote normal carbohydrate and lipid metabolism.
CRISPR-Cas: Development and applications for mammalian genome editing (2014)

The ability to introduce targeted modifications into genomes and engineer model organisms holds enormous promise for biomedical and technological applications, and has driven the development of tools such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). To facilitate genome engineering in mammalian cells, we have engineered the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 programmable nuclease systems from Streptococcus pyogenes SF370 (SpCas9) and S. thermophilus LMD-9 (St1Cas9) for mouse and human cell gene editing through heterologous expression of the minimal protein and RNA components. We have demonstrated that Cas9 nucleases can be guided by several short RNAs (sgRNAs) to introduce double stranded breaks (DSB) in the mammalian genome and induce efficient, multiplexed gene modification through non-homologous end-joining-mediated indels or homology-directed repair. Furthermore, we have engineered SpCas9 into a nicking enzyme (SpCas9n) to facilitate recombination while minimizing mutagenic DNA repair processes, and show that SpCas9n can be guided by pairs of appropriately offset sgRNAs to induce DSBs with high efficiency and specificity. In collaboration with Drs. Osamu Nureki and Hiroshi Nishimasu at the University of Tokyo, we further report the crystal structure of SpCas9 in complex with the sgRNA and target DNA, and elucidate the structure-function relationship of the ribonucleoprotein complex. Finally, through a metagenomic screen of orthologs, we have identified an additional small Cas9 from Staphylococcus aureus subsp. aureus (SaCas9) that cleaves mammalian endogenous DNA with high efficiency. SaCas9 can be packaged into adeno-associated virus for effective gene modification in vivo. Together, these technologies open up exciting possibilities for applications across basic science, biotechnology, and medicine.
Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design (1993)

A stable, non-peptide inhibitor of the protease from type 1 human immunodeficiency virus has been developed, and the stereochemistry of binding defined through crystallographic three-dimensional structure determination.The initial compound, haloperidol, was discovered through computational screening of the Cambridge Structural Database using a shape complementarity algorithm.The subsequent modification is a non-peptidic lateral lead, which belongs to a family of compounds with well characterized pharmacological properties.This thioketal derivative of haloperidol and a halide counterion are bound within the enzyme active site in a mode distinct from that observed for peptidebased inhibitors.A variant of the protease cocrystallized with this inhibitor shows binding in the manner predicted during the initial computer-based search.The structures provide the context for subsequent synthetic modifications of the inhibitor. ~~Inhibition of human immunodeficiency virus (HIV-1)l protease leads to loss of viable viral particles in infected cells (1).The x-ray crystal structure of HIV-1 protease (2-9) permits structure-based searches for specific inhibitors (10,11).The dimeric enzyme presents two aspartic acid side chains, one from each monomer, to form a single catalytic site.Two symmetrically disposed p ribbon "flaps" surround the catalytic center and close around peptide-based inhibitors.The instability of peptidomimetic inhibitors in vivo, the inability to deliver them through oral routes, and their poor bio-Health Grant GM 39552.
Conformation-activity relationship study of 5-HT3 receptor antagonists and a definition of a model for this receptor site (1990)

A conformation-activity relationship study of 5-HT3 receptor antagonists was used to define a pharmacophore and receptor map to qualitatively account for their activity. The design and synthesis of specific keto-amino-indole derivatives that are potent 5-HT3 receptor antagonists gave some support to the model.
Synthesis of neo-glycosylated L-alanyl-D-isoglutamine derivatives as potential immunoadjuvants. (1992)

The synthesis is described for muramyl-dipeptide-related amphiphilic analogs, where 1,10-diaminodecane served as a lipophilic C-terminal linker for the preparation of a bidentated L-alanyl-D-isoglutamine derivative and incorporation of aldonic and uronic acids at the N-termini as hydrophilic cores. For the N-acylation steps via lactones, suitable conditions were elaborated to allow for the use of unprotected or minimally protected aldonic and uronic acid lactones, respectively. These procedures may represent a useful general approach for the synthesis of neoglycopeptides.
Gated-SCNN: Gated Shape CNNs for Semantic Segmentation (2019)

Current state-of-the-art methods for image segmentation form a dense image representation where the color, shape and texture information are all processed together inside a deep CNN. This however may not be ideal as they contain very different type of information relevant for recognition. Here, we propose a new two-stream CNN architecture for semantic segmentation that explicitly wires shape information as a separate processing branch, i.e. shape stream, that processes information in parallel to the classical stream. Key to this architecture is a new type of gates that connect the intermediate layers of the two streams. Specifically, we use the higher-level activations in the classical stream to gate the lower-level activations in the shape stream, effectively removing noise and helping the shape stream to only focus on processing the relevant boundary-related information. This enables us to use a very shallow architecture for the shape stream that operates on the image-level resolution. Our experiments show that this leads to a highly effective architecture that produces sharper predictions around object boundaries and significantly boosts performance on thinner and smaller objects. Our method achieves state-of-the-art performance on the Cityscapes benchmark, in terms of both mask (mIoU) and boundary (F-score) quality, improving by 2% and 4% over strong baselines.
Effects of Salvia sclarea on chronic immobilization stress induced endothelial dysfunction in rats (2014)

Although Salvia sclarea (clary sage) is widely used in aromatherapy and has antioxidant and antimicrobial properties, its mechanisms of action remain poorly understood. We therefore assessed whether clary sage is effective in treating endothelial dysfunction induced by chronic immobilization stress in rats. Rats were intraperitoneally injected with almond oil, clary sage oil (5%, 10% or 20%), or nifedipine once daily, followed by immobilization stress (2 h/day) for 14 days. Systolic blood pressure (SBP) and heart rate (HR) were measured, as were serum concentrations of corticosterone (CORT); a biomarker of chronic stress, malondialdehyde (MDA); a biomarker of oxidative stress. Nitric oxide production was assessed by nitrite assays, and eNOS level, a biomarker of endothelial dysfunction, was measured by western blotting. Endothelial dysfunction was also assayed by measuring the effect of clary sage on the contraction of rat aortae. Treatment with 5% (p = 0.029), 10% (p = 0.008), and 20% (p = 0.008) clary sage significantly reduced SBP and treatment with 20% clary sage significantly reduced HR (p = 0.039) compared with the chronic immobilization stress group. Clary sage decreased CORT serum concentration (10%, p = 0.026; 20%, p = 0.012) and MDA (10%, p = 0.007; 20%, p = 0.027), findings similar to those observed with nifedipine. In addition, 20% clary sage significantly increased nitric oxide production (p <0.001) and eNOS expression level (p <0.001) and relaxed aortic rings in rats subjected to chronic immobilization stress. Clary sage treatment of rats subjected to immobilization stress contributed to their recovery from endothelial dysfunction by increasing NO production and eNOS level as well as by decreasing oxidative stress. Appropriate concentration of clary sage may result in recovery from endothelial dysfunction. These findings indicate that clary sage oil may be effective in the prevention and treatment of stress-induced cardiovascular diseases.
Synthesis and biologic properties of hydrophilic sapphyrins, a new class of tumor-selective inhibitors of gene expression (2007)

Hydrophilic sapphyrins were found to display promise as novel agents that localize to tumors, generate oxidative stress, and inhibit gene expression.
ChemInform Abstract: PHOSPHORYL DERIVATIVES OF GEMINAL NITROSOHEXAFLUORO‐2‐PROPANOL (1980)

Abstract Läßt man auf Hexafluor‐aceton‐N‐(di‐ethoxyphosphoryl)‐imin (I) Salpetrigsäure‐anhydrid (II) einwirken, so erhält man unter Distickstoffmonoxidabspaltung (2‐Nitroso‐hexafluorpropyl‐2)‐diethylphosphat (IIIa) in mäßiger Ausbeute.
Physical manipulation of the Escherichia coli chromosome reveals its soft nature (2012)

Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In this work, we demonstrate experimentally the fundamentally soft nature of the bacterial chromosome and the entropic forces that can compact it in a crowded intracellular environment. We developed a unique "micropiston" and measured the force-compression behavior of single Escherichia coli chromosomes in confinement. Our data show that forces on the order of 100 pN and free energies on the order of 10(5) k(B)T are sufficient to compress the chromosome to its in vivo size. For comparison, the pressure required to hold the chromosome at this size is a thousand-fold smaller than the surrounding turgor pressure inside the cell. Furthermore, by manipulation of molecular crowding conditions (entropic forces), we were able to observe in real time fast (approximately 10 s), abrupt, reversible, and repeatable compaction-decompaction cycles of individual chromosomes in confinement. In contrast, we observed much slower dissociation kinetics of a histone-like protein HU from the whole chromosome during its in vivo to in vitro transition. These results for the first time provide quantitative, experimental support for a physical model in which the bacterial chromosome behaves as a loaded entropic spring in vivo.
Regulation of Antibody Responses via Antibodies, Complement, and Fc Receptors (2000)

Antibodies can completely suppress or enhance the antibody response to their specific antigen by several hundredfold. Immunoglobulin M (IgM) enhances antibody responses via the complement system, and complement activation by IgM probably starts the chain of events leading to antibody responses to suboptimal antigen doses. IgG can enhance primary antibody responses in the absence of the complement system and seems to be dependent on Fc receptors for IgG (FcgammaRs). IgE enhances antibody responses via the low-affinity receptor for IgE (FcepsilonRII/CD23). The precise effector mechanisms that cause enhancement are not known, but direct B-cell signaling, antigen presentation, and increased follicular localization are all possibilities. IgG, IgE, and IgM may also suppress antibody responses when used in certain immunization regimes, and it seems reasonable that an important mechanism behind suppression is the masking of antigenic epitopes by antibodies. In addition, FcgammaRIIB, which contains a cytoplasmic inhibitory motif, acts as a negative regulator of antibody responses. This receptor, however, may prevent the antibody responses from exceeding a certain level rather than causing complete suppression.
Studies on the role of plasminogen activator in ovulation. In vitro response of granulosa cells to gonadotropins, cyclic nucleotides, and prostaglandins. (1976)

A quantitative method is described for measuring the amount of plasminogen activator produced by rat ovarian granulosa cells following exposure to hormones in vivo or in vitro. The results confirm the previously reported observation (Beers, W. H., Strickland, S., and Reich, E. (1975) Cell 6, (387-394) that granulosa cells in vivo produce increasing amounts of plasminogen activator as the time of ovulation approaches and that the enzyme is produced only be cells obtained from follicles destined to ovulate. Inactive cells can be stimulated in vitro by gonadotropins to produce plasminogen activator. This response is time- and dose-dependent, and results in an increase of intracellular and extracellular enzyme. Studies of the specificity of this response indicate that preparations of follicle-stimulating hormone are much more effective than corresponding preparations of luteinizing hormone. The effect of other pituitary hormones is also presented. Molecules other than gonadotropins are also capable of stimulating the cells to produce the enzyme. Prostaglandins E1 and E2 and analogues of cAMP effectively stimulated the cells to produce plasminogen activator, cGMP and its analogues and prostaglandins F1a and F2a were without effect as were the six steroids studied. The inactive compounds also did not inhibit the response of the cells to gonadotropins. The granulosa cell plasminogen activator has been analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and has an apparent molecular weight of 75,000. By this and other criteria, the granulosa cell enzyme is similar to one of the species of plasminogen activators obtained from cultures of simian virus 40-transformed rat embryo fibroblasts.
Discovery of the Macrocycle 11-(2-Pyrrolidin-1-yl-ethoxy)-14,19-dioxa-5,7,26-triaza-tetracyclo[19.3.1.1(2,6).1(8,12)]heptacosa-1(25),2(26),3,5,8,10,12(27),16,21,23-decaene (SB1518), a Potent Janus Kinase 2/Fms-Like Tyrosine Kinase-3 (JAK2/FLT3) Inhibitor for the Treatment of Myelofibrosis and Lymphoma (2011)

Discovery of the activating mutation V617F in Janus Kinase 2 (JAK2(V617F)), a tyrosine kinase critically involved in receptor signaling, recently ignited interest in JAK2 inhibitor therapy as a treatment for myelofibrosis (MF). Herein, we describe the design and synthesis of a series of small molecule 4-aryl-2-aminopyrimidine macrocycles and their biological evaluation against the JAK family of kinase enzymes and FLT3. The most promising leads were assessed for their in vitro ADME properties culminating in the discovery of 21c, a potent JAK2 (IC(50) = 23 and 19 nM for JAK2(WT) and JAK2(V617F), respectively) and FLT3 (IC(50) = 22 nM) inhibitor with selectivity against JAK1 and JAK3 (IC(50) = 1280 and 520 nM, respectively). Further profiling of 21c in preclinical species and mouse xenograft and allograft models is described. Compound 21c (SB1518) was selected as a development candidate and progressed into clinical trials where it is currently in phase 2 for MF and lymphoma.
Feature subimage extraction for cephalogram landmarking (2002)

The significant features corresponding to skull structures on cephalograms are clinically useful for cephalometric diagnosis and superimposition. Accordingly the specific anatomical landmarks need to be firstly located for cephalometric measurements. In this paper, a novel method combining the multilayer perceptron and genetic algorithm is proposed to extract the specific feature areas. Thus, the useful landmarks may then be easily found from these feature areas instead of the whole image. The multilayer perceptron is used to approximate a fitness function for the genetic algorithm. In each iteration, eighty randomly selected subimages are grouped as the population for a GA search. Based on the feature characteristics, the selected subimages with the best fitness will survive to the last. From the experimental results, it is shown that the proposed algorithm does work better than our previous method of correlation.
Biochemical and Immunological Characterization of Bacterially Expressed and RefoldedPlasmodium falciparum42-Kilodalton C-Terminal Merozoite Surface Protein 1 (2003)

Protection against Plasmodium falciparum can be induced by vaccination in animal models with merozoite surface protein 1 (MSP1), which makes this protein an attractive vaccine candidate for malaria. In an attempt to produce a product that is easily scaleable and inexpensive, we expressed the C-terminal 42 kDa of MSP1 (MSP1(42)) in Escherichia coli, refolded the protein to its native form from insoluble inclusion bodies, and tested its ability to elicit antibodies with in vitro and in vivo activities. Biochemical, biophysical, and immunological characterization confirmed that refolded E. coli MSP1(42) was homogeneous and highly immunogenic. In a formulation suitable for human use, rabbit antibodies were raised against refolded E. coli MSP1(42) and tested in vitro in a P. falciparum growth invasion assay. The antibodies inhibited the growth of parasites expressing either homologous or heterologous forms of P. falciparum MSP1(42). However, the inhibitory activity was primarily a consequence of antibodies directed against the C- terminal 19 kDa of MSP1 (MSP1(19)). Vaccination of nonhuman primates with E. coli MSP1(42) in Freund's adjuvant protected six of seven Aotus monkeys from virulent infection with P. falciparum. The protection correlated with antibody-dependent mechanisms. Thus, this new construct, E. coli MSP1(42), is a viable candidate for human vaccine trials.
Role of innate signalling pathways in the immunogenicity of alphaviral replicon-based vaccines (2011)

We show that alphaviral replicon-based vectors activate multiple innate signalling pathways, which both activate and restrict the induced immune response. These results further show that there is a delicate balance in the strength of innate signalling and induction of adaptive immune responses that should be taken into consideration when innate signalling molecules, such as type I IFNs, are used as vaccine adjuvant.