gebhart/patrepeval huggingface dataset:
Theoretical study of the ligand–CYP2B4 complexes: Effect of structure on binding free energies and heme spin state (2004)

The molecular origins of temperature-dependent ligand-binding affinities and ligand-induced heme spin state conversion have been investigated using free energy analysis and DFT calculations for substrates and inhibitors of cytochrome P450 2B4 (CYP2B4), employing models of CYP2B4 based on CYP2C5(3LVdH)/CYP2C9 crystal structures, and the results compared with experiment. DFT calculations indicate that large heme-ligand interactions (ca. -15 kcal/mol) are required for inducing a high to low spin heme transition, which is correlated with large molecular electrostatic potentials (approximately -45 kcal/mol) at the ligand heteroatom. While type II ligands often contain oxygen and nitrogen heteroatoms that ligate heme iron, DFT results indicate that BP and MF heme complexes, with weak substrate-heme interactions (ca. -2 kcal/mol), and modest MEPS minima (>-35 kcal/mol) are high spin. In contrast, heme complexes of the CYP2B4 inhibitor, 4PI, the product of benzphetamine metabolism, DMBP, and water are low spin, have substantial heme-ligand interaction energies (<-15 kcal/mol) and deep MEPS minima (<-45 kcal/mol) near their heteroatoms. MMPBSA analysis of MD trajectories were made to estimate binding free energies of these ligands at the heme binding site of CYP2B4. In order to initially assess the realism of this approach, the binding free energy of 4PI inhibitor was computed and found to be a reasonable agreement with experiment: -7.7 kcal/mol [-7.2 kcal/mol (experiment)]. BP was determined to be a good substrate [-6.3 kcal/mol (with heme-ligand water), -7.3 kcal/mol (without ligand water)/-5.8 kcal/mol (experiment)], whereas the binding of MF was negligible, with only marginal binding binding free energy of -1.7 kcal/mol with 2-MF bound [-3.8 kcal/mol (experiment)], both with and without retained heme-ligand water. Analysis of the free energy components reveal that hydrophobic/nonpolar contributions account for approximately 90% of the total binding free energy of these substrates and are the source of their differential and temperature-dependent CYP2B4 binding. The results indicate the underlying origins of the experimentally observed differential binding affinities of BP and MF, and indicate the plausibility of the use of models derived from moderate sequence identity templates in conjunction with approximate free energy methods in the estimation of ligand-P450 binding affinities.
MEVLÂNÂNIN HOCASI SEYYİD BURHANEDDİN VE BAZI İTİKÂDÎ KELÂMÎ GÖRÜŞLERİNİN DEĞERLENDİRİLMESİ (2016)

Kelâm İlminin esas gâyelerinden biri ve en önemlisi; kişide sağlam bir inanç oluşturmak ve bu inancı, bir takım vaki şüphelerle sarsıntıya uğramayacak şekilde muhafaza, bu yolda Kurân ve sünnet ışığında çeşitli metod ve teknikleri müslümanlara sunma gayretidir. Tasavvuf ilminin gâyesi de nefsi terbiye ederek ahlâk ekseninde bu imânı muhafaza etmeye gayret sarfetmektir. Seyyid Burhâneddîn Tirmizi Xll. yüzyılın sonlarında doğmuş, XIII. asrın ilk yarısında yaşamış, önemli bir mutasavvıftır. Onun kıymeti Mevlana Celâleddîn-i Rumî&amp;#039;yi itikâdî ve tasavvufî yönden şekillendiren uzun süre eğiten ilk hocası olmasındandır. Bu makâlede tasavvuf çevrelerinde ve Anadolu İslâm kültüründe önemli bir konuma sahip Seyyid Burhâneddînin bazı itikâdî ve kelâmî görüşleri incelenecektir.
Effective free distance of turbo codes (1996)

The authors define and study the effective free distance of a turbo code. If a turbo code is constructed from a number of component codes, they argue that the effective free distance can be maximised by choosing the component codes to be IIR convolutional code fragments with maximal input weight-2 free distance. They then present some theoretical bounds for, and some numerical tables of; IIR code fragments with maximal input weight-2 free distance.
Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years (2020)

The future trajectory of the coronavirus disease 2019 (COVID-19) pandemic hinges on the dynamics of adaptive immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, salient features of the immune response elicited by natural infection or vaccination are still uncertain. We use simple epidemiological models to explore estimates for the magnitude and timing of future COVID-19 cases, given different assumptions regarding the protective efficacy and duration of the adaptive immune response to SARS-CoV-2, as well as its interaction with vaccines and nonpharmaceutical interventions. We find that variations in the immune response to primary SARS-CoV-2 infections and a potential vaccine can lead to markedly different immune landscapes and burdens of critically severe cases, ranging from sustained epidemics to near elimination. Our findings illustrate likely complexities in future COVID-19 dynamics and highlight the importance of immunological characterization beyond the measurement of active infections for adequately projecting the immune landscape generated by SARS-CoV-2 infections.
Peptide nucleic acids targeted to the neurotensin receptor and administered i.p. cross the blood–brain barrier and specifically reduce gene expression (1999)

Intraperitoneal injection of an unmodified antisense peptide nucleic acid (PNA) complementary to mRNA of the rat neurotensin (NT) receptor (NTR1) was demonstrated by a gel shift assay to be present in brain, thus indicating that the PNA had in fact crossed the blood-brain barrier. An i.p. injection of this antisense PNA specifically inhibited the hypothermic and antinociceptive activities of NT microinjected into brain. These results were associated with a reduction in binding sites for NT both in brain and the small intestine. Additionally, the sense-NTR1 PNA, targeted to DNA, microinjected directly into the brain specifically reduced mRNA levels by 50% and caused a loss of response to NT. To demonstrate the specificity of changes in behavioral, binding, and mRNA studies, animals treated with NTR1 PNA were tested for behavioral responses to morphine and their mu receptor levels were determined. Both were found to be unaffected in these NTR1 PNA-treated animals. The effects of both the antisense and sense PNAs were completely reversible. This work provides evidence that any antisense strategy targeted to brain proteins can work through i. p. delivery by crossing the normal blood-brain barrier. Equally important was that an antigene strategy, the sense PNA, was shown in vivo to be a potentially effective therapeutic treatment.
Cell-based therapy approaches using dying cells: from tumour immunotherapy to transplantation tolerance induction (2002)

Cell-based therapies are promising approaches to treat uncontrolled pathologies, such as tumours. Apoptotic tumour cells have recently been proposed as a source of tumour-associated antigens to stimulate an efficient immune response. However, a complex relationship exists between apoptosis and the immune system. In this review, the different factors that may influence immune responses against apoptotic cells are detailed and discussed in the light of recent publications. These factors include the nature of the phagocytes and the receptors involved in apoptotic cell uptake, as well as the environment in which cells are dying. A possible distinction between apoptosis and necrosis by immune system sentinels adds a further level of complexity. The potential use of the immunomodulatory properties associated with apoptosis to favour engraftment and induce tolerance in transplantation is then discussed. In conclusion, this review will suggest appropriate conditions to efficiently and safely use apoptotic cells as a new cell therapy product.
Influence of PEGylation on the Release of Low and High Molecular-Weight Proteins from PVA Matrices (1999)

Model proteins of therapeutic interest, ribonuclease, superoxide dismutase, catalase and albumin, extensively PEGylated with linear 5,000 Mw PEG, were entrapped in PVA hydrogels (31,000-50,000 Mw) by means of a cryogel procedure and the rate of release was evaluated. All of the PEGylated proteins were released from the gel, but at a lower rate than the unmodified proteins. The rate for both native and PEGylated species decreases as the molecular weight of the protein increased. Moreover, for both native and PEGylated proteins, the release rate was reduced when the gel was lyophilized before the release evaluation. Release was also dependent on the PVA Mw, in fact, for Mw's of 124,000-186,000, permanent entrapment was achieved. This behaviour was verified with PEGylated glucose oxidase and coline oxidase which were permanently retained in high Mw PVA. This study indicates the potential for the combination of PEGylation and cryogel entrapment of enzymes for the biotechnological and therapeutic applications.
The Occurrence of Single-Stranded DNA in the Serum of Patients with Systemic Lupus Erythematosus and Other Diseases (1973)

Single-stranded DNA (SDNA) occurs in high incidence and in greatest concentration in the sera of patients with systemic lupus erythematosus (SLE), where levels as high as 250 mug/ml were observed. SDNA appears to be an imunogen for anti-SDNA antibodies and forms complexes in vivo of both anti-SDNA-SDNA and anti-NDNA-SDNA types, which apparently play a role in the pathogenesis of the glomerulonephritis found in patients with SLE, SDNA is also found in high incidence but at lower levels in the sera of patients with rheumatoid arthritis. Lesser amounts of SDNA are found in several other diseases in which a low incidence of anti-SDNA antibodies is observed.
Modulation of Cystathionine β-Synthase Level Regulates Total Serum Homocysteine in Mice (2004)

Elevated total plasma homocysteine is an independent risk factor in the development of vascular disease in humans. Cystathionine beta-synthase (CBS) is an enzyme that condenses homocysteine with serine to form cystathionine. In this article, we describe the effects of modulating CBS activity using a transgenic mouse that contains the human CBS cDNA under control of the zinc-inducible metallothionein promoter (Tg-CBS). In the presence of zinc, Tg-CBS mice have a 2- to 4-fold increase in liver and kidney CBS activity compared with nontransgenic littermates. Transgenic mice on standard mouse chow had a 45% decrease in their serum homocysteine (12.1 to 7.2 micromol/L; P<0.0001) when zinc was added to drinking water, although zinc had minimal effect on their nontransgenic siblings (13.2 micromol/L versus 13.0 micromol/L; P=NS). Tg-CBS mice maintained on a high-methionine, low-folate diet also had significantly lower serum homocysteine compared with control animals (179 micromol/L versus 242 micromol/L; P<0.02). CBS overexpression also significantly lowered serum cysteinylglycine (3.6 versus 2.8 micromol/L; P<0.003) levels and reduced the levels of many amino acids in the liver. We also found that expression of Tg-CBS rescued the severe hyperhomocysteinemia and neonatal lethality of Cbs deletion animals. Our results show that elevating CBS activity is an effective method to lower plasma homocysteine levels. In addition, the creation of an inducible mouse system to modulate plasma homocysteine will also be useful in the study of homocysteine-related vascular disease.
Face alignment through subspace constrained mean-shifts (2009)

Deformable model fitting has been actively pursued in the computer vision community for over a decade. As a result, numerous approaches have been proposed with varying degrees of success. A class of approaches that has shown substantial promise is one that makes independent predictions regarding locations of the model's landmarks, which are combined by enforcing a prior over their joint motion. A common theme in innovations to this approach is the replacement of the distribution of probable landmark locations, obtained from each local detector, with simpler parametric forms. This simplification substitutes the true objective with a smoothed version of itself, reducing sensitivity to local minima and outlying detections. In this work, a principled optimization strategy is proposed where a nonparametric representation of the landmark distributions is maximized within a hierarchy of smoothed estimates. The resulting update equations are reminiscent of mean-shift but with a subspace constraint placed on the shape's variability. This approach is shown to outperform other existing methods on the task of generic face fitting.
Destabilization of phosphatidylethanolamine liposomes at the hexagonal phase transition temperature (1986)

We have examined whether there is a relationship between the lamellar-hexagonal phase transition temperature, TH, and the initial kinetics of H+- and Ca2+-induced destabilization of phosphatidylethanolamine (PE) liposomes. The liposomes were composed of dioleoylphosphatidylethanolamine, egg phosphatidylethanolamine (EPE), or phosphatidylethanolamine prepared from egg phosphatidylcholine by transesterification (TPE). These lipids have well-spaced lamellar-hexagonal phase transition temperatures (approximately 12, approximately 45, and approximately 57 degrees C) in a temperature range that allows us to measure the initial kinetics of bilayer destabilization, both below and above TH. The liposomes were prepared at pH 9.5. The TH of EPE and TPE was measured by using differential scanning calorimetry, and it was found that the TH was essentially the same at low pH or at high pH in the presence of 20 mM Ca2+. At temperatures well below TH, either at pH 4.5 or at pH 9.5 in the presence of Ca2+, the liposomes aggregate, leak, and undergo lipid mixing and mixing of contents. We show that liposome/liposome contact is involved in the destabilization of the PE liposomes. The temperature dependence of leakage, lipid mixing, and mixing of contents shows that there is a massive enhancement in the rate of leakage when the temperature approaches the TH of the particular PE and that lipid mixing appears to be enhanced. However, the fusion (mixing of aqueous contents) is diminished or even abolished at temperatures above TH. At and above the TH, a new mechanism of liposome destabilization arises, evidently dependent upon the ability of the PE molecules to adapt new morphological structures at these temperatures. We propose that this destabilization demarks the first step in the pathway to the eventual formation of the HII phase. Thus, the polymorphism accessible to PE is a powerful agent for membrane destabilization, but additional factors are required for fusion.
Risk factors for the development of acute lung injury in patients with septic shock: An observational cohort study* (2008)

When adjusted for known modifiers of ALI expression, delayed treatment of shock and infection were associated with development of ALI.
Molecular cloning of a widely expressed human homologue for the Drosophila trp gene (1995)

The Drosophila transient receptor potential (trp) gene and its homologue, trpl, have been suggested to mediate calcium entry during the insect's phototransduction process. We isolated a human cDNA, human trp-1 (Htrp-1), encoding a polypeptide of 793 amino acids that is 37% identical (62% similar) to Drosophila trp and trpl. Northern analysis showed that the Htrp-1 transcript is approximately 5.5 kb and expressed in most human tissues, with higher amounts in ovary, testis, heart, and brain. Isolation of Htrp-1 suggests that a trp-type protein is present in mammals and should provide a useful tool in studying calcium-depletion induced calcium influx processes.
Clostridium difficile toxin A stimulates intracellular calcium release and chemotactic response in human granulocytes. (1988)

Clostridium difficile, a common enteric pathogen, mediates tissue damage and intestinal fluid secretion by release of two protein exotoxins: toxin A, an enterotoxin, and toxin B, a cytotoxin. Because toxin A elicits an intense inflammatory reaction in vivo, we studied the effects of highly purified C. difficile toxins on activation of human granulocytes. Toxin A at concentrations of 10(-7) to 10(-6) M, but not toxin B, elicited a significant chemotactic and chemokinetic response by granulocytes that was comparable with that induced by the chemotactic factor N-FMLP (10(-7) M). Neither toxin stimulated release of superoxide anion from granulocytes. Toxin A produced a rapid, transient rise in cytosolic [Ca2+]i, as measured by quin 2 fluorescence. Pertussis toxin and depletion of intra- and extracellular calcium blocked the toxin A effect on cytosolic [Ca2+]i. These findings suggest that the inflammatory effects of C. difficile toxin A in the intestine may be related to its ability to mobilize intracellular Ca2+ and elicit a chemotactic response by granulocytes.
Automated site-directed drug design: the concept of spacer skeletons for primary structure generation (1989)

This paper examines the problem of automated structure generation at specified binding sites. The objective is to obtain molecular graphs that span the binding site and incorporate predicted ligand points at their vertices. Three approaches are considered: brute-force techniques, subgraph addition and spacer skeletons. Spacer skeletons are assemblies of molecular subgraphs and are used to reduce the combinatorial problems of structure generation to a practicable level for future analysis. This description is restricted to structure generation in two dimensions. Assemblies of rings are examined for planarity by searching the Cambridge Structural Database. Appropriate spacer skeletons may then be fitted to arrays of site points.
Electrically Controlled Nanostructured Metasurface Loaded with Liquid Crystal: Toward Multifunctional Photonic Switch (2015)

Achieving an efficient spectral tuning in liquid‐crystal (LC)‐loaded active photonic metamaterials has so far remained a challenge due to strong surface anchoring of LC molecules. This paper reports on a novel approach in the development of hybrid metamaterials that enables to overcome this problem and engage for the first time in‐plane switching of liquid‐crystal molecules on the nanoscale. Combined with the usual volume switching, it unlocks the full potential of the liquid crystals as a functional component of active metamaterial hybrids operating at optical frequencies. As a result, the resonant response of an active metasurface can now be controlled both in terms of its magnitude and wavelength with the spectral tunability approaching the theoretical limit of 9%. This mechanism of two‐way active switching of the hybrid metamaterial is also confirmed theoretically by simulating the distribution of the LC director around the metamaterial fabric.
Cyclin‐dependent kinase inhibitor drugs as potential novel anti‐inflammatory and pro‐resolution agents (2009)

The cyclin-dependent kinase inhibitor (CDKi) drugs such as R-roscovitine have emerged as potential anti-inflammatory, pharmacological agents that can influence the resolution of inflammation. Usually, once an inciting inflammatory stimulus has been eliminated, resolution proceeds by prompt, safe removal of dominant inflammatory cells. This is accomplished by programmed cell death (apoptosis) of prominent effector, inflammatory cells typified by the neutrophil. Apoptosis of neutrophils ensures that toxic neutrophil granule contents are securely packaged in apoptotic bodies and expedites phagocytosis by professional phagocytes such as macrophages. A panel of CDKi drugs have been shown to promote neutrophil apoptosis in a concentration- and time-dependent manner and the archetypal CDKi drug, R-roscovitine, overrides the anti-apoptotic effects of powerful survival factors [including lipopolysaccharide (LPS) and granulocyte macrophage-colony stimulating factor (GM-CSF)]. Inflammatory cell longevity and survival signalling is integral to the inflammatory process and any putative anti-inflammatory agent must unravel a complex web of redundancy in order to be effective. CDKi drugs have also been demonstrated to have significant effects on other cell types including lymphocytes and fibroblasts indicating that they may have pleiotropic anti-inflammatory, pro-resolution activity. In keeping with this, CDKi drugs like R-roscovitine have been reported to be efficacious in resolving established animal models of neutrophil-dominant and lymphocyte-driven inflammation. However, the mechanism of action behind these powerful effects has not yet been fully elucidated. CDKs play an integral role in the regulation of the cell cycle but are also recognized as participants in processes such as apoptosis and transcriptional regulation. Neutrophils have functional CDKs, are transcriptionally active and demonstrate augmented apoptosis in response to CDKi drugs, while lymphocyte proliferation and secretory function are inhibited. This review will discuss current understanding of the processes of inflammation and resolution but will focus on CDKis and their potential mechanisms of action.
Membranous Nectin-4 expression is a risk factor for distant relapse of T1-T2, N0 luminal-A early breast cancer (2014)

Nectins are Ca(2+)-independent immunoglobulin-like cell adhesion molecules that compose a family of four members that regulate several cellular activities such as movement, proliferation, survival, differentiation, polarization, and the entry of viruses. Nectin-4 has recently emerged as a metastatis-associated protein in several cancers. Here, we have evaluated the association between the expression of Nectin-4 and the clinical outcome of patients with node-negative, T1/T2 breast cancers.The study group consisted of 197 patients presenting with primary unilateral breast carcinoma (T1/T2), with no evidence of nodal involvement and distant metastases. Nectin-4 protein expression was assessed by immunohistochemistry on tissue microarrays, and the results correlated with the clinical data using Kaplan-Meier curves and multivariate Cox regression analysis. Thirty-four out of 197 tumors (17.3%) exhibited Nectin-4 expression on cell membrane (m-Nectin-4) and 122 out of the 163m-Nectin-4 negative tumors (74.8%) showed high cytoplasmic expression of Nectin-4 (c-Nectin-4(High)). At Kaplan-Meier analysis, m-Nectin-4 positivity was significantly associated with a lower disease-free survival (DFS) and distant relapse-free survival (DRFS) rate in patients with a luminal-A phenotype (P=0.030 and P=0.002, respectively). Multivariate analysis showed that in luminal-A tumors m-Nectin-4 positivity is an independent prognostic factor for DFS (P=0.018) and DRFS (P=0.004), but not for local relapse-free survival (LRFS). On the other hand, c-Nectin-4(High) was significantly associated with higher rates of DFS and LRFS, but not DRFS, in the whole population (P=0.008 and P=0.004, respectively) and in patients with luminal-A tumors (P=0.022 and P=0.018, respectively). In patients with luminal-A tumors, multivariate analysis showed that the prognostic value of c-Nectin-4(Low/Negative) is limited to DFS (P=0.012) and LRFS (P=0.022). We suggest that Nectin-4 represents a prognostic factor and a therapeutic target in luminal-A early stage breast cancer.
Accelerated Bioorthogonal Conjugation:  A Practical Method for the Ligation of Diverse Functional Molecules to a Polyvalent Virus Scaffold (2005)

Covalent bond formation to proteins is made difficult by their multiple unprotected functional groups and normally low concentrations. A water-soluble sulfonated bathophenanthroline ligand (2) was used to promote a highly efficient Cu(I)-mediated azide-alkyne cycloaddition (CuAAC) reaction for the chemoselective attachment of biologically relevant molecules to cowpea mosaic virus (CPMV). The ligated substrates included complex sugars, peptides, poly(ethylene oxide) polymers, and the iron carrier protein transferrin, with routine success even for cases that were previously resistant to azide-alkyne coupling using the conventional ligand tris(triazolyl)amine (1). The use of 4-6 equiv of substrate was sufficient to achieve loadings of 60-115 molecules/virion in yields of 60-85%. Although it is sensitive to oxygen, the reliably efficient performance of the Cu.2 system makes it a useful tool for demanding bioconjugation applications.