gebhart/patrepeval huggingface dataset:
Colletruncoic Acid Methyl Ester, a Unique Meroterpenoid from Colletotrichum truncatum (1986)

Abstract Metabolites isolated from the soybean pathogen Colletotrichum truncatum were identified as meso- and ᴅ-( -)-butane-2,3-diol and the previously unreported compound , colletruncoic acid methyl ester, to which structure 1 is assigned mainly on 1 H - and 13 CMR evidence. The compound has a skeleton unprecedented for a fungal polyketide. The previously unknown 2-hydroxymethylhexa-2,4-dienol was also isolated.
Spatially resolved electronic detection of biopolymers (2004)

An integrated array of field-effect transistor structures is used to detect two oppositely charged biopolymers: poly(L-lysine) and DNA. Local deposition of polymer solutions on part of the array induces sizeable variations in the dc current-voltage characteristics of the transistors exposed to the molecular charge. The whole transistor array is measured in the presence of a common electrolyte. Differential signals are studied as a function of electrolyte salt and polymer concentrations. The measurements provide information on the interface electrostatic potentials of the (semiconductor/biopolymer/electrolyte) system and the experimental data are compared to an analytical model which accounts for screening of the adsorbed charge by mobile ions.
Graph-aware modeling of brain connectivity networks (2023)

Functional connections in the brain are frequently represented by weighted networks, with nodes representing locations in the brain and edges representing the strength of connectivity between these locations. One challenge in analyzing such data is that inference at the individual edge level is not particularly biologically meaningful; interpretation is more useful at the level of so-called functional systems or groups of nodes and connections between them; this is often called “graph-aware” inference in the neuroimaging literature. However, pooling over functional regions leads to significant loss of information and lower accuracy. Another challenge is correlation among edge weights within a subject which makes inference based on independence assumptions unreliable. We address both of these challenges with a linear mixed effects model, which accounts for functional systems and for edge dependence, while still modeling individual edge weights to avoid loss of information. The model allows for comparing two populations, such as patients and healthy controls, both at the functional regions level and at individual edge level, leading to biologically meaningful interpretations. We fit this model to resting state fMRI data on schizophrenic patients and healthy controls, obtaining interpretable results consistent with the schizophrenia literature.
NANOCRYSTAL SUPERLATTICES (1998)

Ordered arrays, or superlattices, of metallic, insulating, or semiconducting quantum dots, represent an exciting new class of materials. These superlattices are often referred to as artificial solids, in which the nanocrystals take the place of atoms in traditional solids, and the packing arrangement of the nanocrystals determines the unit cell parameters of the superstructure. In this review, we discuss various approaches toward assembling nanocrystal superlattices and we discuss their physical properties.
Demethylation of DNA by purified chick embryo 5-methylcytosine-DNA glycosylase requires both protein and RNA (1997)

We have previously purified and characterized a 5-methylcytosine (5-MeC)-DNA glycosylase from 12 day old chick embryos [Jost,J.P. et al. (1995) J. Biol. Chem. 270, 9734-9739]. The activity of the purified enzyme is abolished upon treatment with proteinase K and ribonuclease A. RNA copurifies with 5-MeC-DNA glycosylase activity throughout all chromatographic steps and preparative gel electrophoresis. RNA with a length of approximately 300-500 nucleotides was isolated from the gel purified enzyme. Upon extensive treatment with proteinase K, the gel eluted and labeled RNA did not show any significant change in molecular mass. The purified RNA incubated alone or in the presence of Mg2+and deoxyribonucleotide phosphates had no 5-MeC-DNA glycosylase or demethylating activities. However, activity of 5-MeC-DNA glycosylase could be restored when the purified RNA was incubated with the inactive protein, free of RNA.
Assessment of acute pulmonary edema in dogs by electrical impedance imaging (1996)

Acute pulmonary edema was assessed quantitatively in 12 experiments on six anesthetized dogs. Thirty-two copper foil electrodes were placed around each animal's thorax at the level of the third intercostal space. A real-time electrical impedance tomograph was used to form images of the electrical admittivity of the thorax in and near the plane of these electrodes. The lungs were identified by studying the change in admittivity associated with inspiration. Mean admittivity in these lung regions was assessed at 40-min intervals for the next 3-6 hours. In six control experiments, each having a duration of 200 min, the initial admittivity of the lung regions was 102 +/- 16(SD) mS/m. Lung admittivity usually increased during the first 80 min, and then remained within 2 mS/m of its value at 80 min for the remaining 120 min. In six experiments with pulmonary edema, an initial period of change followed by stability was observed. When stability had been attained, 0.07 ml/kg of oleic acid was injected slowly into a central venous site. Five animals received oleic acid, the sixth received a sham injection of saline. In the five receiving oleic acid, lung admittivity rose steadily for the remainder of the experiment. The increase in lung admittivity in these five animals was between 4 and 16 mS/m. In the sham injected experiment, the lung admittivity changed by 1 mS/m. We conclude that impedance imaging can provide semiquantitative assessment of the development of acute pulmonary edema.
Structural basis for antibody recognition of the NANP repeats in Plasmodium falciparum circumsporozoite protein (2017)

Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)-based vaccine against <i>Plasmodium falciparum</i> that contains 19 NANP repeats followed by a thrombospondin repeat domain. Although RTS,S has undergone extensive clinical testing and has progressed through phase III clinical trials, continued efforts are underway to enhance its efficacy and duration of protection. Here, we determined that two monoclonal antibodies (mAbs 311 and 317), isolated from a recent controlled human malaria infection trial exploring a delayed fractional dose, inhibit parasite development in vivo by at least 97%. Crystal structures of antibody fragments (Fabs) 311 and 317 with an (NPNA)<sub>3</sub> peptide illustrate their different binding modes. Notwithstanding, one and three of the three NPNA repeats adopt similar well-defined type I β-turns with Fab311 and Fab317, respectively. Furthermore, to explore antibody binding in the context of <i>P. falciparum</i> CSP, we used negative-stain electron microscopy on a recombinant shortened CSP (rsCSP) construct saturated with Fabs. Both complexes display a compact rsCSP with multiple Fabs bound, with the rsCSP-Fab311 complex forming a highly organized helical structure. Together, these structural insights may aid in the design of a next-generation malaria vaccine.
AApeptides as a new class of antimicrobial agents (2013)

Antibiotic resistance is an increasing public health concern around the world, and is recognized as one of the greatest threats facing humankind in the 21(st) century. Natural antimicrobial peptides (AMPs) are small cationic amphiphilic peptides found in virtually all living organisms, and play a key role in the defense against bacterial infections. Compared with conventional antibiotics, which target specific metabolic processes, AMPs are able to adopt globally amphipathic conformations, and kill bacteria through disruption of their membranes. As such, AMPs do not readily induce drug-resistance. However, AMPs are associated with intrinsic drawbacks such as low-to-moderate activity, susceptibility to enzymatic degradation, and inconvenience for optimization. Recently, we have developed a new class of peptidomimetics termed "AApeptides". Such peptide mimics are highly resistant to protease degradation and are straightforward for chemical diversification and development. Our current studies show that AApeptides with globally amphipathic structures can mimic the bactericidal mechanism of AMPs, and display potent and broad-spectrum activity against both Gram-positive and -negative multi-drug-resistant bacteria. In this review, we summarize our current findings of antimicrobial AApeptides, and discuss potential future directions on the development of more potent and specific analogues.
Modulation of CRP‐dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti‐activation by the nucleoid proteins FIS and IHF (2003)

acs encodes acetyl-coenzyme A synthetase, a high-affinity enzyme that allows cells to scavenge for acetate during carbon starvation. CRP activates acs transcription by binding tandem DNA sites located upstream of the major promoter, acsP2. Here, we used electrophoretic mobility shift assays and DNase I footprint analyses to demonstrate that the nucleoid proteins FIS and IHF each bind multiple sites within the acs regulatory region, that FIS competes successfully with CRP for binding to their overlapping and neighbouring sites and that IHF binds independently of either FIS or CRP. Using in vitro transcription assays, we demonstrated that FIS and IHF independently reduce CRP-dependent acs transcription. Using in vivo reporter assays, we showed that disruption of DNA sites for FIS or deletion of DNA sites for IHF increases acs transcription. We propose that FIS and IHF each function directly as anti-activators of CRP, each working independently at different times during growth to set the levels of CRP-dependent acs transcription.
TNF-α converting enzyme-mediated ErbB4 transactivation by TNF promotes colonic epithelial cell survival (2011)

Disruption of intestinal epithelial homeostasis, including enhanced apoptosis, is a hallmark of inflammatory bowel disease (IBD). We have recently shown that tumor necrosis factor (TNF) increases the kinase activity of ErbB4, a member of the epidermal growth factor receptor family that is elevated in mucosa of IBD patients and that promotes colon epithelial cell survival. In this study, we tested the hypothesis that TNF transactivates ErbB4 through TNF-α converting enzyme (TACE)-mediated ligand release and that this transactivation is necessary to protect colonic epithelial cells from cytokine-induced apoptosis. Using neutralizing antibodies, we show that heparin-binding EGF-like growth factor (HB-EGF) is required for ErbB4 phosphorylation in response to TNF. Pharmacological or genetic inhibition of the metalloprotease TACE, which mediates HB-EGF release from cells, blocked TNF-induced ErbB4 activation. MEK, but not Src or p38, was also required for transactivation. TACE activity and ligand binding were required for ErbB4-mediated antiapoptotic signaling; whereas mouse colon epithelial cells expressing ErbB4 were resistant to TNF-induced apoptosis, TACE inhibition or blockade of ErbB4 ligand binding reversed the survival advantage. We conclude that TNF transactivates ErbB4 through TACE-dependent HB-EGF release, thus protecting colon epithelial cells from cytokine-induced apoptosis. These findings have important implications for understanding how ErbB4 protects the colon from apoptosis-induced tissue injury in inflammatory conditions such as IBD.
Insulin administration: present strategies and future directions for a noninvasive (possibly more&nbsp;physiological) delivery (2015)

Insulin is a life-saving medication for people with type 1 diabetes, but traditional insulin replacement therapy is based on multiple daily subcutaneous injections or continuous subcutaneous pump-regulated infusion. Nonphysiologic delivery of subcutaneous insulin implies a rapid and sustained increase in systemic insulin levels due to the loss of concentration gradient between portal and systemic circulations. In fact, the liver degrades about half of the endogenous insulin secreted by the pancreas into the venous portal system. The reverse insulin distribution has short- and long-term effects on glucose metabolism. Thus, researchers have explored less-invasive administration routes based on innovative pharmaceutical formulations, which preserve hormone stability and ensure the therapeutic effectiveness. This review examines some of the recent proposals from clinical and material chemistry point of view, giving particular attention to patients' (and diabetologists') ideal requirements that organic chemistry could meet.
Psychosurgery and the limbic system (1973)

Summary The limbic system can be considered to consist of a central ‘core’ from which three well-defined circuits emerge. These are the Papez or medial circuit, the basolateral circuit and the defence reaction circuit. The functions of the primitive limbic brain are modulated by a higher order control—the frontal lobe. Emotional responses and physiological changes have been obtained by stimulation of fronto-limbic pathways and limbic circuits and these have been used for location of target sites in psychosurgery. For the relief of intractable depression and anxiety, lesions are generally made in the lower medial quadrant or posteroorbital part of the frontal lobe, where there is a concentration of fronto-limbic connections. In primary obsessional neurosis lesions at this site produce less satisfactory results, but these illnesses may be helped by lesions in the cingulate gyrus, which is part of the Papez circuit. Patients with epilepsy and aggressive outbursts may respond to temporal lobotomy, or to operations, such as amygdalotomy, where lesions are placed in the defence reaction circuit.
Deglycosylation of flavonoid and isoflavonoid glycosides by human small intestine and liver β‐glucosidase activity (1998)

Flavonoid and isoflavonoid glycosides are common dietary phenolics which may be absorbed from the small intestine of humans. The ability of cell-free extracts from human small intestine and liver to deglycosylate various (iso)flavonoid glycosides was investigated. Quercetin 4'-glucoside, naringenin 7-glucoside, apigenin 7-glucoside, genistein 7-glucoside and daidzein 7-glucoside were rapidly deglycosylated by both tissue extracts, whereas quercetin 3,4'-diglucoside, quercetin 3-glucoside, kaempferol 3-glucoside, quercetin 3-rhamnoglucoside and naringenin 7-rhamnoglucoside remained unchanged. The Km for hydrolysis of quercetin 4'-glucoside and genistein 7-glucoside was approximately 32+/-12 and approximately 14+/-3 microM in both tissues respectively. The enzymatic activity of the cell-free extracts exhibits similar properties to the cytosolic broad-specificity -glucosidase previously described in mammals.
Induction of Peroxisome Proliferator-Activated Receptor γ during the Conversion of 3T3 Fibroblasts into Adipocytes Is Mediated by C/EBPβ, C/EBPδ, and Glucocorticoids (1996)

The differentiation of 3T3 preadipocytes into adipocytes is accompanied by a transient induction of C/EBPbeta and C/EBPdelta expression in response to treatment of the cells with methylisobutylxanthine (MIX) and dexamethasone (DEX), respectively. In this report, we demonstrate that peroxisome proliferator-activated receptor gamma (PPARgamma) expression in 3T3-L1 preadipocytes is induced by MIX and DEX, suggesting that C/EBPbeta and C/EBPdelta may be involved in this process. Using a tetracycline-responsive expression system, we have recently shown that the conditional ectopic expression of C/EBPbeta in NIH 3T3 fibroblasts (beta2 cells) in the presence of DEX activates the synthesis of peroxisome PPARgamma mRNA. Subsequent exposure of these cells to PPAR activators stimulates their conversion into adipocytes; however, neither the expression of C/EBPbeta nor exposure to DEX alone is capable of inducing PPARgamma expression in the beta2 cell line. We find that unlike the case for 3T3 preadipocytes, C/EBPdelta is not induced by DEX in these 3T3 fibroblasts and therefore is not relaying the effect of this glucocorticoid to the PPARgamma gene. To define the role of glucocorticoids in regulating PPARgamma expression and the possible involvement of C/EBPdelta, we have established an additional set of NIH 3T3 cell lines expressing either C/EBPdelta alone (delta23 cells) or C/EBPdelta and C/EBPbeta together (beta/delta39 cells), using the tetracycline-responsive system. Culture of these cells in tetracycline-deficient medium containing DEX, MIX, insulin, and fetal bovine serum shows that the beta/delta39 cells express PPARgamma and aP2 mRNAs at levels that are almost equivalent to those observed in fully differentiated 3T3-L1 adipocytes. These levels are approximately threefold higher than their levels of expression in the beta2 cells. Despite the fact that these beta/delta39 cells produce abundant amounts of C/EBPbeta and C/EBPdelta (in the absence of tetracycline), they still require glucocorticoids to attain maximum expression of PPARgamma mRNA. Furthermore, the induction of PPARgamma mRNA by exposure of these cells to DEX occurs in the absence of ongoing protein synthesis. The delta23 cells, on the other hand, are not capable of activating PPARgamma gene expression when exposed to the same adipogenic inducers. Finally, attenuation of ectopic C/EBPbeta production at various stages during the differentiation process results in a concomitant inhibition of PPARgamma and the adipogenic program. These data strongly suggest that the induction of PPARgamma gene expression in multipotential mesenchymal stem cells (NIH 3T3 fibroblasts) is dependent on elevated levels of C/EBPbeta throughout the differentiation process, as well as an initial exposure to glucocorticoids. C/EBPdelta may function by synergizing with C/EBPbeta to enhance the level of PPARgamma expression.
Materials with a Buried  C 60 Layer Produced by Direct Wafer Bonding (1994)

Si wafers covered with a sublimed layer have been directly bonded to bare or oxidized Si wafers at room temperature via Van der Waals attraction forces. The interface energies of the bonded pairs increase during storage in air at room temperature and approach saturated values after ∼200 h. The typical saturated interface energy of (∼40 erg/cm2) is higher than that of (20–30 erg/cm2). Other material combinations having a buried layer may also be realized by wafer bonding for specific applications.
Estimating Service Lives of Organic Vapor Cartridges (1994)

Procedures were developed for estimating service lives of air-purifying organic vapor respirator cartridges, including methods for untested compounds and use conditions (concentration, temperature, and airflow rate). Correlations of adsorption capacities and adsorption-rate coefficients based on equilibrium and breakthrough curve data were reviewed. These correlations were combined using the Reaction Kinetic (modified Wheeler) equation to estimate breakthrough times. The proposed estimation procedure showed 95% confidence intervals of up to ±50% when no breakthrough data were assumed. It is shown how even limited breakthrough curve data for one vapor/carbon combination can be used to substantially improve accuracy of the estimation. Only dry conditions (below 50% relative humidity) have been considered so far.
Neurite‐promoting activity from fetal skeletal muscle: Partial purification of a high‐molecular‐weight form (1986)

Neurite extension from sensory neuroblasts dissociated from chick embryo dorsal root ganglia can be stimulated by precoating the polylysine culture surface with extracts of skeletal muscle from bovine fetuses. The active factor(s) may be partially purified from cytosolic extracts of muscle by chromatography on Sepharose 6B and affinity chromatography on wheat germ agglutinin or Helix pomatia agglutinin columns. Extract concentrations of 10-50 micrograms protein per 1 ml were active in promoting neurite extension when the neurons were cultured without serum or nerve growth factor (beta NGF). However, levels of 1-10 micrograms/ml produced dramatic neurite extension when 10% (v/v) fetal or newborn calf serum or 0.5 ng/ml beta NGF was added to the medium. The biological activity was not blocked by antiserum that was raised against purified mouse laminin and that abolished the neurite-promoting activity of mouse laminin. The activity of the muscle extract was destroyed by trypsin or heparitinase, in contrast to the biological activity of purified mouse laminin, which was not abolished by heparitinase treatment. The activity could be resolved into two broad peaks on a Sepharose 2B column (apparent Mr between 2 X 10(6) and in 10 X 10(6) in native form). Treatment with dithiothreitol was necessary to dissociate the factor for electrophoresis in 4.25% polyacrylamide-SDS gels, revealing three major polypeptide bands at Mr = 160,000, 195,000 and 200,000. This preliminary characterization indicates that the neurite-promoting activity from bovine skeletal muscle tissue consists of a high-molecular-weight complex, one essential component of which is a heparan sulfate.
Genome-Wide Analysis of Ethylene-Responsive Element Binding Factor-Associated Amphiphilic Repression Motif-Containing Transcriptional Regulators in Arabidopsis (2010)

The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, C2H2, and auxin/indole-3-acetic acid families of transcriptional regulators. Sequence comparison of the core EAR motif sites from these proteins revealed two distinct conservation patterns: LxLxL and DLNxxP. Proteins containing these motifs play key roles in diverse biological functions by negatively regulating genes involved in developmental, hormonal, and stress signaling pathways. Through a genome-wide bioinformatics analysis, we have identified the complete repertoire of the EAR repressome in Arabidopsis (Arabidopsis thaliana) comprising 219 proteins belonging to 21 different transcriptional regulator families. Approximately 72% of these proteins contain a LxLxL type of EAR motif, 22% contain a DLNxxP type of EAR motif, and the remaining 6% have a motif where LxLxL and DLNxxP are overlapping. Published in vitro and in planta investigations support approximately 40% of these proteins functioning as negative regulators of gene expression. Comparative sequence analysis of EAR motif sites and adjoining regions has identified additional preferred residues and potential posttranslational modification sites that may influence the functionality of the EAR motif. Homology searches against protein databases of poplar (Populus trichocarpa), grapevine (Vitis vinifera), rice (Oryza sativa), and sorghum (Sorghum bicolor) revealed that the EAR motif is conserved across these diverse plant species. This genome-wide analysis represents the most extensive survey of EAR motif-containing proteins in Arabidopsis to date and provides a resource enabling investigations into their biological roles and the mechanism of EAR motif-mediated transcriptional regulation.