gebhart/patrepeval huggingface dataset:
Restoration of hormonal action and muscle protein (2007)

This review focuses on the effects of restoring hormonal levels and/or influence on muscle protein metabolism in the stressed state. We have highlighted our clinical experience in the administration of anabolic and anticatabolic agents in stressed clinical populations, primarily adult and pediatric burn injury, as well as patients undergoing elective hip arthroplasty. Our previous experience entails the administration of anabolic hormones, such as testosterone and its derivatives, growth hormone, insulin-like growth factor-1 combined with its binding protein 3, and insulin. Current efforts focus on the administration of anticatabolic agents to reduce the effects of hypercortisolemia. Muscle protein metabolism was determined by stable isotope methodology. Our results indicate that normalization of anabolic hormone concentrations or amelioration of hormonal resistance restores the effects of feeding on skeletal muscle protein metabolism. Anabolic hormone administration results in a more favorable muscle protein balance in severely burned patients. Amelioration of hypercortisolemia in the stressed state leads to an improvement in protein kinetics. To summarize, alterations in hormonal influence that accompany stress states favor the loss of muscle protein. Restoration or normalization of hormonal influence improves muscle protein kinetics and ameliorates the loss of muscle nitrogen. To restore hormonal influence, clinicians should consider reestablishing anabolic stimuli and reducing catabolic stimuli.
Positive end expiratory pressure with increased intra-abdominal pressure. (1985)

Positive pressure ventilation with PEEP may be required in patients with increased IAP. Separately, PEEP and increase IAP have been shown in both man and animals to have significant hemodynamic effects. The results of this study demonstrated that, in dogs, the combination of PEEP with elevated IAP results in markedly increased CVP, PCWP, mean PAP and PVR. CO is depressed but to no greater degree than with the combination of IAP and positive pressure ventilation without PEEP. Interestingly, serum lactate levels markedly increase when both PEEP and IAP are applied, a finding not explained by the fall in CO. Possibly, the combination of PEEP with elevated IAP inhibits hepatic metabolism of lactate. Measures taken to reduce IAP and PEEP may not only improve hemodynamics but may result in reduced serum lactate levels.
New Procedure to Maintain Fecal Microbiota in a Dry Matrix Ready to Encapsulate (2022)

Fecal microbiota transplantation (FMT) is one of the recommended treatments for recurrent <i>Clostridioides difficile</i> infection, but endoscopy and available oral formulations still have several limitations in their preparation, storage, and administration. The need for a viable oral formulation that facilitates the implementation of this highly effective therapy in different settings has led us to test the microcrystalline cellulose particles as an adsorbent of concentrated filtered fresh feces in comparison to lyophilized feces. This free-flowing material can provide protection to bacteria and results in a dried product able to maintain the viability of the microbiota for a long time. Adsorbate formulation showed a stabilizing effect in gut microbiota, maintaining bacteria viability and preserving its diversity, and is a competitive option for lyophilized capsules.
The Design, Synthesis and Application of Stereochemical and Directional Peptide Isomers: A Critical Review (2003)

Physiological processes are regulated to a large extent by physical and chemical interactions between polypeptides. Although many small molecules have been discovered that can modulate such interactions and may be useful as drugs, the design of these agents purely from the knowledge of the details of a given protein-protein interaction, or through screening, remains difficult. Therefore, the peptidomimetic process, which aims at using peptides derived from either polypeptide binding partner directly, or after modification to improve affinity and physicochemical properties, continues to be attractive. The vast majority of naturally occurring polypeptides are composed of L-amino acids. Because natural proteins need to be metabolised, L-amino acid polypeptides are very prone to proteolytic degradation, a property that severely limits their therapeutic application. The proteolytic machinery is not well equipped to deal with D-amino acid polypeptides, however, and it is this finding above all else that has spurned research into stereochemical and directional manipulation of peptide chains. The expectation has been that systematic inversion of the stereochemistry at the peptide backbone alpha-carbon atoms, if accompanied by chain reversal, should yield proteolytically stable retro-inverso peptide isomers, whose side chain topology, in the extended conformation, corresponds closely to that of a native sequence, and whose biological activity emulates that of a parent polypeptide. The actual structural implications of modifying amino acid stereochemistry and peptide bond direction are reviewed critically here and the reasons for the lack of general success with this strategy are discussed. The application of polypeptides is particularly pertinent to synthetic vaccine design. Interestingly, the retro-inverso strategy has been more successful for immunological applications than elsewhere; recent finding are collated in this review. Partial rather than global retro-inversion holds much promise since the loss of crucial backbone hydrogen-bonding through peptide bond reversal can be avoided, while still permitting stabilisation of selected hydrolysis-prone peptide bonds. Generically applicable synthetic methods for such partially modified retro-inverso peptides are not as yet available; progress towards this goal is also summarised.
Boosting antibody developability through rational sequence optimization (2015)

The application of monoclonal antibodies as commercial therapeutics poses substantial demands on stability and properties of an antibody. Therapeutic molecules that exhibit favorable properties increase the success rate in development. However, it is not yet fully understood how the protein sequences of an antibody translates into favorable in vitro molecule properties. In this work, computational design strategies based on heuristic sequence analysis were used to systematically modify an antibody that exhibited a tendency to precipitation in vitro. The resulting series of closely related antibodies showed improved stability as assessed by biophysical methods and long-term stability experiments. As a notable observation, expression levels also improved in comparison with the wild-type candidate. The methods employed to optimize the protein sequences, as well as the biophysical data used to determine the effect on stability under conditions commonly used in the formulation of therapeutic proteins, are described. Together, the experimental and computational data led to consistent conclusions regarding the effect of the introduced mutations. Our approach exemplifies how computational methods can be used to guide antibody optimization for increased stability.
Rho and RNA: models for recognition and response (1994)

Escherichia coli Rho factor is required for termination of transcription at certain sites by RNA polymerase. Binding to unstructured cytosine-containing RNA target sites, subsequent RNA-dependent ATP hydrolysis, and an RNA-DNA helicase activity that presumably facilitates termination, are considered essential for Rho function. Yet the RNA recognition elements have remained elusive, the parameters relating RNA binding to ATPase activation have been obscure, and the mechanistic steps that integrate Rho's characteristics with its termination function in vitro and in vivo have been largely undefined. Recent work offers new insights into these interactions with results that are both surprising and satisfying in the context of Rho's emerging structure. These include the requirements for binding and ATPase activation by a variety of RNA substrates, dynamic analyses of Rho tracking, helicase and termination activity, and the participation of a new factor (NusG) that interacts with Rho. Models for Rho function are considered in the light of these recent revelations.
Beyond Necrotizing Enterocolitis: Other Clinical Advantages of an Exclusive Human Milk Diet (2018)

Incorporation of any cow milk-based nutrition into the diet of extremely premature infants correlates with more days on PN and a longer time to achieve full feeds. There was a nonstatistically significant trend toward increased ventilator days. These represent additional clinical consequences of the use of any cow milk-based protein in feeding EP infants.
Neutrophil nicotinamide adenine dinucleotide phosphate oxidase assembly. Translocation of p47-phox and p67-phox requires interaction between p47-phox and cytochrome b558. (1991)

Two of the cytosolic NADPH oxidase components, p47-phox and p67-phox, translocate to the plasma membrane in normal neutrophils stimulated with phorbol myristate acetate (PMA). We have now studied the translocation process in neutrophils of patients with chronic granulomatous disease (CGD), an inherited syndrome in which the oxidase system fails to produce superoxide due to lesions affecting any one of its four known components: the gp91-phox and p22-phox subunits of cytochrome b558 (the membrane-bound terminal electron transporter of the oxidase), p47-phox, and p67-phox. In contrast to normal cells, neither p47-phox nor p67-phox translocated to the membrane in PMA-stimulated CGD neutrophils which lack cytochrome b558. In one patient with a rare X-linked form of CGD caused by a Pro----His substitution in gp91-phox, but whose neutrophils have normal levels of this mutant cytochrome b558, translocation was normal. In two patients with p47-phox deficiency, p67-phox failed to translocate, whereas p47-phox was detected in the particulate fraction of PMA-stimulated neutrophils from two patients deficient in p67-phox. Our data suggest that cytochrome b558 or a closely linked factor provides an essential membrane docking site for the cytosolic oxidase components and that it is p47-phox that mediates the assembly of these components on the membrane.
Two-Level Morphology: A General Computational Model for Word-Form Recognition and Production (1983)

This dissertation presents a new computationally implemented linguistic model for morphological analysis and synthesis. The model incorporates a general formalism for making morphological descriptions of particular languages, and a language-independent program implementing the model. The two-level formalism and the structure of the program are formally defined. The program can utilize descriptions of various languages, including highly inflected ones such as Finnish, Russian, or Sanskrit. The new model is unrestricted in scope and it is capable of handling the entire language system as well as ordinary running text. A full description of Finnish inflectional morphology is presented in order to validate the model. The two-level model is based on a lexicon system and a set of two-level rules. It differs from generative phonology in the following respects. The rules are parallel, as opposed to being sequentially ordered, as is the case with the rewriting rules of generative phonology. The two-level model is fully bidirectional both conceptually and processually. It can also be interpreted as a morphological model of the performance processes of word-form recognition and production. The model and the descriptions are based on computationally simple machinery, mostly on small finite state automata. The computational complexity of the model is discussed, and the description of Finnish is evaluated with respect to external evidence from child language acquisition.
A Dominant Negative Inhibitor Indicates that Monocyte Chemoattractant Protein 1 Functions as a Dimer (1995)

Monocyte chemoattractant protein 1 (MCP-1) is a member of the chemokine family of proinflammatory cytokines, all of which share a high degree of amino acid sequence similarity. Aberrant expression of chemokines occurs in a variety of diseases that have an inflammatory component, such as atherosclerosis. Although structural analyses indicate that chemokines form homodimers, there is controversy about whether dimerization is necessary for activity. To address this question for MCP-1, we obtained evidence in four steps. First, coprecipitation experiments demonstrated that MCP-1 forms dimers at physiological concentrations. Second, chemically cross-linked MCP-1 dimers attract monocytes in vitro with a 50% effective concentration of 400 pM, identical to the activity of non-cross-linked MCP-1. Third, an N-terminal deletion variant of MCP-1 (called 7ND) that inhibits MCP-1-mediated monocyte chemotaxis specifically forms heterodimers with wild-type MCP-1. Finally, although 7ND inhibits wild-type MCP-1 activity, it has no effect on cross-linked MCP-1. These results indicate that 7ND is a dominant negative inhibitor, implying that MCP-1 activates its receptor as a dimer. In addition, chemical cross-linking restores activity to an inactive N-terminal insertional variant of MCP-1, further supporting the need for dimerization. Since the reported Kd for MCP-1 monomer dissociation is much higher than its 50% effective concentration or Kd for receptor binding, active dimer formation may require high local concentrations of MCP-1. Our data further suggest that the dimer interface can be a target for MCP-1 inhibitory drugs.
Cross-Linked Supramolecular Polymer Gels Constructed from Discrete Multi-pillar[5]arene Metallacycles and Their Multiple Stimuli-Responsive Behavior (2014)

A new family of discrete hexakis-pillar[5]arene metallacycles with different sizes have been successfully prepared via coordination-driven self-assembly, which presented very few successful examples of preparation of discrete multiple pillar[n]arene derivatives. These newly designed hexakis-pillar[5]arene metallacycles were well characterized with one-dimensional (1-D) multinuclear NMR ((1)H and (31) P NMR), two-dimensional (2-D) (1)H-(1)H COSY and NOESY, ESI-TOF-MS, elemental analysis, and PM6 semiempirical molecular orbital methods. Furthermore, the host-guest complexation of such hexakis-pillar[5]arene hosts with a series of different neutral ditopic guests G1-6 were well investigated. Through host-guest interactions of hexakis-pillar[5]arene metallacycles H2 or H3 with the neutral dinitrile guest G5, the cross-linked supramolecular polymers H2⊃(G5)3 or H3⊃(G5)3 were successfully constructed at the high-concentration region, respectively. Interestingly, these cross-linked supramolecular polymers transformed into the stable supramolecular gels upon increasing the concentrations to a relatively high level. More importantly, by taking advantage of the dynamic nature of metal-ligand bonds and host-guest interactions, the reversible multiple stimuli-responsive gel-sol phase transitions of such polymer gels were successfully realized under different stimuli, such as temperature, halide, and competitive guest, etc. The mechanism of such multiple stimuli-responsive processes was well illustrated by in situ multinuclear NMR investigation. This research not only provides a highly efficient approach to the preparation of discrete multiple pillar[n]arene derivatives but also presents a new family of multiple stimuli-responsive "smart" soft matters.
Long-term safety aspects of systemic therapy with fumaric acid esters in severe psoriasis (2003)

The present study indicates that FAE can be considered as a safe long-term treatment in patients with severe psoriasis.
ROLE OF NEUTROPHIL ELASTASE IN DEVELOPMENT OF PULMONARY VASCULAR INJURY AND SEPTIC SHOCK IN RATS (2008)

Prostacyclin prevents pulmonary vascular injury and shock by inhibiting increases in lung tissue levels of TNF in rats administered endotoxin. We previously reported that NO derived from eNOS increases endothelial production of prostacyclin. Because neutrophil elastase has been shown to decrease endothelial production of prostacyclin by inhibiting NOS activity, we examined whether neutrophil elastase inhibitors reduce pulmonary vascular injury and hypotension by inhibiting the decrease in pulmonary endothelial production of prostacyclin in rats administered endotoxin. Animals were pretreated with sivelestat or L-658,758, neutrophil elastase inhibitors, before endotoxin administration. Lung tissue levels of 6-keto-prostaglandin F1alpha were markedly increased after endotoxin administration, followed by a rapid decrease to baseline levels. Sivelestat and L-658,758 inhibited these decreases as well as inhibiting increases in lung tissue levels of TNF and lung wet-to-dry weight ratios in animals administered endotoxin. These inhibitors also reduced hypotension and inhibited increases in lung tissue levels of mRNA of the inducible form of NOS in animals administered endotoxin. The effects of neutrophil elastase inhibitors were completely reversed by pretreatment with nitro-L-arginine methyl ester, an inhibitor of NOS, or indomethacin, a nonspecific cyclooxygenase inhibitor. These observations suggested that neutrophil elastase might decrease the pulmonary endothelial production of prostacyclin by inhibiting endothelial NO production, thereby contributing to the development of pulmonary vascular injury and shock through increases in lung tissue levels of TNF in rats administered endotoxin.
Efficient non-viral transfection of adult neural stem/progenitor cells, without affecting viability, proliferation or differentiation (2005)

These data demonstrate that non-viral transfection may be used to genetically manipulate neural stem/progenitor cells, without adversely affecting their growth or perturbing lineage selection. Such a method is valuable for examining the molecular mechanisms of cell fate determination in vitro. Furthermore, this protocol may be exploited in the development of cell-based gene therapy strategies.
Ovarian and Adrenal Hyperandrogenism (2006)

Because in normal women androgens are secreted in almost equal quantities by both adrenals and ovaries, for many years many studies have tried to distinguish the source of androgen excess. However, in the last 10-15 years, the diagnoses of ovarian or adrenal hyperandrogenism have almost disappeared. This is due to the lack of specificity of dynamic tests as well as to the emphasis given on clinical information and ovarian sonography for the diagnosis of hyperandrogenic syndromes. However, determination of the source of increased androgens may still be useful for improving the classification and the understanding of androgen excess disorders. The aim of this review is to examine the source of androgen excess in the three more common androgen excess disorders: polycystic ovary syndrome (PCOS), idiopathic hyperandrogenism; and nonclassic 21-hydroxylase deficiency (NCAH). The ovary is the main androgen source in PCOS and idiopathic hyperandrogenism while adrenal androgen secretion is prevalent in NCAH. However, androgen secretion from more than one source is common in all main forms of hyperandrogenism as is the case in 70-80% of patients with NCAH, in 35% of women with PCOS, and in 50% of patients with idiopathic hyperandrogenism. Secondary PCOS is the main cause of ovarian androgen excess in nonclassic 21-hydroxylase deficiency while adrenal hyperandrogenism in PCOS and idiopathic hyperandrogenism is probably the consequence of multiple factors including hyperinsulinemia, altered cortisol metabolism, and increased ovarian steroid production. The clinical image is not generally affected by the source of androgen excess. However, hyperandrogenic patients with increased dehydroepiandrosterone sulfate (DHEAS) tend to have lower body weight and insulin levels and a better metabolic profile.
Carbohydrate-binding properties of human neo-CRP and its relationship to phosphorylcholine-binding site (2002)

Binding characteristics of two types of ligands for human neo-C-reactive protein (neo-CRP), which is a conformationally altered but physiologically relevant form of CRP, were studied fluorometrically by probing CRP immobilized on a polystyrene surface with europium-labeled ligands. Two Eu-ligands used were bovine serum albumin derivatives that contain on average 40 residues of ligand structures, one derivative containing phosphorylcholine (PC) and the other lactosyl residues. The PC-containing ligands required the presence of calcium for binding, whereas galactose-containing derivatives bound in the absence of calcium. The optimal pH for the PC-dependent binding was broad (pH 6-8), whereas the best binding pH for the galactose-dependent binding was around 6. The carbohydrate-mediated binding is rather nonspecific: the binding site prefers galactose configuration, but other hexoses can be accommodated. The two best monosaccharide inhibitors at this site were galactose-6-phosphate and galacturonic acid, suggesting the importance of having a negatively charged group at C-6 position of galactose. In fact, the phosphate-binding site is common to both PC and sugar phosphates, and the choline- and the sugar-binding sites are probably located on either side of the phosphate-binding site. Binding characteristics of Eu-labeled PC-BSA to neo-CRP are quite similar to that found for native CRP in solution phase [Lee et al. (2002) J. Biol. Chem., 277, 225-232], whereas binding of sugar phosphates by neo-CRP shows considerably less stringent requirements compared to native CRP. For instance, galactose-alpha1-phosphate was not inhibitory at all in the native CRP binding assay, whereas it was a good inhibitor in the neo-CRP assay.
Anti–TNF-α therapy induces a distinct regulatory T cell population in patients with rheumatoid arthritis via TGF-β (2007)

The induction of regulatory T (T reg) cells holds considerable potential as a treatment for autoimmune diseases. We have previously shown that CD4+CD25hi T reg cells isolated from patients with active rheumatoid arthritis (RA) have a defect in their ability to suppress proinflammatory cytokine production by CD4+CD25- [corrected] T cells. This defect, however, was overcome after anti-tumor necrosis factor (TNF)-alpha antibody (infliximab) therapy. Here, we demonstrate that infliximab therapy gives rise to a CD4+CD25hiFoxP3+ T reg cell population, which mediates suppression via transforming growth factor (TGF)-beta and interleukin 10, and lacks CD62L expression, thereby distinguishing this T reg cell subset from natural T reg cells present in healthy individuals and patients with active RA. In vitro, infliximab induced the differentiation of CD62L- T reg cells from CD4+CD25- T cells isolated from active RA patients, a process dependent on TGF-beta. In spite of the potent suppressor capacity displayed by this CD62L- T reg cell population, the natural CD62L+ T reg cells remained defective in infliximab-treated patients. These results suggest that anti-TNF-alpha therapy in RA patients generates a newly differentiated population of T reg cells, which compensates for the defective natural T reg cells. Therefore, manipulation of a proinflammatory environment could represent a therapeutic strategy for the induction of T reg cells and the restoration of tolerance.