gebhart/patrepeval huggingface dataset:
Development of pilus organelle subassemblies in vitro depends on chaperone uncapping of a beta zipper (1996)

The major subassemblies of virulence-associated P pili, the pilus rod (comprised of PapA) and tip fibrillum (comprised of PapE), were reconstituted from purified chaperone-subunit complexes in vitro. Subunits are held in assembly-competent conformations in chaperone-subunit complexes prior to their assembly into mature pili. The PapD chaperone binds, in part, to a conserved motif present at the C terminus of the subunits via a beta zippering interaction. Amino acid residues in this conserved motif were also found to be essential for subunit-subunit interactions necessary for the formation of pili, thus revealing a molecular mechanism whereby the PapD chaperone may prevent premature subunit-subunit interactions in the periplasm. Uncapping of the chaperone-protected C terminus of PapA and PapE was mimicked in vitro by freeze-thaw techniques and resulted in the formation of pilus rods and tip fibrillae, respectively. A mutation in the leading edge of the beta zipper of PapA produces pilus rods with an altered helical symmetry and azimuthal disorder. This change in the number of subunits per turn of the helix most likely reflects involvement of the leading edge of the beta zipper in forming a right-handed helical cylinder. Organelle development is a fundamental process in all living cells, and these studies shed new light on how immunoglobulin-like chaperones govern the formation of virulence-associated organelles in pathogenic bacteria.
Trends in Hospitalizations Associated With Pediatric Traumatic Brain Injuries (2008)

Although pediatric hospitalization rates for mild traumatic brain injuries have decreased over the past 15 years, rates for moderate and severe traumatic brain injuries are relatively unchanged. Our study provides national estimates of pediatric traumatic brain injury hospitalizations that can be used as benchmarks to increase injury prevention effectiveness through targeting of effective strategies.
Identification of Candida albicans ALS2 and ALS4 and Localization of Als Proteins to the Fungal Cell Surface (1998)

Additional genes in the growing ALS family of Candida albicans were isolated by PCR screening of a genomic fosmid library with primers designed from the consensus tandem-repeat sequence of ALS1. This procedure yielded fosmids encoding ALS2 and ALS4. ALS2 and ALS4 conformed to the three-domain structure of ALS genes, which consists of a central domain of tandemly repeated copies of a 108-bp motif, an upstream domain of highly conserved sequences, and a domain of divergent sequences 3' of the tandem repeats. Alignment of five predicted Als protein sequences indicated conservation of N- and C-terminal hydrophobic regions which have the hallmarks of secretory signal sequences and glycosylphosphatidylinositol addition sites, respectively. Heterologous expression of an N-terminal fragment of Als1p in Saccharomyces cerevisiae demonstrated function of the putative signal sequence with cleavage following Ala17. This signal sequence cleavage site was conserved in the four other Als proteins analyzed, suggesting identical processing of each protein. Primary-structure features of the five Als proteins suggested a cell-surface localization, which was confirmed by indirect immunofluorescence with an anti-Als antiserum. Staining was observed on mother yeasts and germ tubes, although the intensity of staining on the mother yeast decreased with elongation of the germ tube. Similar to other ALS genes, ALS2 and ALS4 were differentially regulated. ALS4 expression was correlated with the growth phase of the culture; ALS2 expression was not observed under many different in vitro growth conditions. The data presented here demonstrate that ALS genes encode cell-surface proteins and support the conclusion that the size and number of Als proteins on the C. albicans cell surface vary with strain and growth conditions.
Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal (2019)

These findings suggest a novel paradigm in which specific strains of a gut commensal may contribute to the immune pathogenesis of lupus nephritis.
Constructing an adenocarcinoma vaccine: Immunization of mice with synthetic KH‐1 nonasaccharide stimulates anti‐KH‐1 and anti‐Le y antibodies (2002)

There is mounting evidence to suggest that immunization-based strategies can be used to mobilize the human immune system against specific carbohydrate antigens displayed on the surface of cancer cells. Following isolation and identification, such antigens can be administered as conjugate vaccines. The tumor-associated carbohydrate antigen KH-1 is 1 such antigen and may serve as a potential target for immunization against adenocarcinoma. However, a serious impediment to the application of a vaccine-based approach involving this antigen is that its availability from natural sources is severely limited. In order to overcome this limitation, we have developed an efficient total synthesis of this complex glycolipid. We have extended our synthesis to reach a structurally related analog in which the ceramide portion of KH-1 is replaced with an allyl substituent. These synthetic advances have led to the preparation of 2 potential vaccine constructs, each based on the conjugation of the KH-1 nonasaccharide and the carrier protein keyhole limpet hemocyanin (KLH). In 1 construct (KH-1-Et-KLH), the nonasaccharide is conjugated to KLH via a simple ethyl linkage, while in the other (KH-1-MMCCH-KLH), conjugation is mediated by a 4-(4-N-maleimidomethyl)cyclohexane-1-carboxyl hydrazide (MMCCH) cross-linker. We report here the immunological properties of these 2 constructs. Mice were immunized with either of the 2 KH-1-KLH vaccine candidates or the KH-1 ceramide, along with the immunological adjuvant QS-21. Immunization with the ceramide served as a negative control and, as expected, failed to stimulate the production of antibodies against the KH-1 glycolipid. The construct in which the KH-1 nonasaccharide is linked to KLH via a simple alkyl chain stimulated significant quantities of IgM antibodies, whereas the construct linked to KLH by MMCCH induced high titers of both IgM and IgG antibodies. Inhibition data demonstrated that antibodies generated in response to immunization with the KH-1-KLH constructs recognize not only the KH-1 antigen but also the Lewis(y) (Le(y)) antigen, which, from a structural perspective, is similar to the 4 residues located at the non-reducing end of the KH-1 nonasaccharide. Thus, the KH-1-KLH constructs elicit an immune response that successfully targets 2 adenocarcinoma markers. As assessed by FACS analysis, the antibodies raised were strongly reactive with the KH-1/Le(y) positive cell line MCF-7 but not with KH-1 and Le(y) negative melanoma cell lines. Based on the results of our study, a KH-1-KLH plus QS-21 vaccine is being prepared for clinical evaluation.
Creation of Saccular Aneurysms in the Rabbit (2000)

Arterial aneurysms with intact endothelium and deficient elastic lamina were reliably created in an area of high shear stress in New Zealand white rabbits. Three of these aneurysms remained patent for at least 6 months. We found a simple procedure that can be readily applied to the testing of new endovascular devices for a reliable creation of aneurysms in rabbits.
Antigenic variation of Anaplasma marginale msp2 occurs by combinatorial gene conversion (2002)

The rickettsial pathogen Anaplasma marginale establishes lifelong persistent infection in the mammalian reservoir host, during which time immune escape variants continually arise in part because of variation in the expressed copy of the immunodominant outer membrane protein MSP2. A key question is how the small 1.2 Mb A. marginale genome generates sufficient variants to allow long-term persistence in an immunocompetent reservoir host. The recombination of whole pseudogenes into the single msp2 expression site has been previously identified as one method of generating variants, but is inadequate to generate the number of variants required for persistent infection. In the present study, we demonstrate that recombination of a whole pseudogene is followed by a second level of variation in which small segments of pseudogenes recombine into the expression site by gene conversion. Evidence for four short sequential changes in the hypervariable region of msp2 coupled with the identification of nine pseudogenes from a single strain of A. marginale provides for a combinatorial number of possible expressed MSP2 variants sufficient for lifelong persistence.
Palladium-Catalyzed Alkylation-Alkenylation Reactions: Rapid Access to Tricyclic Mescaline Analogues (2006)

A norbornene-mediated palladium-catalyzed sequence is described in which two alkyl-aryl bonds and one alkenyl-aryl bond are formed in one pot. A variety of symmetrical and unsymmetrical tricyclic heterocycles were synthesized in good yields from a Heck acceptor and an aryl iodide containing two tethered alkyl bromides. This methodology was applied to the synthesis of a tricyclic mescaline analogue.
High-performance photonic analog-to-digital converters (2002)

The advantages of photonics combined with advances in electronics has led to recent progress toward the realization of photonic analog-to-digital converters with wide-bandwidth and high-resolution. Applications, advantages, issues and recent results will be presented.
Prostaglandin E2Induces Vascular Relaxation by E-Prostanoid 4 Receptor-Mediated Activation of Endothelial Nitric Oxide Synthase (2007)

The present experiments were designed to test the hypothesis that prostaglandin (PG) E(2) causes vasodilatation through activation of endothelial NO synthase (eNOS). Aortic rings from mice with targeted deletion of eNOS and E-prostanoid (EP) receptors were used for contraction studies. Blood pressure changes in response to PGE(2) were measured in conscious mice. Single doses of PGE(2) caused concentration-dependent relaxations during contractions to phenylephrine (EC(50)=5*10(-8) mol/L). Relaxation after PGE(2) was absent in rings without endothelium and in rings from eNOS(-/-) mice and was abolished by N(G)-nitro-l-arginine methyl ester and the soluble guanylate cyclase inhibitor 1H(1,2,4)-oxadiazolo-[4,3-a]quinoxalin-1-one. In PGE(2)-relaxed aortic rings, the cGMP content increased significantly. PGE(2)-induced relaxations were abolished by the EP4 receptor antagonist AE3-208 (10(-8) mol/L) and mimicked by an EP4 agonist (AE1-329, 10(-7) mol/L) in the presence of endothelium and eNOS only. Relaxations were attenuated significantly in rings from EP4(-/-) mice but normal in EP2(-/-). Inhibitors of the cAMP-protein kinase A pathway attenuated, whereas the inhibitor of protein phosphatase 1C, calyculin (10(-8) mol/L), abolished the PGE(2)-mediated relaxation. In aortic rings, PGE(2) dephosphorylated eNOS at Thr(495). Chronically catheterized eNOS(-/-) mice were hypertensive (137+/-3.6 mm Hg, n=13, versus 101+/-3.9 mm Hg, n=9) and exhibited a lower sensitivity of blood pressure reduction in response to PGE(2) compared with wild-type mice. There was no difference in the blood pressure response to nifedipine. These findings show that PGE(2) elicits EP4 receptor-mediated, endothelium-dependent stimulation of eNOS activity by dephosphorylation at Thr(495) resulting in guanylyl cyclase-dependent vasorelaxation and accumulation of cGMP in aortic rings.
Deblocking of Proteins Containing N-Terminal PyroglutamicAcid (2003)

Pyroglutamic acid (pGlu) is the product of cyclization of N-terminal glutamine and is one of the common modifications found at the N-termini of proteins. This modification is typical for immunoglobulins, especially IgGs, since they contain glutamine at the amino terminus of the heavy chain. This chemical modification, in addition to other modifications of the N-terminus results in a “blocked“ protein which cannot be sequenced using Edman degradation. Many deblocking procedures have been reported to remove common modifications at the N-terminal end of proteins for the sequence determination by Edman chemistry (1). Deblocking of N-terminal pGlu is usually achieved by the use of either chemical methods (2,3) or by the use of pyroglutamate aminopeptidase (PGAP) (1,4,5). Removal of pGlu from peptides by PGAP with high yield has been described (1,6–10) and recommended as a standard procedure (1). However, when this protocol is applied to large proteins such as IgGs, it results in relatively low yield (<40%) of the deblocked protein. The most commonly cited procedure of Podell and Abraham (11) for removal of pGlu from proteins is also recommended in the handbooks (1,12). However, this procedure is not consistent with the results, which demonstrated that incubation at 4°C did not yield any deblocking (13). Other existing protocols use PGAP for digestion in solution or for proteins blotted onto PVDF membranes and result in variable yields of deblocked protein (2,11,12,15,16).
Adenovirus-mediated generation of cAMP-stimulated Cl- transport in cystic fibrosis airway epithelia in vitro: effect of promoter and administration method. (1996)

Cystic fibrosis (CF) is a common autosomal recesses disease in which loss of CFTR-Cl- channel function of defective cAMP-stimulated Cl- transport transfer across airway epithelia. Recombinant adenoviruses have shown progress as vectors with which to transfer CFTR cDNA to CF airway epithelia. Here we investigated variables involved in adenovirus-mediated transfer of CFTR by measuring cAMP- stimulated Cl- transport in CF airway epithelia grown as monolayers on permeable filter supports. When we compared the effects of different promoters, we found that persistent correction of Cl- transport was obtained when the vector contained the E1a promoter, or to a lesser extent the PGK promoter. Vector containing the CMV promoter produced a greater initial cAMP-stimulated Cl- current, but the duration of correction was shorter and the infection procedure itself increased CFTR expression, suggesting that high input doses of virus stimulate expression. We compared the level of expression, measured with a beta-galactosidase reporter of CFTR mRNA, with CFTR-mediated Cl- transport. Even low levels of expression generated significant Cl- current and marked increases in expression produced only modest increments in Cl- current. Correction of the CF Cl- transport defect was also improved when the concentration of adenovirus vector was high and when the duration of contact with the epithelium was prolonged. These findings may help optimize the ability of adenovirus vectors encoding CFTR to correct the CF Cl- transport defect.
Activity and stability of human kallikrein‐2‐specific linear and cyclic peptide inhibitors (2007)

Human glandular kallikrein (KLK2) is a highly prostate-specific serine protease, which is mainly excreted into the seminal fluid, but part of which is also secreted into circulation from prostatic tumors. Since the expression level of KLK2 is elevated in aggressive tumors and it has been suggested to mediate the metastasis of prostate cancer, inhibition of the proteolytic activity of KLK2 is of potential therapeutic value. We have previously identified several KLK2-specific linear peptides by phage display technology. Two of its synthetic analogs, A R R P A P A P G (KLK2a) and G A A R F K V W W A A G (KLK2b), show specific inhibition of KLK2 but their sensitivity to proteolysis in vivo may restrict their potential use as therapeutic agents. In order to improve the stability of the linear peptides for in vivo use, we have prepared cyclic analogs and compared their biological activity and their structural stability. A series of cyclic variants with cysteine bridges were synthesized. Cyclization inactivated one peptide (KLK2a) and its derivatives, while the other peptide (KLK2b) and its derivatives remained active. Furthermore, backbone cyclization of KLK2b improved significantly the resistance against proteolysis by trypsin and human plasma. Nuclear magnetic resonance studies showed that cyclization of the KLK2b peptides does not make the structures more rigid. In conclusion, we have shown that backbone cyclization of KLK2 inhibitory peptides can be used to increase stability without losing biological activity. This should render the peptides more useful for in vivo applications, such as tumor imaging and prostate cancer targeting.
Secretion and Intracellular Generation of Truncated Aβ in β-Site Amyloid-β Precursor Protein-cleaving Enzyme Expressing Human Neurons (2003)

Insoluble pools of the amyloid-beta peptide (Abeta) in brains of Alzheimer's disease patients exhibit considerable N- and C-terminal heterogeneity. Mounting evidence suggests that both C-terminal extensions and N-terminal truncations help precipitate amyloid plaque formation. Although mechanisms underlying the increased generation of C-terminally extended peptides have been extensively studied, relatively little is known about the cellular mechanisms underlying production of N-terminally truncated Abeta. Thus, we used human NT2N neurons to investigate the production of Abeta11-40/42 from amyloid-beta precursor protein (APP) by beta-site APP-cleaving enzyme (BACE). When comparing undifferentiated human embryonal carcinoma NT2- cells and differentiated NT2N neurons, the secretion of sAPP and Abeta correlated with BACE expression. To study the effects of BACE expression on endogenous APP metabolism in human cells, we overexpressed BACE in undifferentiated NT2- cells and NT2N neurons. Whereas NT2N neurons produced both full-length and truncated Abeta as a result of normal processing of endogenous APP, BACE overexpression increased the secretion of Abeta1-40/42 and Abeta11-40/42 in both NT2- cells and NT2N neurons. Furthermore, BACE overexpression resulted in increased intracellular Abeta1-40/42 and Abeta11-40/42. Therefore, we conclude that Abeta11-40/42 is generated prior to deposition in senile plaques and that N-terminally truncated Abeta peptides may contribute to the downstream effects of amyloid accumulation in Alzheimer's disease.
Activation of an apical Cl- conductance by Ca2+ ionophores in cystic fibrosis airway epithelia (1989)

Cystic fibrosis (CF) airway epithelia express a defect in adenosine 3',5'-cyclic monophosphate (cAMP)-dependent regulation of apical membrane Cl- channels. Recent patch-clamp studies have raised the possibility that Ca2+ -dependent mechanisms for the activation of Cl- secretion may be preserved in CF airway epithelia. To determine 1) whether intact normal (N1) and CF airway epithelia exhibit a Ca2+ -dependent mechanism for activation of Cl- secretion and 2) whether Ca2+ -dependent mechanism for activation of Cl- secretion and 2) whether Ca2+ -dependent mechanisms initiate Cl- secretion via activation of an apical membrane Cl- conductance (GCl-), nasal epithelia from N1 and CF subjects were cultured on collagen membranes, and responses to isoproterenol or Ca2- ionophores [A23187 10(-6) M; ionomycin (10(-5)M)] were measured with transepithelial and intracellular techniques. Isoproterenol induced activation of an apical membrane GCl- in N1 cultures but was ineffective in CF. In contrast, in both N1 and CF amiloride-pretreated cultures, A23187 induced an increase in the equivalent short-circuit current that was associated with an activation of an apical membrane Gc1- and was bumetanide inhibitable. A23187 addition during superfusion of the lumen with a low Cl- (3 mM) solution reduced intracellular Cl- activity of CF cells. A Ca2+ ionophore of different selectivity properties, ionomycin, was also an effective Cl- secretagogue in both N1 and CF cultures. We conclude that 1) the A23187 induced Cl- secretion via activation of an apical GCl- in N1 human nasal epithelium, and 2) in contrast to an isoproterenol-dependent path, a Ca2+ -dependent path for GCl- activation is preserved in CF epithelia.
Indoleamine 2,3‐dioxygenase (IDO) activity influence tumor growth in the TRAMP prostate cancer model (2010)

Our results argue for a role for IDO mediated immune suppression in the early stages of prostate cancer progression. However, since the intra-tumor IDO expression in J(-/-) mice was indistinguishable from that of C57BL/6 animals the IDO expression in the tumor tissue appears to be irrelevant for TRAMP tumor incidence.
Factors associated with increased frequency of HIV‐related oral candidiasis (1991)

HIV-related oral candidiasis was investigated in 71 HIV-seropositive patients who received interviews, oral examinations and hematologic investigation. Diagnosis of candidiasis was based on clinical signs and examination of PAS-stained smears. The frequency of candidiasis was 24/71 (34%). The clinical presentations were pseudomembranous 8 (11%), erythematous 14 (20%), angular cheilitis 3 (4%). Twenty-six patients (37%) had candidiasis or were receiving antifungal treatment for recurrent pseudomembranous type. Twelve of 13 (92%) patients with AIDS and 14/58 (24%) without AIDS were affected. Bivariate analyses showed significant associations with AIDS, the use of zidovudine, low T4-count, xerostomia; marital status (sometime married), restricted performance status and age of greater than 35 yr. Multivariate logistic regression analysis showed that the presence of xerostomia was an independent and statistically significant predictor of HIV-related oral candidiasis. T4-count and restricted performance status were the second and third most important predictors.
Foldable Printed Circuit Boards on Paper Substrates (2009)

Abstract This paper describes several low‐cost methods for fabricating flexible electronic circuits on paper. The circuits comprise i) metallic wires (e.g., tin or zinc) that are deposited on the substrate by evaporation, sputtering, or airbrushing, and ii) discrete surface‐mountable electronic components that are fastened with conductive adhesive directly to the wires. These electronic circuits—like conventional printed circuit boards—can be produced with electronic components that connect on both sides of the substrate. Unlike printed circuit boards made from fiberglass, ceramics, or polyimides, however, paper can be folded and creased (repeatedly), shaped to form three‐dimensional structures, trimmed using scissors, used to wick fluids (e.g., for microfluidic applications) and disposed of by incineration. Paper‐based electronic circuits are thin and lightweight; they should be useful for applications in consumer electronics and packaging, for disposable systems for uses in the military and homeland security, for applications in medical sensing or low‐cost portable diagnostics, for paper‐based microelectromechanical systems, and for applications involving textiles.