Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the Carbohydrate Moieties and Glycosylation Motifs in Campylobacter jejuni Flagellin*

Flagellins from three strains ofCampylobacter jejuni and one strain of Campylobacter coli were shown to be extensively modified by glycosyl residues, imparting an approximate 6000-Da shift from the molecular mass of the protein predicted from the DNA sequence. Tryptic peptides from C. jejuni 81–176 flagellin were subjected to capillary liquid chromatography-electrospray mass spectrometry with a high/low orifice stepping to identify peptide segments of aberrant masses together with their corresponding glycosyl appendages. These modified peptides were further characterized by tandem mass spectrometry and preparative high performance liquid chromatography followed by nano-NMR spectroscopy to identify the nature and precise site of glycosylation. These analyses have shown that there are 19 modified Ser/Thr residues in C. jejuni 81–176 flagellin. The predominant modification found onC. jejuni flagellin was O-linked 5,7-diacetamido-3,5,7,9-tetradeoxy-l -glycero- l -manno-nonulosonic acid (pseudaminic acid, Pse5Ac7Ac) with additional heterogeneity conferred by substitution of the acetamido groups with acetamidino and hydroxyproprionyl groups. In C. jejuni 81–176, the gene Cj1316c, encoding a protein of unknown function, was shown to be involved in the biosynthesis and/or the addition of the acetamidino group on Pse5Ac7Ac. Glycosylation is not random, since 19 of the total 107 Ser/Thr residues are modified, and all but one of these are restricted to the central, surface-exposed domain of flagellin when folded in the filament. The mechanism of attachment appears unrelated to a consensus peptide sequence but is rather based on surface accessibility of Ser/Thr residues in the folded protein.
Oxidative damage to mitochondrial DNA and glutathione oxidation in apoptosis: studies in vivo and in vitro

Free radicals may be involved in apoptosis although this is the subject of some controversy. Furthermore, the source of free radicals in apoptotic cells is not certain. The aim of this study was to elucidate the role of oxidative stress in the induction of apoptosis in serum‐deprived fibroblast cultures and in weaned lactating mammary glands as in vitro and in vivo experimental models, respectively. Oxidative damage to mtDNA is higher in apoptotic cells than in controls. Oxidized glutathione (GSSG) levels in mitochondria from lactating mammary gland are also higher in apoptosis. There is a direct relationship between mtDNA damage and the GSSG/reduced glutathione (GSH) ratio. Furthermore, whole cell GSH is decreased and GSSG is increased in both models of apoptosis. Glutathione oxidation precedes nuclear DNA fragmentation. These signs of oxidative stress are caused, at least in part, by an increase in peroxide production by mitochondria from apoptotic cells. We report a direct relationship between glutathione oxidation and mtDNA damage in apoptosis. Our results support the role of mitochondrial oxidative stress in the induction of apoptosis—Esteve, J. M. , Mompo, J., Garcia de la Asuncion, J., Sastre, J., Asensi, M. , Boix, J., Viña, J. R. , Viña, J., Pallardó, F. V. Oxidative damage to mitochondrial DNA and glutathione oxidation in apoptosis: studies in vivo and in vitro. FASEB J. 13, 1055–1064 (1999)
Pathophysiology of shock and hemorrhage in a fulminating viral infection (Ebola).

Eleven rhesus monkeys were monitored intensively during experimental infection with Ebola virus. Prominent neutrophilia with left shift and lymphopenia were the earliest abnormalities and were statistically significant by day 4 (P less than .02 and P less than .01, respectively). By day 4 falls in platelet counts were not statistically significant, whereas in vitro platelet aggregation was markedly depressed, progressing rapidly to complete failure by the time of maximum illness. Intraplatelet protein studies suggested this event was the result of in vivo activation and degranulation. Coagulation cascade defects were mainly in the intrinsic system and were surprisingly mild, with no evidence of selective consumption or production deficit of factor VII or VIII. When the possibility of indirectly mediated damage to endothelium possibly by a nonspecific immune response was examined, weight loss was less severe in drug-treated monkeys, and all had detectable plasma prostacyclin metabolites, but there was no improvement in survival.
Sites of interaction between SecA and the chaperone SecB, two proteins involved in export

SecB, a small tetrameric cytosolic chaperone in Escherichia coli, facilitates the export of precursor poly‐peptides by maintaining them in a nonnative conformation and passing them to SecA, which is a peripheral member of the membrane‐bound translocation apparatus. It has been proposed by several laboratories that as SecA interacts with various components along the export pathway, it undergoes conformational changes that are crucial to its function. Here we report details of molecular interactions between SecA and SecB, which may serve as conformational switches. One site of interaction involves the final C‐terminal 21 amino acids of SecA, which are positively charged and contain zinc. The C terminus of each subunit of the SecA dimer makes contact with the flat β‐sheet that is formed by each dimer of the SecB tetramer. Here we demonstrate that a second interaction exists between the extreme C‐terminal α‐helix of SecB and a site on SecA, as yet undefined but different from the C terminus of SecA. We investigated the energetics of the interactions by titration calorimetry and characterized the hydrodynamic properties of complexes stabilized by both interactions or each interaction singly using sedimentation velocity centrifugation.
Angiotensin II Receptor Blockade Administered after Injury Improves Muscle Regeneration and Decreases Fibrosis in Normal Skeletal Muscle

Background Several therapeutic agents have been shown to inhibit fibrosis and improve regeneration after injury in skeletal muscle by antagonizing transforming growth factor-β1. Angiotensin receptor blockers have been shown to have a similar effect on transforming growth factor-β1 in a variety of tissues. Hypothesis Systemic treatment of animals after injury of skeletal muscle with an angiotensin receptor blocker may decrease fibrosis and improve regeneration, mainly through transforming growth factor-β1 blockade, and can be used to improve skeletal muscle healing after injury. Study Design Controlled laboratory study. Methods Forty mice underwent bilateral partial gastrocnemius lacerations. Mice were assigned randomly to a control group (tap water), a low-dose angiotensin receptor blocker group (losartan, 0.05 mg/mL), or a high-dose angiotensin receptor blocker group (0.5 mg/mL). The medication was dissolved in tap water and administered enterally. Mice were sacrificed 3 or 5 weeks after injury, and the lacerated muscles were examined histologically for muscle regeneration and fibrosis. Results Compared with control mice at 3 and 5 weeks, angiotensin receptor blocker-treated mice exhibited a histologic dose-dependent improvement in muscle regeneration and a measurable reduction in fibrous tissue formation within the area of injury. Conclusion By modulating the response to local and systemic angiotensin II, angiotensin receptor blocker therapy significantly reduced fibrosis and led to an increase in the number of regenerating myofibers in acutely injured skeletal muscle. The clinical implications for this application of angiotensin receptor blockers are potentially far-reaching and include not only sports- and military-related injuries, but also diseases such as the muscular dystrophies and trauma- and surgery-related injury. Clinical Relevance Angiotensin receptor blockers may provide a safe, clinically available treatment for improving healing after skeletal muscle injury.
Identification of Differentially Regulated Francisella tularensis Genes by Use of a Newly Developed Tn5-Based Transposon Delivery System

ABSTRACT Francisella tularensis is the etiologic agent of an intracellular systemic infection of the lymphatic system in humans called tularemia. The organism has become the subject of considerable research interest due to its classification as a category A select agent by the CDC. To aid genetic analysis of this pathogen, we have constructed a temperature-sensitive Tn5-based transposon delivery system that is capable of generating chromosomal reporter fusions with lacZ or luxCDABE, enabling us to monitor gene expression. Transposition is catalyzed by the hyperactive Tn5 transposase, whose expression is driven by the Francisella groES promoter. When high-temperature selection (42°C) is applied to a bacterial culture carrying the transposon delivery plasmid, ∼0.1% of the population is recovered with Tn5 insertions in the chromosome. Nucleotide sequence analysis of a sample of mutants revealed that the insertions occur randomly throughout the chromosome. The kanamycin-selectable marker of the transposon is also flanked by FLP recombination target sequences that allow deletion of the antibiotic resistance gene when desired. This system has been used to generate transposon mutant libraries for the F. tularensis live vaccine strain as well as two different virulent F. tularensis strains. Chromosomal reporters delivered with the transposon were used to identify genes upregulated by growth in Chamberlain's defined medium. Genes in the fsl operon, reported to be involved in iron acquisition, as well as genes in the igl gene cluster were among those identified by the screen. Further experiments implicate the ferric uptake regulator (Fur) protein in the negative regulation of fsl but not igl reporters, which occurs in an iron-dependent manner. Our results indicate that we have created a valuable new transposon that can be used to identify and characterize virulence genes in F. tularensis strains.
Elevated Cancer-Specific Mortality Among HIV-Infected Patients in the United States.

PURPOSE Despite advances in the treatment of HIV, HIV-infected people remain at increased risk for many cancers, and the number of non-AIDS-defining cancers is increasing with the aging of the HIV-infected population. No prior study has comprehensively evaluated the effect of HIV on cancer-specific mortality. PATIENTS AND METHODS We identified cases of 14 common cancers occurring from 1996 to 2010 in six US states participating in a linkage of cancer and HIV/AIDS registries. We used Cox regression to examine the association between patient HIV status and death resulting from the presenting cancer (ascertained from death certificates), adjusting for age, sex, race/ethnicity, year of cancer diagnosis, and cancer stage. We included 1,816,461 patients with cancer, 6,459 (0.36%) of whom were HIV infected. RESULTS Cancer-specific mortality was significantly elevated in HIV-infected compared with HIV-uninfected patients for many cancers: colorectum (adjusted hazard ratio [HR], 1.49; 95% CI, 1.21 to 1.84), pancreas (HR, 1.71; 95% CI, 1.35 to 2.18), larynx (HR, 1.62; 95% CI, 1.06 to 2.47), lung (HR, 1.28; 95% CI, 1.17 to 1.39), melanoma (HR, 1.72; 95% CI, 1.09 to 2.70), breast (HR, 2.61; 95% CI, 2.06 to 3.31), and prostate (HR, 1.57; 95% CI, 1.02 to 2.41). HIV was not associated with increased cancer-specific mortality for anal cancer, Hodgkin lymphoma, or diffuse large B-cell lymphoma. After further adjustment for cancer treatment, HIV remained associated with elevated cancer-specific mortality for common non-AIDS-defining cancers: colorectum (HR, 1.40; 95% CI, 1.09 to 1.80), lung (HR, 1.28; 95% CI, 1.14 to 1.44), melanoma (HR, 1.93; 95% CI, 1.14 to 3.27), and breast (HR, 2.64; 95% CI, 1.86 to 3.73). CONCLUSION HIV-infected patients with cancer experienced higher cancer-specific mortality than HIV-uninfected patients, independent of cancer stage or receipt of cancer treatment. The elevation in cancer-specific mortality among HIV-infected patients may be attributable to unmeasured stage or treatment differences as well as a direct relationship between immunosuppression and tumor progression.
Obesity and type 2 diabetes: which patients are at risk?

An estimated 72.5 million American adults are obese, and the growing US obesity epidemic is responsible for substantial increase in morbidity and mortality, as well as increased health care costs. Obesity results from a combination of personal and societal factors, but is often viewed as a character flaw rather than a medical condition. This leads to stigma and discrimination towards obese individuals and decreases the likelihood of effective intervention. Conditions related to obesity are increasingly common, such as metabolic syndrome, impaired fasting glucose (IFG) and impaired glucose tolerance (IGT), all of which indicate high risk for type 2 diabetes (T2DM). This paper reviews the progression from obesity to diabetes, identifying physiological changes that occur along this path as well as opportunities for patient identification and disease prevention. Patients with prediabetes (defined as having IFG, IGT or both) and/or metabolic syndrome require interventions designed to preserve insulin sensitivity and β‐cell function, both of which start to deteriorate prior to T2DM diagnosis. Lifestyle modification, including both healthy eating choices and increased physical activity, is essential for weight management and diabetes prevention. Although sustained weight loss is often considered by patients and physicians as being impossible to achieve, effective interventions do exist. Specifically, the Diabetes Prevention Program (DPP) and programs modelled along its parameters have shown repeated successes, even with long‐term maintenance. Recent setbacks in the development of medications for weight loss further stress the importance of lifestyle management. By viewing obesity as a metabolic disorder rather than a personal weakness, we can work with patients to address this increasingly prevalent condition and improve long‐term health outcomes.
Efficiency of Internal Capital Allocation and the Success of Acquisitions

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A force feedback glove based on Magnetorheological Fluid: Preliminary design issues

This work first provides an overview of haptic gloves found in the literature, with a focus on their applications and their requirements. This information is then used to justify the use of Magnetorheological Fluid (MRF), a smart fluid which reversibly changes viscosity proportionally to an applied magnetic field, to effect the force feedback in a haptic glove. This is followed by the development of a linear damper to form part of the proposed glove, as well as a report on our selection of MRF through experiments performed on a number of fluids with different iron content, developed in-house. Finally, the paper describes the position sensing system and the preliminary design of the force feedback glove.
Survivin gene expression in early‐stage non‐small cell lung cancer

Survivin is an inhibitor of apoptosis protein, overexpressed in most human malignancies and implicated in mitosis regulation and preservation of cell viability. In order to investigate the prevalence and clinical significance of survivin in early‐stage non‐small cell lung carcinoma (NSCLC), survivin mRNA levels and protein expression were evaluated, using quantitative real‐time RT‐PCR and immunohistochemistry, respectively, in a series of 83 patients with stage I (IA and IB) surgically resected NSCLC. Detectable survivin mRNA levels could be demonstrated in all non‐neoplastic lung tissue samples and in the tumours analysed. Survivin mRNA levels were elevated in 80 carcinomas (96%) compared to normal lung (p = 0.008). Among all tumours, survivin transcripts were present at a higher level in squamous cell carcinomas (p = 0.0022). Cytoplasmic and nuclear immunoreactivity was found in 70% and 80% of tumours, respectively and both were present in 54%. Cytoplasmic immunoreactivity correlated with tumour stage (p = 0.019). Survivin expression levels did not correlate with patient survival. In one specimen, cytoplasmic and focal nuclear immunostaining was observed in dysplastic bronchial squamous metaplasia. These results document that survivin overexpression is almost always present in early‐stage NSCLC, suggesting that this protein may play a role in lung tumourigenesis. This ubiquitous expression makes survivin an appealing new target for novel therapies in lung cancer. In addition, this study also documents that survivin overexpression could be exploited for diagnostic purposes and that quantitative real‐time RT‐PCR can be a useful tool for evaluating survivin activation in NSCLC. Copyright © 2003 John Wiley & Sons, Ltd.
Black men who have sex with men and the association of down-low identity with HIV risk behavior.

Black men "on the down low" have been considered prime agents of HIV transmission in the Black community despite little empirical evidence. We assessed the relationship between down-low identification and sexual risk outcomes among 1151 Black MSM. Down-low Identification was not associated with unprotected anal or vaginal sex with male or female partners. Future HIV prevention programs and research should target sexual risk behaviors of Black men, irrespective of identity, and not focus on the "down low. "
How Social Capital Facilitates Clan Control on Software Platforms to Enhance App-Developers' Performance and Success

Although platform operators such as Google or Apple are facing a trade-off between retaining and relinquishing control to manage a myriad of third-party developers and development projects, little is known about how clan control—a particularly relevant informal control mode in decentralized multi-project software development—can be facilitated on software platforms and how it affects developer performance. Drawing on control literature and social capital theory, we conducted an online survey with 218 app developers of Google’s Android platform in which we examined how social capital facilitates the exercise of clan control to enhance crucial developer performance outcomes. Our study not only shows that all three dimensions of social capital (i.e., structural, cognitive and relational social capital) are critical levers for exercising clan control on software platforms, but also that clan control leads to higher development performance and app ratings on the platform. Theoretical and practical implications are discussed.
Sorting of actin isoforms in chicken auditory hair cells.

Most nonmuscle cells of higher vertebrates contain two different actin isoforms, beta- and gamma-cytoplasmic actin. The beta-isoform is with few exceptions the predominant isoform in nonmuscle cells and tissues. Perturbation of the beta:gamma ratio has been shown to affect the organization of bundled actin filaments indicating that the beta- and gamma-genes encode functionally distinct cytoarchitectural information. In the present study we localized by immunostaining beta- and gamma-actin in chicken auditory hair cells. These highly specialized cells serve as model system for studying certain developmental and structural aspects of a complex actin filament system with high architectural precision. We show that gamma-actin is the predominant actin isoform in auditory hair cells with an apparent beta:gamma ratio of approximately 1:2. gamma-Actin is not sorted and occurs in all three actin assemblies of the hair border, i.e. the cores of sensory hairs (stereocilia), the subjacent gel-like actin filament meshwork (cuticular plate) and the zonula adherens ring. In contrast to gamma-actin, the beta-isoform is specifically sorted to the actin filament core bundle of stereocilia that is extensively crosslinked by fimbrin. In view of recent studies showing that L-plastin, the leukocyte homolog of fimbrin, has a higher binding affinity for beta-actin than for gamma-actin, a mechanism is proposed for how hair cells might restrict formation of actin filament bundles to a single cellular site (i.e. the stereocilia). The limited level of expression of beta-actin in hair cells may help to prevent ectopic bundle formation in other cellular compartments.
Unified Variance Bounds and a Stein-Type Identity

Let X be an absolutely continuous (a.c.) random variable (r.v.) with finite variance σ2. Then, there exists a new r.v. X∗ (which can be viewed as a transform on X) with a unimodal density, satisfying the extended Stein-type covariance identity Cov[X, g(X)] = σ IE[g′(X∗)] for any a.c. function g with derivative g′, provided that IE|g′(X∗)| < ∞. Properties of X∗ are discussed and, also, the corresponding unified upper and lower bounds for the variance of g(X) are derived. AMS 1991 subject classifications. Primary 60E15; secondary 60E05.
Signal Anchor Sequence Provides Motive Force for Polypeptide Chain Translocation through the Endoplasmic Reticulum Membrane*

Many proteins are translocated across and integrated into the endoplasmic reticulum membrane. The type I signal anchor sequence mediates the translocation of its preceding region through the endoplasmic reticulum membrane, but the source of the motive force has been unclear. Here, we characterized the motive force for N-terminal domain translocation using two probes. First, an Ig-like domain of the muscle protein titin (I27 domain) or its mutants were fused to the N termini, and translocation was examined in a cell-free translation system supplemented with rough microsomal membrane. The N-terminal translocation efficiencies correlated with the mechanical instabilities of the I27 mutants. When the I27 domain was separated from the signal anchor sequence by inserting a spacer, even the most unstable mutant stalled on the cytoplasmic side, whereas its downstream portion spanned the membrane. Proline insertion into the signal anchor sequence also caused a large translocation defect. Second, a streptavidin-binding peptide tag was fused to the N terminus. Titration of streptavidin in the translation system allowed us to estimate the translocation motive force operative on the tag. The motive force was decreased by the proline insertion into the signal anchor sequence as well as by separation from the signal anchor sequence. When the streptavidin-binding peptide tag was separated from the signal anchor, the proline insertion did not induce further deficits in the motive force for the tag. On the basis of the findings obtained by using these two independent techniques, we conclude that the signal sequence itself provides the motive force for N-terminal domain translocation within a limited upstream region.