Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulatory gene mutation: a driving force behind group a Streptococcus strain‐ and serotype‐specific variation

Data from multiple bacterial pathogens are consistent with regulator‐encoding genes having higher mutation frequencies than the genome average. Such mutations drive both strain‐ and type‐ (e.g., serotype, haplotype) specific phenotypic heterogeneity, and may challenge public health due to the potential of variants to circumvent established treatment and/or preventative regimes. Here, using the human bacterial pathogen the group A Streptococcus (GAS; S. pyogenes) as a model organism, we review the types and regulatory‐, phenotypic‐, and disease‐specific consequences of naturally occurring regulatory gene mutations. Strain‐specific regulator mutations that will be discussed include examples that transform isolates into hyper‐invasive forms by enhancing expression of immunomodulatory virulence factors, and examples that promote asymptomatic carriage of the organism. The discussion of serotype‐specific regulator mutations focuses on serotype M3 GAS isolates, and how the identified rewiring of regulatory networks in this serotype may be contributing to a decades old epidemiological association of M3 isolates with particularly severe invasive infections. We conclude that mutation plays an outsized role in GAS pathogenesis and has clinical relevance. Given the phenotypic variability associated with regulatory gene mutations, the rapid examination of these genes in infecting isolates may inform with respect to potential patient complications and treatment options.
Functional relatedness in the Inv/Mxi‐Spa type III secretion system family

Type III Secretion Systems (T3SSs) are structurally conserved nanomachines that span the inner and outer bacterial membranes, and via a protruding needle complex contact host cell membranes and deliver type III effector proteins. T3SS are phylogenetically divided into several families based on structural basal body components. Here we have studied the evolutionary and functional conservation of four T3SS proteins from the Inv/Mxi‐Spa family: a cytosolic chaperone, two hydrophobic translocators that form a plasma membrane‐integral pore, and the hydrophilic ‘tip complex’ translocator that connects the T3SS needle to the translocon pore. Salmonella enterica serovar Typhimurium (S. Typhimurium), a common cause of food‐borne gastroenteritis, possesses two T3SSs, one belonging to the Inv/Mxi‐Spa family. We used invasion‐deficient S. Typhimurium mutants as surrogates for expression of translocator orthologs identified from an extensive phylogenetic analysis, and type III effector translocation and host cell invasion as a readout for complementation efficiency, and identified several Inv/Mxi‐Spa orthologs that can functionally substitute for the S. Typhimurium chaperone and translocator proteins. Functional complementation correlates with amino acid sequence identity between orthologs, but varies considerably between the four proteins. This is the first in‐depth survey of the functional interchangeability of Inv/Mxi‐Spa T3SS proteins acting directly at the host‐pathogen interface.
Coordinating a supply chain with negative effect of retailer's local promotion on goodwill and reference price

This paper investigates a distribution channel consisting of a manufacturer and a retailer under a cooperative program, where the manufacturer determines the national advertising and quality improving effort, while the retailer decides the local promotion effort and may undertake parts of the costs of national advertising and quality improving of the manufacturer. It is assumed that the manufacturer’s national advertising and quality improving efforts positively affect the brand goodwill and reference price, whereas the retailer’s local promotion effort damages them. Three scenarios of the non-cooperative and cooperative scenarios in the decentralized supply chain, and the centralized supply chain scenario, are analyzed. The corresponding equilibrium strategies and profits are obtained and compared, which shows that the cooperative program can achieve payoff-Pareto-improving, but cannot coordinate completely the supply chain. Furthermore, a revenue sharing contract combined with two-subsidy policy is designed to coordinate the decentralized supply chain. Numerical simulation and sensitivity analysis of the coordinating results on the key system parameters are provided to verify the effectiveness of the contract, and some managerial insights are provided.
Mycobacterium tuberculosis virulence‐regulator PhoP interacts with alternative sigma factor SigE during acid‐stress response

The ability to sense acid stress and mount an appropriate adaptive response by Mycobacterium tuberculosis, which adapts a long‐term residence in the macrophage phagosome, remains one of the critical features that defines mycobacterial physiology and its intracellular location. To understand the mechanistic basis of adaptation of the intracellular pathogen, we studied global regulation of M. tuberculosis gene expression in response to acid stress. Although recent studies indicate a role for the virulence‐associated phoP locus in pH‐driven adaptation, in this study, we discovered a strikingly novel regulatory mechanism, which controls acid‐stress homeostasis. Using mycobacterial protein fragment complementation and in vitro interaction analyses, we demonstrate that PhoP interacts with acid‐inducible extracytoplasmic SigE (one of the 13 M. tuberculosis sigma factors) to regulate a complex transcriptional program. Based on these results, we propose a model to suggest that PhoP–SigE interaction represents a major requirement for the global acid stress response, absence of which leads to strongly reduced survival of the bacilli under acidic pH conditions. These results account for the significant growth attenuation of the phoP mutant in both cellular and animal models, and unravel the underlying global mechanism of how PhoP induces an adaptive program in response to acid stress.
Anthony van Leeuwenhoek and His Little Animals: Being Some Account of the Father of Protozoology

This paperback reprint of a wonderful book demonstrates from several points of view the truth that science is a passionate enterprise. Cold objectivity is a figment of the imagination. Leeuwenhoek (1632-1723) did not live as a biologist or as a manufacturer of magnifying glasses. He was a draper in Delft, who for over 50 years took a passionate interest in the smallest living things. In 1673 he sent a letter about them to the Royal Society of London. When he died in August, 1723, he had sent some 200 letters—the last one only three months before—on the microscopic appearance of the diaphragm of sheep and oxen. Why about this subject? He was curious about the cause of his own palpitations, and he believed that they arose in the diaphragm. Boitet, his biographer, wrote: "Six-and-thirty hours before his death, when his limbs were already growing numb, the fire of his ardour
Selective ligand-induced intracellular calcium changes in a population of rat isolated gastric endocrine cells.

BACKGROUND & AIMS Peripheral regulation of acid secretion depends mainly on stimulation or inhibition of the three major gastric endocrine cells (enterochromaffin-like, gastrin, and somatostatin). The aim of this paper was to define physiological responses of enterochromaffin-like, gastrin, and somatostatin cells in a mixed endocrine cell population by measuring ligand-selective changes of intracellular calcium ([Ca2+]i) in individual cells. METHODS Endocrine cells were enriched from a rat gastric cell suspension by elutriation, a density-gradient fractionation, and a 48-hour short-term culture. [Ca2+]i responses of individual cells to various ligands such as gastrin/carboxy-terminal cholecystokinin octapeptide and selective cholecystokinin antagonists, carbachol, and gastrin-releasing peptide were monitored using video imaging in a perfusion chamber. Characteristic [Ca2+]i changes distinguished the three cell types, confirmed by immunostaining. RESULTS All enterochromaffin-like cells respond to cholecystokinin-B receptor stimulation, but only a few respond to carbachol. Gastrin cells respond to both gastrin-releasing peptide and carbachol but not to cholecystokinin-receptor agonists. Somatostatin cells have both stimulatory cholecystokinin-A and cholecystokinin-B receptors and inhibitory muscarinic receptors. All cells have inhibitory somatostatin receptors. CONCLUSIONS Calcium-signaling responses of gastric endocrine cells are distinctive. This allows individual cell types in a mixed population to be characterized and permits an analysis of the hormones and transmitters that act directly on a specific cell type.
Excitatory and inhibitory actions of vasopressin on colonic excitation-contraction coupling in dogs.

BACKGROUND & AIMS Vasopressin, a circulating hormone and agent used to treat gastrointestinal bleeding, affects gastrointestinal motility. Both excitatory and inhibitory responses that may be caused by species differences or concentration-dependent effects of this hormone have been reported. This study examined the actions of vasopressin on the canine colon and studied the mechanism underlying the excitatory effects of vasopressin. METHODS Intracellular microelectrodes and isometric force measurements were used to measure vasopressin responses in muscle strips. The patch-clamp technique was used to record arginine vasopressin activation of nonselective cation currents in isolated myocytes. RESULTS Vasopressin (10(-12) to 10(-9) mol/L) increased electrical slow waves and enhanced phasic contractions. Atropine and tetrodotoxin did not alter the responses to vasopressin. In myocytes, vasopressin activated a nonselective cation conductance at concentrations that enhanced slow waves. Vasopressin (> 5 x 10(-8) mol/L) caused a tetrodotoxin- or NG-nitro-L-arginine methyl ester-insensitive inhibition of slow waves and contractile activity. A V1-receptor antagonist shifted the effects of vasopressin to higher concentrations. Immunohistochemistry showed expression of vasopressin-like immunoreactivity within the colonic wall, suggesting that local concentrations may exceed circulating levels. CONCLUSIONS These data document the concentration dependence of the biphasic effects of vasopressin and provide a mechanism for the excitatory effects of vasopressin at physiological levels.
Factors associated with poor health-related quality of life of patients with cirrhosis.

BACKGROUND & AIMS Increasing interest is being given to health-related quality of life in chronic diseases. In cirrhosis, both physical functioning and mental well-being may be altered, but no study has investigated factors associated with a poor perceived health status. METHODS We measured quality of life by Short Form-36 and Nottingham Health Profile questionnaires in 544 patients with cirrhosis. Data were compared with age- and gender-adjusted values of 2 random samples of the Italian population (more than 2000 subjects). Factors associated with poor perceived health status were identified by logistic regression. RESULTS All domains of health-related quality of life, except pain, were altered in cirrhosis (by 9%-42%), mainly in younger patients. There were minor differences in relation to gender, whereas etiology had no effects. Severity of disease (Child-Pugh score) and, above all, muscle cramps were the factors most closely associated with poor health status perception. Self-rating of disease progression was associated with ascites and pruritus, whereas previous variceal sclerotherapy and the use of disaccharides had a protective effect. Most areas of daily life were affected by perceived health problems; this was mainly true for paid employment and sex life in men and home life and social life in women. CONCLUSIONS Quality of life is variably impaired in cirrhosis, also in uncomplicated patients. Non-life-threatening symptoms, such as muscle cramps, are of major concern. These data are the basis for longitudinal studies measuring the effects of therapy and procedures on patient-derived health outcomes.
Leptin is a growth factor for colonic epithelial cells.

BACKGROUND AND AIMS Obesity increases the risk of colon cancer, whereas physical activity reduces the risk. Plasma levels of leptin increase in proportion to the level of obesity and are reduced by physical activity. Leptin acts as a growth factor for several cell types and thus may provide a biological explanation for the observed epidemiological risk factors. The aim of this study was to investigate whether leptin is a growth factor for colonic epithelial cells. METHODS The presence of the leptin receptor in human colon cancer cell lines was assessed using reverse-transcription polymerase chain reaction and immunoblotting, and its presence in human colonic tissue was assessed by immunohistochemistry. The effects of leptin in vitro on HT29 cells were assessed by assessing p42/44 mitogen-activated protein kinase phosphorylation, thymidine incorporation, and cell numbers and in vivo in C57BL/6 mice by colonic bromodeoxyuridine incorporation. RESULTS The leptin receptor is expressed in human colon cancer cell lines and human colonic tissue. Stimulation with leptin leads to phosphorylation of p42/44 mitogen-activated protein kinase and increases proliferation in vitro and in vivo. CONCLUSIONS Leptin is a growth factor in colonic epithelial cells and one that may provide a biological explanation for the observed associations between obesity, physical activity, and colon cancer.
A review of activity indices and efficacy endpoints for clinical trials of medical therapy in adults with Crohn's disease.

WILLIAM J. SANDBORN,*,‡ BRIAN G. FEAGAN,§ STEPHEN B. HANAUER,*,‡ HERBERT LOCHS,* ROBERT LOFBERG,* ROBERT MODIGLIANI,*,\ DANIEL H. PRESENT,*,‡ PAUL RUTGEERTS,* JURGEN SCHOLMERICH,* EDUARD F. STANGE,* and LLOYD R. SUTHERLAND* *The Clinical Trials Task Force of the International Organization of Inflammatory Bowel Disease (IOIBD), ‡The Clinical Alliance of the Crohn’s and Colitis Foundation of America, the §Clinical Network of the Crohn’s and Colitis Foundation of Canada, and the \Groupe d’Etude Therapeutique des Affections Inflammatoires Digestives. See Appendix I for institutional affiliations for each author and for the complete membership of the IOIBD Clinical Trials Task Force
Structural basis for substrate selection by the translocation and assembly module of the β‐barrel assembly machinery

The assembly of proteins into bacterial outer membranes is a key cellular process that we are only beginning to understand, mediated by the β‐barrel assembly machinery (BAM). Two crucial elements of that machinery are the core BAM complex and the translocation and assembly module (TAM), with each containing a member of the Omp85 superfamily of proteins: BamA in the BAM complex, TamA in the TAM. Here, we used the substrate protein FimD as a model to assess the selectivity of substrate interactions for the TAM relative to those of the BAM complex. A peptide scan revealed that TamA and BamA bind the β‐strands of FimD, and do so selectively. Chemical cross‐linking and molecular dynamics are consistent with this interaction taking place between the first and last strand of the TamA barrel domain, providing the first experimental evidence of a lateral gate in TamA: a structural element implicated in membrane protein assembly. We suggest that the lateral gates in TamA and BamA provide different environments for substrates to engage, with the differences observed here beginning to address how the TAM can be more effective than the BAM complex in the folding of some substrate proteins.
The CysB motif of Rev3p involved in the formation of the four‐subunit DNA polymerase ζ is required for defective‐replisome‐induced mutagenesis

Eukaryotic DNA replication is performed by high‐fidelity multi‐subunit replicative B‐family DNA polymerases (Pols) α, δ and ɛ. Those complexes are composed of catalytic and accessory subunits and organized in multicomplex machinery: the replisome. The fourth B‐family member, DNA polymerase zeta (Pol ζ), is responsible for a large portion of mutagenesis in eukaryotic cells. Two forms of Pol ζ have been identified, a hetero‐dimeric (Pol ζ2) and a hetero‐tetrameric (Pol ζ4) ones and recent data have demonstrated that Pol ζ4 is responsible for damage‐induced mutagenesis. Here, using yeast Pol ζ mutant defective in the assembly of the Pol ζ four‐subunit form, we show in vivo that [4Fe‐4S] cluster in Pol ζ catalytic subunit (Rev3p) is also required for spontaneous (wild‐type cells) and defective‐replisome‐induced mutagenesis – DRIM (pol3‐Y708A, pol2‐1 or psf1‐100 cells), when cells are not treated with any external damaging agents.
Needle core biopsy of the breast

Abstract The benefits of preoperative diagnosis in breast cancer are now well established and include appropriate planning of operating lists and patient involvement in therapeutic options. The use of intraoperative frozen section is thus considered by many now to be unacceptable and preoperative diagnostic methods have replaced its use. These include fine needle aspiration cytology and needle core biopsy. We describe in this manuscript the basic principles of needle core biopsy use and recommendations for reporting of these samples into five diagnostic categories as recommended by the National Health Service Breast Screening Programme in the UK. In addition, we address problem areas and potential pitfalls in needle core biopsy diagnosis and describe some of the more common difficulties that the pathologist may encounter. Finally, we briefly describe alternative uses for core biopsy including the potential evaluation of prognostic factors such as histological grade and predictive factors such as oestrogen receptor.
Efficacy and safety of therapy with metformin plus pioglitazone in the treatment of patients with type 2 diabetes: a double-blind, placebo-controlled, clinical trial

ABSTRACT Objective: To assess the efficacy and safety of combination therapy with pioglitazone and metformin in Japanese patients with type 2 diabetes. Research design and methods: During a 12-week observation period 236 patients were treated with metformin 500 or 750 mg/day. 169 patients with a confirmed HbA1c level ≥ 6.5% were randomized (stratified according to metformin dosage) to receive pioglitazone 15 mg/day for 12 weeks then increased to 30 mg/day for a further 16 weeks (n = 83), or placebo (n = 86). Outcome measures included HbA1c, fasting blood glucose (FBG), percentage of patients achieving HbA1c < 6.5%, lipid profile, and other metabolic parameters. Results: Mean HbA1c was reduced by 0.67% in patients receiving pioglitazone plus metformin versus an increase of 0.25% in those receiving metformin alone (p < 0.0001). After 8 weeks’ treatment and until the end of the study, HbA1c was significantly lower with pioglitazone plus metformin and more patients in this group achieved an HbA1c < 6.5% (38.6% vs. 8.1%; p < 0.0001). FBG was also reduced by a significantly greater amount in patients receiving pioglitazone plus metformin compared with metformin monotherapy (−20.5 vs. 1.9 mg/dl; p < 0.0001). Combination therapy was associated with significantly increased HDL-cholesterol, total cholesterol, and adiponectin, and significantly decreased levels of fasting insulin, free fatty acids, and homeostasis model assessment insulin resistance (HOMA-R) compared with metformin monotherapy. Overall, combination therapy and monotherapy were equally well tolerated and the incidence of adverse effects ‘possibly’ related to therapy was 15.7% and 11.6% (p = 0.505), respectively. Edema occurred slightly more often in the combination group (6.0 vs. 1.2%). Conclusion: Pioglitazone plus metformin significantly improved glycemic control (HbA1c and FBG), and markers associated with increased insulin resistance and cardiovascular risk compared with metformin monotherapy. Clinical trial registration number: UMIN 000001110.
Can audiovisual presentations be used to provide health education at primary health care facilities in South Africa?

This study assessed the feasibility and potential effectiveness of using audiovisual presentations in the waiting rooms of busy South African primary health care clinics, to educate patients about STD prevention and treatment. A 24-minute episode of South Africa's popular soap opera, Soul City was played continuously during three consecutive days in the clinic waiting areas. The storyline of the episode chosen was intended to convey key health messages regarding the prevention and treatment of STDs. The research was conducted at four primary health care clinics serving large, poor peri-urban townships in South Africa. Observations of patient behaviour were made, and a random selection of patients were interviewed on exit. A focus-group discussion was held with all of the clinic staff at each clinic site, to assess staff atti tudes towards the use of such audiovisual presentations as part of their future routine duties. The mean proportion of patients who were observed watching the video at any one time varied from 34 to 64 per cent at all four clinics. Based on exit inter views, the presentation was seen by 88.2 per cent of patients attending all four clinics, and its STD content was recognised by 91.5 per cent of those who had seen it. Over 90 per cent of patients found the presentation helpful and interesting. Clinic staff described the use of video-mediated education as a solution to the problem of inad equate health education, and there was unanimous support for it. In future, it will be important to evaluate whether such audiovisual presentations can be effective in improving patients' knowledge and attitudes, and changing their behaviour, without compromising important interactions between clinicians and patients.
The bacterial effector DspA/E is toxic in Arabidopsis thaliana and is required for multiplication and survival of fire blight pathogen.

The type III effector DspA/E is an essential pathogenicity factor of the phytopathogenic bacterium Erwinia amylovora. We showed that DspA/E was required for transient bacterial growth in nonhost Arabidopsis thaliana leaves, as an E. amylovora dspA/E mutant was unable to grow. We expressed DspA/E in A. thaliana transgenic plants under the control of an oestradiol-inducible promoter, and found that DspA/E expressed in planta restored the growth of a dspA/E mutant. DspA/E expression in these transgenic plants led to the modulation by at least two-fold of the expression of 384 genes, mostly induced (324 genes). Both induced and repressed genes contained high proportions of defence genes. DspA/E expression ultimately resulted in plant cell death without requiring a functional salicylic acid signalling pathway. Analysis of A. thaliana transgenic seedlings expressing a green fluorescent protein (GFP):DspA/E fusion indicated that the fusion protein could only be detected in a few cells per seedling, suggesting the degradation or absence of accumulation of DspA/E in plant cells. Consistently, we found that DspA/E repressed plant protein synthesis when injected by E. amylovora or when expressed in transgenic plants. Thus, we conclude that DspA/E is toxic to A. thaliana: it promotes modifications, among which the repression of protein synthesis could be determinant in the facilitation of necrosis and bacterial growth.
Hydroxychloroquine for subglottic stenosis: A novel therapy in the battle for air

Upper airway obstruction due to subglottic edema and granulation tissue proliferation may cause severe morbidity and may be life threatening. Hydroxychloroquine interferes with antigen processing by means of raising lysosomal pH and immune response modulation. Herein, we present the outcome of a steroid‐sparing treatment using hydroxychloroquine in an 80‐year‐old man with acquired subglottic stenosis and steroid dependency. Twice daily oral hydroxychloroquine at 2 mg/kg/day allowed cessation of systemic steroids without recurrence of the stenosis. Successful weaning of the hydroxychloroquine took place over a 5‐month period. Laryngoscope, 2010