Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of adenylate kinase. The "essential lysine" helps to orient the phosphates and the active site residues to proper conformations.

Although how Lys21 interacts with the substrate MgATP of muscle adenylate kinase (AK) can now be deduced from the crystal structure of Escherichia coli AK.MgAP5A [P1,P5-bis(5'-adenosyl) pentaphosphate] [Müller, C. W. , & Schulz, G. E. (1992) J. Mol. Biol. 224, 159-177], its contribution to catalysis has not yet been demonstrated by functional studies since the proton NMR of the K21M mutant was shown to be perturbed significantly [Tian, G. , Yan. , H. , Jiang, R. -T. , Kishi, F. , Nakazawa, A. , & Tsai, M. -D. (1990) Biochemistry 29, 4296-4304]. We therefore undertook further structural and functional analyses of a conservative mutant K21R and a nonconservative mutant K21A. In addition to kinetic analyses, the structures of the mutants were analyzed by one- and two-dimensional proton NMR spectroscopy and (1H, 15N) heteronuclear multiple-quantum coherence (HMQC) experiments. Detailed assignments were performed in reference to the total backbone assignments of the WT AK.MgAP5A complex [Byeon, I. -J. L. , Yan, H. , Edison, A. S. , Mooberry, E. S. , Abildgaard, F. , Markley, J. L. , & Tsai, M. -D. (1993) Biochemistry 32, 12508-12521]. The analysis showed that the residues located near the active site (Gly15, Thr23, Arg97, Gln101, Arg128, Arg132, Asp140, Asp141, and Tyr153) exhibit greater changes in 1H-15N chemical shifts. Finally, two-dimensional 31P-31P COSY experiments were used to examine the effects of the lysine side chain on the phosphate groups in the bound AP5A. Our data have led to the following conclusions independent of the crystal structure: (i) Because the perturbations in the conformation of the mutants are not global and are mainly localized at active site residues and Tyr153, the side chain of Lys21 can be concluded to stabilize the transition state in the catalysis of AK by up to 7 kcal/mol on the basis of the 10(5)-fold decreases in the kcat/Km of mutants. (ii) The results of 31P NMR analyses suggest that Lys21 functions by orienting the triphosphate chain of MgATP to a proper conformation required for catalysis. (iii) The interaction between Lys21 and the phosphate chain in turn dictates the interactions between the substrates and the active site residues. In the K21R.MgATP complex, the NH chemical shifts of many of the active site residues are perturbed. (iv) The catalytic functions of Lys21 cannot be replaced by a conservative residue arginine. In addition, since K21A and K21R behave similarly, the catalytic function of Lys21 should not be merely a charge effect.
Effects of an Invasive Plant on Population Dynamics in Toads

When populations decline in response to unfavorable environmental change, the dynamics of their population growth shift. In populations that normally exhibit high levels of variation in recruitment and abundance, as do many amphibians, declines may be difficult to identify from natural fluctuations in abundance. However, the onset of declines may be evident from changes in population growth rate in sufficiently long time series of population data. With data from 23 years of study of a population of Fowler's toad (Anaxyrus [ = Bufo] fowleri) at Long Point, Ontario (1989–2011), we sought to identify such a shift in dynamics. We tested for trends in abundance to detect a change point in population dynamics and then tested among competing population models to identify associated intrinsic and extrinsic factors. The most informative models of population growth included terms for toad abundance and the extent of an invasive marsh plant, the common reed (Phragmites australis), throughout the toads’ marshland breeding areas. Our results showed density‐dependent growth in the toad population from 1989 through 2002. After 2002, however, we found progressive population decline in the toads associated with the spread of common reeds and consequent loss of toad breeding habitat. This resulted in reduced recruitment and population growth despite the lack of significant loss of adult habitat. Our results underscore the value of using long‐term time series to identify shifts in population dynamics coincident with the advent of population decline.
Improved HF183 Quantitative Real-Time PCR Assay for Characterization of Human Fecal Pollution in Ambient Surface Water Samples

ABSTRACT Quantitative real-time PCR (qPCR) assays that target the human-associated HF183 bacterial cluster within members of the genus Bacteroides are among the most widely used methods for the characterization of human fecal pollution in ambient surface waters. In this study, we show that a current TaqMan HF183 qPCR assay (HF183/BFDrev) routinely forms nonspecific amplification products and introduce a modified TaqMan assay (HF183/BacR287) that alleviates this problem. The performance of each qPCR assay was compared in head-to-head experiments investigating limits of detection, analytical precision, predicted hybridization to 16S rRNA gene sequences from a reference database, and relative marker concentrations in fecal and sewage samples. The performance of the modified HF183/BacR287 assay is equal to or improves upon that of the original HF183/BFDrev assay. In addition, a qPCR chemistry designed to combat amplification inhibition and a multiplexed internal amplification control are included. In light of the expanding use of PCR-based methods that rely on the detection of extremely low concentrations of DNA template, such as qPCR and digital PCR, the new TaqMan HF183/BacR287 assay should provide more accurate estimations of human-derived fecal contaminants in ambient surface waters.
The progressive pathway of microalbuminuria: from early marker of renal damage to strong cardiovascular risk predictor

There is clear evidence that urinary albumin excretion levels, even below the cut-off values currently used to diagnose microalbuminuria, are associated with an increased risk of cardiovascular events. The relationships of microalbuminuria with a variety of risk factors, such as hypertension, diabetes and metabolic syndrome and with several indices of subclinical organ damage, may contribute, at least in part, to explain the enhanced cardiovascular risk conferred by microalbuminuria. Nonetheless, several studies showed that the association between microalbuminuria and cardiovascular disease remains when all these risk factors are taken into account in multivariate analyses. Therefore, the exact pathophysiological mechanisms explaining the association between microalbuminuria and cardiovascular risk remain incompletely understood. The simple search for microalbuminuria in hypertensive patients may enable the clinician to better assess absolute cardiovascular risk, and its identification may induce physicians to encourage patients to make healthy lifestyle changes and perhaps would prompt to more aggressive modification of standard cardiovascular risk factors.
Mycoplasma pneumoniae cytadherence: unravelling the tie that binds

Mycoplasma pneumoniae is the leading cause of pneumonia in older children and young adults. Mycoplasma adherence to the respiratory epithelium (cytadherence) is required for colonization and pathogenesis. Although considered to be among the smallest and simplest known prokaryotes, this cell‐wall‐less bacterium possesses a highly differentiated terminal structure that is thought to be functional in mycoplasma cell division, gliding motility, and cytadherence. Mutant analysis has identified mycoplasma proteins associated with cytadherence, and revealed novel regulatory features. Ultrastructural and biochemical studies have established the subcellular location and interaction of key components, several of which are phosphorylated by ATP‐dependent kinase(s) in a manner that is responsive to changing nutritional conditions. This review summarizes recent progress in defining the composition, organization and regulation of the attachment organelle. What emerges is a picture of M. pneumoniae cytadherence as a multifactorial process that extends well beyond adhesin‐receptor recognition.
A Novel Bacterial Enzyme with d-Glucuronyl C5-epimerase Activity*

Background: d-Glucuronyl C5-epimerase activity is essential in glycosaminoglycan biosynthesis. Results: This is the first demonstration of a bacterial enzyme having d-glucuronyl C5-epimerase activity. Conclusion: This novel enzyme, probably involved in bacterial capsular polysaccharide biosynthesis, shows catalytic properties similar to murine heparan sulfate d-glucuronyl C5-epimerase. Significance: Increased insight into bacterial cell wall biosynthesis and a potential biotechnological tool applicable in chemo-enzymatic synthesis of industrially relevant heparin-like glycosaminoglycans are provided. Glycosaminoglycans are biologically active polysaccharides that are found ubiquitously in the animal kingdom. The biosynthesis of these complex polysaccharides involves complicated reactions that turn the simple glycosaminoglycan backbone into highly heterogeneous structures. One of the modification reactions is the epimerization of d-glucuronic acid to its C5-epimer l-iduronic acid, which is essential for the function of heparan sulfate. Although l-iduronic acid residues have been shown to exist in polysaccharides of some prokaryotes, there has been no experimental evidence for the existence of a prokaryotic d-glucuronyl C5-epimerase. This work for the first time reports on the identification of a bacterial enzyme with d-glucuronyl C5-epimerase activity. A gene of the marine bacterium Bermanella marisrubri sp. RED65 encodes a protein (RED65_08024) of 448 amino acids that has an overall 37% homology to the human d-glucuronic acid C5-epimerase. Alignment of this peptide with the human and mouse sequences revealed a 60% similarity at the carboxyl terminus. The recombinant protein expressed in Escherichia coli showed epimerization activity toward substrates generated from heparin and the E. coli K5 capsular polysaccharide, thereby providing the first evidence for bacterial d-glucuronyl C5-epimerase activity. These findings may eventually be used for modification of mammalian glycosaminoglycans.
Causes and presenting features in 85 consecutive patients with hypersensitivity pneumonitis.

OBJECTIVE To assess the current spectrum of causes and clinical features associated with hypersensitivity pneumonitis (HP). PATIENTS AND METHODS We studied consecutive patients with HP diagnosed at the Mayo Clinic in Rochester, Minn, from January 1, 1997, through December 31, 2002. Diagnostic criteria for HP included the following: (1) presence of respiratory symptoms, (2) radiologic evidence of diffuse lung disease, (3) known exposure or a positive serologic test result to an inciting antigen, and (4) no other identifiable cause for the lung disease. If there was no identifiable inciting antigen, 1 of the following 2 criteria was required: (1) lung biopsy specimen that demonstrated features of HP or (2) bronchoalveolar lavage lymphocytosis and high-resolution computed tomographic evidence of ground-glass opacities or centrilobular nodules bilaterally. RESULTS The mean +/- SD age of the 85 study patients was 53 +/- 14 years; 53 patients (62%) were women. Only 2 patients (2%) were current smokers. Chronic (> or = 4 months) respiratory symptoms were present in 66 patients (78%). Histopathologic confirmation was obtained in 64 patients (75%). The cause was identified in 64 patients (75%), and the most common causes were avian antigens (34%) and Mycobacterium avium complex in hot tub water (21%). Farmer's lung disease accounted for 11% of cases, and an additional 9% were related to household mold exposure. The inciting antigen was not identifiable in 25% of patients. CONCLUSION Most patients with HP seen at this tertiary care referral center in the Midwest region of the United States had chronic HP, and the most common causes were exposure to birds and exposure to hot tubs.
Transient temperature rise in a mouse due to low-frequency regional hyperthermia

A refined nonlinear heat transfer model of a mouse has been developed to simulate the transient temperature rise in a neoplastic tumour and neighbouring tissue during regional hyperthermia using a 150 kHz inductive coil. In this study, we incorporate various bio-energetic enhancements to the heat transfer equation and numerical validations based on experimental findings for the mouse, in terms of nonlinear metabolic heat production, homeothermy, blood perfusion parameters, thermoregulation, psychological and physiological effects. The discretized bio-heat transfer equation has been validated with the commercial software FEMLAB on a canonical multi-sphere object before applying the scheme to the inhomogeneous mouse voxel phantom. The time-dependent numerical results of regional hyperthermia of mouse thigh have been compared with the available experimental temperature results with only a few small disparities. During the first 20 min of local unfocused heating, the temperature in the tumour and the surrounding tissue increased by around 7.5 °C. The objective of this preliminary study was to develop a validated electrothermal numerical scheme for inductive hyperthermia of a small mammal with the intention of expanding the model into a complete numerical solution involving ferromagnetic nanoparticles for targeted heating of tumours at low frequencies. In addition, the numerical scheme herein could assist in optimizing and tailoring of focused electromagnetic fields for hyperthermia.
Differences in Audit Pricing between Voluntary and Mandatory Audits

Purpose Despite the extensive research on the determinants of audit pricing in both public and private settings, there is a lack of research about the differences in audit fees between voluntary audits and mandatory audits. The purpose of this paper is to address this gap. Design/methodology/approach First, a theoretical framework is developed to justify differences in audit pricing between voluntary and mandatory audits. Next, using a sample of Spanish private small and medium enterprises (SMEs) running from 2009 to 2014, the authors empirically test whether the fees charged for voluntary audits differ from those charged for mandatory ones. The authors also examine whether the premium observed among large auditors is persistent in the SME setting, and whether this premium differs depending on whether the audits are voluntary or mandatory. Findings Although a preliminary analysis does not report significant differences in pricing between voluntary and mandatory audits, additional analyses using samples restricted by company size show that voluntary audits are charged with a premium. The authors observe a premium related to large auditors, and find no significant differences in the audit pricing of Big 4 auditors depending on the mandatory/voluntary nature of the audit, but the premium associated with Middle-Tier auditors disappears in the voluntary setting. Originality/value This paper contributes to the previous literature by introducing the examination of differences in audit pricing between voluntary and mandatory audits. As far as the authors know, this is the first study to examine the differences in audit pricing between voluntary and mandatory audits. It also elaborates on studies on audit pricing in SMEs.
Stratification of prostate-specific antigen level and results of transrectal ultrasonography and digital rectal examination as predictors of positive prostate biopsy.

OBJECTIVE To determine which of several variables--age, serum level of prostate-specific antigen (PSA), findings of transrectal ultrasonography (TRUS) and findings of digital rectal examination (DRE)--are the best predictors of positive prostate biopsy results. SETTING An urban, university-affiliated tertiary care hospital. PATIENTS a cohort of 1330 consecutive men referred to the diagnostic imaging department for TRUS and TRUS-guided prostate biopsy. Each patient was referred after examination by a urologist because of clinical suspicion of prostate cancer. METHODS All of the men had undergone prior determination of serum level of PSA. Repeat DRE was performed at the time of imaging. The variables age, PSA level, TRUS findings and DRE findings were tested aline and in combination as predictors of positive biopsy results by means of logistic regression analysis. A summary of percentage risk for positive biopsy results was constructed for each combination of statistically significant variables, stratified for age. RESULTS Cancer was detected in 541 men (40.7%). A strong correlation was observed between serum PSA level and the likelihood of positive biopsy result (p < 0.001). Of 402 men with normal age-specific PSA, 109 (27.1%) had positive biopsy results. Of 403 men with PSA of 10 ng/mL or more, 233 (57.8%) had cancer. The level of serum PSA was also related to the number of prostate sextants harbouring cancer (p < 0.001). TRUS findings at the time of biopsy were a strong predictor of cancer of the PSA level was abnormal (p < 0.001). DRE results alone did not correlate with positive biopsy results, regardless of age, PSA level of TRUS findings. CONCLUSIONS Men in whom there is a clinical concern for prostate cancer should undergo prostate biopsy if there is any elevation of age-specific PSA, particularly if the findings of TRUS are also abnormal. Because DRE alone was not predictive of biopsy outcome, algorithms for prostate cancer detection that rely on abnormal DRE results to identify men who should undergo biopsy will miss a significant number of cancers.
Oral health students as reflective practitioners: changing patterns of student clinical reflections over a period of 12 months.

PURPOSE The purpose of this study was to determine the levels of reflection shown by bachelor of oral health students in relation to their clinical and professional practice. METHODS Reflective learning was embedded as a topic in the oral health curriculum within the discipline of dental hygiene practice. Reflective journal writing was integrated with clinical practice and linked with assessment requirements. Students' reflective writing was analyzed thematically to elucidate levels of reflection based on Boud's 4 Rs of Reflection (review, react, relate and respond) over a period of 12 months. Differences in the levels of reflection at different time intervals were examined. RESULTS Students' ability to critically reflect improved over the period of 12 months. The predominant level of reflection changed from primarily descriptive and superficial at the start of the academic year to primarily critical and relational by the end. As expected, the highest level of critical reflection (respond) occurred infrequently, although it became more frequent as the academic year progressed. CONCLUSION Bachelor of oral health students do reflect critically. Regular reflective writing contributed to the development of critical reflective skills in the context of clinical and professional development.
Blockchain and Digital Currency in the World of Finance

High-tech enables payment evolution and global competition. The ambiguities surround- ing of the digital currency still leave enough space for the analysis of its unreserved acceptance, trust and anticipation, which are the main driver for the spread of the network. Banks should carefully consider the technology underlying these cryptocurrencies as a potential generic new way of transferring ownership of the value over the long term. The chapter provides an analysis of the use of cryptocurrencies in general, especially Bitcoin as the technology adoption in the presence of network externalities. The objective attitude is the future of the digital currency in the moment is still unsolved issue due to the existence of “critical mass”. Further, the chapter explores financial privacy which is very sensitive issue in using digital currency (or cryptocurrency) and discuss about private choices versus political rules. The research has shown that the future of cryptocurrencies can be bright if some institutional-formal conditions are met due to the fact that success evolution of e-money requires building safety payments through three criteria–standardization, com- patibility and innovation.
Benefits of Prenatal Taurine Supplementation in Preventing the Onset of Acute Damage in the Mdx Mouse

Introduction: Duchenne Muscular Dystrophy (DMD) is a debilitating muscle wasting disorder with no cure. Safer supplements and therapies are needed to improve the severity of symptoms, as severe side effects are associated with the only effective treatment, corticosteroids. The amino acid taurine has shown promise in ameliorating dystrophic symptoms in mdx mice, an animal model of DMD, however little work is in 21-28 (d)ay animals, the period of natural peak damage. Methods: This study compares the effect of prenatal taurine supplementation on tibialis anterior (TA) in situ contractile function, histopathological characteristics and the abundance of Ca2+-handling as well as pathologically relevant proteins in non-exercised mdx mice at 28 and 70 d. Results: Supplementation elevated TA taurine content by 25% (p<0.05), ameliorated in situ specific force by 60% (p<0.05) and improved histological characteristics in 28 d mdx mice; however no benefit was seen in 70 d mice, where background pathology was initially stable. Age specific effects in SERCA1, calsequestrin 1 (CSQ1), CSQ2, utrophin and myogenin protein abundances were seen between both 28 and 70 d mdx and mdx taurine-supplemented mice. Discussion: Considering these findings and that taurine is a relatively cost effective, readily accessible and side effect free dietary supplement, we propose further investigation into taurine supplementation during pregnancy in a protective capacity, reminiscent of folate in the prevention of spinal bifida.
Low-Dose Cyclophosphamide Improves Survival in a Murine Treatment Model of Sepsis

ABSTRACT Sepsis is a complex medical condition characterized by a systemic inflammatory response in the setting of infection. We hypothesized that combining antibiotics plus an immunosuppressant would protect against the morbidity and mortality of polymicrobial sepsis in mice better than would antibiotics alone. We used a murine cecal-ligation-and-puncture model in which mice were treated either with imipenem plus cyclophosphamide or imipenem alone. Titration to a low cyclophosphamide dose revealed that combination therapy increased survival by 20% compared with imipenem alone (56% vs. 36%, P < 0.001). To investigate the mechanism by which combination therapy did this, we reviewed quantitative and qualitative markers of the systemic immune response, end-organ damage, and the local immune response at the site of injury. Cyclophosphamide treatment was not associated with depletion of peripheral leukocytes or differences in pulmonary damage. However, mice that received combination therapy had higher plasma granulocyte colony-stimulating factor levels than did those treated with antibiotics alone. In addition, mice treated with cyclophosphamide had higher levels of bacterial colonization in intestinal Peyer’s patch lymph nodes at 72 h after the septic insult. Intraperitoneal macrophage phenotypes and phagocytosis activity did not differ between groups. We conclude that the inflammatory response plays a significant role in the mortality of polymicrobial sepsis and that the regulation of this element is both feasible and beneficial in this disease model.