Bacterial genotyping by 16S rRNA mass cataloging

BACKGROUND: It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. Because mass spectrometry is extremely rapid and widely available such techniques offer significant advantages in some applications. A key element in favor of mass spectrometric analysis of RNA fragmentation patterns is that a reference database for analysis of the results can be generated from sequence information. In contrast to hybridization approaches, the genetic affinity of any unknown isolate can in principle be determined within the context of all previously sequenced 16S rRNAs without prior knowledge of what the organism is. In contrast to the original RNase T(1 )cataloging method, when digestion products are analyzed by mass spectrometry, products with the same base composition cannot be distinguished. Hence, it is possible that organisms that are not closely related (having different underlying sequences) might be falsely identified by mass spectral coincidence. We present a convenient spectral coincidence function for expressing the degree of similarity (or distance) between any two mass-spectra. Trees constructed using this function are consistent with those produced by direct comparison of primary sequences, demonstrating that the inherent degeneracy in mass spectrometric analysis of RNA fragments does not preclude correct organism identification. RESULTS: Neighbor-joining trees for important bacterial pathogens were generated using distances based on mass spectrometric observables and the spectral coincidence function. These trees demonstrate that most pathogens will be readily distinguished using mass spectrometric analyses of RNA digestion products. A more detailed, genus-level analysis of pathogens and near relatives was also performed, and it was found that assignments of genetic affinity were consistent with those obtained by direct sequence comparisons. Finally, typical values of the coincidence between organisms were also examined with regard to phylogenetic level and sequence variability. CONCLUSION: Cluster analysis based on comparison of mass spectrometric observables using the spectral coincidence function is an extremely useful tool for determining the genetic affinity of an unknown bacterium. Additionally, fragmentation patterns can determine within hours if an unknown isolate is potentially a known pathogen among thousands of possible organisms, and if so, which one

How does financial reporting quality relate to investment efficiency?

Prior evidence that higher-quality financial reporting improves capital investment efficiency leaves unaddressed whether it reduces over- or under-investment. This study provides evidence of both in documenting a conditional negative (positive) association between financial reporting quality and investment for firms operating in settings more prone to over-investment (under-investment). Firms with higher financial reporting quality also are found to deviate less from predicted investment levels and show less sensitivity to macro-economic conditions. These results suggest that one mechanism linking reporting quality and investment efficiency is a reduction of frictions such as moral hazard and adverse selection that hamper efficient investment

Conflict of interest reforms and analysts’ research biases

This study examines the consequences of the series of reforms targeting investment banking–related conflicts of interest. The authors compare and contrast optimism biases in analysts’ stock recommendations and earnings forecasts across different types of analyst firms in the postreform period of 2004 to 2007 versus the prereform period of 1998 to 2001. The authors document a significant reduction in the relative optimism of sanctioned investment bank analysts’ stock recommendations but not in their earnings forecasts. Moreover, the authors find little change in the profitability of their stock recommendations but detect a drop in the accuracy of earnings forecasts made by investment bank analysts. In sum, the reforms achieve the objective of mitigating the apparent optimism in investment bank stock recommendations, but they do not provide benefit to investors in terms of more profitable recommendations or more accurate earnings forecasts.Guan appreciates research start-up grant from City University of Hong Kong. Lu and Wong acknowledge financial support from the Rotman School of Management at the University of Toronto and the Social Sciences and Humanities Research Council of Canada

SHIELD: Comparing Gas and Star Formation in Low Mass Galaxies

We analyze the relationships between atomic, neutral hydrogen (HI) and star formation (SF) in the 12 low-mass SHIELD galaxies. We compare high spectral (~0.82 km/s/channel) and spatial resolution (physical resolutions of 170 pc - 700 pc) HI imaging from the VLA with H\alpha and far-ultraviolet imaging. We quantify the degree of co-spatiality between star forming regions and regions of high HI column densities. We calculate the global star formation efficiencies (SFE, $\Sigma_{\rm SFR}$ / $\Sigma_{\rm HI}$), and examine the relationships among the SFE and HI mass, HI column density, and star formation rate (SFR). The systems are consuming their cold neutral gas on timescales of order a few Gyr. While we derive an index for the Kennicutt-Schmidt relation of N ~ 0.68 $\pm$ 0.04 for the SHIELD sample as a whole, the values of N vary considerably from system to system. By supplementing SHIELD results with those from other surveys, we find that HI mass and UV-based SFR are strongly correlated over five orders of magnitude. Identification of patterns within the SHIELD sample allows us to bin the galaxies into three general categories: 1) mainly co-spatial HI and SF regions, found in systems with highest peak HI column densities and highest total HI masses, 2) moderately correlated HI and SF regions, found in systems with moderate HI column densities, and 3) obvious offsets between HI and SF peaks, found in systems with the lowest total HI masses. SF in these galaxies is dominated by stochasticity and random fluctuations in their ISM

SHIELD: Neutral Gas Kinematics and Dynamics

We present kinematic analyses of the 12 galaxies in the "Survey of HI in Extremely Low-mass Dwarfs" (SHIELD). We use multi-configuration interferometric observations of the HI 21cm emission line from the Karl G. Jansky Very Large Array (VLA) to produce image cubes at a variety of spatial and spectral resolutions. Both two- and three-dimensional fitting techniques are employed in an attempt to derive inclination-corrected rotation curves for each galaxy. In most cases, the comparable magnitudes of velocity dispersion and projected rotation result in degeneracies that prohibit unambiguous circular velocity solutions. We thus make spatially resolved position-velocity cuts, corrected for inclination using the stellar components, to estimate the circular rotation velocities. We find circular velocities <30 km/s for the entire survey population. Baryonic masses are calculated using single-dish HI fluxes from Arecibo and stellar masses derived from HST and Spitzer imaging. Comparison is made with total dynamical masses estimated from the position-velocity analysis. The SHIELD galaxies are then placed on the baryonic Tully-Fisher relation. There exists an empirical threshold rotational velocity <15 km/s, below which current observations cannot differentiate coherent rotation from pressure support. The SHIELD galaxies are representative of an important population of galaxies whose properties cannot be described by current models of rotationally-dominated galaxy dynamics

Metastasis to the gluteus maximus muscle from renal cell carcinoma with special emphasis on MRI features

<p>Abstract</p> <p>Background</p> <p>The skeletal muscle is an unusual site for metastasis from renal cell carcinoma (RCC). Metastatic RCC must be differentiated from benign primary soft-tissue tumors because aggressive surgical resection is necessary.</p> <p>Case presentation</p> <p>We present the case of a 65-year-old man with metastatic RCC in the gluteus maximus muscle (3.8 cm in diameter) found on enhanced computed tomography (CT) 6 years after nephrectomy. Retrospectively, the small mass (1 cm in diameter) was overlooked 5 years earlier on enhanced CT. Because the growth of the lesion was slow, benign tumor was a differential diagnosis. However, magnetic resonance imaging (MRI) showed that the mass had high-signal intensity on T1- and T2-weighted images (WIs) compared to that of skeletal muscle, with mild enhancement by Gadolinium. The MRI features were unusual for most soft-tissue tumors having low-signal intensity on T1-WI and high-signal intensity on T2-WI. Therefore, under a diagnosis of metastatic RCC, the lesion was resected together with the surrounding skeletal muscle. The histology was confirmed to be metastatic RCC.</p> <p>Conclusion</p> <p>MRI features of metastatic RCC may be beneficial in differentiating it from primary soft-tissue tumor.</p

Conflicts of Interest in Sell-side Research and The Moderating Role of Institutional Investors

Because sell-side analysts are dependent on institutional investors for performance ratings and trading commissions, we argue that analysts are less likely to succumb to investment banking or brokerage pressure in stocks highly visible to institutional investors. Examining a comprehensive sample of analyst recommendations over the 1994-2000 period, we find that analysts’ recommendations relative to consensus are positively associated with investment banking relationships and brokerage pressure, but negatively associated with the presence of institutional investor owners. The presence of institutional investors is also associated with more accurate earnings forecasts and more timely re-ratings following severe share price falls

Applying Benford’s law to detect accounting data manipulation in the banking industry

We utilise Benford’s Law to test if balance sheet and income statement data broadly used to assess bank soundness were manipulated prior to and also during the global financial crisis. We find that all banks resort to loan loss provisions to manipulate earnings and income upwards. Distressed institutions that have stronger incentives to conceal their financial difficulties resort additionally to manipulating loan loss allowances and non-performing loans downwards. Moreover, manipulation is magnified during the crisis and expands to encompass regulatory capital