Northern Steamship Company: The depreciation problem in the nineteenth century

In 1889 a New Zealand company had to write down its paid-up capital by 27 percent, because, the Chairman stated, previous management had failed to allow for depreciation as an expense. An investigation was conducted to see if this capital reduction could have been avoided had the company followed modern depreciation policy. This revealed that the failure to depreciate adequately was not the main cause of the capital reduction, other firms followed the same practice and contemporary English legislation did not permit depreciation as a tax deductible item, while United States courts were rejecting depreciation as a valid expense

Inspiratory effort and lung mechanics in spontaneously breathing patients with acute respiratory failure due to COVID-19. A matched control study.

Several physical and biological mechanisms can drive progression between the different phases of lung injury due to SARS-CoV-2 infection, thus modifying the mechanical properties and behavior of COVID-19 over time. In this research letter we have presented the findings of a registered clinical trial aimed at describing and comparing the inspiratory effort (primary outcome) and the breathing pattern of spontaneously breathing patients with ARF in COVID-19 and historically matched non-COVID-19 patients, either candidate to NIV. Moreover, we reported the response to a 2 hours NIV trial in the two groups. Spontaneously breathing COVID-19 at their early onset of acute respiratory failure with indication for NIV showed different mechanical characteristics and breathing pattern when compared with non-COVID-19

Bradyzoite pseudokinase 1 is crucial for efficient oral infectivity of the Toxoplasma gondii tissue cyst.

The tissue cyst formed by the bradyzoite stage of Toxoplasma gondii is essential for persistent infection of the host and oral transmission. Bradyzoite pseudokinase 1 (BPK1) is a component of the cyst wall, but nothing has previously been known about its function. Here, we show that immunoprecipitation of BPK1 from in vitro bradyzoite cultures, 4 days postinfection, identifies at least four associating proteins: MAG1, MCP4, GRA8, and GRA9. To determine the role of BPK1, a strain of Toxoplasma was generated with the bpk1 locus deleted. This BPK1 knockout strain (Δbpk1) was investigated in vitro and in vivo. No defect was found in terms of in vitro cyst formation and no difference in pathogenesis or cyst burden 4 weeks postinfection (wpi) was detected after intraperitoneal (i.p.) infection with Δbpk1 tachyzoites, although the Δbpk1 cysts were significantly smaller than parental or BPK1-complemented strains at 8 wpi. Pepsin-acid treatment of 4 wpi in vivo cysts revealed that Δbpk1 parasites are significantly more sensitive to this treatment than the parental and complemented strains. Consistent with this, 4 wpi Δbpk1 cysts showed reduced ability to cause oral infection compared to the parental and complemented strains. Together, these data reveal that BPK1 plays a crucial role in the in vivo development and infectivity of Toxoplasma cysts

Network-assisted protein identification and data interpretation in shotgun proteomics

Protein assembly and biological interpretation of the assembled protein lists are critical steps in shotgun proteomics data analysis. Although most biological functions arise from interactions among proteins, current protein assembly pipelines treat proteins as independent entities. Usually, only individual proteins with strong experimental evidence, that is, confident proteins, are reported, whereas many possible proteins of biological interest are eliminated. We have developed a clique-enrichment approach (CEA) to rescue eliminated proteins by incorporating the relationship among proteins as embedded in a protein interaction network. In several data sets tested, CEA increased protein identification by 8–23% with an estimated accuracy of 85%. Rescued proteins were supported by existing literature or transcriptome profiling studies at similar levels as confident proteins and at a significantly higher level than abandoned ones. Applying CEA on a breast cancer data set, rescued proteins coded by well-known breast cancer genes. In addition, CEA generated a network view of the proteins and helped show the modular organization of proteins that may underpin the molecular mechanisms of the disease

Parity and Components of the Metabolic Syndrome Among US Hispanic/Latina Women

BACKGROUND: Physiological adaptations occurring across successive pregnancies may increase the risk of adverse cardiovascular health outcomes in later life. METHODS AND RESULTS: The association between parity and metabolic syndrome was examined among 7467 Hispanic/Latina women of diverse backgrounds, aged 18 to 74 years, who participated in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) from 2008 to 2011. Metabolic syndrome components were defined according to American Heart Association/National Heart, Lung, and Blood Institute criteria and included abdominal obesity, elevated triglycerides, low high-density lipoprotein cholesterol, high blood pressure, and elevated fasting glucose. Logistic regression models estimated odds ratios (ORs) adjusting for sociodemographic, behavioral, and reproductive characteristics. At HCHS/SOL baseline, women reported none (21.1%), 1 (19.9%), 2 (25.7%), 3 (18.6%), 4 (8.8%), and ≥ 5 (5.9%) live births. When compared with women with 1 birth, those with 4 births had the highest odds of abdominal obesity (OR, 2.0; 95% confidence interval, 1.5-2.8) and overall metabolic syndrome (OR, 1.4; 95% confidence interval, 1.0-2.0) and those with ≥ 5 births had the highest odds of low high-density lipoprotein cholesterol (OR, 1.5; 95% confidence interval, 1.2-2.0) and elevated fasting glucose (OR, 1.6; 95% confidence interval, 1.1-2.4), after adjusting for age, background, education, marital status, income, nativity, smoking, physical activity, menopause, oral contraceptive use, hormone therapy, and field center. Further adjustment for percent body fat attenuated these associations. No associations were observed between parity and elevated triglycerides or high blood pressure. CONCLUSIONS: Higher parity is associated with an increased prevalence of selected components of the metabolic syndrome among Hispanic/Latina women in the US. High parity among Hispanics/Latinas with a high prevalence of abdominal obesity suggests high risk for metabolic dysregulation

A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

<p>Abstract</p> <p>Background</p> <p>High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate <it>de novo </it>sequencing for identification of post-translational modifications and amino acid polymorphisms.</p> <p>Results</p> <p>In this study, a new <it>de novo </it>sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of <it>Rhodopseudomonas palustris</it>. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of <it>de novo </it>sequenced spectra and the sequencing accuracy.</p> <p>Conclusions</p> <p>Here, we improved <it>de novo </it>sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at <url>http://compbio.ornl.gov/Vonode</url>.</p

<i>Schizosaccharomyces pombe</i> Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex

ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEClike complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation

The EGFR family members sustain the neoplastic phenotype of ALK+ lung adenocarcinoma via EGR1.

In non-small cell lung cancer (NSCLC), receptor tyrosine kinases (RTKs) stand out among causal dominant oncogenes, and the ablation of RTK signaling has emerged as a novel tailored therapeutic strategy. Nonetheless, long-term RTK inhibition leads invariably to acquired resistance, tumor recurrence and metastatic dissemination. In ALK+ cell lines, inhibition of ALK signaling was associated with coactivation of several RTKs, whose pharmacological suppression reverted the partial resistance to ALK blockade. Remarkably, ERBB2 signaling synergized with ALK and contributed to the neoplastic phenotype. Moreover, the engagement of wild-type epidermal growth factor receptor or MET receptors could sustain cell viability through early growth response 1 (EGR1) and/or Erk1/2; Akt activation and EGR1 overexpression prevented cell death induced by combined ALK/RTK inhibition. Membrane expression of ERBB2 in a subset of primary naive ALK+ NSCLC could be relevant in the clinical arena. Our data demonstrate that the neoplastic phenotype of ALK-driven NSCLC relays ‘ab initio' on the concomitant activation of multiple RTK signals via autocrine/paracrine regulatory loops. These findings suggest that molecular and functional signatures are required in de novo lung cancer patients for the design of efficacious and multi-targeted ‘patient-specific' therapies