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Introduction: The United States Medical Licensing Examination (USMLE) Step 1 test evolved into a key metric utilized by program directors (PDs) in assessing candidates for residency. The transition to a USMLE Step 1 binary pass/fail scoring system has resulted in a loss of an important objective assessment. With national movements toward pass/fail systems for clerkship grading and trends toward abandonment of class ranking, assessing residency applications has become increasingly challenging., Methods: The Society of Academic Urologists convened a task force to, in part, assess the perspectives of urology PDs regarding the importance of various aspects of a residency application for predicting clinical performance. An anonymous survey was disseminated to all urology PDs in the US. Perspectives on 11 potential application predictors of clinical performance and demographics were recorded. Descriptive statistics characterized PD responses. Friedman test and pairwise Wilcoxon tests were used to evaluate the relative ranks assigned to application elements by PDs., Results: There was a 60.5% response rate (89/147). Letters of recommendation (LORs) were ranked as the most important predictor, with a mean rank of 2.39, median of 2 (IQR 1-3). Clerkship grades and USMLE Step 1 were comparable and ranked second. Medical school reputation ranked the lowest. There was significant subjective heterogeneity among categories; however, this was less so for LORs, which predominated as the most important factor among application elements ( P < .001)., Conclusions: To our knowledge, this is the largest sample size assessing PD perspectives on application factors that predict clinical performance. The second (clerkship grades) and third (USLME Step 1) most important factors moving toward binary pass/fail systems create an opportunity for actionable change to improve assessment objectivity. Our data demonstrate LORs to be the most important factor of residency applications, making a compelling argument for moving toward a standardized LOR to maximize this tool, mitigate bias, and improve interreviewer reliability.

We demonstrate the generation of extreme-ultraviolet (XUV) free-electron laser (FEL) pulses with time-dependent polarization. To achieve polarization modulation on a femtosecond timescale, we combine two mutually delayed counterrotating circularly polarized subpulses from two cross-polarized undulators. The polarization profile of the pulses is probed by angle-resolved photoemission and above-threshold ionization of helium; the results agree with solutions of the time-dependent Schrödinger equation. The stability limit of the scheme is mainly set by electron-beam energy fluctuations, however, at a level that will not compromise experiments in the XUV. Our results demonstrate the potential to improve the resolution and element selectivity of methods based on polarization shaping and may lead to the development of new coherent control schemes for probing and manipulating core electrons in matter.

Purpose of Review: Currently, the increasing diversity of our society is poorly reflected in the urology workforce. In this review, we sought to address this disparity by highlighting key components involved in forming an academic urology department and training program that is focused on diversity, equity, and inclusion (DEI) as well as recruitment and retention of underrepresented in medicine (URiM) trainees and faculty., Recent Findings: We identified obstacles and provided approaches to enhance the ability of a department in creating a DEI-based curriculum and recruitment strategy with a key focus on understanding and addressing unconscious biases and microaggressions in the workplace. Substantive changes in the level of diversity within the urologic community can be made through the organization of a structured approach to increasing DEI. It starts with a commitment from each department to form achievable goals surrounding early mentorship of URiM students and trainees, an inclusive curriculum that is rooted in DEI, and targeted benchmarks for recruitment and retention of diverse staff., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Objectives: To assess the utility of genomic testing in risk-stratifying Black patients with low and intermediate risk prostate cancer., Methods: We retrospectively identified 63 Black men deemed eligible for active surveillance based on National Comprehensive Cancer Network (NCCN) guidelines, who underwent OncotypeDx Genomic Prostate Score testing between April 2016 and July 2020. Nonparametric statistical testing was used to compare relevant features between patients reclassified to a higher NCCN risk after genomic testing and those who were not reclassified., Results: The median age was 66 years and median pre-biopsy PSA was 7.3. Initial risk classifications were: very low risk: 7 (11.1%), low risk: 24(38.1%), favorable intermediate risk: 31(49.2%), and unfavorable intermediate risk: 1 (1.6%). Overall, NCCN risk classifications after Genomic Prostate Score testing were significantly higher than initial classifications (P=.003, Wilcoxon signed-rank). Among patients with discordant risk designations, 28(28/40, 70%) were reclassified to a higher NCCN risk after genomic testing. A pre-biopsy prostate specific antigen of greater than 10 did not have significantly higher odds of HBR (OR:2.16 [95% CI: 0.64,7.59, P=.2). Of favorable intermediate risk patients, 20(64.5%) were reclassified to a higher NCCN risk. Ultimately, 18 patients underwent definitive treatment., Conclusions: Incorporation of genomic testing in risk stratifying Black men with low and intermediate-risk prostate cancer resulted in overall higher NCCN risk classifications. Our findings suggest a role for increased utilization of genomic testing in refining risk-stratification within this patient population. These tests may better inform treatment decisions on an individualized basis., (Copyright © 2021. Published by Elsevier Inc.)

Introduction: Bladder cancer care has been increasingly concentrated in high-volume metropolitan medical centres (ie, "regionalisation" of care). We aimed to assess the potential role of geographic factors, including facility region and distance to treatment centre, as determinants of neoadjuvant chemotherapy (NAC) delivery in patients with non-metastatic urothelial muscle-invasive bladder cancer (MIBC) using nationally representative data from the United States., Methods: We queried the National Cancer Database to identify patients with cT2-cT4a, N0M0 urothelial MIBC who underwent radical cystectomy (RC) from 2006 to 2015. Patients who received radiation therapy, single-agent chemotherapy, adjuvant chemotherapy or systemic therapies other than multi-agent chemotherapy were excluded. Multivariate logistic regression analysis was performed to identify independent predictors of receiving NAC., Results: A total of 5986 patients met the criteria for inclusion, of whom 1788 (29.9%) received NAC and 4108 received RC alone. Younger age, increased Charlson-Deyo score, increased cT stage, increased annual income, increased distance from cancer treatment centre, treatment at an Academic Research Program or Integrated Network Cancer Program and a later year of diagnosis were independently predictive of NAC receipt. Older age, Medicare insurance and treatment in the East South Central or West South Central regions were independently associated with decreased odds of NAC receipt., Conclusions: Distance to treatment centre and United States geographic region were found to affect the likelihood of NAC receipt independently of other established predictors of success in this quality-of-care metric. Access to transportation and related resources merits consideration as additional pertinent social determinants of health in bladder cancer care., (© 2021 John Wiley & Sons Ltd.)

Purpose: Pathologic upstaging in renal cell carcinoma (RCC) is common and confers a significant risk of poor surgical and survival outcomes. Preoperative predictors of upstaging are of great clinical relevance but empirical evidence specific to racial minorities remains scarce., Methods: National Cancer Database (NCDB) analysis of T3a-specific upstaging among White, African-American, Hispanic and Asian Pacific Islander (API) patients with AJCC cT1N0M0 RCC who underwent partial or radical nephrectomy between 2010 and 2015. Independent preoperative predictors of tumour upstaging were identified using multivariate logistic regression analyses., Results: A total of 81 002 patients met the criteria for inclusion (5.6% T3a-specific upstaging). Increased age, increased Charlson-Deyo comorbidity index, clinical stages cT1b and unspecified cT1, and increased Fuhrman nuclear grade were identified as independent risk factors for upstaging. Independent protective factors for upstaging were younger age, female sex, African-American race and papillary, chromophobe, and unspecified RCC histologic subtypes. Significant risk factors and protective factors within individual racial subgroups were highly consistent with those observed in the overall study sample. All independent factors identified on race-specific subgroup analyses were significant in the same direction relative to the overall study sample. Variables found to be non-significant in the overall study sample remained non-significant across all racial subgroup analyses., Conclusion: The present study of nationally representative data found no clinically significant differences in upstaging risk across individual racial subgroups relative to the overall study sample. Preoperative factors that can be used to predict pT3a-specific tumour upstaging in CT1N0M0 RCC likely persist across different racial groups., (© 2020 John Wiley & Sons Ltd.)

Radical cystectomy (RC) is associated with significant morbidity. Neuraxial analgesia is recommended by enhanced recovery after surgery guidelines, but largely supported by evidence extrapolated from colorectal surgery outcomes. We synthesized current evidence regarding short- and long-term outcomes associated with neuraxial analgesia versus patient controlled non-neuraxial analgesia following RC. PubMed, Embase, and Cochrane databases were searched for relevant studies published up to May 2020. Studies reporting complications, length of stay (LOS), pain score, opioid usage within 72 hours, overall survival, cancer-specific survival, and recurrence rate were included. Of 550 identified studies, 9 met criteria for inclusion. Four studies demonstrated a higher percentage of 90-day complications in the neuraxial analgesia cohort. Out of 6 studies reporting information regarding LOS, 4 demonstrated no improvement in LOS in the neuraxial cohort. A reduction in 72 hours post-RC opioid usage was observed in 2 out of 3 studies with available data. Information regarding post-RC pain scores were variable up to 3 days post-RC. One out of 2 studies with available data reported a significant association between neuraxial analgesia and an earlier time to recurrence. No significant associations were seen with respect to overall survival or cancer-specific survival. A majority of low-to-moderate quality evidence demonstrates neuraxial analgesia is associated with a higher rate of complications, variable information regarding pain control, no improvements in LOS, and no significant association with long-term oncological outcomes. Further research regarding the incorporation of nonopiate-based analgesic modalities into RC ERAS protocols is warranted., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Purpose: Recent literature has separately identified multiple determinants of the use of neoadjuvant chemotherapy (NAC) and adherence to pelvic lymph node dissection (PLND) guidelines in the management of non-metastatic bladder cancer. However, such NAC/PLND analyses tend not to account for the other modality, despite the fact that NAC may impact the extent of dissectible lymph nodes. We aimed to determine the predictors of adequate PLND in patients with non-metastatic urothelial muscle-invasive bladder cancer (MIBC) undergoing radical cystectomy (RC) following receipt of NAC., Methods: We queried the National Cancer Database to identify patients from 2006-2015 with cT2-cT4a/N0M0 urothelial MIBC who underwent RC and were pre-treated with NAC. Multivariate logistic regression analysis was used to identify independent predictors of undergoing an adequate PLND (defined as > 8 nodes)., Results: A total of 1518 patients met the criteria for inclusion (74.4% underwent adequate PLND). Adequate PLND was associated with treatment at an academic research facility (OR 2.762 [95% CI 2.119-3.599], p < 0.001). The likelihood of adequate PLND was significantly decreased in patients of older age (0.607 [0.441-0.835], p = 0.002 for age 70-79 years; 0.459 [0.245-0.860], p = 0.015 for age ≥ 80 years), a Charlson-Deyo score of 1 (0.722 [0.537-0.971], p = 0.031), and those who were uninsured (0.530 [0.292-0.964], p = 0.038)., Conclusions: Established predictors of PLND may not necessarily be generalizable to all patients undergoing treatment for bladder cancer. The interplay between PLND and NAC merits further study, particularly in view of recent literature calling into question the survival benefit of PLND in patients pre-treated with NAC.

Background: Primary small cell carcinoma of the kidney (PSCCK) is exceedingly rare and data on disease characteristics and outcomes are sparse. This study examines a nationally-representative cancer registry to better characterize PSCCK. Methods: We queried the National Cancer Database to identify patients with histology-confirmed PSCCK from 2004 to 2015. Adjusted Cox proportional hazards regression and Kaplan-Meier analyses were employed to assess predictors of mortality and estimate median survival time, respectively. Results: A total of 110 patients were included (47:53% female:male, 77% ≥60 years of age, 86% Caucasian). Significant predictors of mortality included female sex, age 60-69 years, treatment at an Integrated Network Cancer Program, stage cM1, and lack of surgical and chemoradiotherapy treatment. Independent protective factors were high socioeconomic status and treatment at an Academic Research Program. The estimated median overall survival time was 9.31 (95% CI 7.28-10.98) months for all patients. No differences in estimated survival time were observed across individual treatment modalities among those patients who underwent treatment ( p = 0.214). Conclusions: PSCCK is an aggressive malignancy with a median survival time of less than one year. Future studies that correlate clinical tumor staging with specific treatment modalities are needed to optimize and individualize management.

Research at modern light sources continues to improve our knowledge of the natural world, from the subtle workings of life to matter under extreme conditions. Free-electron lasers, for instance, have enabled the characterization of biomolecular structures with sub-ångström spatial resolution, and paved the way to controlling the molecular functions. On the other hand, attosecond temporal resolution is necessary to broaden our scope of the ultrafast world. Here we discuss attosecond pulse generation beyond present capabilities. Furthermore, we review three recently proposed methods of generating attosecond x-ray pulses. These novel methods exploit the coherent radiation of microbunched electrons in undulators and the tailoring of the emitted wavefronts. The computed pulse energy outperforms pre-existing technologies by three orders of magnitude. Specifically, our simulations of the proposed Soft X-ray Laser at MAX IV (Lund, Sweden) show that a pulse duration of 50-100 as and a pulse energy up to 5 [Formula: see text]J is feasible with the novel methods. In addition, the methods feature pulse shape control, enable the incorporation of orbital angular momentum, and can be used in combination with modern compact free-electron laser setups.

Introduction: Physician burnout is linked to decreased job performance, increased medical errors, interpersonal conflicts and depression. Two recent multispecialty studies showed that urologists had the highest rate of burnout. However, these reports were limited by a low sample size of urologists (119). We aimed to establish the prevalence of urologist burnout and associated factors., Methods: In the 2016 American Urological Association Census, Maslach Burnout Inventory questions were randomly assigned to half of the respondents. Using matrix sampling, the 1,126 practicing urologists who received and answered the Maslach Burnout Inventory questions represented the entire 2,301 who completed the census. Burnout was defined as scoring high on the scales of emotional exhaustion or depersonalization. Demographic and practice variables were assessed to establish factors correlating to burnout., Results: Overall 38.8% of urologists met the criteria for burnout, with 17.2% scoring high for emotional exhaustion and 37.1% scoring high for depersonalization. Multivariate analysis revealed that urologist burnout is associated with more patient visits per week, younger age, being in a subspecialty area other than pediatric or oncology, in solo or multispecialty practice, practice size greater than 2 and greater number of work hours per week., Conclusions: These results suggest that the burnout rate for urologists is lower than previously reported, and are consistent with rates reported in other medical and surgical specialties. However, burnout continues to be an important issue. Greater workload correlated with increased burnout while other practice patterns appeared to be protective. It is critical to keep urologists in the workforce to help lessen projected shortages.

Introduction: We compared characteristics of patients undergoing prostate biopsy in a high-risk inner city population before and after the 2012 USPSTF recommendation against PSA based prostate cancer screening to determine its effect on prostate biopsy practices., Materials and Methods: This was a retrospective study including patients who received biopsies after an abnormal PSA measurement from October 2008-December 2015. Patients with previously diagnosed prostate cancer were excluded. Chi-square tests of independence, two sample t-tests, Mann-Whitney U tests, and Fisher's exact tests were performed., Results: There were 202 and 208 patients in the pre-USPSTF and post-USPSTF recommendation cohorts, respectively. The post-USPSTF cohort had higher median PSA (7.8 versus 7.1ng/mL, p=0.05), greater proportion of patients who were black (96.6% versus 90.5%, p=0.01), and greater percentage of biopsy cores positive for disease (58% versus 29.5%, p<0.001). Multivariable analysis supported that the increase in PSA was independent of the increase in the proportion of patients who were black. The proportion of patients who were classified as D'Amico intermediate and high-risk disease increased in the post-USPSTF cohort and approached statistical significance (70.1% versus 58.8%, p=0.12)., Conclusions: Our study suggests that the USPSTF recommendations may have led to na increase in pre-biopsy PSA as well as greater volume of disease. Also, a greater proportion of patients were being classified with intermediate or high risk disease. While the clinical significance of these findings is unknown, what the data suggests is somewhat troubling. Future research should further examine these changes in a larger cohort as well as resultant long-term outcomes., Competing Interests: Conflict of interest: None declared., (Copyright® by the International Brazilian Journal of Urology.)

As underdeveloped nations continue to industrialize and world population continues to increase, the need for energy, natural resources, and goods will lead to ever increasing inorganic contaminants, such as heavy metals, in various waste streams that can have damaging effects on plant life, wildlife, and human health. This work is focused on the evaluation of the potential of Nannochloropsis salina to be integrated with contaminated water sources for the concurrent production of a biofuel feedstock while providing an environmental service through bioremediation. Individual contaminants (As, Cd, Cr, Co, Cu, Pb, Ni, Hg, Se, and Zn) at various concentrations ranging from a low concentration (1X) to higher concentrations (10X, and 40X) found in contaminated systems (mine tailings, wastewater treatment plants, produced water) were introduced into growth media. Biological growth experimentation was performed in triplicate at the various contaminant concentrations and at 3 different light intensities. Results show that baseline concentrations of each contaminant slightly decreased biomass growth to between 89% and 99% of the control with the exception of Ni which dramatically reduced growth. Increased contaminant concentrations resulted in progressively lower growth rates for all contaminants tested. Lipid analysis shows most baseline contaminant concentrations slightly decrease or have minimal effects on lipid content at all light levels. Trace contaminant analysis on the biomass showed Cd, Co, Cu, Pb, and Zn were sorbed by the microalgae with minimal contaminants remaining in the growth media illustrating the effectiveness of microalgae to bioremediate these contaminants when levels are sufficiently low to not detrimentally impact productivity. The microalgae biomass was less efficient at sorption of As, Cr, Ni, and Se., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Corynebacterium glutamicum (C. glutamicum) is a highly promising alternative prokaryotic host for recombinant protein expression, as it possesses several significant advantages over Escherichia coli (E. coli), the currently leading bacterial protein expression system. During the past decades, several experimental techniques and vector components for genetic manipulation of C. glutamicum have been developed and validated, including strong promoters for tightly regulating target gene expression, various types of plasmid vectors, protein secretion systems and methods of genetically modifying the host strain genome to improve protein production potential. This review critically discusses current progress in establishing C. glutamicum as a host for recombinant protein expression, and examines, in depth, some successful case studies of actual application of this expression system. The established "expression tool box" for developing novel constructs based on C. glutamicum as a host are also evaluated. Finally, the existing issues and solutions in process development with C. glutamicum as a host are specifically addressed.

Ganoderma lucidum BCCM 31549 has a long established role for its therapeutic activities. In this context, much interest has focused on the possible functions of the (1,3)-β-D-glucan (G) produced by these cultures in a stirred-tank bioreactor and extracted from their underutilized mycelium. In the existing study, we report on the systematic production of G, and its sulfated derivative (GS). The aim of this study was to investigate G and its GS from G. lucidum in terms of their antibacterial properties and cytotoxicity spectrum against human prostate cells (PN2TA) and human caucasian histiocytic lymphoma cells (U937). (1)H NMR for both G and GS compounds showed β-glycosidic linkages and structural similarities when compared with two standards (laminarin and fucoidan). The existence of characteristic absorptions at 1,170 and 867 cm(-1) in the FTIR (Fourier Transform Infrared Spectroscopy) for GS demonstrated the successful sulfation of G. Only GS exhibited antimicrobial activity against a varied range of test bacteria of relevance to foodstuffs and human health. Moreover, both G and GS did not show any cytotoxic effects on PN2TA cells, thus helping demonstrate the safety of these polymers. Moreover, GS showed 40% antiproliferation against cancerous U937 cells at the low concentration (60 μg/ ml) applied in this study compared with G (10%). Together, this demonstrates that sulfation clearly improved the solubility and therapeutic activities of G. The water-soluble GS demonstrates the potential multifunctional effects of these materials in foodstuffs.

Promoter of alcohol oxidase I (PAOX1) is the most efficient promoter involved in the regulation of recombinant protein expression in Pichia pastoris (P. pastoris). PAOX1 is tightly repressed by the presence of glycerol in the culture medium; thus, glycerol must be exhausted before methanol can be taken up by P. pastoris and the expression of the heterologous protein can be induced. In this study, a candidate glycerol transporter (GT1, GeneID: 8197545) was identified, and its role was confirmed by further studies (e.g. bioinformatics analysis, heterologous complementation in Schizosaccharomyces pombe (S. pombe)). When GT1 is co-expressed with enhanced green fluorescent protein (EGFP), it localizes to the membrane and S. pombe carrying gt1 but not the wild-type strain can grow on medium containing glycerol as the sole carbon source. The present study is the first to report that AOX1 in the X-33Δgt1 mutant can achieve constitutive expression in medium containing glycerol; thus, knocking down gt1 can eliminate the glycerol repression of PAOX1 in P. pastoris These results suggest that the glycerol transporter may participate in the process of PAOX1 inhibition in glycerol medium., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Retroperitoneal hemorrhage and an associated hematoma are uncommon but potentially serious complications following ureteroscopy with laser lithotripsy. However, no reports of serious bleeding complications have been published regarding ureteroscopy without laser lithotripsy in the management of stone disease. We report of such a case here and then review the current literature in order to discuss the incidence, risk factors, and management of such events.

Prostate cancer (PCa) is the most commonly diagnosed cancer as well as the greatest source of cancer-related mortality in males of African ancestry (MoAA). Interestingly, this has been shown to be associated with single nucleotide polymorphisms around regions 2 and 3 of the 8q24 human chromosomal region. The non-protein coding gene locus Plasmacytoma Variant Translocation 1 (PVT1) is located at 8q24 and is overexpressed in PCa and, therefore, is also a candidate biomarker to explain the well-known disparity in this group. PVT1 has at least 12 exons that make separate transcripts which may have different functions, all of which are at present unknown in PCa. Our aim was to determine if any PVT1 transcripts play a role in aggressiveness and racial disparity in PCa. We used a panel of seven PCa cell lines including three derived from MoAA. Ribonucleic acid extraction, complementary deoxyribonucleic acid synthesis, and quantitative polymerase chain reaction (qPCR) were performed to evaluate expression of all 12 PVT1 exons. Each qPCR was performed in quadruplicates. At least four separate qPCR experiments were performed. Expression of PVT1 exons was inconsistent except for exon 9. There was no significant difference in exon 9 expression between cell lines derived from Caucasian males (CM), and an indolent cell line derived from MoAA. However, exon 9 expression in the aggressive MDA PCa 2b and E006AA-hT cell lines derived from MoAA was significantly higher than in other cell lines. Consequently, we observed differential expression of exon 9 of PVT1 in a manner that suggests that PVT1 exon 9 may be associated with aggressive PCa in MoAA.

Thermostability has been considered as a requirement in the starch processing industry to maintain high catalytic activity of pullulanase under high temperatures. Four data driven rational design methods (B-FITTER, proline theory, PoPMuSiC-2.1, and sequence consensus approach) were adopted to identify the key residue potential links with thermostability, and 39 residues of Bacillus acidopullulyticus pullulanase were chosen as mutagenesis targets. Single mutagenesis followed by combined mutagenesis resulted in the best mutant E518I-S662R-Q706P, which exhibited an 11-fold half-life improvement at 60 °C and a 9.5 °C increase in Tm. The optimum temperature of the mutant increased from 60 to 65 °C. Fluorescence spectroscopy results demonstrated that the tertiary structure of the mutant enzyme was more compact than that of the wild-type (WT) enzyme. Structural change analysis revealed that the increase in thermostability was most probably caused by a combination of lower stability free-energy and higher hydrophobicity of E518I, more hydrogen bonds of S662R, and higher rigidity of Q706P compared with the WT. The findings demonstrated the effectiveness of combined data-driven rational design approaches in engineering an industrial enzyme to improve thermostability., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Increasing demand for renewable fuels has researchers investigating the feasibility of alternative feedstocks, such as microalgae. Inherent advantages include high potential yield, use of non-arable land and integration with waste streams. The nutrient requirements of a large-scale microalgae production system will require the coupling of cultivation systems with industrial waste resources, such as carbon dioxide from flue gas and nutrients from wastewater. Inorganic contaminants present in these wastes can potentially lead to bioaccumulation in microalgal biomass negatively impact productivity and limiting end use. This study focuses on the experimental evaluation of the impact and the fate of 14 inorganic contaminants (As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, Sb, Se, Sn, V and Zn) on Nannochloropsis salina growth. Microalgae were cultivated in photobioreactors illuminated at 984 µmol m(-2) sec(-1) and maintained at pH 7 in a growth media polluted with inorganic contaminants at levels expected based on the composition found in commercial coal flue gas systems. Contaminants present in the biomass and the medium at the end of a 7 day growth period were analytically quantified through cold vapor atomic absorption spectrometry for Hg and through inductively coupled plasma mass spectrometry for As, Cd, Co, Cr, Cu, Mn, Ni, Pb, Sb, Se, Sn, V and Zn. Results show N. salina is a sensitive strain to the multi-metal environment with a statistical decrease in biomass yieldwith the introduction of these contaminants. The techniques presented here are adequate for quantifying algal growth and determining the fate of inorganic contaminants.

Contamination of food and feed by Aflatoxin B1 (AFB1) is a cause of serious economic and health problems. Different processes have been used to degrade AFB1. In this study, biological degradation of AFB1 was carried out using three Actinomycete species, Rhodococcus erythropolis ATCC 4277, Streptomyces lividans TK 24, and S. aureofaciens ATCC 10762, in liquid cultures. Biodegradation of AFB1 was optimised under a range of temperatures from 25 to 40 °C and pH values of 4.0 to 8.0. An initial concentration of 20 µg/mL of AFB1 was used in this study. The amount of AFB1 remaining was measured against time by thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC), coupled with UV and mass spectrometry (LC-MS). All species were able to degrade the AFB1, and no significant difference was found between them. AFB1 remained in the liquid culture for R. erythropolis, S. lividans and S. aureofaciens were 0.81 µg/mL, 2.41 µg/mL and 2.78 µg/mL respectively, at the end of the first 24 h. Degradation occurred at all incubation temperatures and the pH with the optimal conditions for R. erythropolis was achieved at 30 °C and pH 6, whereas for S. lividans and S. aureofaciens the optimum conditions for degradation were 30 °C and pH 5. Analysis of the degradative route indicated that each microorganism has a different way of degrading AFB1. The metabolites produced by R. erythropolis were significantly different from the other two microorganisms. Products of degradation were identified through metabolomic studies by utilizing high-resolution mass spectral data. Mass spectrometric analysis indicated that the degradation of AFB1 was associated with the appearance of a range of lower molecular weight compounds. The pathway of degradation or chemical alteration of AFB1 was followed by means of high resolution Fourier transform mass spectrometry (HR-FTMS) analysis as well as through the MS2 fragmentation to unravel the degradative pathway for AFB1. AFB1 bio-degradation was coupled with the accumulation of intermediates of fatty acid metabolism and glycolysis. A plausible mechanism of degradation of AFB1 by Rhodococcus was hypothesized.

This review focuses on recent progress in the technology of high throughput (HTP) cultivation and its increasing application in quality by design (QbD) -driven bioprocess development. Several practical HTP strategies aimed at shortening process development (PD) timelines from DNA to large scale processes involving commercially available HTP technology platforms, including microtiter plate (MTP) culture, micro-scale bioreactors, and in parallel fermentation systems, etc., are critically reviewed in detail. This discussion focuses upon the relative strengths and weaknesses or limitations of each of these platforms in this context. Emerging prototypes of micro-bioreactors reported recently, such as milliliter (mL) scale stirred tank bioreactors, and microfludics integrated micro-scale bioreactors, and their potential for practical application in QbD-driven HTP process development are also critically appraised. The overall aim of such technology is to rapidly gain process insights, and since the analytical technology deployed in HTP systems is critically important to the achievement of this aim, this rapidly developing area is discussed. Finally, general future trends are critically reviewed., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Background: Among genitourinary malignancies, bladder cancer (BCa) ranks second in both prevalence and cause of death. Biomarkers of BCa for diagnosis, prognosis and disease surveillance could potentially help prevent progression, improve survival rates and reduce health care costs. Among several oncogenic signaling pathways implicated in BCa progression is that of hepatocyte growth factor (HGF) and its cell surface receptor, Met, now targeted by 25 experimental anti-cancer agents in human clinical trials. The involvement of this pathway in several cancers is likely to preclude the use of urinary soluble Met (sMet), which has been correlated with malignancy, for initial BCa screening. However, its potential utility as an aid to disease surveillance and to identify patients likely to benefit from HGF/Met-targeted therapies provide the rationale for this preliminary retrospective study comparing sMet levels between benign conditions and primary BCa, and in BCa cases, between different disease stages., Methods: Normally voided urine samples were collected from patients with BCa (Total: 183; pTa: 55, pTis: 62, pT1: 24, pT2: 42) and without BCa (Total: 83) on tissue-procurement protocols at three institutions and sMet was measured and normalized to urinary creatinine. Normalized sMet values grouped by pathologic stage were compared using non-parametric tests for correlation and significant difference. ROC analyses were used to derive classification models for patients with or without BCa and patients with or without muscle-invasive BCa (MIBCa or NMIBCa)., Results: Urinary sMet levels accurately distinguished patients with BCa from those without (p<0.0001, area under the curve (AUC): 0.7008) with limited sensitivity (61%) and moderate specificity (76%), and patients with MIBCa (n=42) from those with NMIBCa (n=141; p<0.0001, AUC: 0.8002) with moderate sensitivity and specificity (76% and 77%, respectively) and low false negative rate (8%)., Conclusions: Urinary sMet levels distinguish patients with BCa from those without, and patients with or without MIBCa, suggesting the potential utility of urinary sMet as a BCa biomarker for surveillance following initial treatment. Further studies are warranted to determine its potential value for prognosis in advanced disease, predicting treatment response, or identifying patients likely to benefit from Met-targeted therapies.

Objective: To analyze patients from an underserved area who presented initially with metastatic prostate cancer in order to identify patients in our population who would suffer greatly if PSA screening was eliminated., Materials and Methods: A prospectively maintained androgen deprivation therapy database from an inner city municipal hospital was queried to identify patients who presented with metastatic prostate cancer. We identified 129 individuals from 1999 to 2009 eligible for study. Those who underwent previous treatment for prostate cancer were excluded. We examined metastatic distribution and analyzed survival using Kaplan Meier probability curves., Results: The median age of presentation was 68 with a median Gleason sum of 8 per prostate biopsy. Thirty-two patients presented with hydronephrosis with a median creatinine of 1.79, two of whom required emergent dialysis. Of those patients who underwent radiographic imaging at presentation, 35.5% (33/93) had lymphadenopathy suspicious for metastasis, 16.1% (15/93) had masses suspicious for visceral metastases. Of the patients who underwent a bone scan 93% (118/127) had positive findings with 7.9% (10/127) exhibiting signs of cord compression. The 2 and 5- year cancer specific survival was 92.1% and 65.6%, respectively., Conclusions: In this study we have highlighted a group of men in an underserved community who presented with aggressive and morbid PCa despite widespread acceptance of PSA screening.

Background: Novel analytical tools, which shorten the long and costly development cycles of biopharmaceuticals are essential. Metabolic flux analysis (MFA) shows great promise in improving our understanding of the metabolism of cell factories in bioreactors, but currently only provides information post-process using conventional off-line methods. MFA combined with real time multianalyte process monitoring techniques provides a valuable platform technology allowing real time insights into metabolic responses of cell factories in bioreactors. This could have a major impact in the bioprocessing industry, ultimately improving product consistency, productivity and shortening development cycles., Results: This is the first investigation using Near Infrared Spectroscopy (NIRS) in situ combined with metabolic flux modelling which is both a significant challenge and considerable extension of these techniques. We investigated the feasibility of our approach using the industrial workhorse Pichia pastoris in a simplified model system. A parental P. pastoris strain (i.e. which does not synthesize recombinant protein) was used to allow definition of distinct metabolic states focusing solely upon the prediction of intracellular fluxes in central carbon metabolism. Extracellular fluxes were determined using off-line conventional reference methods and on-line NIR predictions (calculated by multivariate analysis using the partial least squares algorithm, PLS). The results showed that the PLS-NIRS models for biomass and glycerol were accurate: correlation coefficients, R2, above 0.90 and the root mean square error of prediction, RMSEP, of 1.17 and 2.90 g/L, respectively. The analytical quality of the NIR models was demonstrated by direct comparison with the standard error of the laboratory (SEL), which showed that performance of the NIR models was suitable for quantifying biomass and glycerol for calculating extracellular metabolite rates and used as independent inputs for the MFA (RMSEP lower than 1.5 × SEL). Furthermore, the results for the MFA from both datasets passed consistency tests performed for each steady state, showing that the precision of on-line NIRS is equivalent to that obtained by the off-line measurements., Conclusions: The findings of this study show for the first time the potential of NIRS as an input generating for MFA models, contributing to the optimization of cell factory metabolism in real-time.

Rationale: Allostatic load (AL), a novel measure of the physiologically dysregulated response of the body to stress, represents a biomarker of chronic stress exposure., Objectives: To determine whether preadolescent children with high AL are more susceptible to asthma as adolescents., Methods: This was a prospective evaluation of children recruited at 7 to 10 years of age in the nested case-control arm of the Study of Asthma, Genes and Environment and followed until 11 to 14 years of age. AL was measured using eight biomarkers: fasting glucose, total cholesterol, high-density lipoprotein cholesterol, dehydroepiandrosterone sulfate, cortisol, systolic and diastolic blood pressure, and waist-to-hip ratio. AL, created from the sum of biomarkers in a high-risk quartile, was related to prevalence and incidence of asthma using logistic regression., Measurements and Main Results: Among 352 participants followed until 11 to 14 years of age, prevalent asthma was four times more likely in boys with high (>3) versus low (≤2) AL after adjusting for current asthma/atopy, age, ethnicity, parental history of asthma, and overweight status. Similar results were observed in the analysis of new-onset asthma in boys (adjusted odds ratio, 4.35; 95% confidence interval, 1.19-15.9). In girls, there were no associations between AL and asthma. In the analysis of a subset of biomarkers, combinations of total cholesterol, glucose, and cortisol were associated with similar or greater risk of asthma prevalence or onset in boys., Conclusions: AL and its biomarkers are associated with an increased likelihood of asthma in adolescent boys. The observed association between AL and asthma may be attributable to a combined subset of AL biomarkers.

The effects of mild conventional food-processing conditions on Listeria monocytogenes survival to pulsed UV (PUV) irradiation and virulence-associated characteristics were investigated. Specifically, this study describes the inability of 10 strains representative of 3 different culture forms or morphotypes of L. monocytogenes to adapt to normally lethal levels of PUV-irradiation after exposure to sub-lethal concentrations of salt (7.5% (w/v) NaCl for 1 h), acid (pH 5.5 for 1 h), heating (48 °C for 1 h) or PUV (UV dose 0.08 μJ/cm(2)). Findings showed that the order of increasing sensitivity of L. monocytogenes of non-adapted and stressed morphotypes to low pH (pH 3.5 for 5 h, adjusted with lactic), high salt (17.5% w/v NaCl for 5 h), heating (60 °C for 1 h) and PUV-irradiation (100 pulses at 7.2 J and 12.8 J, equivalent to UV doses of 2.7 and 8.4 μJ/cm(2) respectively) was typical wild-type smooth (S/WT), atypical filamentous rough (FR) and atypical multiple-cell-chain (MCR) variants. Exposure of L. monocytogenes cells to sub-lethal acid, salt or heating conditions resulted in similar or increased susceptibility to PUV treatments. Only prior exposure to mild heat stressing significantly enhanced invasion of Caco-2 cells, whereas subjection of L. monocytogenes cells to combined sub-lethal salt, acid and heating conditions produced the greatest reduction in invasiveness. Implications of these findings are discussed. This constitutes the first study to show that pre-exposure to mild conventional food-processing stresses enhances sensitivity of different culture morphotypes of L. monocytogenes to PUV, which is growing in popularity as an alternative or complementary approach for decontamination in the food environment., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Objective: Due to imprecise clinical staging, the finding of extravesical and node-positive disease at the time of radical cystectomy (RC) for patients with clinically localized bladder cancer is not uncommon. Circulating tumor cells (CTCs) have been shown to be present in the peripheral blood of patients with metastatic urothelial carcinoma. The object of this study was to evaluate the ability of CTCs to predict extravesical disease in bladder cancer patients prior to RC., Materials and Methods: Peripheral blood samples from 43 patients with bladder cancer were evaluated using the CellSearch (Veridex, LLC, Raritan, NJ) CTC assay prior to RC. The sensitivity, specificity, and positive predictive value (PPV) of CTC status in predicting extravesical disease was calculated. Receiver operating characteristic (ROC) curves were generated to quantify the ability of CTCs to predict extravesical and node-positive disease., Results: CTCs were detected in 9 (21%) patients prior to RC. The sensitivity, specificity, and PPV of CTC status in predicting extravesical disease were 27%, 88% and 78%, respectively. The accuracy of CTC status in predicting extravesical (≥pT3 or node-positive) disease for the entire cohort was 0.576. In a model incorporating preoperative hydronephrosis, CTC status did not improve the predictive accuracy for extravesical disease (0.576 vs. 0.585, P = 0.915)., Conclusion: CTCs were detected in low numbers in a small percentage (21%) of patients prior to undergoing RC at our institution. CTC status was not a robust predictor of extravesical or node-positive disease in this cohort. CTC status is not likely to be a clinically useful parameter for directing therapeutic decisions in patients with ≤cT2 bladder cancer., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Debate still surrounds the physiological roles of the alternative respiratory enzymes found in many fungi and plants. It has been proposed that alternative NADH:ubiquinone oxidoreductases (NADH dehydrogenases) may protect against oxidative stress, conversely, elevated activity of these enzymes has been linked to senescence. Here we show that inhibition of these enzymes in a fungal protein expression system (Aspergillus niger) leads to significantly enhanced specific growth rate, substrate uptake, carbon dioxide evolution, higher protein content, and more efficient use of substrates. These findings are consistent with a protective role of the NADH dehydrogenases against oxidative stress, thus, when electron flow via these enzymes is blocked, flux through the main respiratory pathway rises, leading to enhanced ATP generation. We anticipate that our findings will stimulate further studies in fungal and plant cultures leading to significant improvements in these expression systems, and to deeper insights into the cellular roles of alternative respiration.

There is considerable interest in exploiting the novel physical and biological properties of microbial exopolysaccharides in industry and medicine. For economic and scientific reasons, large scale production under carefully monitored and controlled conditions is required. Producing exopolysaccharides in industrial fermenters poses several complex bioengineering and microbiological challenges relating primarily to the very high viscosities of such culture media, which are often exacerbated by the producing organism's morphology. What these problems are, and the strategies for dealing with them are discussed critically in this review, using pullulan, curdlan, xanthan, and fungal β-glucans as examples of industrially produced microbial exopolysaccharides. The role of fermenter configuration in their production is also examined.

Despite the importance of filamentous fungi in the biotechnology industry, little is known about their metabolism under the stressful conditions experienced in typical production fermenters. In the present study, oxygen enrichment was used to recreate an industrial batch process, and the effects of the increasing dissolved oxygen tension were studied as regards the cellular metabolism. It was found that elevated dissolved oxygen tension led to an oxidatively stressful environment, as detailed by rapid initial increases in reactive oxygen species (ROS) concentrations and antioxidant enzyme activities. Intracellular protein concentrations also decreased in oxygenated cultures; this appeared to be concomitant with a decrease in the adenosine-5'-triphosphate (ATP) pool in these cultures. Oxygenated cultures showed early senescence and death compared to aerated control cultures. Despite earlier studies proposing various mechanisms for such findings in fungal cultures subjected to oxidative stress, these findings can best be explained by the fact that in such cultures the activity of alternative NADH dehydrogenases was significantly increased, which served to maintain lower ROS concentrations throughout the duration of the process but in doing so also reduced the ability of the organism to create a proton motive force by which to drive ATP synthesis. The findings of the present study help further our understanding of the central roles of these highly conserved enzymes within fungal metabolism under oxidative stress., (Copyright © 2011 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.)

Large-scale commercial bioprocesses that manufacture biopharmaceutical products such as monoclonal antibodies generally involve multiple bioreactors operated in parallel. Spectra recorded during in situ monitoring of multiple bioreactors by multiplexed fiber-optic spectroscopies contain not only spectral information of the chemical constituents but also contributions resulting from differences in the optical properties of the probes. Spectra with variations induced by probe differences cannot be efficiently modeled by the commonly used multivariate linear calibration models or effectively removed by popular empirical preprocessing methods. In this study, for the first time, a calibration model is proposed for the analysis of complex spectral data sets arising from multiplexed probes. In the proposed calibration model, the spectral variations introduced by probe differences are explicitly modeled by introducing a multiplicative parameter for each optical probe, and then their detrimental effects are effectively mitigated through a "dual calibration" strategy. The performance of the proposed multiplex calibration model has been tested on two multiplexed spectral data sets (i.e., MIR data of ternary mixtures and NIR data of bioprocesses). Experimental results suggest that the proposed calibration model can effectively mitigate the detrimental effects of probe differences and hence provide much more accurate predictions than commonly used multivariate linear calibration models (such as PLS) with and without empirical data preprocessing methods such as orthogonal signal correction, standard normal variate, or multiplicative signal correction.

Controlling the dissolved oxygen (DO) in the fed-batch culture of the medicinal mushroom Ganoderma lucidum led to a two-fold increase of the maximum biomass productivity compared to uncontrolled DO conditions. By contrast, extracellular polysaccharide (EPS) production was two times higher under oxygen limitation (uncontrolled DO) than under increased oxygen availability (controlled DO). Morphologically, dispersed mycelium was predominant under controlled DO conditions, with highly branched hyphae, consistent with the enhanced culture growth noted under these conditions. While in the uncontrolled DO processes mycelial clumps were the most common morphology throughout the culture. However, in both cultures clamp connections were found. This is an exciting new finding, which widens the applicability of this basidiomycete in submerged fermentation. In rheological terms, broths demonstrated shear-thinning behaviour with a yield stress under both DO conditions. The flow curves were best described by the Herschel-Bulkley model: flow index down to 0.6 and consistency coefficient up to 0.2 and 0.6 Pa sn in uncontrolled and controlled cultures DO, respectively. The pseudoplastic behaviour was entirely due to the fungal biomass, and not to the presence of EPS (rheological analysis of the filtered broth showed Newtonian behaviour). It is clear that dissolved oxygen tension is a critical process parameter that distinctly influences G. lucidum morphology and rheology, affecting the overall performance of the process. This study contributes to an improved understanding of the process physiology of submerged fermentation of G. lucidum.

Purpose: We determined whether serial prostate needle biopsies predispose men to erectile dysfunction and/or lower urinary tract symptoms over time., Materials and Methods: Men with prostate cancer on an active surveillance protocol were administered the 5-item Sexual Health Inventory for Men and International Prostate Symptom Score questionnaires on protocol entry, and at a cross-sectional point in 2008. All men had at least 1, 10 to 12-core prostate biopsy at protocol entry and yearly surveillance biopsies thereafter were recommended., Results: Of 333 men 231 returned the followup questionnaires. Correlations were found between biopsy number and erectile dysfunction, with increasing biopsy number associated with a decrease in Sexual Health Inventory for Men score (p = 0.04) and a history of 3 or more biopsies associated with a greater decrease in Sexual Health Inventory for Men score than after 2 or fewer biopsies (p = 0.02). Multivariable analysis for biopsy number, age, prostate volume and prostate specific antigen showed that only biopsy number was associated with decreasing Sexual Health Inventory for Men score (p = 0.02). When men were stratified by baseline Sexual Health Inventory for Men, those without preexisting erectile dysfunction (Sexual Health Inventory for Men score 22 to 25) trended toward steeper decreases in Sexual Health Inventory for Men score after 3 or more biopsies (p = 0.06) than did men with baseline mild to moderate erectile dysfunction (Sexual Health Inventory for Men score 8 to 21). No correlation was found between biopsy number and International Prostate Symptom Score., Conclusions: Serial prostate biopsies appear to have an adverse effect on erectile function in men with prostate cancer on active surveillance but do not affect lower urinary tract symptoms.