Laboratory Focus on Improving the Culture of Biosafety: Statewide Risk Assessment of Clinical Laboratories That Process Specimens for Microbiologic Analysis

The Wisconsin State Laboratory of Hygiene challenged Wisconsin laboratories to examine their biosafety practices and improve their culture of biosafety. One hundred three clinical and public health laboratories completed a questionnaire-based, microbiology-focused biosafety risk assessment. Greater than 96% of the respondents performed activities related to specimen processing, direct microscopic examination, and rapid nonmolecular testing, while approximately 60% performed culture interpretation. Although they are important to the assessment of risk, data specific to patient occupation, symptoms, and travel history were often unavailable to the laboratory and, therefore, less contributory to a microbiology-focused biosafety risk assessment than information on the specimen source and test requisition. Over 88% of the respondents complied with more than three-quarters of the mitigation control measures listed in the survey. Facility assessment revealed that subsets of laboratories that claim biosafety level 1, 2, or 3 status did not possess all of the biosafety elements considered minimally standard for their respective classifications. Many laboratories reported being able to quickly correct the minor deficiencies identified. Task assessment identified deficiencies that trended higher within the general (not microbiology-specific) laboratory for core activities, such as packaging and shipping, direct microscopic examination, and culture modalities solely involving screens for organism growth. For traditional microbiology departments, opportunities for improvement in the cultivation and management of highly infectious agents, such as acid-fast bacilli and systemic fungi, were revealed. These results derived from a survey of a large cohort of small- and large-scale laboratories suggest the necessity for continued microbiology-based understanding of biosafety practices, vigilance toward biosafety, and enforcement of biosafety practices throughout the laboratory setting

Phosphorus bioavailability in soil profiles of a long-term fertilizer experiment: The evaluation of their bioaccessibility

Global agricultural productivity depends on the use of finite phosphorus (P) resources of which not only the topsoil, but also subsoil, can hold immense reserves. To assess potential soil contribution to plant nutrition, we compared the P status of Stagnic Cambisol profiles in experimental plots that received different P fertilizer applications (control, triple superphosphate (TSP), compost, compost+TSP) for 16 years. Sequential fractionation was combined with P K-edge X-ray absorption near edge structure (XANES) spectroscopy to identify the chemical P speciation. Fertilized topsoils (21 to 69 kg P ha-1 a-1) showed P reserves larger by a factor of 1.2 to 1.4, and subsoil P reserves larger by a factor of 1.3 to 1.5 than those of the control. P-XANES revealed the predominance of inorganic P species such as moderately labile Fe- (46 to 92%), Al- (0 to 40%), and Ca- (0 to 15%) P compounds besides organic P (0 to 13%) in all treatments. The fertilizer application slightly altered P speciation throughout the profiles, but the type of fertilizer had no significant effect on it. Optimal plant growth requirements are restricted by the exchangeable P from the solid phase within the soil solution. Therefore, ongoing research focuses on the accessibility of P from P loaded amorphous Fe- and Al-hydroxides, previously identified as the predominant abiotic P forms. To assess their P desorption potential, P-33 rhizotron experiments combined with P-33 isotopic exchange kinetics (IEK) are underway. Preliminary results indicated that besides differences in P binding capacity of soil hydroxides, physical soil parameters, such as the matric potential, strongly control soil P availability, thus plant P acquisition rates can vary among different soil types. Our results gained new detailed information about P bioavailability under agricultural practice. The investigations towards P bioaccessibility may contribute to improved interpretation of soil P tests and reduced fertilizer recommendations

Juxtaposition of system dynamics and agent-based simulation for a case study in immunosenescence

Advances in healthcare and in the quality of life significantly increase human life expectancy. With the aging of populations, new un-faced challenges are brought to science. The human body is naturally selected to be well-functioning until the age of reproduction to keep the species alive. However, as the lifespan extends, unseen problems due to the body deterioration emerge. There are several age-related diseases with no appropriate treatment; therefore, the complex aging phenomena needs further understanding. It is known that immunosenescence is highly correlated to the negative effects of aging. In this work we advocate the use of simulation as a tool to assist the understanding of immune aging phenomena. In particular, we are comparing system dynamics modelling and simulation (SDMS) and agent-based modelling and simulation (ABMS) for the case of age-related depletion of naive T cells in the organism. We address the following research questions: Which simulation approach is more suitable for this problem? Can these approaches be employed interchangeably? Is there any benefit of using one approach compared to the other? Results show that both simulation outcomes closely fit the observed data and existing mathematical model; and the likely contribution of each of the naive T cell repertoire maintenance method can therefore be estimated. The differences observed in the outcomes of both approaches are due to the probabilistic character of ABMS contrasted to SDMS. However, they do not interfere in the overall expected dynamics of the populations. In this case, therefore, they can be employed interchangeably, with SDMS being simpler to implement and taking less computational resources

Comparing SurePath, ThinPrep, and conventional cytology as primary test method: SurePath is associated with increased CIN II+ detection rates

Purpose: Within the last decade, SurePath and ThinPrep [both liquid-based cytology (LBC) tests] have replaced conventional cytology (CC) as primary test method in cervical cancer screening programs of multiple countries. The aim of our study was to examine the effect in the Dutch screening program. Methods: All primary smears taken within this program from 2000 to 2011 were analyzed using the nationwide registry of histo- and cytopathology (PALGA) with a follow-up until March 2013. The percentage of smears classified as borderline/mildly dyskaryotic (BMD) and >BMD as well as CIN and cervical cancer detection rates were compared between SurePath and ThinPrep versus CC by logistic regression analyses (adjusted for age, screen region, socioeconomic status, and calendar time). Results: We included 3,118,685 CC, 1,313,731 SurePath, and 1,584,587 ThinPrep smears. Using SurePath resulted in an increased rate of primary smears classified as >BMD [odds ratio (OR) = 1.12 (95% confidence interval (CI) 1.09–1.16)]. CIN I and II+ detection rates increased by 14 % [OR = 1.14 (95% CI 1.08–1.20)] and 8 % [OR = 1.08 (95% CI 1.05–1.12)]. Cervical cancer detection rates were unaffected. Implementing ThinPrep did not result in major alterations of the cytological classification of smears, and it did not affect CIN detection rates. While not significant, cervical cancer detection rates were lower [OR = 0.87 (95% CI 0.75–1.01)]. Conclusions: The impact of replacing CC by LBC as primary test method depends on the type of LBC test used. Only the use of SurePath was associated with increased CIN II+ detection, although it simultaneously increased the detection of CIN I

Towards the development of a simulator for investigating the impact of people management practices on retail performance

               \ud           \ud 

Identifying Heavy Goods Vehicle Driving Styles in the United Kingdom

Although driving behavior has been largely studied amongst private motor vehicles drivers, the literature addressing heavy goods vehicle (HGV) drivers is scarce. Identifying the existing groups of driving stereotypes and their proportions enables researchers, companies, and policy makers to establish group-specific strategies to improve safety and economy. In addition, insight into driving styles can help predict drivers' reactions and therefore enable the modeling of interactions between vehicles and the possible obstacles encountered on a journey. Consequently, there are also contributions to the research and development of autonomous vehicles and smart roads. In this paper, our interest lies in investigating driving behavior within the HGV community in the United Kingdom (U.K.). We conduct analysis of a telematics dataset containing the incident information on 21 193 HGV drivers across the U.K. We are interested in answering two research questions: 1) What groups of behavior are we able to uncover? 2) How do these groups complement current findings in the literature? To answer these questions, we apply a two-stage data analysis methodology involving consensus clustering and ensemble classification to the dataset. Through the analysis, eight patterns of behavior are uncovered. It is also observed that although our findings have similarities to those from previous work on driving behavior, further knowledge is obtained, such as extra patterns and driving traits arising from vehicle and road characteristics

Introduction of primary screening using high-risk HPV DNA detection in the Dutch cervical cancer screening programme:a population-based cohort study

Background: In January 2017, the Dutch cervical cancer screening programme transitioned from cytomorphological to primary high-risk HPV (hrHPV) DNA screening, including the introduction of self-sampling, for women aged between 30 and 60 years. The Netherlands was the first country to switch to hrHPV screening at the national level. We investigated the health impact of this transition by comparing performance indicators from the new hrHPV-based programme with the previous cytology-based programme. Methods: We obtained data from the Dutch nationwide network and registry of histo- and cytopathology (PALGA) for 454,573 women eligible for screening in 2017 who participated in the hrHPV-based programme between 1 January 2017 and 30 June 2018 (maximum follow-up of almost 21 months) and for 483,146 women eligible for screening in 2015 who participated in the cytology-based programme between 1 January 2015 and 31 March 2016 (maximum follow-up of 40 months). We compared indicators of participation (participation rate), referral (screen positivity; referral rate) and detection (cervical intraepithelial neoplasia (CIN) detection; number of referrals per detected CIN lesion). Results: Participation in the hrHPV-based programme was significantly lower than that in the cytology-based programme (61% vs 64%). Screen positivity and direct referral rates were significantly higher in the hrHPV-based programme (positivity rate: 5% vs 9%; referral rate: 1% vs 3%). CIN2+ detection increased from 11 to 14 per 1000 women screened. Overall, approximately 2.2 times more clinical irrelevant findings (i.e. ≤CIN1) were found in the hrHPV-based programme, compared with approximately 1·3 times more clinically relevant findings (i.e. CIN2+); this difference was mostly due to a national policy change recommending colposcopy, rather than observation, of hrHPV-positive, ASC-US/LSIL results in the hrHPV-based programme. Conclusions: This is the first time that comprehensive results of nationwide implementation of hrHPV-based screening have been reported using high-quality data with a long follow-up. We have shown that both benefits and potential harms are higher in one screening round of a well-implemented hrHPV-based screening programme than in an established cytology-based programme. Lower participation in the new hrHPV programme may be due to factors such as invitation policy changes and the phased roll-out of the new programme. Our findings add further to evidence from trials and modelling studies on the effectiveness of hrHPV-based screening

Author Correction: identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling

Correction to: Communications Biology https://doi.org/10.1038/s42003-022-04141-x, published online 16 November 2022.In the original version of the Article, an incorrect additional description of panel b in Figure 1 was included. The following sentence has now been removed:b Lignocellulose is a complex and recalcitrant polymer built up from cellulose, xylan (hemicellulose), and lignin. Its degradation requires the synergistic action of various different enzymes.Bio-organic Synthesi

Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling

Activity-based protein profiling is used to screen lignocellulose-degrading enzymes from the white rot fungus Phanerochaete chrysosporium to identify those specifically active in the presence of wood substrate.Activity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.Bio-organic Synthesi