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Quality management and innovation are priority issues in research facilities that close the cycle from research to products delivery for its social use. The objective of this work is to diagnose the conditions for the implementation of the Integrated Quality and Innovation Management System in the Biomaterials Center of the University of Havana, based on the standards: NCISO 9001:2015; NC-ISO 13485:2018 and NC 1307:2019. To do this, the stages to manage the change were established, and a diagnostic tool based on the integration of the mentioned standards was designed and applied. As a result, it was identified the need to strengthen the aspects related to: the strategies for achieving the vision, the management of ideas, the execution of projects by product, the transfer of results, the monitoring and measurement of the management of research, development and innovation activities and their results. In addition, the existing documents in the Center's management system must be modified in order to detail the implementation and monitoring of innovation activities. The integrated management, of the regulatory requirements for biomaterials, and the quality and innovation management, constitutes an organizational innovation that will facilitate the development of innovative products for the National Health System, contributing to the achievement of the organization's vision and the fulfillment of strategic objectives. [ABSTRACT FROM AUTHOR]

Mice thermoneutral zone lies at temperatures much higher than expected when considering the geographical extension of the species. Growing evidence shows that mouse-dependent thermogenesis experimentation needs to cope with temperatures below those at which the animals are most comfortable. The associated physiological changes interfere with experimental results, thereby highlighting the apparently trivial subject of room-temperature. Working at above 25 °C is difficult for researchers and animal care technicians. Herein, we explore alternative solutions related to living habits of wild mice that could improve translation of research on mice to humans. Standard murine environments are often colder than those in laboratory facilities and their behavior is mainly characterized by a gregarious, nesting and exploratory way of life. Optimization of their thermal environment can thus also be achieved by avoiding individual housing and providing high-quality nesting material and devices that would allow locomotor activity, hence muscle thermogenesis. These options have additional relevance in terms of animal welfare. When precise monitoring of the temperature is required, temperature-controlled cabinets can be used for the duration of the experiments. During the manipulation of mice, a heated laminar flow hood or tray could create an optimized microenvironment. The specification of temperature-related data in publications should contain information on the translatability of the described mouse models to humans. Furthermore, publications should describe the premises of the laboratory in relation to housing possibilities and murine behavior. [ABSTRACT FROM AUTHOR]

Numerous doctoral degree holders were trained in African archaeometallurgy in the Global North as well as on the African continent. African archaeometallurgy continues to attract a significant number of researchers from Europe and North America. This paper is based on our lived experiences as resident African archaeometallurgists. We argue that out of frustration because of unequal power relations and lack of access to archaeological science laboratories and funding, most African archaeometallurgists are now pursuing other research areas and careers altogether. We propose some solutions to ensure sustainability in the training and practice of archaeological scientists on the African continent. We conclude that African scholars need to develop home-grown and long-term research capacities and strategies. [ABSTRACT FROM AUTHOR]

The article looks at organizational and financial regulation of construction and operation of large-scale research plants. It analyzes and describes general provisions and peculiarities of mega-science projects, and their definitions. It also studies organizational forms of their cooperation both at the national and international levels and looks at financial mechanisms applied to the funding of research facilities on the territory of Russia and abroad. While working on the article the authors have established that financial and legal norms are applied to social relations targeted at financing mega-science projects. Social relations include the issues of financing from state budget and tax relief applied to the organizations that construct and operate large research plants. The article also looks at financial control, which is put in place during the implementation of mega-science projects. As a result of the conducted research a conclusion has been made about the efficiency of joint projects by both international government organizations and Russian organizations where research facilities will be located. The article also draws attention to a misplaced approach, when mega-science projects are implemented on the premises of research institutions funded from state budget. [ABSTRACT FROM AUTHOR]

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies. [ABSTRACT FROM AUTHOR]

The transition to PEPFAR 2.0 with its focus on country ownership was accompanied by substantial funding cuts. We describe the impact of this transition on HIV care in a large network of HIV clinics in Nigeria. We surveyed 30 comprehensive HIV treatment clinics to assess services supported before (October 2013-September 2014) and after (October 2014-September 2015) the PEPFAR funding policy change, the impact of these policy changes on service delivery areas, and response of clinics to the change. We compared differences in support for staffing, laboratory services, and clinical operations pre- and post-policy change using paired t-tests. We used framework analysis to assess answers to open ended questions describing responses to the policy change. Most sites (83%, n = 25) completed the survey. The majority were public (60%, n = 15) and secondary (68%, n = 17) facilities. Clinics had a median of 989 patients in care (IQR: 543–3326). All clinics continued to receive support for first and second line antiretrovirals and CD4 testing after the policy change, while no clinics received support for other routine drug monitoring labs. We found statistically significant reductions in support for viral load testing, staff employment, defaulter tracking, and prevention services (92% vs. 64%, p = 0.02; 80% vs. 20%, 100% vs. 44%, 84% vs. 16%, respectively, p<0.01 for all) after the policy change. Service delivery was hampered by interrupted laboratory services and reduced wages and staff positions leading to reduced provider morale, and compromised quality of care. Almost all sites (96%) introduced user fees to address funding shortages. Clinics in Nigeria are experiencing major challenges in providing routine HIV services as a result of PEPFAR’s policy changes. Funding cutbacks have been associated with compromised quality of care, staff shortages, and reliance on fee-based care for historically free services. Sustainable HIV services funding models are urgently needed. [ABSTRACT FROM AUTHOR]

Differential Evolution (DE) is powerful for global optimization problems. Among DE algorithms, JADE and its variants, whose mutation strategy is DE/current-to-pbest/1 with optional archive, have good performance. A significant feature of the above mutation strategy is that one individual for difference operation comes from the union of the optional external archive and the population. In existing DE algorithms based on the mutation strategy—JADE and its variants, individuals eliminated from the population are send to the archive. In this paper, we propose a scheme for managing the optional external archive. According to our scheme, two subpopulations are maintained in the population. Each of them regards the other as the archive. In experiments, our scheme is applied in JADE and two of its variants—SHADE and L-SHADE. Experimental results show that our scheme can enhance JADE and its variants. Moreover, it can be seen that L-SHADE with our scheme performs significantly better than four DE algorithms, CoBiDE, MPEDE, EDEV, and MLCCDE. [ABSTRACT FROM AUTHOR]

Amphibians, the most threatened group of vertebrates, are seen as indicators of the sixth mass extinction on earth. Thousands of species are threatened with extinction and many have been affected by an emerging infectious disease, chytridiomycosis, caused by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). However, amphibians exhibit different responses to the pathogen, such as survival and population persistence with infection, or mortality of individuals and complete population collapse after pathogen invasion. Multiple factors can affect host pathogen dynamics, yet few studies have provided a temporal view that encompasses both the epizootic phase (i.e. pathogen invasion and host collapse), and the transition to a more stable co-existence (i.e. recovery of infected host populations). In the Sierra Nevada mountains of California, USA, conspecific populations of frogs currently exhibit dramatically different host/ Bd-pathogen dynamics. To provide a temporal context by which present day dynamics may be better understood, we use a Bd qPCR assay to test 1165 amphibian specimens collected between 1900 and 2005. Our historical analyses reveal a pattern of pathogen invasion and eventual spread across the Sierra Nevada over the last century. Although we found a small number of Bd-infections prior to 1970, these showed no sign of spread or increase in infection prevalence over multiple decades. After the late 1970s, when mass die offs were first noted, our data show Bd as much more prevalent and more spatially spread out, suggesting epizootic spread. However, across the ~400km2 area, we found no evidence of a wave-like pattern, but instead discovered multiple, nearly-simultaneous invasions within regions. We found that Bd invaded and spread in the central Sierra Nevada (Yosemite National Park area) about four decades before it invaded and spread in the southern Sierra Nevada (Sequoia and Kings Canyon National Parks area), and suggest that the temporal pattern of pathogen invasion may help explain divergent contemporary host pathogen dynamics. [ABSTRACT FROM AUTHOR]

Biobanks have evolved, and their governance procedures have undergone important transformations. Our paper examines this issue by focusing on the perspective of the professionals working in management or scientific roles in research-based biobanks, who have an important impact on shaping these transformations. In particular, it highlights that recent advances in molecular medicine and genomic research have raised a range of ethical, legal and societal implications (ELSI) related to biobank-based research, impacting directly on regulations and local practices of informed consent (IC), private-public partnerships (PPPs), and engagement of participants. In our study, we investigate the ways that these concerns influence biobanking practices and assess the level of satisfaction of the cross-national biobanking research communities with the ELSI related procedures that are currently in place. We conducted an online survey among biobankers and researchers to investigate secondary use of data, informing and/or re-contacting participants, sharing of data with third parties from industry, participant engagement, and collaboration with industrial partners. Findings highlight the need for a more inclusive and transparent biobanking practice where biobanks are seen in a more active role in providing information and communicating with participants; the need to improve the current IC procedures and the role of biobanks in sharing of samples and data with industry partners and different countries, and the need for practical, tangible and hands-on ethical and legal guidance. [ABSTRACT FROM AUTHOR]

Early industrialization and the development of cheap production processes for paper have led to an exponential accumulation of paper-based documents during the last two centuries. Archives and libraries harbor vast amounts of ancient and modern documents and have to undertake extensive endeavors to protect them from abiotic and biotic deterioration. While services for mechanical preservation such as ex post de-acidification of historic documents are already commercially available, the possibilities for long-term protection of paper-based documents against fungal attack (apart from temperature and humidity control) are very limited. Novel processes for mechanical enhancement of damaged cellulosic documents use Ionic Liquids (IL) as essential process components. With some of these ILs having azole-functionalities similar to well-known fungicides such as Clotrimazole, the possibility of antifungal activities of these ILs was proposed but has not yet been experimentally confirmed. We evaluated the potency of four ILs with potential application in paper restoration for suppression of fungal growth on five relevant paper-infesting molds. The results revealed a general antifungal activity of all ILs, which increased with the size of the non-polar group. Physiological experiments and ultimate elemental analysis allowed to determine the minimal inhibitory concentration of each IL as well as the residual IL concentration in process-treated paper. These results provide valuable guidelines for IL-applications in paper restoration processes with antifungal activity as an added benefit. With azoles remaining in the paper after the process, simultaneous repair and biotic protection in treated documents could be facilitated. [ABSTRACT FROM AUTHOR]

Practical laboratory classes teaching molecular pharmacology approaches employed in the development of therapeutic strategies are of great interest for students of courses in Biotechnology, Applied Biology, Pharmaceutic and Technology Chemistry, Translational Oncology. Unfortunately, in most cases the technology to be transferred to learning students is complex and requires multi-step approaches. In this respect, simple and straightforward experimental protocols might be of great interest. This study was aimed at presenting a laboratory exercise focusing (a) on a very challenging therapeutic strategy, i.e. microRNA therapeutics, and (b) on the employment of biomolecules of great interest in applied biology and pharmacology, i.e. peptide nucleic acids (PNAs). The aims of the practical laboratory were to determine: (a) the possible PNA-mediated arrest in RT-qPCR, to be eventually used to demonstrate PNA targeting of selected miRNAs; (b) the possible lack of activity on mutated PNA sequences; (c) the effects (if any) on the amplification of other unrelated miRNA sequences. The results which can be obtained support the following conclusions: PNA-mediated arrest in RT-qPCR can be analyzed in a easy way; mutated PNA sequences are completely inactive; the effects of the employed PNAs are specific and no inhibitory effect occurs on other unrelated miRNA sequences. This activity is simple (cell culture, RNA extraction, RT-qPCR are all well-established technologies), fast (starting from isolated and characterized RNA, few hours are just necessary), highly reproducible (therefore easily employed by even untrained students). On the other hand, these laboratory lessons require some facilities, the most critical being the availability of instruments for PCR. While this might be a problem in the case these instruments are not available, we would like to underline that determination of the presence or of a lack of amplified product can be also obtained using standard analytical approaches based on agarose gel electrophoresis. [ABSTRACT FROM AUTHOR]

Parasites and pathogens are often aggregated in a minority of susceptible hosts within a population, with a majority of individuals harboring low infection intensities. However, determining the relative importance of host traits to explain this heterogeneity is a challenge. One ecologically important pathogen is Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis and has been associated with many amphibian population declines worldwide. For many hosts, post-metamorphic stages are generally more susceptible than the larval stage. Yet, examination of the effects of Bd infection at different ages within a life stage, has received little attention. This study investigated the hypothesis that recently-post-metamorphic frogs were more sensitive to chytridiomycosis than older frogs, and that sensitivity to Bd infection decreased as frogs aged. We examined this relationship with Pacific treefrogs (Pseudacris regilla) and red legged frogs (Rana aurora). Age had a strong effect on susceptibility to infection, infection intensity, and survival–but not in the directions we had predicted. In both host species, an increase in age was associated with frogs becoming more susceptible to Bd infection, harboring larger infection intensities, and greater risk of mortality. This suggests that the timing of Bd exposure may influence amphibian population dynamics. [ABSTRACT FROM AUTHOR]

Scientists across disciplines must often work together to address pressing global issues facing our societies. For interdisciplinary projects to flourish, scientists must recognise the potential contribution of other disciplines in answering key research questions. Recent research suggested that social sciences may be appreciated less than hard sciences overall. Building on the extensive evidence of ingroup bias and ethnocentrism in intergroup relations, however, one could also expect scientists, especially those belonging to high status disciplines, to play down the contributions of other disciplines to important research questions. The focus of the present research was to investigate how hard and social scientists perceive one another and the impact of interdisciplinary collaborations on these perceptions. We surveyed 280 scientists at Wave 1 and with 129 of them followed up at Wave 2 to establish how ongoing interdisciplinary collaborations underpinned perceptions of other disciplines. Based on Wave 1 data, scientists who report having interdisciplinary experiences more frequently are also more likely to recognise the intellectual contribution of other disciplines and perceive more commonalities with them. However, in line with the intergroup bias literature, group membership in the more prestigious hard sciences is related to a stronger tendency to downplay the intellectual contribution of social science disciplines compared to other hard science disciplines. This bias was not present among social scientists who produced very similar evaluation of contribution of hard and social science disciplines. Finally, using both waves of the survey, the social network comparison of discipline pairs shows that asymmetries in the evaluation of other disciplines are only present among discipline pairs that do not have any experience of collaborating with one another. These results point to the need for policies that incentivise new collaborations between hard and social scientists and foster interdisciplinary contact. [ABSTRACT FROM AUTHOR]

Sharing research equipment and personnel across investigators and laboratories has a long-standing history within research universities. However, the coordinated management of centralized, shared resources (i.e., core facilities) that provide access to instruments, technologies, services, expert consultation, and/or other scientific and clinical capabilities by Chief Research Officers (CROs) represents a more recent shift within the academy. While a number of recent surveys and studies have focused on the experiences of core facility directors and users, there has not yet been a targeted survey of CROs. Partnering with the Association for Public and Land Grant Universities Council on Research, fiftyeight CROs (or their designee) from research universities completed an electronic survey on core facilities (response rate = 35%). Core facilities formally reported to a range of entities within the university (and many to multiple entities), including the CRO office (83%), colleges/schools (67%), institutes/centers (42%), and departments (42%). Forty percent of respondents indicated that their university does not have a formal process to become and/or retain status as a recognized core facility. CROs also perceived that different types of core facilities directors differed in their general effectiveness (F(3,179)=6.88, p<.001); professional staff and administrators were rated as significantly more effective at directing/supervising core facilities than were tenure/tenure-track faculty (Tukey's post-hoc; p<.005). Core facilities were funded through a variety of mechanisms, with the most common being use fees (96%), central and/or decentralized funding of directors or staff (77%), annual general fund allocation (62%), a designated portion of Facilities & Administration (F&A) reimbursements (46%), and internal grant programs (31%). Funds for purchasing new equipment within core facilities came from a number of sources, with the most common being external grants (87%), central institutional funds (83%), college/school/department funds (73%), use fees (50%), F&A resources (50%), and donations (27%). There are significant challenges to managing and funding core facilities; the present study provides new insights into the various strategies and tactics being taken by CROs to address these real and perceived challenges. [ABSTRACT FROM AUTHOR]

Background: Large numbers of young people die yearly due to homicide, but little is known about homicide during adolescence. Research primarily focuses on youth violence among young men and masks important gender-related factors inherent in the adolescent age group. Although young women are less likely to be victims of homicide, violence against women is an important form of violence experienced during adolescence. In this paper, we describe the prevalence of and gender difference in adolescent homicide in South Africa in 2009. Methods: We conducted a retrospective national mortuary-based study to identify all child homicides (boys and girls < 18 years) in 2009 in a proportionate sample of mortuaries. Victim, perpetrator and crime data were collected in three phases: cases were identified from the mortuary register, the autopsy report and from police interviews. In this paper we focus on the adolescent group, aged 10 to 17 years. Findings: We identified 674 (95% CI: 520–823) adolescent homicides for 2009, with more male (520) than female (154) homicides. This gender disparity increased as children aged, with the male homicide rate 27.9/100 000 population (95% CI: 20.3–35.5), nearly 5 times the female rate (4.5:1) of 6.5/ 100 000 population (95% CI: 4.7–8.2) in older adolescents (15–17 year old). Adolescent males were significantly more likely (61.2%) to die in a public space compared to female adolescents (39.3%) but more adolescent females (48.4%) died at home compared to adolescent males (32.9%). Adolescent females (42.1%) were mainly killed by a family member or intimate partner while adolescent males were predominantly (58%) killed by an acquaintance. Conclusion: We found a distinct gender pattern for adolescent homicide in South Africa. This pattern appears to be driven by gender norms that support violence. South Africa requires an investment in developing evidence informed interventions to reduce violence. [ABSTRACT FROM AUTHOR]

A growing body of evidence has shown that active learning has a considerable advantage over traditional lecture for student learning in undergraduate STEM classes, but there have been few large-scale studies to identify the specific types of activities that have the greatest impact on learning. We therefore undertook a large-scale, curriculum-wide study to investigate the effects of time spent on a variety of classroom activities on learning gains. We quantified classroom practices and related these to student learning, assessed using diagnostic tests written by over 3700 students, across 31 undergraduate biology classes at a research-intensive university in the Pacific Northwest. The most significant positive predictor of learning gains was the use of group work, supporting the findings of previous studies. Strikingly, we found that the addition of worksheets as an active learning tool for in-class group activities had the strongest impact on diagnostic test scores. This particular low-tech activity promotes student collaboration, develops problem solving skills, and can be used to inform the instructor about what students are struggling with, thus providing opportunities for valuable and timely feedback. Overall, our results indicate that group activities with low barriers to entry, such as worksheets, can result in significant learning gains in undergraduate science. [ABSTRACT FROM AUTHOR]

Introduction: For HIV-positive individuals on antiretroviral therapy (ART), the World Health Organization (WHO) recommends routine viral load (VL) monitoring. We report on the cascade of care in individuals with unsuppressed VL after introduction of routine VL monitoring in a district in Lesotho. Materials and methods: In Butha-Buthe district 12 clinics (11 rural, 1 hospital) send samples for VL testing to the district laboratory. We included data from patients aged ≥15 years from Dec 1, 2015 to November 1, 2018. As per WHO guidelines VL <1000 copies/mL are considered suppressed, those ≥1000copies/mL unsuppressed. Patients with unsuppressed VL receive adherence counseling and follow-up VL within 8–12 weeks. Two consecutively unsuppressed VLs should trigger switch to second-line ART. For analysis of the VL monitoring cascade we defined care to be “according to guidelines” if patients with unsuppressed VL received a follow-up VL within <180 days and follow-up VL was either re-suppressed, or again unsuppressed and the individual was switched to second-line within 90 days. Results: For 9,949 individuals 24,948 VL tests were available. The majority were female (73%), median age 41 years (interquartile range 33–52), and 58% seen at rural clinics. Overall, 25% (260/1028) of individuals were managed according to guidelines: 40% (410/1028) had a follow-up VL within 180 days of their initial unsuppressed VL and 25% (260/1028) of those either re-suppressed or switched to second-line within 90 days. Female patients were more likely to have a follow-up VL done, (p = 0.015). In rural clinics rates of two consecutively unsuppressed VLs were higher than in the hospital (64% vs. 44%, p<0.001), and rural clinics were less likely to switch these patients to second-line (35% vs. 66%, p<0001). Conclusions: Our data show that in a real-life setting availability of routine VL monitoring may not be exploited to its potential. A lack of timely follow-up after a first unsuppressed VL and reluctance to switch patients with confirmed virological failure, reduce the benefit of VL monitoring, i.e. in the rural clinics. Future studies will have to assess models of care which ensure that VL results are met with an action and make use of scalable innovative approaches. [ABSTRACT FROM AUTHOR]

Once a fixture of research in the social and behavioral sciences, volunteer subjects are now only rarely used in human subjects research. Yet volunteers are a potentially valuable resource, especially for research conducted online. We argue that online volunteer laboratories are able to produce high-quality data comparable to that from other online pools. The scalability of volunteer labs means that they can produce large volumes of high-quality data for multiple researchers, while imposing little or no financial burden. Using a range of original tests, we show that volunteer and paid respondents have different motivations for participating in research, but have similar descriptive compositions. Furthermore, volunteer samples are able to replicate classic and contemporary social science findings, and produce high levels of overall response quality comparable to paid subjects. Our results suggest that online volunteer labs represent a potentially significant untapped source of human subjects data. [ABSTRACT FROM AUTHOR]

Vegetation is a key determinant of wildfire behaviour at field scales as it functions as fuel. Past studies in the laboratory show that plant flammability, the ability of plants to ignite and maintain combustion, is a function of their traits. However, the way the traits of individual plants combine in a vegetation community to affect field flammability has received little attention. This study aims to bridge the gap between the laboratory and field by linking plant traits to metrics of field-scale flammability. Across three prescribed burns, in Eucalyptus-dominated damp and dry forest, we measured pre-burn plant species abundance and post-burn field flammability metrics (percentage area burnt, char and scorch height). For understory species with dominant cover-abundance, we measured nine traits that had been demonstrated to influence flammability in the laboratory. We used fourth-corner ordination to evaluate covariation between the plant traits, species abundance and flammability. We found that several traits covaried at the species level. In some instances, these traits (e.g. specific leaf area and bulk density) could have cumulative effects on the flammability of a species while in other instances (e.g. moisture and specific leaf area) they may have counteractive effects, assuming trait effects on flammability are akin to previous research. At field scales, species with similar traits tended to co-occur, suggesting that the effects of individual traits accumulate within a plant community. Fourth-corner analyses found the trait-field flammability relationship to be statistically significant. Traits significantly associated with increasing field flammability metrics were: bulk density (negatively associated) and hydrocarbon quantity, specific leaf area and surface area to volume ratio (all positively associated). Our study demonstrates that some traits known to influence flammability in the laboratory can be associated with field-scale flammability metrics. Further research is needed to isolate the contributions of individual traits to understand how species composition drives forest flammability. [ABSTRACT FROM AUTHOR]

Introduction: Viral load (VL) monitoring programs have been scaled up rapidly, but are now facing the challenge of providing access to the most remote facilities (the “last mile”). For the hardest-to-reach facilities in Zambia, we compared the cost of placing point of care (POC) viral load instruments at or near facilities to the cost of an expanded sample transportation network (STN) to deliver samples to centralized laboratories. Methods: We extended a previously described geospatial model for Zambia that first optimized a STN for centralized laboratories for 90% of estimated viral load volumes. Amongst the remaining 10% of volumes, facilities were identified as candidates for POC placement, and then instrument placement was optimized such that access and instrument utilization is maximized. We evaluated the full cost per test under three scenarios: 1) POC placement at all facilities identified for POC; 2)an optimized combination of both on-site POC placement and placement at facilities acting as POC hubs; and 3) integration into the centralized STN to allow use of centralized laboratories. Results: For the hardest-to-reach facilities, optimal POC placement covered a quarter of HIV-treating facilities. Scenario 2 resulted in a cost per test of $39.58, 6% less than the cost per test of scenario 1, $41.81. This is due to increased POC instrument utilization in scenario 2 where facilities can act as POC hubs. Scenario 3 was the most costly at $53.40 per test, due to high transport costs under the centralized model ($36 per test compared to $12 per test in scenario 2). Conclusions: POC VL testing may reduce the costs of expanding access to the hardest-to-reach populations, despite the cost of equipment and low patient volumes. An optimal combination of both on-site placement and the use of POC hubs can reduce the cost per test by 6–35% by reducing transport costs and increasing instrument utilization. [ABSTRACT FROM AUTHOR]

Background: The purpose of this paper was to analyze the general diagnostic strength and performance of in vitro diagnostics for C-reactive protein and procalcitonin based on the results of external quality assessment schemes (EQAs). Methods: We analyzed qualitative and quantitative data on both markers collected by the Society for Promotion Quality Assurance in Medical Laboratories (INSTAND e.V.) from 20 EQAs. The C-reactive protein evaluation was method-specific and the procalcitonin evaluation manufacturer-specific (pseudonymized). Coefficients of variation were determined in order to evaluate interlaboratory comparability and the performance of individual laboratories during the analyzed period was examined. Results: Overall most of our participants were able to correctly distinguish the positive from the negative samples, but we occasionally observed also false-positive results for the immunological detection of C-reactive protein. For the semi-quantitative results of C-reactive protein we observed an overall median difference below 5% except for dry chemistry methods (≤ 21%). For procalcitonin two manufacturer collectives showed a good comparability, while one manufacturer detected up to 42% higher results. The coefficients of variation are promising for both analytes even though they surpass the manufacturer’s indication for some collectives. The performance of individual laboratories during the analyzed period was more stable for C-reactive protein than for procalcitonin. Conclusion: In-vitro diagnostic testing for C-reactive protein and procalcitonin showed promising results in our EQAs but still further improvements are needed. We recommend stepping up research on reference measurement methods for both parameters to possibly enhancing the accuracy and diagnostic strength of such assays. [ABSTRACT FROM AUTHOR]

Introduction: Laboratory rat welfare is critically influenced by laboratory animal personnel through their implementation, or lack of implementation, of various enrichment techniques. One such promising technique is heterospecific play, or “rat tickling”, which mimics aspects of rat rough-and-tumble play and can contribute to improving welfare, but may be infrequently implemented. The theory of planned behavior can be used to study implementation by measuring intentions and beliefs about rat tickling, including behavioral attitudes (whether it is good or bad), subjective norms (whether there is social/professional pressure to provide it), and control beliefs (whether they feel in control of providing it). Therefore, the objective of this study was to identify current rat tickling prevalence and predictors among laboratory animal personnel in the United States and Canada. Our hypothesis was that rat tickling prevalence would be low and associated with beliefs about the practice, enrichment, and laboratory animals in general. Methods: Laboratory animal personnel were recruited from widespread online promotion. A total of 794 personnel (mean = 40±11 years, 80% white, 80% female) completed at least 50% of the mixed methods online survey and met inclusion criteria of currently working with laboratory rats in the USA or Canada. The survey included questions about demographics, enrichment practices and beliefs, attitudes towards rats, general positive behaviors (e.g. talking to laboratory animals), and both practices and beliefs about rat tickling. Qualitative data were coded using thematic analysis. Quantitative data were analyzed using general linear models. Results: Laboratory personnel reported low levels of rat tickling implementation, with 89% of participants reporting using it never or rarely. Laboratory personnel reported 2 key benefits (handling: 61%, welfare: 55%) and 3 key barriers (time: 59%, personnel: 22%, and research: 22%) to rat tickling using qualitative analysis. Current and planned rat tickling were positively associated with more positive beliefs (social/professional pressure p<0.0001, control of providing tickling p<0.0001) and familiarity with tickling (p<0.0001). Current rat tickling was also positively associated with more positive general behaviors towards laboratory animals, such as naming animals (p<0.0001). Future rat tickling was positively associated with more positive attitudes about it (p<0.0001) and a desire to implement more enrichment (p<0.01). Conclusion: Our findings show that even though rat tickling implementation is currently low, it is positively associated with personnel beliefs, familiarity, general attitudes, and a desire for more enrichment. That is, laboratory animal personnel were more likely to provide rat tickling if they were more familiar with it, thought providing it was both good and under their control, and felt subject to social/professional pressure, as well as if they wanted to provide more enrichment and generally had more positive behaviors towards laboratory animals. There is potential to increase rat tickling by increasing personnel familiarity with the procedure through training, decreasing the time required, and changing personnel beliefs–thereby improving rat welfare. [ABSTRACT FROM AUTHOR]

Murine Astrovirus is one of the most prevalent viral agents in laboratory rodent facilities worldwide, but its influence on biomedical research results is poorly examined. Due to possible influence on research results and high seroprevalence rates in mice, it appears useful to include this virus into routine health monitoring programs. In order to establish exhaust air particle PCR as a reliable detection method for Murine Astrovirus infections in mice kept in individually ventilated cages (IVC) and compare the method to sentinel mice monitoring regarding reproducibility and detection limit, we conducted a study with defined Murine Astrovirus cage prevalence. In parallel, the efficacy of both detection strategies (soiled-bedding sentinel (SBS) and exhaust air dust (EAD) analysis) was tested for Myocoptes musculinus. The fur mite was used as a reference organism during the whole study period to ensure the validity of this method. Because some publications already demonstrated successful detection of several pathogens, including murine fur mite species, via EAP-PCR. Detection of Murine Astrovirus infections at low prevalence is possible with both methods tested. Detection by exhaust air particles (EAP) is faster, more sensitive and more reliable compared to soiled bedding sentinels (SBS). Exhaust air particle PCR also detected the reference organism Myocoptes musculinus, which was not detected at all by sentinel mice, not even by high sensitivity fur swab qPCR. In conclusion, Murine Astrovirus can be detected by both exhaust air particle PCR and soiled bedding sentinels. We recommend exhaust air particle PCR as the better detection technique for Murine Astrovirus, because it is more reliable. Environmental samples are the method of choice for detection of Myocoptes musculinus because relying on soiled bedding sentinels harbors a big risk of missing existing infestations. [ABSTRACT FROM AUTHOR]

Early infant diagnosis (EID) of HIV provides an opportunity for early HIV detection and access to appropriate Antiretroviral treatment (ART). Dried Blood Spot (DBS) samples are used for EID of exposed infants, born to HIV-positive mothers. However, DBS rejection rates in Zimbabwe have been exceeding the target of less than 2% per month set by the National Microbiology Reference Laboratory (NMRL), in Harare. The aim of this study was to determine the DBS sample rejection rate, the reasons for rejection and the possible associations between rejection and level of health facility where the samples were collected. This is an analytical cross-sectional study using routine DBS sample data from the NMRL in Harare, Zimbabwe, between January and December 2017.A total of 34 950 DBS samples were received at the NMRL. Of these, 1291(4%) were rejected. Reasons for rejection were insufficient specimen volume (72%), missing request form (11%), missing sample (6%), cross-contamination (6%), mismatch of information (4%) and clotted sample (1%). Samples collected from clinics/rural health facilities were five times more likely to be rejected compared to those from a central hospital. Rejection rates were above the set target of <2%. The reasons for rejection were ‘pre-analytical’ errors including labelling errors, missing or inconsistent data, and insufficient blood collected. Samples collected at primary healthcare facilities had higher rejection rates. [ABSTRACT FROM AUTHOR]

Estimation of influenza-like illness (ILI) using search trends activity was intended to supplement traditional surveillance systems, and was a motivation behind the development of Google Flu Trends (GFT). However, several studies have previously reported large errors in GFT estimates of ILI in the US. Following recent release of time-stamped surveillance data, which better reflects real-time operational scenarios, we reanalyzed GFT errors. Using three data sources—GFT: an archive of weekly ILI estimates from Google Flu Trends; ILIf: fully-observed ILI rates from ILINet; and, ILIp: ILI rates available in real-time based on partial reporting—five influenza seasons were analyzed and mean square errors (MSE) of GFT and ILIp as estimates of ILIf were computed. To correct GFT errors, a random forest regression model was built with ILI and GFT rates from the previous three weeks as predictors. An overall reduction in error of 44% was observed and the errors of the corrected GFT are lower than those of ILIp. An 80% reduction in error during 2012/13, when GFT had large errors, shows that extreme failures of GFT could have been avoided. Using autoregressive integrated moving average (ARIMA) models, one- to four-week ahead forecasts were generated with two separate data streams: ILIp alone, and with both ILIp and corrected GFT. At all forecast targets and seasons, and for all but two regions, inclusion of GFT lowered MSE. Results from two alternative error measures, mean absolute error and mean absolute proportional error, were largely consistent with results from MSE. Taken together these findings provide an error profile of GFT in the US, establish strong evidence for the adoption of search trends based 'nowcasts' in influenza forecast systems, and encourage reevaluation of the utility of this data source in diverse domains. [ABSTRACT FROM AUTHOR]

The contemporary scientific community places a growing emphasis on the reproducibility of research. The projects R package is a free, open-source package created in the interest of facilitating reproducible research workflows. It adds to existing software tools for reproducible research and introduces several practical features that are helpful for scientists and their collaborative research teams. For each individual project, it supplies a framework for storing raw and cleaned study data sets, and it provides script templates for protocol creation, data cleaning, data analysis and manuscript development. Internal databases of project and author information are generated and displayed, and manuscript title pages containing author lists and their affiliations are automatically generated from the internal database. File management tools allow teams to organize multiple projects. When used on a shared file system, multiple researchers can harmoniously contribute to the same project in a less punctuated manner, reducing the frequency of misunderstandings and the need for status updates. [ABSTRACT FROM AUTHOR]

Background: Considerable upscaling of malaria control efforts have taken place over the last 15 years in the Democratic Republic of Congo, the country with the second highest malaria case load after Nigeria. Malaria control interventions have been strengthened in line with the Millenium Development Goals. We analysed the effects of these interventions on malaria cases at health facility level, using a retrospective trend analysis of malaria cases between 2005 and 2014. Data were collected from outpatient and laboratory registers based on a sample of 175 health facilities that represents all eco-epidemiological malaria settings across the country. Methods: We applied a time series analysis to assess trends of suspected and confirmed malaria cases, by health province and for different age groups. A linear panel regression model controlled for non-malaria outpatient cases, rain fall, nightlight intensity, health province and time fixed effects, was used to examine the relationship between the interventions and malaria case occurrences, as well as test positivity rates. Results: Overall, recorded suspected and confirmed malaria cases in the DRC have increased. The sharp increase in confirmed cases from 2010 coincides with the introduction of the new treatment policy and the resulting scale-up of diagnostic testing. Controlling for confounding factors, the introduction of rapid diagnostic tests (RDTs) was significantly associated with the number of tested and confirmed cases. The test positivity rate fluctuated around 40% without showing any trend. Conclusion: The sharp increase in confirmed malaria cases from 2010 is unlikely to be due to a resurgence of malaria, but is clearly associated with improved diagnostic availability, mainly the introduction of RDTs. Before that, a great part of malaria cases were treated based on clinical suspicion. This finding points to a better detection of cases that potentially contributed to improved case management. Furthermore, the expansion of diagnostic testing along with the increase in confirmed cases implies that before 2010, cases were underreported, and that the accuracy of routine data to describe malaria incidence has improved. [ABSTRACT FROM AUTHOR]

Harmonia axyridis (Coleoptera, Coccinellidae) is a globally invasive ladybird. It has been intentionally introduced in many countries as a biological control agent, whereas it has been unintentionally released in many others. Climatic factors are important in limiting the spread of H. axyridis. For example, very few records are known from tropical or desert regions. Currently, no published reports are known from Central America. Here, we report H. axyridis from Costa Rica, Guatemala, Honduras, Panama, and Puerto Rico. Specimens were either observed by the authors, discovered in dried insect collections, or retrieved from searching through online photographs available from the citizen science project iNaturalist and the photo-sharing website Flickr. These new records and the wide distribution of H. axyridis in Latin America suggest several invasion events, which have gone unnoticed until now. We stress the need for further, large-scale monitoring and show the advantage of citizen science to assess the presence of invasive alien species. [ABSTRACT FROM AUTHOR]

Recent molecular systematic studies of arvicoline voles of the genera Neodon, Lasiopodomys, Phaiomys, and Microtus from Central Asia suggest the inclusion of Phaiomys leucurus, Microtus clarkei, and Lasiopodomys fuscus into Neodon and moving Neodon juldaschi into Microtus (Blanfordimys). In addition, three new species of Neodon (N. linzhiensis, N. medogensis, and N. nyalamensis) have recently been described from Tibet. Analyses of concatenated mitochondrial (Cytb, COI) and nuclear (Ghr, Rbp3) genes recovered Neodon as a well-supported monophyletic clade including all the recently described and relocated species. Kimura-2-parameter distance between Neodon from western Nepal compared to N. sikimensis (K2P = 13.1) and N. irene (K2P = 13.4) was equivalent to genetic distances observed between recognized species of this genus. The specimens sampled from western Nepal were recovered sister to N. sikimensis in the concatenated analysis. However, analyses conducted exclusively with mitochondrial loci did not support this relationship. The occlusal patterns of the first lower (m1) and third upper (M3) molars were simpler in specimens from western Nepal in comparison to N. sikimensis from eastern Nepal and India. Twelve craniodental characters and four external field measurements were examined from specimens of N. sikimensis from eastern Nepal and India, N. irene, and Neodon from western Nepal. Neodon from western Nepal were significantly different from N. sikimensis from eastern Nepal and India in ten out of 16 characters measured and from N. irene for all characters except ear height. Specimens from western Nepal were smaller in size than N. sikimensis from Eastern Nepal and India and larger than N. irene. Together the results of the molecular and morphological analyses indicate that Neodon from western Nepal are distinct under the phylogenetic, genetic and morpho species concepts. [ABSTRACT FROM AUTHOR]

Social learning has important ecological and evolutionary consequences but the role of certain factors, such as social rank, neophobia (i.e., avoidance of novel stimuli), persistence, and task-reward association, remain less understood. We examined the role of these factors in social learning by captive coyotes (Canis latrans) via three studies. Study 1 involved individual animals and eliminated object neophobia by familiarizing the subjects to the testing apparatus prior to testing. Studies 2 and 3 used mated pairs to assess social rank, and included object neophobia, but differed in that study 3 decoupled the food reward from the testing apparatus (i.e., altered task-reward association). For all three studies, we compared performance between coyotes that received a demonstration from a conspecific to control animals with no demonstration prior to testing. Coyotes displayed social learning during study 1; coyotes with a demonstrator were faster and more successful at solving the puzzle box but did not necessarily use the same modality as that observed to be successful. In study 2, there was no difference in success between treatment groups but this is likely because only one coyote within each pair was successful so successful coyote results were masked by their unsuccessful mate. In study 3, there was no difference in success between treatment groups; only two coyotes, both dominant, hand-reared males with demonstrators were able to perform the task. However, coyotes with a demonstrator were less neophobic, measured as latency to approach the object, and more persistent, measured as time spent working on the apparatus. Social rank was the best predictor of neophobia and persistence and was also retained in the best model for time to eat inside the apparatus, a post-trial measurement of object neophobia. These results suggest coyotes are capable of social learning for novel tasks but social rank, neophobia, and persistence influence their social-learning capabilities. This study contributes to understanding the mechanisms underlying how animals gain information about their environment. [ABSTRACT FROM AUTHOR]

Research is an intellectual activity which not only improves the existing services but also secures the future generation by putting forward valuable recommendations. The quality of research is co-related with the research attitude of the researcher. The research attitude of the researcher depends upon several aspects. The study at hand is an effort to investigate the relationship of on-campus facilities with the research attitude of students. To conduct the survey MPhil and PhD level students of social sciences departments from 20 public and private universities were the target population. Conveniently selected 300 respondents were approached through two questionnaires to reveal that students' research attitudes and on-campus facilities were significantly co-related. [ABSTRACT FROM AUTHOR]

Background: In recent months, multiple publications have demonstrated the use of convolutional neural networks (CNN) to classify images of skin cancer as precisely as dermatologists. However, these CNNs failed to outperform the International Symposium on Biomedical Imaging (ISBI) 2016 challenge which ranked the average precision for classification of dermoscopic melanoma images. Accordingly, the technical progress represented by these studies is limited. In addition, the available reports are impossible to reproduce, due to incomplete descriptions of training procedures and the use of proprietary image databases or non-disclosure of used images. These factors prevent the comparison of various CNN classifiers in equal terms. Objective: To demonstrate the training of an image-classifier CNN that outperforms the winner of the ISBI 2016 CNNs challenge by using open source images exclusively. Methods: A detailed description of the training procedure is reported while the used images and test sets are disclosed fully, to insure the reproducibility of our work. Results: Our CNN classifier outperforms all recent attempts to classify the original ISBI 2016 challenge test data (full set of 379 test images), with an average precision of 0.709 (vs. 0.637 of the ISBI winner) and with an area under the receiver operating curve of 0.85. Conclusion: This work illustrates the potential for improving skin cancer classification with enhanced training procedures for CNNs, while avoiding the use of costly equipment or proprietary image data. [ABSTRACT FROM AUTHOR]

Due to the Expanded Program on Immunization (EPI) and supplementary immunization activities (SIAs) in China, the incidence of measles in China has decreased extensively. The incidence reached its lowest levels in contemporary history in 2012 and 2017, with incidence rates of 4.6 and 4.3 per million population, respectively. However, more than 147,000 measles cases were reported from 2013 to 2016. Furthermore, the proportions of cases in infants < 8 months and adults have been increasing since 2013, representing a considerable challenge for measles elimination in China. A total of 14,868 measles viruses were isolated from confirmed measles cases from 2011 to 2017, of which 14,631 were identified as the predominant endemic genotype, H1; 87 were identified as genotype A viruses that were vaccine associated strains; and 150 were identified as non-H1 genotype viruses. The non-H1 genotype viruses included 62 D8 viruses, 70 D9 viruses, 3 D11 viruses, 14 B3 viruses, and 1 G3 virus, which were identified as imported or import-related viruses that caused sporadic cases or small outbreaks. Most of the transmission chains detected during the period 2011–2012 were interrupted and were followed by many new transmission chains of unknown origin that spread, causing a large measles resurgence in China during 2013–2016. After 4 years of measles resurgence and continuous implementation of the routine immunization program and SIAs, the population immunity reached a sufficiently high level to interrupt most of the transmission chains; only a few strains survived, which continued to be sporadically detected in China in 2017. In the present study, the results from the combined epidemiological and molecular virological data demonstrated the great progress towards measles elimination in China by the further analysis of circulation dynamics for the endemic H1 genotype measles virus from 2011 to 2017. And this study accumulated critical baseline data on circulating wild-type measles viruses in China and provides comprehensive information to the world. These comprehensive baseline data provide evidence to support measles elimination in the future, not only in China but also in other countries worldwide. In addition, the information will be very useful to other countries for tracing their sources of measles cases and for identifying transmission links, which can help prevent potential measles outbreaks. [ABSTRACT FROM AUTHOR]

In tasks that demand rapid performance, actions must be executed as efficiently as possible. Theories of expert motor performance such as the motor chunking framework suggest that efficiency is supported by automatization, where many serial actions are automatized into smaller chunks, or groups of commonly co-occuring actions. We use the fast-paced, professional eSport StarCraft 2 as a test case of the explanatory power of the motor chunking framework and assess the importance of chunks in explaining expert performance. To do so, we test three predictions motivated by a simple motor chunking framework. (1) StarCraft 2 players should exhibit an increasing number of chunks with expertise. (2) The proportion of actions falling within a chunk should increase with skill. (3) Chunks should be faster than non-chunks containing the same atomic behaviours. Although our findings support the existence of chunks, they also highlight two problems for existing accounts of rapid motor execution and expert performance. First, while better players do use more chunks, the proportion of actions within a chunks is stable across expertise and expert sequences are generally more varied (the diversity problem). Secondly, chunks, which are supposed to enjoy the most extreme automatization, appear to save little or no time overall (the time savings problem). Instead, the most parsimonious description of our latency analysis is that players become faster overall regardless of chunking. [ABSTRACT FROM AUTHOR]

An appreciation of body size allometry is central for understanding insect pollination ecology. A recent model utilises allometric coefficients for five of the seven extant bee families (Apoidea: Anthophila) to include crucial but difficult-to-measure traits, such as proboscis length, in ecological and evolutionary studies. Melittidae were not included although they are important pollinators in South Africa where they comprise an especially rich and morphologically diverse fauna. We measured intertegular distance (correlated with body size) and proboscis length of 179 specimens of 11 species from three genera of Melittidae. With the inclusion of Melittidae, we tested the between family differences in the allometric scaling coefficients. AIC model selection was used to establish which factors provide the best estimate of proboscis length. We explored a hypothesis that has been proposed in the literature, but which has not been tested, whereby body and range sizes of bees are correlated with rainfall regions. We tested this by using body size measurements of 2109 museum specimens from 56 species of Melittidae and applied the model coefficients to estimate proboscis length and foraging distance. Our results from testing differences across bee families show that with the addition of Melittidae, we retained the overall pattern of significant differences in the scaling coefficient among Apoidea, with our model explaining 98% of the variance in species-level means for proboscis length. When testing the relationship between body size and rainfall region we found no relationship for South African Melittidae. Overall, this study has added allometric scaling coefficients for an important bee family and shown the applicability of using these coefficients when linked with museum specimens to test ecological hypothesis. [ABSTRACT FROM AUTHOR]

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A new test rig has been designed, built and commissioned, and is now jointly pursued to facilitate experimental investigations into advanced combustion processes (i.e., dual fuel, multi-mode) under turbulent conditions at high, engine-like temperature and pressure levels. Based on a standard diesel engine block, it offers much improved optical access to the in-cylinder processes due to its separated and rotated arrangement of the compression volume and combustion chamber, respectively. A fully variable pneumatic valve train and the appropriate preconditioning of the intake air allows it to represent a wide range of engine-like in-cylinder conditions regarding pressures, temperatures and turbulence levels. The modular design of the test rig facilitates easy optimizations of the combustion chamber/cylinder head design regarding different experimental requirements. The name of the new test rig, Flex-OeCoS, denotes its Flexibility regarding Optical engine Combustion diagnostics and/or the development of corresponding Sensing devices and applications. Measurements regarding in-cylinder gas pressures, temperatures and the flow field under typical operating conditions are presented to complete the description and assessment of the new test rig.

Background: We describe CD4 count recovery among HIV positive individuals who initiated antiretroviral therapy (ART) with and without severe immune suppression using complete laboratory data from South Africa’s national HIV treatment programme between 2010 and 2014 and discuss implications for CD4 count monitoring. Methods: Retrospective analysis of routinely collected laboratory data from South Africa’s National Health Laboratory Service (NHLS). A probabilistic record linkage algorithm was used to create a cohort of HIV positive individuals who initiated ART between 2010 and 2014 based on timing of CD4 count and viral load measurements. A CD4 count < 50 copies/μl at ART initiation was considered severe immunosuppression. A multivariable piecewise mixed-effects linear regression model adjusting for age, gender, year of starting ART, viral suppression in follow up and province was used to predict CD4 counts during follow up. Results: 1,070,900 individuals had evidence of starting ART during 2010–2014 and met the criteria for inclusion in the cohort -46.6% starting ART with CD4 < 200 cells/μl and 10.1% with CD4 < 50 cells/ μl. For individuals with CD4 counts < 200 cells/μl, predicted CD4 counts > 200 cells/μl, >350 cells/μl and >500 cells/μl corresponded with mean follow up durations of 1.5 years (standard deviation [s.d] 1.1), 1.9years (s.d 1.2) and 2.1 years (s.d 1.3 years). For those with CD4 counts < 50 cells/μl, predicted CD4 count above these threshold corresponded with mean follow up durations of 2.5 years (s.d 0.9 years), 4.4 years (s.d 0.4 years) and 5.0 years (s.d 0.1years) for recovery to the same thresholds. CD4 count recovery varied mostly with duration on ART, CD4 count at the start of ART and gender. Conclusion: For individuals starting with ART with severe immunosuppression, CD4 recovery to 200cells/μl did not occur or took longer than 12 month for significant proportions. CD4 monitoring and interventions recommended for advanced HIV disease should continue until full recovery. [ABSTRACT FROM AUTHOR]

The 2011 report, Vision and Change in Undergraduate Biology Education: A Call to Action, provided the impetus to mobilize the undergraduate life sciences education community to affect change in order to enhance the educational experiences of life sciences majors. The work of the appointed Partnership for Undergraduate Life Sciences Education (PULSE) Vision and Change (V&C) Leadership Fellows has focused on the development of programs and resources to support departmental change. In this report, we present a qualitative assessment of several documents generated from the PULSE V&C Leadership Fellow Recognition Team. The Recognition Team developed two initiatives to provide departments with feedback on their change process. The first initiative, the validated PULSE V&C Rubrics, enables departments to collaboratively self-assess their progress in enacting change. The second initiative, the PULSE Recognition Program, involves completion of the aforementioned Rubrics and a site-visit by two Recognition Team members to provide external insights and suggestions to foster a department’s change process. Eight departments participated in the Recognition Program in 2014. An evaluation of the documents yielded from the Recognition Program review of seven of the eight departments and a comparison of Rubric scores from before and three years following the site-visits uncovered several common elements required for successful department level change. These elements include an institutional culture that values and supports excellence in teaching and learning with resources and infrastructure, a departmental emphasis on program and course level assessment, and, most importantly, a departmental champion who actively supports endeavors that enhance teaching excellence. [ABSTRACT FROM AUTHOR]

Soil-transmitted helminths (STHs) affect more than 1.5 billion people. The global strategy to control STH infections requires periodic mass drug administration (MDA) based on prevalence among populations at risk determined by diagnostic testing. Widely used copromicroscopy methods to detect infection, however, have low sensitivity as the prevalence and intensity of STH infections decline with repeated MDA. More sensitive diagnostic tools are needed to inform program decision-making. Using an integrated product development process, PATH conducted qualitative and quantitative formative research to inform the design and development of a more sensitive test for STH infections. The research, grounded in a conceptual framework for ensuring access to health products, involved stakeholder analysis, key opinion leader interviews, observational site visits of ongoing STH surveillance programs, and market research including market sizing, costing and willingness-to-pay analyses. Stakeholder analysis identified key groups and proposed strategic engagement of stakeholders during product development. Interviews highlighted features, motivations and concerns that are important for guiding design and implementation of new STH diagnostics. Process mapping outlined current STH surveillance workflows in Kenya and the Philippines. Market sizing in 2016 was estimated around half a million tests for lower STH burden countries, and 1–2 million tests for higher STH burden countries. The cost of commodities per patient for a molecular STH diagnostic may be around $10, 3–4 times higher than copromicroscopy methods, though savings may be possible in time and staffing requirements. The market is highly price sensitive as even at $5 per test, only 27% of respondents thought the test would be used by surveillance programs. A largely subsidized STH control strategy and a semi-functional Kato-Katz test may have created few incentives for manufacturers to innovate in STH diagnostics. Diverse partnerships, as well as balancing needs and expectations for new STH diagnostics are necessary to ensure access to needed products. [ABSTRACT FROM AUTHOR]

In a Policy Forum, Peter Ehrenkranz and colleagues discuss the contribution of CD4 and viral load testing to outcomes for people with HIV in low- and middle-income countries. [ABSTRACT FROM AUTHOR]

Recent high throughput omics technology has been used to assemble large biomedical omics datasets. Clustering of single omics data has proven invaluable in biomedical research. For the task of patient sub-classification, all the available omics data should be utilized combinedly rather than treating them individually. Clustering of multi-omics datasets has the potential to reveal deep insights. Here, we propose a late integration based multiobjective multi-view clustering algorithm which uses a special perturbation operator. Initially, a large number of diverse clustering solutions (called base partitionings) are generated for each omic dataset using four clustering algorithms, viz., k means, complete linkage, spectral and fast search clustering. These base partitionings of multi-omic datasets are suitably combined using a special perturbation operator. The perturbation operator uses an ensemble technique to generate new solutions from the base partitionings. The optimal combination of multiple partitioning solutions across different views is determined after optimizing the objective functions, namely conn-XB, for checking the quality of partitionings for different views, and agreement index, for checking agreement between the views. The search capability of a multiobjective simulated annealing approach, namely AMOSA is used for this purpose. Lastly, the non-dominated solutions of the different views are combined based on similarity to generate a single set of non-dominated solutions. The proposed algorithm is evaluated on 13 multi-view cancer datasets. An elaborated comparative study with several baseline methods and five state-of-the-art models is performed to show the effectiveness of the algorithm. [ABSTRACT FROM AUTHOR]

Scientific data recording and reporting systems are of a great interest for endorsing reproducibility and transparency practices among the scientific community. Current research generates large datasets that can no longer be documented using paper lab notebooks (PLNs). In this regard, electronic laboratory notebooks (ELNs) could be a promising solution to replace PLNs and promote scientific reproducibility and transparency. We previously analyzed five ELNs and performed two survey-based studies to implement an ELN in a biomedical research institute. Among the ELNs tested, we found that Microsoft OneNote presents numerous features related to ELN best functionalities. In addition, both surveyed groups preferred OneNote over a scientifically designed ELN (PerkinElmer Elements). However, OneNote remains a general note-taking application and has not been designed for scientific purposes. We therefore provide a quick guide to adapt OneNote to an ELN workflow that can also be adjusted to other nonscientific ELNs. [ABSTRACT FROM AUTHOR]

Air temperature data retrieved from global atmospheric models may show a systematic bias with respect to measurements from weather stations. This is a common concern in local climate studies. The current study presents two methods based upon copulas and Conditional Probability (CP) to predict bias-corrected mean air temperature in a data-scarce environment: CP-I offers a single conditional probability as a predictor, CP-II is a pixel-wise version of CP-I and offers spatially varying predictors. The methods were applied on daily air temperature in the Qazvin Plain, Iran that were collected at 24 weather stations and 150 ECMWF ERA-interim grid cells from a single month (June) over 11 years. We compared the methods with the commonly applied conditional expectation and conditional median methods. Leave-k-out cross-validation and correlation scores show that the new methods reduced the bias with 44–68% for the full data set and with 34–74% on a homogeneous subarea. We conclude that the two methods are able to locally improve ECMWF air temperatures in a data-scarce area. [ABSTRACT FROM AUTHOR]

Background: Better research data management (RDM) provides the means to analyze data in new ways, effectively build on another researcher’s results, and reproduce the results of an experiment. Librarians are recognized by many as a potential resource for assisting researchers in this area, however this potential has not been fully realized in the biomedical research community. While librarians possess the broad skill set needed to support RDM, they often lack specific knowledge and time to develop an appropriate curriculum for their research community. The goal of this project was to develop and pilot educational modules for librarians to learn RDM and a curriculum for them to subsequently use to train their own research communities. Materials and methods: We created online modules for librarians that address RDM best practices, resources and regulations, as well as the culture and practice of biomedical research. Data was collected from librarians through questions embedded in the online modules on their self-reported changes in understanding of and comfort level with RDM using a retrospective pre-post design. We also developed a Teaching Toolkit which consists of slides, a script, and an evaluation form for librarians to use to teach an introductory RDM class to researchers at their own institutions. Researchers’ satisfaction with the class and intent to use the material they had learned was collected. Actual changes in RDM practices by researchers who attended was assessed with a follow-up survey administered seven months after the class. Results and discussion: The online curriculum increased librarians’ self-reported understanding of and comfort level with RDM. The Teaching Toolkit, when employed by librarians to teach researchers in person, resulted in improved RDM practices. This two-tiered curriculum provides concise training and a ready-made curriculum that allows working librarians to quickly gain an understanding of RDM, and translate this knowledge to researchers through training at their own institutions. [ABSTRACT FROM AUTHOR]