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Research is characterized as detailed consideration of some subject or concept utilizing logical techniques with an intention to provide useful knowledge to concerned department or society. Research usually uses inductive or deductive methods to verify or recognize the practical phenomenon. Inductive approaches are associated with qualitative research and deductive methods are more commonly associated with quantitative research. All the universities require some ratings in terms of their infrastructure and learning facilities, curriculum and teaching methods, Research, Innovation and Extensions, and services provided to its surrounding societies. This rating helps the parents to know and evaluate the universities before admitting their ward or children‘s to respective universities. In these connections, National Assessment and Accreditation Committee play a major role and it‘s one of most common ranking agency or organization in India. In higher educational institutions or universities the process of promoting research culture among faculties and students is very important and essential for the overall development and to enhance creative and innovative thinking. The institution or university should provide a substantial amount of support in terms of financial, academic and human resources to promote research activities. This paper discusses the different facilities currently available for promotion of research and resource mobilization in Srinivas University. This paper explains what are the innovation and best practices adopted in universities to score good marks under research mobilization and research facilities-key indicators of Research, Innovation and Extension Criteria of NAAC.

Background Medicine quality screening devices hold great promise for post-market surveillance (PMS). However, there is little independent evidence on their field utility and usability to inform policy decisions. This pilot study in the Lao PDR tested six devices’ utility and usability in detecting substandard and falsified (SF) medicines. Methodology/principal findings Observational time and motion studies of the inspections by 16 Lao medicine inspectors of 1) the stock of an Evaluation Pharmacy (EP), constructed to resemble a Lao pharmacy, and 2) a sample set of medicines (SSM); were conducted without and with six devices: four handheld spectrometers (two near infrared: MicroPHAZIR RX, NIR-S-G1 & two Raman: Progeny, Truscan RM); one portable mid-infrared spectrometer (4500a), and single-use paper analytical devices (PAD). User experiences were documented by interviews and focus group discussions. Significantly more samples were wrongly categorised as pass/fail with the PAD compared to the other devices in EP inspections (p, Author summary Substandard and falsified (SF) medicines threaten the lives of millions of people, especially where pharmaceutical legislation and regulation are limited. Screening for SF medicines in supply chains (‘post-market surveillance’) by medicine inspectors is crucial but currently relies only on subjective visual inspection of medicines in most countries. Many innovative portable screening technologies now exist and could be key additional assets to the current practice, but none have been extensively evaluated for medicine quality post-market surveillance. We assessed the utility and usability of six screening devices in the hands of Lao medicines inspectors in a pharmacy constructed to resemble a Lao pharmacy. Five spectrometers showed promising accuracies to identify falsified medicines, but difficulties to correctly set them up before running tests were observed. Reading and interpreting colour barcodes of the ‘paper analytical cards’–a lab-on-a-chip test by inspectors were difficult, leading to lower accuracy than with spectrometers. The study suggests that overconfidence in devices may cause harm by reducing inspectors’ investment in visual inspection—a crucial step to identify falsified medicines. Advantages/limitations of the devices are also documented to inform policy.

Céline Caillet and co-authors discuss a Collection on use of portable devices for the evaluation of medicine quality and legitimacy.

Serum insulin-like growth factor-1 (IGF-I) and IGF binding protein-3 (IGFBP-3) levels can be used to monitor the safety of recombinant human growth hormone (rhGH) therapy. In this study, we evaluated the changes in serum IGF-I and IGFBP-3 levels during rhGH therapy as a marker of height outcome in prepubertal children. Totally, 705 prepubertal children with short stature were enrolled from the LG Growth Study Database. Data for three groups of subjects were obtained as follows: Idiopathic GH deficiency (IGHD; n = 486); idiopathic short stature (n = 66); small for gestational age (n = 153). Serum IGF-I and IGFBP-3 levels at the baseline and after the 1st and 2nd year of rhGH therapy, as well as the Δheight standard deviation score (SDS), were obtained. Δheight SDS after the 1st and 2nd year of rhGH therapy had notably increased compared to that at the baseline for all three groups. IGF-I and IGFBP-3 levels in all three groups were significantly increased compared to those at the baseline (p st year of therapy, ΔIGFBP-3 SDS after the 2nd year of therapy in the IGHD group, and ΔIGF-I SDS and ΔIGFBP-3 SDS after the 2nd year of therapy (p < 0.05), regardless of whether the height at the baseline was a covariate. The increase in IGF-I and IGFBP-3 levels during rhGH therapy was related to the growth response in children with IGHD. Therefore, it may be valuable to measure the change in serum IGF-I and IGFBP-3 levels, especially the latter, during rhGH treatment to predict the growth response upon long-term treatment.

Introduction Acute Q fever is endemic in Israel, yet the clinical and laboratory picture is poorly defined. Methods A retrospective study reviewing the medical records of acute Q fever patients, conducted in a single hospital in the Sharon district, Israel. Serum samples from suspected cases were preliminary tested by a qualitative enzyme immunoassay (EIA). Confirmatory testing at the reference laboratory used an indirect immunofluorescence assay (IFA). Positive cases were defined as fever with at least one other symptom and accepted laboratory criteria such as a single-phase II immunoglobulin G (IgG) antibody titer ≥1:200. Cases not fulfilling these criteria and in which acute Q fever was excluded, served as a control group. Results Between January 2012 and May 2018, 484 patients tested positive. After confirmatory testing, 65 (13.4%) were positive for acute Q fever (with requisite clinical picture), 171 (35.3%) were definitely not infected, the remaining 248 were excluded because of past/chronic/undetermined infection. The average age was 58 years and 66% were males. Most resided in urban areas with rare animal exposure. Pneumonia was seen in 57% of cases and a combination with headache/hepatitis was highly suggestive of acute Q fever diagnosis. Syncope/presyncope, fall and arthritis were more common in acute Q fever cases. Laboratory indexes were similar to the control group, except for erythrocyte sedimentation rate (ESR) which was more common and higher in the study group. Conclusion Acute Q fever in the Sharon district could be better diagnosed by using a syndromic approach in combination with improved rapid diagnostic testing., Author summary Acute Q fever is endemic in Israel, yet the clinical and laboratory picture is poorly defined. We performed a retrospective study reviewing medical records of acute Q fever patients compared to those for whom acute Q fever was excluded. Serum samples from suspected cases were preliminary tested by a qualitative enzyme immunoassay (EIA). Confirmatory testing at the reference laboratory used an indirect immunofluorescence assay (IFA). Positive cases were defined as fever with at least one other symptom and accepted laboratory criteria. Cases not fulfilling these criteria and in which acute Q fever was excluded, served as a control group. Over 6 years, 484 patients tested positive by EIA. After confirmatory testing, 65 (13.4%) were positive for acute Q fever (with requisite clinical picture), 171 (35.3%) were definitely not infected, the remaining 248 were excluded because of past/chronic/undetermined infection. Most resided in urban areas without animal exposure. Pneumonia was seen in 57% of cases and a combination with headache/hepatitis was highly suggestive of acute Q fever diagnosis. Syncope/presyncope, fall and arthritis were more common in acute Q fever cases. We conclude that a syndromic approach to acute Q fever in combination with improved rapid diagnostic testing would be beneficial.

Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is very complex and depends on a large number of variables. We noticed a lack of detailed guides for STA processing. Also, current publications in this field often lack a documentation that is practical enough to reproduce the results with reasonable effort, which is necessary for the scientific community to grow. We therefore provide a complete, detailed, and fully reproducible processing protocol that covers all aspects of particle picking and particle alignment in STA. The command line–based workflow is fully based on the popular Dynamo software for STA. Within this workflow, we also demonstrate how large parts of the processing pipeline can be streamlined and automatized for increased throughput. This protocol is aimed at users on all levels. It can be used for training purposes, or it can serve as basis to design user-specific projects by taking advantage of the flexibility of Dynamo by modifying and expanding the given pipeline. The protocol is successfully validated using the Electron Microscopy Public Image Archive (EMPIAR) database entry 10164 from immature HIV-1 virus-like particles (VLPs) that describe a geometry often seen in electron tomography., This study presents a complete and detailed step-by-step guide for subtomogram averaging using Dynamo software, with a special focus on particle picking and particle averaging; this will enable efficient processing for all experience levels, and lays a foundation for user-specific projects.

The accurate identification of urban functional areas is of great significance for optimizing urban spatial structure, rationally allocating spatial elements, and promoting the sustainable development of the city. This paper proposes a method to precisely identify urban functional areas by coupling Open Street Map (OSM) and Point of Interest (POI) data. It takes the central urban area of Hangzhou as a case study to analyze the spatial distribution characteristics of the functional areas. The results show that: (1) The central urban areas of Hangzhou are divided into 21 functional areas (6 single functional areas, 14 mixed functional areas and 1 comprehensive functional area). (2) The single functional areas and the mixed functional areas show the geographical distribution characteristics of the looping stratification, which means “Core-periphery” differentiation is obvious, and the comprehensive functional area is relatively scattered. (3) The mixed degree of regional function with ecological function and production function is low while comprehensive functional areas are usually associated with higher potential and vitality. (4) The identification results are in great agreement with the actual situation of Hangzhou central urban area, and the method is feasible. Therefore, this paper can provide a reference for urban development planning and management.

Automated analysis of video can now generate extensive time series of pose and motion in freely-moving organisms. This requires new quantitative tools to characterize behavioural dynamics. For the model roundworm Caenorhabditis elegans, body pose can be accurately quantified from video as coordinates in a single low-dimensional space. We focus on this well-established case as an illustrative example and propose a method to reveal subtle variations in behaviour at high time resolution. Our data-driven method, based on empirical dynamic modeling, quantifies behavioural change as prediction error with respect to a time-delay-embedded ‘attractor’ of behavioural dynamics. Because this attractor is constructed from a user-specified reference data set, the approach can be tailored to specific behaviours of interest at the individual or group level. We validate the approach by detecting small changes in the movement dynamics of C. elegans at the initiation and completion of delta turns. We then examine an escape response initiated by an aversive stimulus and find that the method can track return to baseline behaviour in individual worms and reveal variations in the escape response between worms. We suggest that this general approach – defining dynamic behaviours using reference attractors and quantifying dynamic changes using prediction error – may be of broad interest and relevance to behavioural researchers working with video-derived time series.

Increasing attention is being paid to the operation of biomedical data repositories in light of efforts to improve how scientific data is handled and made available for the long term. Multiple groups have produced recommendations for functions that biomedical repositories should support, with many using requirements of the FAIR data principles as guidelines. However, FAIR is but one set of principles that has arisen out of the open science community. They are joined by principles governing open science, data citation and trustworthiness, all of which are important aspects for biomedical data repositories to support. Together, these define a framework for data repositories that we call OFCT: Open, FAIR, Citable and Trustworthy. Here we developed an instrument using the open source PolicyModels toolkit that attempts to operationalize key aspects of OFCT principles and piloted the instrument by evaluating eight biomedical community repositories listed by the NIDDK Information Network (dkNET.org). Repositories included both specialist repositories that focused on a particular data type or domain, in this case diabetes and metabolomics, and generalist repositories that accept all data types and domains. The goal of this work was both to obtain a sense of how much the design of current biomedical data repositories align with these principles and to augment the dkNET listing with additional information that may be important to investigators trying to choose a repository, e.g., does the repository fully support data citation? The evaluation was performed from March to November 2020 through inspection of documentation and interaction with the sites by the authors. Overall, although there was little explicit acknowledgement of any of the OFCT principles in our sample, the majority of repositories provided at least some support for their tenets.

The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing, compiling, integrating and interpreting data, information and knowledge. In order to accelerate research towards effective medical treatments and optimizing health, it is critical that efficient and automated tools for identifying key research concepts and their experimentally discovered interrelationships are developed. As an activity within the feasibility phase of a project called “Translator” (https://ncats.nih.gov/translator) funded by the National Center for Advancing Translational Sciences (NCATS) to develop a biomedical science knowledge management platform, we designed a Representational State Transfer (REST) web services Application Programming Interface (API) specification, which we call a Knowledge Beacon. Knowledge Beacons provide a standardized basic API for the discovery of concepts, their relationships and associated supporting evidence from distributed online repositories of biomedical knowledge. This specification also enforces the annotation of knowledge concepts and statements to the NCATS endorsed the Biolink Model data model and semantic encoding standards (https://biolink.github.io/biolink-model/). Implementation of this API on top of diverse knowledge sources potentially enables their uniform integration behind client software which will facilitate research access and integration of biomedical knowledge. Availability The API and associated software is open source and currently available for access at https://github.com/NCATS-Tangerine/translator-knowledge-beacon.

Objective Digital nudging has been mooted as a tool to alter user privacy behavior. However, empirical studies on digital nudging have yielded divergent results: while some studies found nudging to be highly effective, other studies found no such effects. Furthermore, previous studies employed a wide range of digital nudges, making it difficult to discern the effectiveness of digital nudging. To address these issues, we performed a systematic review of empirical studies on digital nudging and information disclosure as a specific privacy behavior. Method The search was conducted in five digital libraries and databases: Scopus, Google Scholar, ACM Digital Library, Web of Science, and Science Direct for peer-reviewed papers published in English after 2006, examining the effects of various nudging strategies on disclosure of personal information online. Results The review unveiled 78 papers that employed four categories of nudge interventions: presentation, information, defaults, and incentives, either individually or in combination. A meta-analysis on a subset of papers with available data (n = 54) revealed a significant small-to-medium sized effect of the nudge interventions on disclosure (Hedges’ g = 0.32). There was significant variation in the effectiveness of nudging (I2 = 89%), which was partially accounted for by interventions to increase disclosure being more effective than interventions to reduce disclosure. No evidence was found for differences in the effectiveness of nudging with presentation, information, defaults, and incentives interventions. Conclusion Identifying ways to nudge users into making more informed and desirable privacy decisions is of significant practical and policy value. There is a growing interest in digital privacy nudges for disclosure of personal information, with most empirical papers focusing on nudging with presentation. Further research is needed to elucidate the relative effectiveness of different intervention strategies and how nudges can confound one another.

Background Post-market surveillance is a key regulatory function to prevent substandard and falsified (SF) medicines from being consumed by patients. Field deployable technologies offer the potential for rapid objective screening for SF medicines. Methods and findings We evaluated twelve devices: three near infrared spectrometers (MicroPHAZIR RX, NIR-S-G1, Neospectra 2.5), two Raman spectrometers (Progeny, TruScan RM), one mid-infrared spectrometer (4500a), one disposable colorimetric assay (Paper Analytical Devices, PAD), one disposable immunoassay (Rapid Diagnostic Test, RDT), one portable liquid chromatograph (C-Vue), one microfluidic system (PharmaChk), one mass spectrometer (QDa), and one thin layer chromatography kit (GPHF-Minilab). Each device was tested with a series of field collected medicines (FCM) along with simulated medicines (SIM) formulated in a laboratory. The FCM and SIM ranged from samples with good quality active pharmaceutical ingredient (API) concentrations, reduced concentrations of API (80% and 50% of the API), no API, and the wrong API. All the devices had high sensitivities (91.5 to 100.0%) detecting medicines with no API or the wrong API. However, the sensitivities of each device towards samples with 50% and 80% API varied greatly, from 0% to 100%. The infrared and Raman spectrometers had variable sensitivities for detecting samples with 50% and 80% API (from 5.6% to 50.0%). The devices with the ability to quantitate API (C-Vue, PharmaChk, QDa) had sensitivities ranging from 91.7% to 100% to detect all poor quality samples. The specificity was lower for the quantitative C-Vue, PharmaChk, & QDa (50.0% to 91.7%) than for all the other devices in this study (95.5% to 100%). Conclusions The twelve devices evaluated could detect medicines with the wrong or none of the APIs, consistent with falsified medicines, with high accuracy. However, API quantitation to detect formulations similar to those commonly found in substandards proved more difficult, requiring further technological innovation., Author summary Criminally falsified or poorly manufactured medicines can lead to patients becoming sicker and losing trust in the health system. Portable tools beyond just documentation checks and visual inspection (the current practices in many low- and middle-income countries) can help pharmacy inspectors with early detection of poor quality medicines. Currently, many tools are available to detect poor quality medicines, but their performances have not been properly assessed and compared. In this study, 12 different devices ranging from disposable single use tests to portable spectrometers were tested in a laboratory. All the tested devices could identify medicines that contained none or the wrong active ingredient(s), a common trait of falsified medicines. Disposable tests required few resources to be implemented, but had difficulties identifying medicines with reduced amounts of active ingredients. Spectrometers used ‘out-of-the-box’ required minimal consumables had varying degrees of success at detecting medicines with reduced amounts of active ingredients. Finally, instruments with more quantitative abilities, such as benchtop simple chromatographs or mass spectrometers, offered the best sensitivity for detecting medicines with reduced amounts of active ingredients, but required the most resources and training and were deemed to be more suitable for centralized testing.

Background In March 2020, an influx of admissions in COVID-19 positive patients threatened to overwhelm healthcare facilities in East Baton Rouge Parish, Louisiana. Exacerbating this problem was an overall shortage of diagnostic testing capability at that time, resulting in a delay in time-to-result return. An improvement in diagnostic testing availability and timeliness was necessary to improve the allocation of resources and ultimate throughput of patients. The management of a COVID-19 positive patient or patient under investigation requires infection control measures that can quickly consume personal protective equipment (PPE) stores and personnel available to treat these patients. Critical shortages of both PPE and personnel also negatively impact care in patients admitted with non-COVID-19 illnesses. Methods A multisectoral partnership of healthcare providers, facilities and academicians created a molecular diagnostic lab within an academic research facility dedicated to testing inpatients and healthcare personnel for SARS-CoV-2. The purpose of the laboratory was to provide a temporary solution to the East Baton Rouge Parish healthcare community until individual facilities were self-sustaining in testing capabilities. We describe the partnership and the impacts of this endeavor by developing a model derived from a combination of data sources, including electronic health records, hospital operations, and state and local resources. Findings Our model demonstrates two important principles: the impact of reduced turnaround times (TAT) on potential differences in inpatient population numbers for COVID-19 and savings in PPE attributed to the more rapid TAT.

While archaeological sciences have made great advances over the last decades through combining archaeological evidence and natural sciences in order to push borders for the understanding of archaeological contexts, traditional archaeology still holds an immense latent potential. Such potential can be realized through baseline projects that pull together unexplored bodies of material culture and study these in detail in order to investigate their significance for the understanding of the human past. This paper presents such a large-scale baseline study and focuses on the presentation of the results emerging from the recently compiled corpus of more than 3700 funerary portraits stemming from one location in the ancient world, Roman Palmyra, an oasis city in the Syrian Desert. The analysis of the chronological development of the numerous portraits allows us to follow the fluctuations in the production of these portraits over approximately 300 years. Here we discuss and review the developments in connection with historical sources and discuss until now unknown events, which have emerged through the data analysis. The paper brings to the forefront the significance of social science baseline projects, which often do not receive enough attention or funding, but which in fact are fundamental for furthering our understanding of the human past and push borders for the directions in which we can take such studies in the future.

Complex IT outsourcing relationships aptitude several benefits such as increased cost likelihood and lowered costs, higher scalability and flexibility upon demand. However, by virtue of its complexity, the complex outsourcing typically necessitates the interactions among various stakeholders from diverse regions and cultures, making it significantly more challenging to manage than traditional outsourcing. Furthermore, when compared to other types of outsourcing, complex outsourcing is extremely difficult because it necessitates a variety of control and coordination mechanisms for project management, which proportionally increases the risk of project failure. In order to overcome the failure of projects in complex outsourcing relationships, there is a need of robust systematic research to identify the key challenges and practices in this area. Therefore, this research implements systematic literature review as a research method and works as a pioneer attempt to accomplish the aforementioned objectives. Upon furnishing the SLR results, the authors identified 11 major challenges with 67 practices in hand from a total of 85 papers. Based on these findings, the authors intend to construct a comprehensive framework in the future by incorporating robust methodologies such as AHP and fuzzy logic, among others. Qatar National Library and Qatar University - grant No. IRCC- 2021-010.

The air humidity in Antarctica is very low and this peculiar weather parameter make the use of flame retardants in research facilities highly needed for safety reasons, as fires are a major risk. Legacy and novel flame retardants (nFRs) including polybrominated diphenyl ethers (PBDEs), hexabromocyclododecanes (HBCDs), 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE), Dechlorane Plus (DP), and other nFRs were measured in indoor dust samples collected at research Stations in Antarctica: Gabriel de Castilla, Spain (GCS), Julio Escudero, Chile (JES), and onboard the RRS James Clark Ross, United Kingdom (RRS JCR). The GC-HRMS and LC-MS-MS analyses of dust samples revealed ∑PBDEs of 41.5 ± 43.8 ng/g in rooms at GCS, 18.7 ± 11.6 ng/g at JES, and 27.2 ± 37.9 ng/g onboard the RRS JCR. PBDE pattern was different between the sites and most abundant congeners were BDE-183 (40%) at GCS, BDE-99 (50%) at JES, and BDE-153 (37%) onboard the RRS JCR. The ∑HBCDs were 257 ± 407 ng/g, 14.9 ± 14.5 ng/g, and 761 ± 1043 ng/g in indoor dust collected in rooms at GCS, JES, and RRS JCR, respectively. The ∑nFRs were 224 ± 178 ng/g at GCS, 14.1 ± 13.8 ng/g at JES, and 194 ± 392 ng/g on the RRS JCR. Syn- and anti-DP were detected in most of the samples and both isomers showed the highest concentrations at GCS: 163 ± 93.6 and 48.5 ± 61.1 ng/g, respectively. The laboratory and living room showed the highest concentration of HBCDs, DPs, BTBPE. The wide variations in FR levels in dust from the three research facilities and between differently used rooms reflect the different origin of furnishing, building materials and equipment. The potential health risk associated to a daily exposure via dust ingestion was assessed for selected FRs: BDEs 47, 99, and 153, α-, β-, and γ-HBCD, BTBPE, syn- and anti-DP. Although the estimated exposures are below the available reference doses, caution is needed given the expected increasing use of novel chemicals without a comprehensive toxicological profile., This work was supported by Project SENTINEL-CTM2015- 70535-P (JD and BJ), Projects ANID-FONDECYT 1130329 (KP) and 1161673 (KP), 11150548 (CGM), ANID-FONDAP 15110027 (RA-H), ANID-PIA-INACh-ACT192057 (CGM), INACH RT_12_17 (CGM), and INACH RT_08_13 (RA-H), PNRA 2013/C1.04 (SC). We thank the Project PLANET (PNRA 14_0009) in collaboration with the British Antarctic Survey- Ecosystems Team for the collection of samples on board the RRS James Clarke Ross (EB). This research was also supported by the RECETOX Research Infrastructure (Czech Ministry of Education, Youth and Sports: LM2018121), RECETOX RI (CZ.02.1.01/0.0/0.0/16_013/ 0001761), and CETOCOEN EXCELLENCE Teaming 2 project supported by Horizon2020 (857560) and the Czech Ministry of Education, Youth and Sports (02.1.01/0.0/0.0/18_046/0015975).

In the Unites States, the public has a constitutional right to access criminal trial proceedings. In practice, it can be difficult or impossible for the public to exercise this right. We present JUSTFAIR: Judicial System Transparency through Federal Archive Inferred Records, a database of criminal sentencing decisions made in federal district courts. We have compiled this data set from public sources including the United States Sentencing Commission, the Federal Judicial Center, the Public Access to Court Electronic Records system, and Wikipedia. With nearly 600,000 records from the years 2001 - 2018, JUSTFAIR is the first large scale, free, public database that links information about defendants and their demographic characteristics with information about their federal crimes, their sentences, and, crucially, the identity of the sentencing judge.

Loss in intraspecific diversity can alter ecosystem functions, but the underlying mechanisms are still elusive, and intraspecific biodiversity–ecosystem function (iBEF) relationships have been restrained to primary producers. Here, we manipulated genetic and functional richness of a fish consumer (Phoxinus phoxinus) to test whether iBEF relationships exist in consumer species and whether they are more likely sustained by genetic or functional richness. We found that both genotypic and functional richness affected ecosystem functioning, either independently or interactively. Loss in genotypic richness reduced benthic invertebrate diversity consistently across functional richness treatments, whereas it reduced zooplankton diversity only when functional richness was high. Finally, losses in genotypic and functional richness altered functions (decomposition) through trophic cascades. We concluded that iBEF relationships lead to substantial top-down effects on entire food chains. The loss of genotypic richness impacted ecological properties as much as the loss of functional richness, probably because it sustains “cryptic” functional diversity., Global change is expected to generate a loss of intraspecific diversity worldwide. This mesocosm study explores whether loss of genetic and functional diversity in a predator species affects community and ecosystem functioning of lower trophic levels in pond ecosystems, revealing that diversity loss in a single consumer species can impact an entire ecosystem, reducing its functionality.

Background Since the first cases reported in Wuhan, China, in December 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread worldwide. In Indonesia, the first case was reported in early March 2020, and the numbers of confirmed infections have been increasing until now. Efforts to contain the virus globally and in Indonesia are ongoing. This is the very first manuscript using a spatial-temporal model to describe the SARS-CoV-2 transmission in Indonesia, as well as providing a patient profile for all confirmed COVID-19 cases. Method Data was collected from the official website of the Indonesia National Task Force for the Acceleration of COVID-19, from the period of 02 March 2020–02 August 2020. The data from RT-PCR confirmed, SARS-CoV-2 positive patients was categorized according to demographics, symptoms and comorbidities based on case categorization (confirmed, recovered, dead). The data collected provides granular and thorough information on time and geographical location for all 34 Provinces across Indonesia. Results A cumulative total of 111,450 confirmed cases of were reported in Indonesia during the study period. Of those confirmed cases 67.79% (75,551/111,450) were shown as recovered and 4.83% (5,382/111,450) of them as died. Patients were mostly male (50.52%; 56,300/111,450) and adults aged 31 to 45 years old (29.73%; 33,132/111,450). Overall patient presentation symptoms of cough and fever, as well as chronic disease comorbidities were in line with previously published data from elsewhere in South-East Asia. The data reported here, shows that from the detection of the first confirmed case and within a short time period of 40 days, all the provinces of Indonesia were affected by COVID-19. Conclusions This study is the first to provide detailed characteristics of the confirmed SARS-CoV-2 patients in Indonesia, including their demographic profile and COVID-19 presentation history. It used a spatial-temporal analysis to present the epidemic spread from the very beginning of the outbreak throughout all provinces in the country. The increase of new confirmed cases has been consistent during this time period for all provinces, with some demonstrating a sharp increase, in part due to the surge in national diagnostic capacity. This information delivers a ready resource that can be used for prediction modelling, and is utilized continuously by the current Indonesian Task Force in order to advise on potential implementation or removal of public distancing measures, and on potential availability of healthcare capacity in their efforts to ultimately manage the outbreak.

Within the HIV clinical trial field, there are gaps in existing ethical regulations in relation to post-trial care. There is need to develop post-trial care guidelines that are flexible and sensitive to local contexts and to the specific needs of different groups of participants, particularly in low income contexts. Evidence regarding HIV trial closure and post-trial care is required to underpin the development of appropriate policies in this area. This article reports research from Uganda that develops a new model of ‘Facilitated Transition’ to conceptualize the transition process of HIV positive trial participants from ‘research’ to ‘usual care’ health facilities after trial conclusion. This was a qualitative grounded theory study that included 21 adult HIV positive post-trial participants and 22 research staff, undertaken between October 2014 and August 2015. The findings showed that trial closure is a complex process for HIV positive participants which includes three phases: the pre-closure, trial-closure, and post-trial phases. The model highlights a range of different needs of research participants and suggests specific and person-centred interventions that can be delivered at different phases with the aim of improving health outcomes and experiences for trial participants in low income settings during trial closure. Further research needs to be done to verify the model in other contexts and for other conditions.

Soil archives are an important resource in agronomic and ecosystem sciences. If microbial communities could be reconstructed from archived soil DNA, as prehistoric plant communities are reconstructed via pollen data, soil archive resources would assume even greater value for reconstructing land-use history, forensic science, and biosphere modelling. Yet, the effects of long-term soil archival on the preservation of microbial DNA is still largely unknown. To address this, we assessed the capacity of high-throughput sequencing (Illumina MiSeq) of ITS (internal transcribed spacer) and prokaryotic 16S rRNA genes for reconstructing soil microbial communities across a 20 years time-series. We studied air-dried soil archives and fresh soil samples taken from Populus bioenergy and deciduous forest research plots at the Kellogg Biological Station. Habitat and archival time explained significant amounts of variation in soil microbial α- and β-diversity both in fungal and prokaryotic communities. We found that microbial richness, diversity, and abundance generally decreased with storage time, but varied between habitat and taxonomic groups. The high relative abundance of ectomycorrhizal species including Hebeloma and Cortinarius detected in older soil archives raises questions regarding traits such as long-term persistence and viability of ectomycorrhizal propagules in soils, with relevance to forest health and ecosystem succession. Talaromyces, Paecilomyces and Epicoccum spp. were detected in fresh and across 20-year-old archived soils and were also cultured from these soils demonstrating their long-term spore viability. In summary, we found that microbial DNA in air-dried soils archived over the past 20 years degraded with time, in a manner that differed between soil types and phylogenetic groups of microbes.

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression-factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

The Coronavirus Disease 2019 (COVID-19) has swept the whole world with high mortality. Since droplet transmission is the main route of transmission, wearing a mask serves as a crucial preventive measure. However, the virus has spread quite quickly, causing severe mask shortage. Finding alternative materials for homemade masks while ensuring the significant performance indicators will help alleviate the shortage of masks. Referring to the national standard for the “Surgical Mask” of China, 17 materials to be selected for homemade masks were tested in four key indicators: pressure difference, particle filtration efficiency, bacterial filtration efficiency and resistance to surface wetting. Eleven single-layer materials met the standard of pressure difference (≤49 Pa), of which 3 met the standard of resistance to surface wetting (≥3), 1 met the standard of particle filtration efficiency (≥30%), but none met the standard of bacterial filtration efficiency (≥95%). Based on the testing results of single-layer materials, fifteen combinations of paired materials were tested. The results showed that three double-layer materials including double-layer medical non-woven fabric, medical non-woven fabric plus non-woven shopping bag, and medical non-woven fabric plus granular tea towel could meet all the standards of pressure difference, particle filtration efficiency, and resistance to surface wetting, and were close to the standard of the bacterial filtration efficiency. In conclusion, if resources are severely lacking and medical masks cannot be obtained, homemade masks using available materials, based on the results of this study, can minimize the chance of infection to the maximum extent.

In invasion team sports, scoring efficiency depends on the ability to create scoring opportunities and to convert them into goals or points. Scoring performance varies across sports and comparisons among them are little. In this paper we compare creation and conversion of scoring opportunities in different team sports and genders. Box-score data from six sports [basketball, handball, water polo, field hockey, football, ice hockey] (328 teams, 5723 games, both genders) were standardized by "per ball possession". We applied Bayesian methods to compute the posterior distributions of shots per possession (SHTpPOS), points per shot (PTSpSHT) and points per possession (PTSpPOS). We evaluated differences for these three variables among sports, between genders and the correlation between every pair of them. Inter-sports evaluation evidenced basketball, handball, ice hockey and water polo are sports with a high probability of creating shots (SHTpPOS-p(robability) > 0.65). Complementary, ice hockey, field hockey and football are sports with a low probability of converting shots (PTSpSHT-0.05 < p < 0.26). Despite the distinct results among sports for creating and converting opportunities, all sports in both genders, converged to a scoring efficiency (PTSpPOS) below 0.5. In the genders' comparison, men are more efficient in creating opportunities than women, except in water polo. For scoring efficiency, differences between men and women are fewer. Results prevent generalization about differences in scoring efficiency between genders. Finally, creation and conversion have low correlation in sports with high shot creation probabilities (basketball and ice hockey). In these sports, scoring is not limited by the number of shots taken but rather by their accuracy. For sports with low shot creation probabilities (soccer and men field hockey), creation and conversion presented higher correlation. Evidences contribute to increase coaches' understanding about scoring tactics' challenges in team sports and design practices accordingly.

Mycetoma is considered a neglected tropical disease globally. However, data on its burden and the associated complications in Uganda are limited. Hence we aimed to estimate its burden in Uganda. Firstly, a systematic PubMed search for all studies of any design on mycetoma in Uganda without restriction to the year of publication was conducted. A retrospective review of all the biopsy reports at the Pathology Reference Laboratory, Department of Pathology, Makerere University, Kampala, Uganda from January 1950 to September 2019 was conducted to identify any reports on mycetoma histological diagnosis. During the 70-years study period, 30 cases were identified by the literature review, with 249 additional cases identified by review of biopsy reports (total of 279 cases). The average incidence was estimated at 0.32/100,000 persons and prevalence of 8.32/100,000 persons per decade. However, there was a general decline in the number of cases detected recently. Males and the age group of 21–30 years were the most affected by mycetoma in Uganda, and only 7% of the cases were children. The highest number of cases was recorded from Kampala (n = 30) and Jinja (n = 19) districts. The majority of the cases (68%) were referred from surgical units. The foot was the most affected part of the body (72%). Ten per cent of the cases had bone involvement of which 58% required amputation. Fungi were the most common causative agents (89%) followed by Nocardia species (5%) and Actinomycetes (4%). The index of clinical suspicion of mycetoma was low (45%) with a very large differential diagnosis. Mycetoma is a relatively rare disease in Uganda, mostly caused by fungi, and there is a big gap in data and epidemiological studies. More systematic studies are warranted to define the true burden of mycetoma in Uganda., Author summary Recently, the World Health Organisation recognized mycetoma, a chronic, progressively destructive morbid inflammatory disease usually of the foot as a neglected tropical disease. However, mycetoma is not a notifiable disease and thus the global burden of the disease remains poorly defined. It is therefore important that any collection of available data on this disease is brought forward to highlight the extent and magnitude of the burden of mycetoma. We retrospectively gathered data on the burden and aetiology of mycetoma in a country (Uganda) within the mycetoma belt based on histological diagnosis and systematic review. We found that fungal pathogens are the most common cause of mycetoma in this region. However, the distribution of the lesions is consistent with global data with the foot being the most affected site. We also noticed that clinicians have low index of clinical suspicion for mycetoma leading to under-diagnosis. Mycetoma is uncommon but not rare in Uganda; more research is obligatory to precisely define the distribution and determinants of the disease as well as primary and secondary preventative measures in endemic areas.

In real world situations, decision makers prefer to have multiple optimal solutions before making a final decision. Aiming to help the decision makers even if they are non-experts in optimization algorithms, this study proposes a new and simple multimodal optimization (MMO) algorithm called the gravitational particle swarm algorithm (GPSA). Our GPSA is developed based on the concept of “particle clustering in the absence of clustering procedures”. Specifically, it simply replaces the global feedback term in classical particle swarm optimization (PSO) with an inverse-square gravitational force term between the particles. The gravitational force mutually attracts and repels the particles, enabling them to autonomously and dynamically generate sub-swarms in the absence of algorithmic clustering procedures. Most of the sub-swarms gather at the nearby global optima, but a small number of particles reach the distant optima. The niching behavior of our GPSA was tested first on simple MMO problems, and then on twenty MMO benchmark functions. The performance indices (peak ratio and success rate) of our GPSA were compared with those of existing niching PSOs (ring-topology PSO and fitness Euclidean-distance ratio PSO). The basic performance of our GPSA was comparable to that of the existing methods. Furthermore, an improved GPSA with a dynamic parameter delivered significantly superior results to the existing methods on at least 60% of the tested benchmark functions.

In this study the near-infrared reflectance (NIR) spectra signals (750-2,500 nm) of soil samples was compared with the NIR signals of the biogenic aggregates produced in the lab by three earthworm species, i.e., Aporrectodea rosea (Savigny 1826), Lumbricus friendi Cognetti, 1904 and Prosellodrilus pyrenaicus (Cognetti, 1904) from subalpine meadows in the Central Pyrenees. NIR spectral signatures of biogenic aggregates, root-aggregates, and non-aggregated soil were obtained together with soil carbon (C), nitrogen (N), [Formula: see text] and [Formula: see text] determinations. The concentrations of C, N and C:N ratio in the three types of soil aggregates identified were not statistically significant (ANOVA, p>0.05) although non-macroaggregated soil had slightly higher C concentrations (66.3 g kg-1 dry soil) than biogenic aggregates (earthworm- and root-aggregates, 64.9 and 63.5 g kg-1 dry soil, respectively), while concentrations of [Formula: see text] and [Formula: see text] were highest in the root-attached aggregates (3.3 and 0.31 mg kg dry soil-1). Total earthworm density and biomass in the sampled area was 137.6 ind. m-2, and 55.2 g fresh weight m-2, respectively. The biomass of aggregates attached to roots and non-macroaggregated soil was 122.3 and 134.8 g m-2, respectively, while biomass of free (particulate) organic matter and invertebrate biogenic aggregates was 62.9 and 41.7 g m-2, respectively. Multivariate analysis of NIR spectra signals of field aggregates separated root aggregates with high concentrations of [Formula: see text] and [Formula: see text] (41.5% of explained variance, axis I) from those biogenic aggregates, including root aggregates, with large concentrations of C and high C:N ratio (21.6% of total variability, axis II). Partial Least Square (PLS) regressions were used to compare NIR spectral signals of samples (casts and soil) and develop calibration equations relating these spectral data to those data obtained for chemical variables in the lab. After a derivatization process, the NIR spectra of field aggregates were projected onto the PLS factorial plane of the NIR spectra from the lab incubation. The projection of the NIR spectral signals onto the PLSR models for C, N, [Formula: see text] and [Formula: see text] from casts produced and incubated in the lab allowed us to identify the species and the age of the field biogenic aggregates. Our hypothesis was to test whether field aggregates would match or be in the vicinity of the NIR signals that corresponded to a certain species and the age of the depositions produced in the lab. A NIRS biogenic background noise (BBN) is present in the soil as a result of earthworm activity. This study provides insights on how to analyse the role of these organisms in important ecological processes of soil macro-aggregation and associated organic matter dynamics by means of analyzing the BBN in the soil matrix.

The amphibian skin disease chytridiomycosis, caused by the pathogenetic fungus Batrachochytrium dendrobatidis (Bd) has become one of the major contributors to global amphibian population declines and extinctions. This fungus has spread globally and has caused mortalities in nearly every continent. In South America, Suriname, Guyana and Paraguay are among the remaining three countries where Bd has not been detected to date. To complete the assessment of the possible presence of Bd in Suriname, 205 specimens from the Zoological Collection of Suriname, compromising 6 frog families and 15 genera were sampled for chytrid fungus. No specimens were found to be infected by this fungus and as such the outcome strengthens the previous result of field sampling that there is no support that Bd has spread to Suriname.

Freshwater wetlands of the temperate north are exposed to a range of pollutants that may alter their function, including nitrogen (N)-rich agricultural and urban runoff, seawater intrusion, and road salt contamination, though it is largely unknown how these drivers of change interact with the vegetation to affect wetland carbon (C) fluxes and microbial communities. We implemented a full factorial mesocosm (378.5 L tanks) experiment investigating C-related responses to three common wetland plants of eastern North America (Phragmites australis, Spartina pectinata, Typha latifolia), and four water quality treatments (fresh water control, N, road salt, sea salt). During the 2017 growing season, we quantified carbon dioxide (CO2) and methane (CH4) fluxes, above- and below-ground biomass, root porosity, light penetration, pore water chemistry (NH4+, NO3-, SO4-2, Cl-, DOC), soil C mineralization, as well as sediment microbial communities via 16S rRNA gene sequencing. Relative to freshwater controls, N enrichment stimulated plant biomass, which in turn increased CO2 uptake and reduced light penetration, especially in Spartina stands. Root porosity was not affected by water quality, but was positively correlated with CH4 emissions, suggesting that plants can be important conduits for CH4 from anoxic sediment to the atmosphere. Sediment microbial composition was largely unaffected by N addition, whereas salt amendments induced structural shifts, reduced sediment community diversity, and reduced C mineralization rates, presumably due to osmotic stress. Methane emissions were suppressed by sea salt, but not road salt, providing evidence for the additional chemical control (SO4-2 availability) on this microbial-mediated process. Thus, N may have stimulated plant activity while salting treatments preferentially enriched specific microbial populations. Together our findings underpin the utility of combining plant and microbial responses, and highlight the need for more integrative studies to predict the consequences of a changing environment on freshwater wetlands.

The pollution of the natural environment, especially the world’s oceans, with conventional plastic is of major concern. Biodegradable plastics are an emerging market bringing along potential chances and risks. The fate of these materials in the environment and their possible effects on organisms and ecosystems has rarely been studied systematically and is not well understood. For the marine environment, reliable field test methods and standards for assessing and certifying biodegradation to bridge laboratory respirometric data are lacking. In this work we present newly developed field tests to assess the performance of (biodegradable) plastics under natural marine conditions. These methods were successfully applied and validated in three coastal habitats (eulittoral, benthic and pelagic) and two climate zones (Mediterranean Sea and tropical Southeast Asia). Additionally, a stand-alone mesocosm test system which integrated all three habitats in one technical system at 400-L scale independent from running seawater is presented as a methodological bridge. Films of polyhydroxyalkanoate copolymer (PHA) and low density polyethylene (LD-PE) were used to validate the tests. While LD-PE remained intact, PHA disintegrated to a varying degree depending on the habitat and the climate zone. Together with the existing laboratory standard test methods, the field and mesocosm test systems presented in this work provide a 3-tier testing scheme for the reliable assessment of the biodegradation of (biodegradable) plastic in the marine environment. This toolset of tests can be adapted to other aquatic ecosystems.

The valley elderberry longhorn beetle (VELB), Desmocerus californicus dimorphus (Coleoptera: Cerambycidae), is a federally threatened subspecies endemic to the Central Valley of California. The VELB range partially overlaps with that of its morphologically similar sister taxon, the California elderberry longhorn beetle (CELB), Desmocerus californicus californicus (Coleoptera: Cerambycidae). Current surveying methods are limited to visual identification of larval exit holes in the VELB/CELB host plant, elderberry (Sambucus spp.), into which larvae bore and excavate feeding galleries. Unbiased genetic approaches could provide a much-needed complementary approach that has more precision than relying on visual inspection of exit holes. In this study we developed a DNA sequencing-based method for indirect detection of VELB/CELB from frass (insect fecal matter), which can be easily and non-invasively collected from exit holes. Frass samples were collected from 37 locations and the 12S and 16S mitochondrial genes were partially sequenced using nested PCR amplification. Three frass-derived sequences showed 100% sequence identity to VELB/CELB barcode references from museum specimens sequenced for this study. Database queries of frass-derived sequences also revealed high similarity to common occupants of old VELB feeding galleries, including earwigs, flies, and other beetles. Overall, this non-invasive approach is a first step towards a genetic assay that could augment existing VELB monitoring and accurately discriminate between VELB, CELB, and other insects. Furthermore, a phylogenetic analysis of 12S and 16S data from museum specimens revealed evidence for the existence of a previously unrecognized, genetically distinct CELB subpopulation in southern California.

The influence of the health-related behavior of one spouse on that of the other is an important research question with public policy reprecussions. Yet, we are unaware of any previous study, which considered endogeneity problems between couples. Moreover, only a few studies considered ethnic origin differences among couples. Based on the 2016 wave of the Israeli longitudinal survey, we observe the cross-sectional correlation between the married couples' BMI, age, and accumulated wealth. The BMI (= [Formula: see text]) is a conventional measure of obesity, where BMI≥25 is considered overweight. Using a 3SLS methodology (in an effort to correct the endogeneity problem associated with BMI couples), the analysis tests the mutual obesity hypothesis among married couples. This hypothesis states that the BMI of the male influences that of a female and vice versa. Results indicate that on the one hand, a one-percent BMI increase among Arab Israeli males is associated with a projected 0.969 percent BMI increase among Arab Israeli females (p = 0.017); and in the case that an Arab Israeli male suffers from overweight, the projected probability of his Arab Israeli female counterpart to suffer from overweight as well rises (p = 0.050). On the other hand, one cannot reject the null hypothesis that projected BMI of the Arab Israeli male is unaffected by that of his Arab Israeli female counterpart (p = 0.907 and p = 0.853). As for the Jewish Israeli population, in the case that the 3SLS methodology is employed, so that the endogeneity problem among couples is considered, a one-percent BMI increase among Jewish Israeli females is associated with a projected 0.639 percent BMI increase among Jewish Israeli males (p = 0.091). Unlike Arab Israeli couples, no support is found to indicate the influence in the other direction, namely, the BMI of the male influences that of the female spouse. Research findings may thus be of relevance to public health and policy planners. Two limitations of this research lie in: 1) the self-reported BMI (which might be different from the measured BMI); and 2) missing confounders, such as regional dummies, which are not available in the dataset.

In solar tower plants, thousands of heliostats reflect sunlight into a central receiver. Heliostats consist of a subset of mirrors called facets that must be perfectly oriented (i.e., canted) to concentrate as much solar radiation as possible. This study presents and validates the so-called flux map fitting technique to detect and correct canting errors. The computed distributions were matched to a series of images through an optimization algorithm. According to the sensitivity analysis, three images spread along a single day provide sufficient information for the algorithm to succeed. Using this methodology, four heliostats at the THEMIS research facility were recanted, thereby substantially increasing the optical quality in three of them. The procedure to infer the heliostat aimpoint was assessed. Universidad Carlos III de Madrid (2020/00051); European Commission (823802); Horizon 2020 Framework Programme (727762). We thank the CNRS-PROMES laboratory, UPR 8521, belonging to the French National Center for Scientific Research (CNRS), for providing access to its facilities, the support of its scientific and technical staff, and the financial support of the SFERA-III project (Grant Agreement No. 823802). We thank the technical help provided by Yann Volut, William Baltus, and Antoine Pérez. The research project VISHELIO-CM-UC3M has been funded by the call "Programa de apoyo a la realización de proyectos interdisciplinares de I+D para jóvenes investigadores de la Universidad Carlos III de Madrid 2019-2020" under the framework of the "Convenio Plurianual Comunidad de Madrid-Universidad Carlos III de Madrid". This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 727762, project acronym NEXT-CSP. Publicado

Introduction Health facility-based records offer a rich source of information to understand trends and changes in malaria cases over time. This study is aimed at determining the changes in malaria occurrence over the last 28 years, from 1989 to 2016 in Dakar, Senegal. Methods Laboratory suspected and confirmed malaria records from 1989 to 2016 were reviewed from the laboratory registers of the Laboratory of Parasitology and Mycology of Aristide Le Dantec Hospital. Interrupted time series (ITS) analysis was used to estimate the changes by comparing malaria cases post-intervention (2006–2016) with that of the pre-intervention (1989–2005) period. Results A total of 5,876 laboratory confirmed malaria cases were reported out of 29,852 tested cases, with total slide positivity rate (SPR) of 19.7%. Malaria case counts exhibited a fluctuating trend with major peaks occurring in the years 1995 and 2003 with SPR of 42.3% and 42.5%, respectively. Overall, a remarkable decline in the total number of laboratory confirmed malaria cases was observed over the last 28 years. P. falciparum was almost the only reported species, accounting for 99.98% of cases. The highest SPR was observed in the age group of under five years during the pre-intervention period while this shifted to the age group of 6–15 years old for the subsequent years. Two major malaria peak seasons were observed: one in September during the pre-intervention period and the other in November for the post-intervention period. The ITS analysis showed a dramatic decline of 83.6% in SPR following the scale-up of interventions in 2006. Conclusion A remarkable decline in laboratory confirmed malaria cases in Dakar over 28 years was observed. The period of rapid decline in malaria SPR coincided with the scale-up in interventions beginning in 2006 with the introduction of ACTs, followed by the widespread introduction in 2008 of bed nets treated with insecticides. Robust surveillance data should be maintained in the context of malaria elimination efforts.

As a result of a shift in the world of technology, the combination of ubiquitous mobile networks and cloud computing produced the mobile cloud computing (MCC) domain. As a consequence of a major concern of cloud users, privacy and data protection are getting substantial attention in the field. Currently, a considerable number of papers have been published on MCC with a growing interest in privacy and data protection. Along with this advance in MCC, however, no specific investigation highlights the results of the existing studies in privacy and data protection. In addition, there are no particular exploration highlights trends and open issues in the domain. Accordingly, the objective of this paper is to highlight the results of existing primary studies published in privacy and data protection in MCC to identify current trends and open issues. In this investigation, a systematic mapping study was conducted with a set of six research questions. A total of 1711 studies published from 2009 to 2019 were obtained. Following a filtering process, a collection of 74 primary studies were selected. As a result, the present data privacy threats, attacks, and solutions were identified. Also, the ongoing trends of data privacy exercise were observed. Moreover, the most utilized measures, research type, and contribution type facets were emphasized. Additionally, the current open research issues in privacy and data protection in MCC were highlighted. Furthermore, the results demonstrate the current state-of-the-art of privacy and data protection in MCC, and the conclusion will help to identify research trends and open issues in MCC for researchers and offer useful information in MCC for practitioners.

Optimizing barley (hordeum vulgare L.) production in Idaho and other parts of the Pacific Northwest (PNW) should focus on farm resource management. The effect of post-harvest residue management on barley residue decomposition has not been adequately studied. Thus, the objective of this study was to determine the effect of residue placement (surface vs. incorporated), residue size (chopped vs. ground-sieved) and soil type (sand and sandy loam) on barley residue decomposition. A 50-day(d) laboratory incubation experiment was conducted at a temperature of 25°C at the Aberdeen Research and Extension Center, Aberdeen, Idaho, USA. Following the study, a Markov-Chain Monte Carlo (MCMC) modeling approach was applied to investigate the first-order decay kinetics of barley residue. An accelerated initial flush of residue carbon(C)-mineralization was measured for the sieved (Day 1) compared to chopped (Day 3 to 5) residues for both surface incorporated applications. The highest evolution of carbon dioxide (CO2)-C of 8.3 g kg-1 dry residue was observed on Day 1 from the incorporated-sieved application for both soils. The highest and lowest amount of cumulative CO2-C released and percentage residue decomposed over 50-d was observed for surface-chopped (107 g kg-1 dry residue and 27%, respectively) and incorporated-sieved (69 g kg-1 dry residue and 18%, respectively) residues, respectively. There were no significant differences in C-mineralization from barley residue based on soil type or its interactions with residue placement and size (p >0.05). The largest decay constant k of 0.0083 d-1 was calculated for surface-chopped residue where the predicted half-life was 80 d, which did not differ from surface sieved or incorporated chopped. In contrast, incorporated-sieved treatments only resulted in a k of 0.0054 d-1 and would need an additional 48 d to decompose 50% of the residue. Future residue decomposition studies under field conditions are warranted to verify the residue C-mineralization and its impact on residue management.

Many blood donation services around the globe maintain large archives of serum and/or plasma specimens of blood donations which could potentially be used for serologic surveillance and risk assessment of influenza. Harnessing this potential requires robust evidence that the outcomes of influenza serology in plasma, which is rarely used, is consistent with that in serum, which is the conventional choice of specimens for influenza serology. We harvested EDTA-plasma specimens from the blood donation archives of Hong Kong Red Cross Transfusion Services, where EDTA is the type of anticoagulant used for plasma collection, compared their antibody titers and responses to that in serum. Influenza A/H1N1/California/7/2009 and A/H3N2/Victoria/208/2009 were the test strains. Our results showed that antibody titers in 609 matched serum/EDTA-plasma specimens (i.e. obtained from the same donor at the same time) had good agreement inferred by Intraclass Correlation Coefficient, the value of which was 0.82 (95% CI: 0.77-0.86) for hemagglutination inhibition assay and 0.95 (95% CI: 0.93-0.96) for microneutralization assay; seroconversion rates (based on hemagglutination inhibition titers) during the 2010 and 2011 influenza seasons in Hong Kong inferred from paired EDTA-plasma were similar to that inferred from paired sera. Our study provided the proof-of-concept that blood donation archives could be leveraged as a valuable source of longitudinal blood specimens for the surveillance, control and risk assessment of both pandemic and seasonal influenza.

Background The Indian Council of Medical Research set up a pan-national laboratory network to diagnose and monitor Coronavirus disease 2019 (COVID-19). Based on these data, we describe the epidemiology of the pandemic at national and sub-national levels and the performance of the laboratory network. Methods We included surveillance data for individuals tested and the number of tests from March 2020 to January 2021. We calculated the incidence of COVID-19 by age, gender and state and tests per 100,000 population, the proportion of symptomatic individuals among those tested, the proportion of repeat tests and test positivity. We computed median (Interquartile range—IQR) days needed for selected surveillance activities to describe timeliness. Results The analysis included 176 million individuals and 188 million tests. The overall incidence of COVID-19 was 0.8%, and 12,584 persons per 100,000 population were tested. 6.1% of individuals tested returned a positive result. Ten of the 37 Indian States and Union Territories accounted for about 75.6% of the total cases. Daily testing scaled up from 40,000 initially to nearly one million in March 2021. The median duration between symptom onset and sample collection was two (IQR = 0,3) days, median duration between both sample collection and testing and between testing and data entry were less than or equal to one day. Missing or invalid entries ranged from 0.01% for age to 0.7% for test outcome. Conclusion The laboratory network set-up by ICMR was scaled up massively over a short period, which enabled testing a large section of the population. Although all states and territories were affected, most cases were concentrated in a few large states. Timeliness between the various surveillance activities was acceptable, indicating good responsiveness of the surveillance system.

The Democratic Republic of the Congo (DRC) declared an Ebola virus disease (EVD) outbreak in North Kivu in August 2018. By June 2019, the outbreak had spread to 26 health zones in northeastern DRC, causing >2,000 reported cases and >1,000 deaths. On June 10, 2019, three members of a Congolese family with EVD-like symptoms traveled to western Uganda’s Kasese District to seek medical care. Shortly thereafter, the Viral Hemorrhagic Fever Surveillance and Laboratory Program (VHF program) at the Uganda Virus Research Institute (UVRI) confirmed that all three patients had EVD. The Ugandan Ministry of Health declared an outbreak of EVD in Uganda’s Kasese District, notified the World Health Organization, and initiated a rapid response to contain the outbreak. As part of this response, UVRI and the United States Centers for Disease Control and Prevention, with the support of Uganda’s Public Health Emergency Operations Center, the Kasese District Health Team, the Superintendent of Bwera General Hospital, the United States Department of Defense’s Makerere University Walter Reed Project, and the United States Mission to Kampala’s Global Health Security Technical Working Group, jointly established an Ebola Field Laboratory in Kasese District at Bwera General Hospital, proximal to an Ebola Treatment Unit (ETU). The laboratory consisted of a rapid containment kit for viral inactivation of patient specimens and a GeneXpert Instrument for performing Xpert Ebola assays. Laboratory staff tested 76 specimens from alert and suspect cases of EVD; the majority were admitted to the ETU (89.3%) and reported recent travel to the DRC (58.9%). Although no EVD cases were detected by the field laboratory, it played an important role in patient management and epidemiological surveillance by providing diagnostic results in, Author summary Following an imported outbreak of Ebola virus disease in Uganda’s western Kasese District, the Uganda Virus Research Institute and the United States Centers for Disease Control and Prevention jointly established a frontline field laboratory to test specimens collected from alert and suspect cases for Ebola virus disease. Using a single room equipped with a rapid containment kit to safely inactivate patient specimens and a GeneXpert to perform the Xpert Ebola Assay, the field laboratory rapidly ruled-out Ebola virus disease as the cause of illness in 76 patients during its 46 operational days. All specimens were also referred to Uganda Virus Research Institute (Entebbe) for confirmatory Ebola virus testing and testing against a panel of viruses known to cause hemorrhagic fever in Uganda, in line with the National Viral Hemorrhagic Fever Program’s testing protocol and mandate. The Ebola field laboratory served as a valuable asset in the outbreak response by supporting patient management and epidemiological surveillance.

The open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function and even anthropogenic activities such as the widespread use of antimicrobials. However, these data consist of genomes assembled with different tools and levels of quality checking, and of large volumes of completely unprocessed raw sequence data. In both cases, considerable computational effort is required before biological questions can be addressed. Here, we assembled and characterised 661,405 bacterial genomes retrieved from the European Nucleotide Archive (ENA) in November of 2018 using a uniform standardised approach. Of these, 311,006 did not previously have an assembly. We produced a searchable COmpact Bit-sliced Signature (COBS) index, facilitating the easy interrogation of the entire dataset for a specific sequence (e.g., gene, mutation, or plasmid). Additional MinHash and pp-sketch indices support genome-wide comparisons and estimations of genomic distance. Combined, this resource will allow data to be easily subset and searched, phylogenetic relationships between genomes to be quickly elucidated, and hypotheses rapidly generated and tested. We believe that this combination of uniform processing and variety of search/filter functionalities will make this a resource of very wide utility. In terms of diversity within the data, a breakdown of the 639,981 high-quality genomes emphasised the uneven species composition of the ENA/public databases, with just 20 of the total 2,336 species making up 90% of the genomes. The overrepresented species tend to be acute/common human pathogens, aligning with research priorities at different levels from individual interests to funding bodies and national and global public health agencies., This study presents the first uniformly assembled, comprehensively described and searchable dataset of 661,405 bacterial genomes; this resource will empower more scientists to harness the multitude of data in public sequencing archives, but also reveals the biased composition of these archives, with 90% of the data originating from just 20 species.

Health research in low-income settings must prioritize sustainability to truly impact target diseases in the long term. Here, I satirically summarize how biomedical investigators from high-income countries can collaboratively work to (not) accomplish this., Health research in low‐income settings must prioritize sustainability in order to truly impact target diseases in the long term; this Perspective article satirically summarizes how biomedical investigators from high-income countries can collaboratively work to (not) accomplish this.

The reconstruction of fire history is essential to understand the palaeoclimate and human history. Polycyclic aromatic hydrocarbons (PAHs) have been extensively used as a fire marker. In this work, the distribution of PAHs in Borneo peat archives was investigated to understand how PAHs reflect the palaeo-fire activity. In total, 52 peat samples were analysed from a Borneo peat core for the PAH analysis. Pyrogenic PAHs consist of 2–7 aromatic rings, some of which have methyl and ethyl groups. The results reveal that the concentration of pyrogenic PAHs fluctuated with the core depth. Compared to low-molecular-weight (LMW) PAHs, the high-molecular-weight (HMW) PAHs had a more similar depth variation to the charcoal abundance. This finding also suggests that the HMW PAHs were mainly formed at a local fire near the study area, while the LMW PAHs could be transported from remote locations.

Background Severe fever with thrombocytopenia syndrome (SFTS) is a serious infectious disease with a fatality of up to 30%. To identify the severity of SFTS precisely and quickly is important in clinical practice. Methods From June to July 2020, 71 patients admitted to the Infectious Department of Joint Logistics Support Force No. 990 Hospital were enrolled in this study. The most frequently observed symptoms and laboratory parameters on admission were collected by investigating patients’ electronic records. Decision trees were built to identify the severity of SFTS. Accuracy and Youden’s index were calculated to evaluate the identification capacity of the models. Results Clinical characteristics, including body temperature (p = 0.011), the size of the lymphadenectasis (p = 0.021), and cough (p = 0.017), and neurologic symptoms, including lassitude (p Conclusion Decision trees can be applied to predict the severity of SFTS.

The global Coronavirus or COVID-19 pandemic exposed the weakness of healthcare systems including laboratory systems and is a call to action for unprecedented collaboration and partnerships to deal with the global crisis. The United States (U.S.) President’s Emergency Plan for AIDS Relief (PEPFAR) establishes the global HIV/AIDS treatment agenda in alignment with the UNAIDS 90-90-90 treatment targets to achieve epidemic control related to enhanced testing, treatment, and viral suppression. A strategic PEPFAR priority area recognizes that large-scale collective efforts and sharing of resources bear greater potential impact for lasting change than any single organization or entity can achieve alone. An important vehicle utilized within the global public health context is the public-private partnership (PPP) model whereby multiple international organizations forge unified project charters to collectively reach mutually agreed goals. While touted as an ideal mechanism to synthesize resources and maximize gain in numerous applications, little is known from a seasoned stakeholder perspective regarding PPP implementation and sustainability issues. The purpose of this research is to holistically examine perceptions of PPP model sustainability related to inputs and impacts among a collective network of stakeholders experienced with PEPFAR workforce development, laboratory-system strengthening project implementation. Interviews were conducted with frontline stakeholders from public and private sector organizations based in the US and select PEPFAR-supported priority countries. Analysis revealed three dominant themes: PPP impacts, keys of successful collaboration, and logistical challenges and opportunities to enhance sustainability of PPP outcomes in the future.

By the time the etiologic agent of the COVID-19 was identified as a novel coronavirus, no country in the Americas Region had laboratory capacity for detecting this new virus. A strategic multilevel approach with specific reagent purchase and delivery, regional trainings, in-country missions, and the provision of technical support was established for timely preparedness of national reference laboratories for SARS-CoV-2 detection. All countries should be prepared to timely detect any potential pandemic emerging agent. The rapid SARS-CoV-2 molecular detection implementation throughout the Americas showed the importance of an efficient and coordinated laboratory response for preparedness. Here we present how in 25 days the Americas Region went from no SARS-CoV-2 diagnostic capacity, to molecular detection fully implemented in 28 Member States, under the coordinated strategy of the Pan American Health Organization and collaborative work at regional and country level with national authorities and public health laboratories.

Background This study aimed to assess the comparability among assays using freshly frozen human sera and external quality assessment (EQA) data in China. Methods Twenty-nine serum samples and two commercial EQA materials, obtained from the National Center for Clinical Laboratories (NCCL), were analyzed in triplicate using eight routine TSH assays. The commutability of commercial EQA materials (NCCL materials) was evaluated in accordance with the CLSI EP30-A and IFCC bias analysis. Median values obtained for the NCCL EQA materials were used to determine the systematic and commutability-related biases among immunoassays through back-calculation. The comparability of TSH measurements from a panel of clinical samples and NCCL EQA data was determined on the basis of Passing–Bablok regression. Furthermore, human serum pools were used to perform commutable EQA. Results NCCL EQA materials displayed commutability among three or five of seven assay combinations according CLSI or IFCC approach, respectively. The mean of systematic bias ranged from -13.78% to 9.85% for the eight routine TSH assays. After correcting for systematic bias, averaged commutability-related biases ranged between -42.26% and 12.19%. After correction for systematic and commutability -related biases, the slopes indicating interassay relatedness ranged from 0.801 to 1.299 using individual human sera, from 0.735 to 1.254 using NCCL EQA data, and from 0.729 to 1.115 using pooled human serum EQA(the commutable EQA). Conclusions The harmonization of TSH measurement is challenging; hence, systematic and commutability-related biases should be determined and corrected for accurate comparisons among assays when using human individual serum and the commercial EQA materials.

Yellow fever (YF), an arboviral disease, affects an estimated 200,000 people and causes 30,000 deaths per year and recently has caused major epidemics in Africa and South America. Timely and accurate diagnosis of YF is critical for managing outbreaks and implementing vaccination campaigns. A YF immunoglobulin M (IgM) antibody-capture (MAC) enzyme-linked immunosorbent assay (ELISA) kit, the YF MAC-HD, was successfully introduced starting in 2018 to laboratories in Africa and South America. The YF MAC-HD kit can be performed in 3.5 hours, test up to 24 samples, and includes all reagents necessary to perform the test, except for water used to dilute wash buffer. In 2018 and 2019, a total of 56 laboratory personnel from 39 countries in Africa and South America were trained to use the kit during workshops, followed by take-home YF IgM proficiency testing (PT) exercises. Participants received either a 10- or 20-sample YF PT panel and performed testing using the YF MAC-HD kit. All countries obtained 90% or higher correct results. These results verified the technical viability and transferability of YF MAC-HD kit use for laboratories in YF-endemic countries., Author summary Yellow fever is a vaccine-preventable disease transmitted by mosquitoes that annually affects an estimated 200,000 people and causes 30,000 deaths. Being able to quickly and accurately identify people infected with yellow fever virus by laboratory confirmation is critical for managing outbreaks and vaccination campaigns. A test developed by the Centers for Disease Control and Prevention can identify yellow fever antibodies in a person’s blood within approximately four hours. In order to assure this test could be used in laboratories located in regions with yellow fever transmission, workshops were held to train laboratorians from Africa and South America on how to use the test. Laboratorians were then given a panel of samples and performed the test in their own laboratories. Of the 39 countries that performed testing, all countries scored 90% or higher concordant results, demonstrating the successful transfer of this yellow fever antibody detection test.

Background The decision of whether to pursue a tenure-track faculty position has become increasingly difficult for undergraduate, graduate, and postdoctoral trainees considering a career in research. Trainees express concerns over job availability, financial insecurity, and other perceived challenges associated with pursuing an academic position. Methods To help further elucidate the benefits, challenges, and strategies for pursuing an academic career, a diverse sample of postdoctoral scholars (“postdocs”) from across the United States were asked to provide advice on pursuing a research career in academia in response to an open-ended survey question. 994 responses were qualitatively analyzed using both content and thematic analyses. 177 unique codes, 20 categories, and 10 subthemes emerged from the data and were generalized into two thematic areas: Life in Academia and Strategies for Success. Results On life in academia, postdoc respondents overwhelmingly agree that academia is most rewarding when you are truly passionate about scientific research and discovery. ‘Passion’ emerged as the most frequently cited code, referenced 189 times. Financial insecurity, work-life balance, securing grant funding, academic politics, and a competitive job market emerged as challenges of academic research. The survey respondents note that while passion and hard work are necessary, they are not always sufficient to overcome these challenges. The postdocs encourage trainees to be realistic about career expectations and to prepare broadly for career paths that align with their interests, skills, and values. Strategies recommended for perseverance include periodic self-reflection, mental health support, and carefully selecting mentors. Conclusions For early-career scientists along the training continuum, this advice deserves critical reflection before committing to an academic research career. For advisors and institutions, this work provides a unique perspective from postdoctoral scholars on elements of the academic training path that can be improved to increase retention, career satisfaction, and preparation for the scientific workforce.