Miracle-dz/UniFAR-FTUs huggingface dataset:
Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems

Underwater sediments are a natural archive of biological information. Reconstruction of past fauna has been conducted for various taxonomic groups using morphological remains and DNA derived from these remains. However, information on past occurrences of fish species, the top predator of lake ecosystems, could have been reproduced only in exceptional environments, and past quantitative information on fish, particularly in lake ecosystems, has been a knowledge gap in reconstructing past fauna. Tracking the quantitative fluctuations of fish is essential for reconstructing multiple trophic levels of organisms in lake ecosystems. To acquire past quantitative fish information from lake sediments, we collected approximately 30 cm-length of underwater sediments in Lake Biwa. We extracted sedimentary environmental DNA (eDNA) and measured temporal fluctuations in the eDNA concentration of the native and fishery target species Plecoglossus altivelis and Gymnogobius isaza. For P. altivelis, we examined the possibility of tracking quantitative fluctuations by comparing sedimentary eDNA with recorded catch per unit effort (CPUE). The chronology of the sediments allowed us to obtain information on sediments collected in Lake Biwa over the past 100 years. The deepest depths at which sedimentary eDNA was detected were 30 and 13 cm for P. altivelis and G. isaza from the surface, corresponding to approximately 100 and 30 years ago, respectively. In the comparison of sedimentary eDNA concentrations and biomass, we found a significant correlation between the CPUE of P. altivelis and its sedimentary eDNA concentration adjusted to compensate for DNA degradation. Sedimentary eDNA fluctuations were observed in P. altivelis, possibly reflecting the abundance fluctuation due to variations in the main food resources of zooplankton. Our findings provide essential pieces for the reconstruction of past fauna of lake ecosystems. The addition of quantitative information on fish species will reach a new phase, for instance, by investigating population shifts or biological interactions in the reconstruction of past fauna in lake ecosystems.
Physiology and structure of pathogenic Escherichia coli pOmpT reveal two substrate-binding sites

The pathogenicity of bacteria can be achieved by cleaving antimicrobial peptides (AMPs) through the outer membrane protease family (Omptins) to evade or resist the host’s innate immune response. The OmpT-like proteins in Escherichia coli are members of Omptins, which have highly conserved proteolytic activity. Here, sequence alignment and physiological studies have determined that pOmpT is a virulence factor with atypical proteolytic activity. Comparing pOmpT with cOmpT in terms of structure, proteolytic activity and target substrates, it is found that Asp267 and Ser276 of cOmpT are substrate-binding sites and help its catalytic center to cleave substrates (protamine,synthetic peptide or RNase 7). However, special structural features and the nature of residues Ser267 and Thr276 of pOmpT caused the inability of cleavage protamine, but allows it to specifically cleave the human AMP RNase 7. It is suggested that two sites are related with the substrate specificity. In short, we found that pOmpT presents a new structural basis for the specific recognition of substrates, and providing new clues for the development of antimicrobial drugs.
Inferring CTCF binding patterns and anchored loops across human tissues and cell types

CCCTC-binding factor (CTCF) is a transcription regulator which is involved in many cellular processes. How CTCF recognizes DNA sequence to exert chromosome barrier or enhancer blocking effects remains to be fully interrogated. Despite many computational tools were developed to predict CTCF-mediated loops qualitatively or quantitatively, few could specially evaluate the regulatory potential of DNA sequence at CTCF binding sites (CBSs) and how it affects chromatin loop formation. Here, we developed a deep learning model, DeepAnchor, to precisely characterize the binding patterns for different types of CBSs. By incorporating base-wise genomic/epigenomic features, we revealed distinct chromatin and sequence features for CTCF-mediated insulation and looping at a high resolution, such as two sequence motifs flanking the core CTCF motif at loop-associated CBSs. Besides, we leveraged the predicted anchor score to optimize the loop extrusion model and achieved the best performance in predicting CTCF-anchored loops. We established a compendium of context-specific CTCF-anchored loops across 52 human tissue/cell types and found that genomic disruption of CTCF-anchored loops may represent a general causal mechanism of disease pathogenesis. These computational models, together with the established resource, could facilitate the mechanistic research on how the CTCF-mediated cis-regulatory elements (CREs) shapes context-specific gene regulation in cell development and disease progression.
Fast super-resolution estimation of DOA and DOD in bistatic MIMO Radar with off-grid targets

ABSTRACT In this paper, we focus on the problem of joint DOA and DOD estimation in Bistatic MIMO Radar using sparse reconstruction method. In traditional ways, we usually convert the 2D parameter estimation problem into 1D parameter estimation problem by Kronecker product which will enlarge the scale of the parameter estimation problem and bring more computational burden. Furthermore, it requires that the targets must fall on the predefined grids. In this paper, a 2D-off-grid model is built which can solve the grid mismatch problem of 2D parameters estimation. Then in order to solve the joint 2D sparse reconstruction problem directly and efficiently, three kinds of fast joint sparse matrix reconstruction methods are proposed which are Joint-2D-OMP algorithm, Joint-2D-SL0 algorithm and Joint-2D-SOONE algorithm. Simulation results demonstrate that our methods not only can improve the 2D parameter estimation accuracy but also reduce the computational complexity compared with the traditional Kronecker Compressed Sensing method.
IMPACT OF FUNGAL INFECTIONS AND SIGNIFICANT COUNT STATUSES ON FERTILITY PARAMETERS IN COMMERCIAL MOTORCYCLISTS AND NON- CYCLISTS IN NNEWI, NIGERIA

Fungal infections cause male assessory gland infections (MAGI) affecting male fertility especially in high risk occupations. A casecontrol study on the impact of fungal infection and significant count statuses on fertility parameters was conducted in commercial motorcyclists and non-cyclists in Nnewi, Nigeria. A total of 304 samples consisting of 152 semen and blood samples from 49 commercial motorcyclists and 103 non-cyclists, aged 19-79 years old were analyzed. Subjects were recruited using non-probability sampling technique, data was collected using questionnaire, yeasts isolated using semen-dilution method and identified. Significant counts were calculated, semen quality and biomarkers assessed using WHO methods, serum hormone by ELISA technique. Fertility index was mathematically deducted and statistics analyzed with SPSS version 21. Results identified seven kinds of yeast isolates; Candida guilliermondii (47.2%), C. tropicalis(30.3%), C. albicans(13.2%), C. glabrata (2.6%), C. famata (2.0%), C. krunzi (1.3%) and Cryptococcus laurentii (0.7%), with C. guilliermondii highest in both groups, more types isolated from controls (7) than test groups (6). Fungal (73.5%) and mixed fungal infections (MFI) (42.9%) were higher in test groups; significant single and mixed fungal count statuses (FCS 1 and FCS 2) were higher in controls (60.9%; 58.6%). Age-wise, 45-64 years old groups had higher (FCS 1) (64.3%), while for (FCS 2), it was 1944 years (38.7%). Mean ranks of some serum hormones, semen qualities and biomarkers were affected by fungal infections and their significant count statuses in both groups, P < 0.05, and affected fertility index of test groups. Middle-aged and younger males are at risk for fungal infections which in significant count affected fertility parameters, more in semen quality and fertility index in test groups. Prompt treatment and awareness is necessary.
Analysis of optical scheme for medium-range directed energy laser weapon system

The relations between range of operation and aperture of laser weapon system were investigated, taking into account diffraction and technical limitations as beam quality, accuracy of point tracking, technical quality of optical train, etc. As a result for the medium ranges of 1 - 2 km we restricted the analysis to apertures not wider than 150 mm and the optical system without adaptive optics. To choose the best laser beam shape, the minimization of aperture losses and thermooptical effects inside optics as well as the effective width of laser beam in far field should be taken into account. We have analyzed theoretically such a problem for the group of a few most interesting from that point of view profiles including for reference two limiting cases of Gaussian beam and ‘top hat’ profile. We have found that the most promising is the SuperGaussian profile of index p = 2 for which the surfaces of beam shaper elements can be manufactured in the acceptable cost-effective way and beam quality does not decrease noticeably. Further, we have investigated the thermo-optic effects on the far field parameters of Gaussian and ‘top hat’ beams to determine the influence of absorption in optical elements on beam quality degradation. The simplified formulae were derived for beam quality measures (parameter M2 and Strehl ratio) which enables to estimate the influence of absorption losses on degradation of beam quality.
Agile Software Development

Agile software development represents a major departure from traditional, plan-based approaches to software engineering. The selections of appropriate software development methodologies for a given project and tailoring the methodologies to a specific requirement have been a challenge since the establishment of software development as a discipline. The research speaks about what is currently known about the benefits and limitations of agile methods and methodologies. Agile software development is a particularly important topic in software engineering and information systems. We approach the idea of the four core of agile software development that are essential to ease the process of software development.
A systematic approach for enterprise systems upgrade decision-making: Outlining the decision processes

Purpose Enterprise systems (ES) upgrade is fundamental to maintaining a system’s continuous improvement and stability. However, while the extant literature is replete with research on ES upgrade decision-making, there is scant knowledge about how different decision processes facilitate this decision to upgrade. This paper aims to investigate and better understand these processes from an organisational perspective. Design/methodology/approach The study adopted a qualitative survey design, and used a Web-based questionnaire and semi-structured interviews to collect data from 23 large organisations. Data accrued were qualitatively analysed and manually coded to identify the various decision processes undertaken during ES upgrade decisions. Findings Analysis results reveal complex interrelations between the upgrade drivers, the need to evaluate the new version’s functionality and the upgrade impact. Understanding the interaction between these elements influences the upgrade decision process. Research limitations/implications The study proposes ES upgrade processes that support a decision to upgrade major releases. Further research is required to offer either similar or conflicting arguments on the upgrade decision-making and provide a probabilistic generalisation of the decision-making processes. Originality/value The research offers a comprehensive and empirically supported methodical approach that embraces an evaluation of a new version’s functionality, technical requirements and concomitant upgrade implications as intrinsic decision processes. This approach assists in the decisions to establish the upgrade need and determine the level of change, effort required, impacts and associated benefits.
Experimental Identification of an Electronic Throttle Body

Detailed off-line experimental identification of an automotive electronic throttle body (ETB) servo drive is carried out with the aim to aid design of a high-performance electronic throttle control strategy. The linear and nonlinear parts of the ETB model are conveniently identified separately. Identification of ETB linear dynamics includes a multi-step identification method based on the physical ETB model form, and single-step methods based on the black-box continuous-time and discrete-time ETB model forms. The nonlinear effects identified include static and dynamic friction effects, and distinctive limp-home nonlinearity.
S2045796022000233jra 1..8

Aims. There is currently little nationally representative diagnostic data available to quantify how many Aboriginal and Torres Strait Islander people may need a mental health service in any given year. Without such information, health service planners must rely on less direct indicators of need such as service utilisation. The aim of this paper is to provide a starting point by estimating the prevalence ratio of 12-month common mental disorders (i.e. mood and anxiety disorders) for Indigenous peoples compared to the general Australian population. Methods. Analysis of the four most recent Australian Indigenous and corresponding general population surveys was undertaken. Kessler-5 summary scores by 10-year age group were computed as weighted percentages with corresponding 95% confidence intervals. A series of meta-analyses were conducted to pool prevalence ratios of Indigenous to general population significant psychological distress by 10-year age groups. The proportion of respondents with self-reported clinician diagnoses of mental disorders was also extracted from the most recent survey iterations. Results. Indigenous Australians are estimated to have between 1.6 and 3.3 times the national prevalence of anxiety and mood disorders. Sensitivity analyses found that the prevalence ratios did not vary across age group or survey wave. Conclusions. To combat the current landscape of inequitable mental health in Australia, priority should be given to populations in need, such as Indigenous Australians. Having a clear idea of the current level of need for mental health services will allow planners to make informed decisions to ensure adequate services are available.
Spaces of Governance for Sustainable Transformation of Local Food Systems: the Case of 8 biodistricts in Tuscany

8 Faced with higher risks from climate change, food systems will need to transition 9 away from dominant industrial paradigms and move towards a more sustainable 10 way of producing, distributing, and consuming food. For sustainability 11 transitions to happen, there is increased acknowledgment that lower 12 administrative levels and local territorial arrangements are fundamental for 13 policymaking, implementation, and impactful action. To go beyond two well14 known criticisms of local food sustainable initiatives, i.e., to be rather small and 15 to be developed outside policy frameworks and/or in stark opposition to current 16 food systems, we argue in this paper to look at new meso-spaces of 17 transformation at local level such as biodistricts, where community members, 18 professionals, and governments get together to share knowledge, deliberate, and 19 collectively devise place-based strategies to address complex food systems issues. 20 We analyse 8 biodistricts in Tuscany and, as a result of the analysis, we argue that 21 biodistricts can potentially act as territorial meso-spaces at local level, favouring 22 the transformation towards sustainability of food systems. 23
Effective Electricity Cost Management in a Manufacturing Operation by Using Optimal ETOU Tariff Formulation

82 Abstract—In this study, simultaneous Demand Side Management (DSM) strategies are proposed for energy consumption cost reduction and peak load mitigation to industrial’s consumers. By which, a real test case study of a manufacturing electricity load profile had been used to prove the concept. A superior bio-inspired algorithm, Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO) had been implemented and compared in order to optimize the upright load profile of load management strategy. Subsequently, significant simulation results of operation profit gain through 24 hours power consumption had been analyzed properly. The proposed method had shown reduction of electricity energy consumption cost at all pricing zones; and Maximum Demand (MD) cost mitigation when load management weightages were applied to the identified 10% controlled loads consequently. The investigation has found that, the loads are manageable through the improvement of Load Factor Index (LFI) while Buildings’ Electricity Economic Responsive Index (BEERI) has been the indicator to find the minimum requirement for the optimum load management weightages. Thus, it is hoped that the finding of this study can help to poise the industrial operation in terms of electricity cost effectiveness as well as support the national demand side management program.
Designing Personal Visualizations for Different People: Lessons from a Study with Elite Soccer Teens

A BSTRACT This paper describes a study that sought to understand elite soccer teenagers’ use of information visualizations to learn about their own sports performance, how this might motivate them to change behavior, and thus potentially improve their own performance. We specifically investigate how information visualizations support the players’ data comprehension, and how their level of comprehension might depend on factors such as their general literacy, visualization literacy and maturity. We show unsurprisingly that elite soccer teenagers are able to use information visualizations to gain new information about their performance. Based on our investigation, we define a classification of the level of data comprehension. Secondly, we demonstrate a method which allows visualization researchers and practitioners to design and evaluate visualization concepts based on real data over a short time-span. Finally, we argue that designers of personal information visualizations need to consider the range of visualization literacies that are to be expected in many target populations. Our lessons provide new insights in peoples’ use of visualizations and more broadly in visualization literacy. From these insights, we discuss implications for design of visualizations that consider peoples’ level of visualization literacy.
An Enhanced Artificial Electric Field Algorithm with Sine Cosine Mechanism for Logistics Distribution Vehicle Routing

Aiming at the scheduling problem of logistics distribution vehicles, an enhanced artificial electric field algorithm (SC-AEFA) based on the sine cosine mechanism is proposed. The development of the SC-AEFA was as follows. First, a map grid model for enterprise logistics distribution vehicle path planning was established. Then, an enhanced artificial electric field algorithm with the sine cosine mechanism was developed to simulate the logistics distribution vehicle scheduling, establish the logistics distribution vehicle movement law model, and plan the logistics distribution vehicle scheduling path. Finally, a distribution business named fresh enterprise A in the Fuzhou Strait Agricultural and Sideline Products Trading Market was selected to test the effectiveness of the method proposed. The theoretical proof and simulation test results show that the SC-AEFA has a good optimization ability and a strong path planning ability for enterprise logistics vehicle scheduling, which can improve the scheduling ability and efficiency of logistics distribution vehicles and save transportation costs.
Metabolome Alterations Linking Sugar-Sweetened Beverage Intake with Dyslipidemia in Youth: The Exploring Perinatal Outcomes among CHildren (EPOCH) Study

The objective of this study was to assess intermediary metabolic alterations that link sugar-sweetened beverage (SSB) intake to cardiometabolic (CM) risk factors in youth. A total of 597 participants from the multi-ethnic, longitudinal Exploring Perinatal Outcomes among CHildren (EPOCH) Study were followed in childhood (median 10 yrs) and adolescence (median 16 yrs). We used a multi-step approach: first, mixed models were used to examine the associations of SSB intake in childhood with CM measures across childhood and adolescence, which revealed a positive association between SSB intake and fasting triglycerides (β (95% CI) for the highest vs. lowest SSB quartile: 8.1 (−0.9,17.0); p-trend = 0.057). Second, least absolute shrinkage and selection operator (LASSO) regression was used to select 180 metabolite features (out of 767 features assessed by untargeted metabolomics) that were associated with SSB intake in childhood. Finally, 13 of these SSB-associated metabolites (from step two) were also prospectively associated with triglycerides across follow-up (from step one) in the same direction as with SSB intake (Bonferroni-adj. p < 0.0003). All annotated compounds were lipids, particularly dicarboxylated fatty acids, mono- and diacylglycerols, and phospholipids. In this diverse cohort, we identified a panel of lipid metabolites that may serve as intermediary biomarkers, linking SSB intake to dyslipidemia risk in youth.
The Effectiveness of Behavioral Interventions in Adults with Post-Traumatic Stress Disorder during Clinical Rehabilitation: A Rapid Review

Background: This review examined the effectiveness of behavioral interventions for adults with post-traumatic stress disorder (PTSD) triggered by physical injury or medical trauma. It discusses implications in support of rehabilitation management for COVID-19 survivors diagnosed with PTSD. Methods: This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and the Interim Guidance from the Cochrane Rapid Reviews Methods Group. The authors searched for randomized control trials in PubMed, Embase, and CENTRAL databases up to 31 March 2021. Results: Five studies (n = 459) met the inclusion criteria. Each study measured a different comparison of interventions. The certainty of the evidence was judged to be very low for all outcomes. Post-traumatic stress disorder symptom reduction was found to be in favor of trauma-focused cognitive-behavioral therapy, cognitive therapy, and cognitive-behavioral therapy. Cognitive function improvements were observed in favor of the cognitive processing therapy control intervention. Conclusions: Overall, there is uncertainty about whether behavioral interventions are effective in reducing PTSD symptoms and improving functioning and quality of life when the disorder is triggered by a physical or medical trauma rather than a psychological trauma. Further research should investigate their efficacy in the context of rehabilitation management and gather evidence on this population.