Recruitment of crustose coralline algae on tiles material for monitoring coral larvae settlement’s consolidators at Nature Reserve Pulau Sempu, East Java, Indonesia

Crustose coralline algae (Corallinophycideae) are red algae that produced calcium carbonate and are well recognized as foundation species in the epipelagic zone of the marine ecosystem. These algae induced settlement juvenile of coral by released chemical cues from bacterial communities on the surface of their colonies. Their extracellular calcium carbonate also can stabilize reef structure that influencing many invertebrate attaches and growth in the seabed. Crustose coralline algae (CCA) have obtained attention because of their distribution and health compromise to increasing seawater temperature, ocean acidification, and pollutant. As a cryptic species in the ecosystem, the presence of CCA recruit sometimes doesn’t have attention, especially on their capability to occupy the empty space. This study aimed to document coverage and number of CCA recruit in two different recruitment tile’s material. The highest CCA percentage of the cover was showed inside surface than others surface in all stations. Light intensity and low sedimentation were suggested as a key factor of success of high coverage. Overall, station higher CCA recruits have shown from Tiga Warna. Low sedimentation and protection from aerial exposure became the main reason for it. No significant difference number of CCA recruits between marble and sandstone in this study. Successful CCA recruitment in this study can give a wide picture that natural recruitment of coral and other reef biodiversity in Southern Malang might be will succeed because of the abundance of coralline algae that support their life history stage.

Development of real-time indoor human tracking system using LoRa technology

<p>Industrial growth has increased the number of jobs hence increase the number of employees. Therefore, it is impossible to track the location of all employees in the same building at the same time as they are placed in a different department. In this work, a real-time indoor human tracking system is developed to determine the location of employees in a real-time implementation. In this work, the long-range (LoRa) technology is used as the communication medium to establish the communication between the tracker and the gateway in the developed system due to its low power with high coverage range besides requires low cost for deployment. The received signal strength indicator (RSSI) based positioning method is used to measure the power level at the receiver which is the gateway to determine the location of the employees. Different scenarios have been considered to evaluate the performance of the developed system in terms of precision and reliability. This includes the size of the area, the number of obstacles in the considered area, and the height of the tracker and the gateway. A real-time testbed implementation has been conducted to evaluate the performance of the developed system and the results show that the system has high precision and are reliable for all considered scenarios.</p>

Standard Flow Multiplexed Proteomics (SFloMPro)—An Accessible Alternative to NanoFlow Based Shotgun Proteomics

Multiplexed proteomics using isobaric tagging allows for simultaneously comparing the proteomes of multiple samples. In this technique, digested peptides from each sample are labeled with a chemical tag prior to pooling sample for LC-MS/MS with nanoflow chromatography (NanoLC). The isobaric nature of the tag prevents deconvolution of samples until fragmentation liberates the isotopically labeled reporter ions. To ensure efficient peptide labeling, large concentrations of labeling reagents are included in the reagent kits to allow scientists to use high ratios of chemical label per peptide. The increasing speed and sensitivity of mass spectrometers has reduced the peptide concentration required for analysis, leading to most of the label or labeled sample to be discarded. In conjunction, improvements in the speed of sample loading, reliable pump pressure, and stable gradient construction of analytical flow HPLCs has continued to improve the sample delivery process to the mass spectrometer. In this study we describe a method for performing multiplexed proteomics without the use of NanoLC by using offline fractionation of labeled peptides followed by rapid “standard flow” HPLC gradient LC-MS/MS. Standard Flow Multiplexed Proteomics (SFloMPro) enables high coverage quantitative proteomics of up to 16 mammalian samples in about 24 h. In this study, we compare NanoLC and SFloMPro analysis of fractionated samples. Our results demonstrate that comparable data is obtained by injecting 20 µg of labeled peptides per fraction with SFloMPro, compared to 1 µg per fraction with NanoLC. We conclude that, for experiments where protein concentration is not strictly limited, SFloMPro is a competitive approach to traditional NanoLC workflows with improved up-time, reliability and at a lower relative cost per sample.

Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap

Many software packages and pipelines had been developed to handle the sequence data of the model species. However, Genotyping from complex heterozygous plant genome needs further improvement on the previous methods. Here we present a new pipeline available at https://github.com/Ncgrhg/HetMapv1) for variant calling and missing genotype imputation from low coverage sequence data for heterozygous plant genomes. To check the performance of the HetMap on the real sequence data, HetMap was applied to both the F1 hybrid rice population which consists of 1495 samples and wild rice population with 446 samples. Four high coverage sequence hybrid rice accessions and two high coverage sequence wild rice accessions, which were also included in low coverage sequence data, are used to validate the genotype inference accuracy. The validation results showed that HetMap archived significant improvement in heterozygous genotype inference accuracy (13.65% for hybrid rice, 26.05% for wild rice) and total accuracy compared with other similar software packages. The application of the new genotype with the genome wide association study also showed improvement of association power in two wild rice phenotypes. It could archive high genotype inference accuracy with low sequence coverage with a small population size with both the natural population and constructed recombination population. HetMap provided a powerful tool for the heterozygous plant genome sequence data analysis, which may help the discover of new phenotype regions for the plant species with complex heterozygous genome.

Mining Simple Path Traversal Patterns in Knowledge Graph

The data mining has remained a subject of unfailing charm for research. The knowledge graph is rising and showing infinite life force and strong developing potential in recent years, where it is observed that acyclic knowledge graph has capacity for enhancing usability. Though the development of knowledge graphs has provided an ample scope for appearing the abilities of data mining, related researches are still insufficient. In this paper, we introduce path traversal patterns mining to knowledge graph. We design a novel simple path traversal pattern mining framework for improving the representativeness of result. A divide-and-conquer approach of combining each path is proposed to discover the most frequent traversal patterns in knowledge graph. To support the algorithm, we design a linked list structure indexed by the length of sequences with handy operations. The correctness of algorithm is proven. Experiments show that our algorithm reaches a high coverage with low output amounts compared to existing frequent sequence mining algorithms.

Pertussis in Children: Clinical and Epidemiological Features, the Possibilities of Vaccine Preventio

Relevance. Despite the specific immunization carried out, pertussis still has great medical and social significance for pediatricians, since it continues to remain a common bacterial infection, involving children of different age groups in the epidemic process. The lack of persistent immunity to whooping cough, combined with a high susceptibility index, contributes to an increase in the incidence among schoolchildren and adolescents, who are diagnosed only during epidemiological and laboratory examinations, and who, in most cases, serve as sources of infection for young children. Aim. To study the clinical and epidemiological features of whooping cough in children aged 0 to 14 years hospitalized in an infectious diseases hospital under conditions of mass vaccine prevention, as well as to identify the features of the disease in vaccinated people using the example of an outbreak of the disease in an organized group. Materials and methods. A retrospective analysis of 164 case histories of children diagnosed with Pertussis hospitalized in the infectious hospital of the Regional Interdistrict Children’s Clinical Hospital № 1 in Krasnoyarsk in 2015–2019, as well as 25 outpatient records of patients identified during the epidemiological investigation of the focus of infection in December 2019 was carried out. For the etiological interpretation of the diagnosis of whooping cough, a comprehensive laboratory examination was carried out using bacteriological, serological and molecular genetic research methods. Results. According to official statistics, in the Krasnoyarsk territory in 2019, among children with pertussis, patients aged 7 to 17 prevailed (38,7%). At the same time, in the age structure of patients hospitalized in a hospital, the primary importance was occupied by children of the first year of life, unvaccinated against this disease. Most of them were diagnosed with a moderate form of the disease with frequent development of complications from the respiratory and nervous systems. At the same time, among schoolchildren and adolescents, as a rule, who have received a completed course of vaccination, there is an atypical, erased course of the disease, while the difficulties of its diagnosis lead to a high incidence of pertussis in children of the first year of life who have not yet been protected by vaccination. Conclusions. Despite the high coverage of decreed groups with preventive vaccinations against whooping cough in the Krasnoyarsk territory, an assessment of the state of specific immunity based on the results of a serological survey conducted in 2019 revealed 50.6% of seronegative individuals already at the age of 3–4 years, which confirms the need to improve the schemes immunization against this disease; and inclusion of pertussis vaccination in the regional immunization schedule.

Implications of AlphaFold2 for crystallographic phasing by molecular replacement

The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models.

An empirical evaluation of genotype imputation of ancient DNA

With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle 4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference and study sample size. Making use of five ancient samples with high-coverage data available, we evaluated imputed data with respect to accuracy, reference bias and genetic affinities as captured by PCA. We obtained genotype concordance levels of over 99% for data with 1x coverage, and similar levels of accuracy and reference bias at levels as low as 0.75x. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1x. We also show that a large and varied phased reference set as well as the inclusion of low- to moderate-coverage ancient samples can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for post-processing and validation prior to downstream analysis.

Effect of Major Illness Insurance on Vulnerability to Poverty: Evidence From China

Disease is the primary cause of poverty in China. Health insurance is an essential mechanism for managing health risks and addressing the risk of financial loss. Using data from the China Family Panel Studies (CFPS) waves from 2010 to 2016, this study develops a random forest method to assess households' vulnerability to poverty and then examines the impact of major illness insurance on vulnerability to poverty by focusing on the rollout period of a major illness insurance scheme. The research also examines the impact of increased major illness insurance coverage on poverty reduction by focusing on the change from low- to high-coverage health insurance. The findings indicate that major illness insurance and improvements in the degree of coverage significantly reduce vulnerability to poverty. In addition, major illness insurance is found to alleviate the vicious cycle of poverty and disease through the mechanism of increasing household income, and its effect has strengthened over time. Compared to other poverty reduction policies, major illness insurance has a greater influence on poverty alleviation.