bluuebunny/crossref_metadata_2025 huggingface dataset:
Is foot deformity associated with developmental dysplasia of the hip?
Authors: Håberg Øvind , Foss Olav A. , Lian Østein Bjerkestrand , Holen Ketil Jarl
Published: November 2020

Aims

To assess if congenital foot deformity is a risk factor for developmental dysplasia of the hip (DDH).

Methods

Between 1996 and 2012, 60,844 children were born in Sør-Trøndelag county in Norway. In this cohort study, children with risk factors for DDH were examined using ultrasound. The risk factors evaluated were clinical hip instability, breech delivery, a family history of DDH, a foot deformity, and some syndromes. As the aim of the study was to examine the risk for DDH and foot deformity in the general population, children with syndromes were excluded. The information has been prospectively registered and retrospectively analyzed.

Results

Overall, 494 children (0.8%) had DDH, and 1,132 (1.9%) a foot deformity. Of the children with a foot deformity, 49 (4.3%) also demonstrated DDH. There was a statistically significant increased association between DDH and foot deformity (p < 0.001). The risk of DDH was highest for talipes calcaneovalgus (6.1%) and club foot (3.5%), whereas metatarsus adductus (1.5%) had a marginal increased risk of DDH.

Conclusion

Compared with the general population, children with a congenital foot deformity had a significantly increased risk for DDH and therefore we regard foot deformity as a true risk factor for DDH. Cite this article: Bone Joint J 2020;102-B(11):1582–1586.
STATE-OF-THE-ART AND TRENDS IN THE SYSTEMATIC DEVELOPMENT OF RICH INTERNET APPLICATIONS
Authors: TOFFETTI GIOVANNI , COMAI SARA , PRECIADO JUAN CARLOS , LINAJE MARINO
Published: November 2020

Rich Internet Applications (RIAs) are widely adopted Web applications that add the richer interaction, presentation, and client-side computation capabilities of desktop applications to the Web. However, the evolution from Web applications towards RIAs comes at the cost of increased complexity in their development. For this reason, a wide variety of tools and technologies have been proposed in order to streamline their development effort. This paper investigates the current state of the art of the RIA development approaches. The review shows that the current industrial development practice lacks a comprehensive approach to RIA development, supporting all the development steps from the design to implementation, test and maintenance, and helping identifying correct design choices. This is in part due to the severe fragmentation of current RIA technologies that prevents the adoption of a commonly recognized set of best practices resulting in ad-hoc development processes. These aspects are in part treated by research methodologies and some innovative industrial solutions, but also these approaches present some limitations. The paper identifies future research directions for RIAs to fully support their development process and to support their design in a more comprehensive and systematic way, from both industrial and research perspectives.
Validating Structural Metrics for BPEL Process Models
Authors: Muketha Geoffrey Muchiri , Azim Abd Ghani Abdul , Atan  Rodziah
Published: November 2020

Business process models tend to get more and more complex with age, which hurts the ease with which designers can understand and modify them. Few metrics have been proposed to measure this complexity, and even fewer have been tested in the Business Process Execution Language (BPEL) context. In this paper, we present three related experimental studies whose aim was to analyse the ability of four selected structural metrics to predict BPEL process model understandability and modifiability. We used Spearman’s rho and regression analysis in all three experiments. All metrics passed the correlation tests meaning that they can serve as understandability and modifiability indicators. Further, four of the metrics passed the regression test for understanding time implying that they can serve as understandability predictors. Finally, only one metric passed the regression test for modification time implying that it can serve as a modifiability predictor.
Design of a Hybrid Digital Watermarking Algorithm with High Robustness
Authors: Xie Yi , Wang Yulin , Ma Maode
Published: November 2020

With the development of the Internet, storage and transmission technologies such as printers and scanners, digital multimedia products are rapidly transmitted through the Internet broadcasting, multimedia works becoming easy to obtain and illegally tampering and copying. The copyright of media works urgently needs to be protected. As an important information security scheme, digital watermarking technology provides a powerful solution to the protection of multimedia works. In this paper, we propose an image digital watermarking algorithm combining discrete wavelet transform, discrete cosine transform and matrix singular value decomposition and new scrambling technique. Furthermore, to improve the robustness of the algorithm, grayscale scrambling and pseudo magic square transform are used. To evaluate our proposed algorithm, we realize the simulation based on Python 3.7.  All the simulation results show that our proposed algorithm has strong imperceptibility and robustness.
Whispering gallery modes in triple microdisks of triangular configurations: publisher’s note
Authors: Ryu Jung-Wan , Rim Sunghwan
Published: November 2020

This publisher’s note corrects the funding section in J. Opt. Soc. Am. B
37, 2382 (2020)JOBPDE0740-322410.1364/JOSAB.392994.
Using B cell receptor lineage structures to predict affinity
Authors: Ralph Duncan K. , Matsen Frederick A.
Published: November 2020

We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of thepartisBCR inference package, available athttps://github.com/psathyrella/partis.

Comments

Please post comments or questions on this paper as new issues athttps://git.io/Jvxkn.
Deep learning predicts short non-coding RNA functions from only raw sequence data
Authors: Noviello Teresa Maria Rosaria , Ceccarelli Francesco , Ceccarelli Michele , Cerulo Luigi
Published: November 2020

Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is determinant to know RNA function and machine learning based approaches have been successfully proven to predict RNA function from secondary structure information. Here we show that RNA function can be predicted with good accuracy from a lightweight representation of sequence information without the necessity of computing secondary structure features which is computationally expensive. This finding appears to go against the dogma of secondary structure being a key determinant of function in RNA. Compared to recent secondary structure based methods, the proposed solution is more robust to sequence boundary noise and reduces drastically the computational cost allowing for large data volume annotations. Scripts and datasets to reproduce the results of experiments proposed in this study are available at: https://github.com/bioinformatics-sannio/ncrna-deep.
Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans
Authors: Evans Kathryn S. , Zdraljevic Stefan , Stevens Lewis , Collins Kimberly , Tanny Robyn E. , Andersen Erik C.
Published: November 2020

Zinc is an essential trace element that acts as a co-factor for many enzymes and transcription factors required for cellular growth and development. Altering intracellular zinc levels can produce dramatic effects ranging from cell proliferation to cell death. To avoid such fates, cells have evolved mechanisms to handle both an excess and a deficiency of zinc. Zinc homeostasis is largely maintained via zinc transporters, permeable channels, and other zinc-binding proteins. Variation in these proteins might affect their ability to interact with zinc, leading to either increased sensitivity or resistance to natural zinc fluctuations in the environment. We can leverage the power of the roundworm nematodeCaenorhabditis elegansas a tractable metazoan model for quantitative genetics to identify genes that could underlie variation in responses to zinc. We found that the laboratory-adapted strain (N2) is resistant and a natural isolate from Hawaii (CB4856) is sensitive to micromolar amounts of exogenous zinc supplementation. Using a panel of recombinant inbred lines, we identified two large-effect quantitative trait loci (QTL) on the left arm of chromosome III and the center of chromosome V that are associated with zinc responses. We validated and refined both QTL using near-isogenic lines (NILs) and identified a naturally occurring deletion insqst-5, a sequestosome-related gene, that is associated with resistance to high exogenous zinc. We found that this deletion is relatively common across strains within the species and that variation insqst-5is associated with zinc resistance. Our results offer a possible mechanism for how organisms can respond to naturally high levels of zinc in the environment and how zinc homeostasis varies among individuals.
Circulating microtranscriptome profiles reveal distinct expression of microRNAs in severe leptospirosis
Authors: Limothai Umaporn , Dinhuzen Janejira , Payongsri Titipon , Tachaboon Sasipha , Tangkijvanich Pisit , Chuaypen Natthaya , Srisawat Nattachai
Published: November 2020

Biomarkers to predict the severity of leptospirosis are still lacking. This study aimed to identify and validate microRNAs in patients with severe leptospirosis, that could potentially be used as biomarkers for predicting an unfavorable outcome. Serum samples were collected from participants with definite diagnosis of leptospirosis. The participants were divided into two groups, non-severe and severe leptospirosis, as defined by the Specific Organ Sequential Organ Failure (SOFA) Score of more than two in any organ. Microtranscriptome analysis was performed using the NanoString miRNA Expression Assay. The expression level of candidate miRNAs was then validated by quantitative RT-PCR. Based on the NanoString, the microtranscriptome profile of the severe group was significantly different from that of the non-severe group. Upregulation of miR155-5p, miR362-3p, miR502-5p, miR601, miR1323, and miR630 in the severe group were identified, and further investigated. A total of 119 participants were enrolled in the validation cohort. Serum miR155-5p and miR630 levels were significantly higher in the severe group compared to the non-severe group. The combined use of miR155-5p or miR-630 with serum bicarbonate levels had an AUC of 0.79 (95%CI; 0.69–0.89, p<0.001) in identifying the severity of the disease. This data provides the first evidence that the microtranscriptome profiles of patients with severe leptospirosis were different from the non-severe group. Serum miR155-5p and miR630 levels might be novel biomarkers for identifying severe leptospirosis.
The risk of adverse clinical outcomes following treatment of Plasmodium vivax malaria with and without primaquine in Papua, Indonesia
Authors: Thriemer Kamala , Poespoprodjo Jeanne-Rini , Kenangalem Enny , Douglas Nicholas M. , Sugiarto Paulus , Anstey Nicholas M. , Simpson Julie Anne , Price Ric N.
Published: November 2020

The widespread use of primaquine (PQ) radical cure for P. vivax, is constrained by concerns over its safety. We used routinely collected patient data to compare the overall morbidity and mortality in patients treated with and without PQ without prior testing of Glucose-6-Phosphate-Dehydrogenase (G6PD) deficiency in Papua, Indonesia, where there is a low prevalence of G6PD deficiency. Records were collated from patients older than 1 year, with P. vivax infection, who were treated with an artemisinin combination therapy (ACT). The risks of re-presentation, hospitalization, major fall in haemoglobin and death within 30 days were quantified and compared between patients treated with and without PQ using a Cox regression model. In total 26,216 patients with P. vivax malaria presented to the hospital with malaria during the study period. Overall 27.56% (95% Confidence Interval (95%CI): 26.96–28.16) of 21,344 patients treated with PQ re-presented with any illness within 30 days and 1.69% (1.51–1.88) required admission to hospital. The corresponding risks were higher in the 4,872 patients not treated with PQ; Adjusted Hazard Ratio (AHR) = 0.84 (0.79–0.91; p<0.001) and 0.54 (0.41–0.70; p<0.001) respectively. By day 30, 14.15% (12.45–16.05) of patients who had received PQ had a fall in haemoglobin (Hb) below 7g/dl compared to 20.43% (16.67–24.89) of patients treated without PQ; AHR = 0.66 (0.45–0.97; p = 0.033). A total of 75 (0.3%) patients died within 30 days of treatment with a mortality risk of 0.27% (0.21–0.35) in patients treated with PQ, compared to 0.38% (0.24–0.60) without PQ; AHR = 0.79 (0.43–1.45; p = 0.448). In Papua, Indonesia routine administration of PQ radical cure without prior G6PD testing, was associated with lower risk of all cause hospitalization and other serious adverse clinical outcomes. In areas where G6PD testing is not available or cannot be delivered reliably, the risks of drug induced haemolysis should be balanced against the potential benefits of reducing recurrent P. vivax malaria and its associated morbidity and mortality.
RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef
Authors: Leal-Gutiérrez Joel D. , Elzo Mauricio A. , Carr Chad , Mateescu Raluca G.
Published: November 2020

RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured inlongissimus dorsimuscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.
Genome-wide pathway-based quantitative multiple phenotypes analysis
Authors: Deng Yamin , Wu Shiman , Fan Huifang
Published: November 2020

For complex diseases, genome-wide pathway association studies have become increasingly promising. Currently, however, pathway-based association analysis mainly focus on a single phenotype, which may insufficient to describe the complex diseases and physiological processes. This work proposes a combination model to evaluate the association between a pathway and multiple phenotypes and to reduce the run time based on asymptotic results. For a single phenotype, we propose a semi-supervised maximum kernel-based U-statistics (mSKU) method to assess the pathway-based association analysis. For multiple phenotypes, we propose the fisher combination function with dependent phenotypes (FC) to transform the p-values between the pathway and each marginal phenotype individually to achieve pathway-based multiple phenotypes analysis. With real data from the Alzheimer Disease Neuroimaging Initiative (ADNI) study and Human Liver Cohort (HLC) study, the FC-mSKU method allows us to specify which pathways are specific to a single phenotype or contribute to common genetic constructions of multiple phenotypes. If we only focus on single-phenotype tests, we may miss some findings for etiology studies. Through extensive simulation studies, the FC-mSKU method demonstrates its advantages compared with its counterparts.
Comparison of the efficiency of Deebag and jute made bag for faecal sludge management and wastewater treatment
Authors: Mishuk Mehedi Hasan , Islam S. M. Tariqul , Alamgir Muhammed
Published: November 2020

Faecal Sludge Management (FSM) has become a prominent environmental concern in the today’s world. Dewatering of sludge and the treatment of wastewater (WW) are the prime spiny issue because of the deleterious essence of faecal sludge (FS) and WW in the environment. The main focus of this study was on FSM by ‘Deebag’ and ‘Jute Bag’ through dewatering and filtering. Deebag is a dewatering as well as filtering media which is made with geotextile and polypropylene. Contrariwise, three types of jute bags were made of jute fiber for using as the same purposes of Deebag. A polyacrylamide polymer was used in this study and both filtering and dewatering were done in two ways—with and without the presence of polymer. Biochemical Oxygen Demand at 5 days (BOD5), Chemical Oxygen Demand (COD), pH, Electrical Conductivity (EC), Chloride (Cl-), Phosphate (PO43-), Nitrate (NO3-), Total Suspended Solid (TSS) and Total Dissolved Solid (TDS) parameters of raw and filtering samples were analyzed to assess the performance of WW treatment by Deebag and jute bags. Only using polymer was observed as one kind of treatment of WW. Deebag has been found to show the maximum dewatering capacity as well as treatment efficiency comparing with the jute bags. However, among three types of jute bags, double jute layered bag has shown the best performance. Maximum dewatering for Deebag and jute bags were found 88% and 83% respectively while using the polymer.
Motivational interviewing to support modifiable risk factor change in individuals at increased risk of cardiovascular disease: A systematic review and meta-analysis
Authors: Mifsud Justin Lee , Galea Joseph , Garside Joanne , Stephenson John , Astin Felicity
Published: November 2020

Background

Programmes using motivational interviewing show potential in facilitating lifestyle change, however this has not been well established and explored in individuals at risk of, yet without symptomatic pre-existent cardiovascular disease. The objective of this systematic review and meta-analysis was to determine the effectiveness of motivational interviewing in supporting modifiable risk factor change in individuals at an increased risk of cardiovascular disease.

Methods

Systematic review and meta-analysis with results were reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Health-related databases were searched for randomised controlled trials from 1980 to March 2020. Criteria for inclusion included; preventive programmes, motivational interviewing principles, modification of cardiovascular risk factors in adults of both genders, different ethnicities and employment status, and having at least 1 or more modifiable cardiovascular risk factor/s. Two reviewers independently extracted data and conducted a quality appraisal of eligible studies using an adapted Cochrane framework. The Cochrane framework supports to systematically identify, appraise and synthesize all the empirical evidence that meets the pre-specified eligibility criteria to answer a specific question.

Findings

A total of 12 studies met the inclusion criteria. While completeness of intervention reporting was found to be adequate, the application of motivational interviewing was found to be insufficiently reported across all studies (mean overall reporting rate; 68%, 26% respectively). No statistical difference between groups in smoking status and physical activity was reported. A random effects analysis from 4 studies was conducted, this determined a synthesized estimate for standardised mean difference in weight of -2.00kg (95% CI -3.31 to -0.69 kg; p = 0.003), with high statistical heterogeneity. Pooled results from 4 studies determined a mean difference in LDL-c of -0.14mmol/l (5.414mg/dl), which was non-significant. The characteristics of interventions more likely to be effective were identified as: use of a blended approach delivered by a nurse expert in motivational interviewing from an outpatient-clinic. The application of affirmation, compassion and evocation, use of open questions, summarising, listening, supporting and raising ambivalence, combining education and barrier change identification with goal setting are also important intervention characteristics.

Conclusions

While motivational interviewing may support individuals to modify their cardiovascular risk through lifestyle change, the effectiveness of this approach remains uncertain. The strengths and limitations of motivational interviewing need to be further explored through robust studies.
Risk assessment in patients with functional class II pulmonary arterial hypertension: Comparison of physician gestalt with ESC/ERS and the REVEAL 2.0 risk score
Authors: Sahay Sandeep , Tonelli Adriano R. , Selej Mona , Watson Zachary , Benza Raymond L.
Published: November 2020

Background

Accurate and regular risk assessment is important for evaluation and treatment of pulmonary arterial hypertension (PAH) patients, including those with functional class (FC) II symptoms, a population considered at low risk for disease progression. Risk assessment methods include subjective and objective evaluations. Multiparametric assessments include tools based on the European Society of Cardiology/European Respiratory Society (ESC/ERS) guidelines (COMPERA and FPHR methods, respectively) and the Registry to Evaluate Early and Long-Term PAH Disease Management (REVEAL; REVEAL 2.0 tool). To better understand risk status determination in FC II patients, we compared physician-reported risk assessments with objective multiparameter assessment tools.

Methods

This retrospective chart analysis included PAH patients with FC II symptoms receiving monotherapy or dual therapy. Physicians were surveyed (via telephone) to obtain an assessment of patient risk using their typical methodology, which might have been informed by objective risk assessment. Patient risk was then calculated independently using COMPERA, FPHR and REVEAL 2.0 tools. Factors associated with incongruent risk assessment were identified.

Results

Of the 153 patients, 41%, 46%, and 13% were classified as low, intermediate, and high risk, respectively, by physicians. Concordance between physician gestalt and objective methods ranged from 43%–54%. Among patients considered as low risk by physician gestalt, 4%–28% were categorized as high risk using objective methods. The most common physician factor associated with incongruent risk assessment was less frequent echocardiography during follow-up (every 7–12 months vs. every 3 months; p = 0.01).

Conclusions

More than half of FC II PAH patients were classified as intermediate/high risk using objective multiparameter assessments. Incorporating objective risk-assessment algorithms into clinical practice may better inform risk assessment and treatment strategies.
Evaluating the small-scale epidemiology of the stony-coral -tissue-loss-disease in the middle Florida Keys
Authors: Sharp William C. , Shea Colin P. , Maxwell Kerry E. , Muller Erinn M. , Hunt John H.
Published: November 2020

Along the Florida reef tract, stony-coral-tissue-loss disease (SCTLD) has caused extensive mortality of more than 20 scleractinian coral species. The pathogen is unknown, but its epizoology indicates that the disease, facilitated by water currents, has progressed linearly along the tract, affecting reefs at the scale of hundreds of kilometers. To inform ongoing disease mitigation efforts, we examined the small-scale spatial and temporal epidemiology of SCTLD. We established a series of sites in the middle Florida Keys at offshore and inshore locations that had not yet shown signs of SCTLD. We then conducted high-frequency monitoring from February 2018 through September 2019 and documented the onset of SCTLD and its progression through the sites. SCTLD was first observed at one site during early February 2018 and by early March 2018 all sites showed signs of the disease. A dynamic multistate model suggested that disease transmission was independent of coral density and found little evidence of a positive association between a colony showing signs of SCTLD and the condition or distance to its neighboring colonies. The model did, however, indicate that the probability of a colony showing signs of SCTLD increased with increasing colony surface area. These results are consistent with the water-borne transmission of a pathogen that progressed rapidly through the survey area. However, by the end of our survey the progression of SCTLD had slowed, particularly at inshore sites. Many affected colonies no longer exhibited progressive tissue mortality typical of the disease, suggesting the existence of differentially resilient colonies or coral communities, meriting their use for future coral rescue and propagation and disease research. These results are useful for refining ongoing SCTLD mitigation strategies, particularly by determining when disease rates are sufficiently low for direct intervention efforts designed to arrest disease progression on individual coral colonies will be most effective.
Reproductive number of coronavirus: A systematic review and meta-analysis based on global level evidence
Authors: Billah Md. Arif , Miah Md. Mamun , Khan Md. Nuruzzaman
Published: November 2020

Background

The coronavirus (SARS-COV-2) is now a global concern because of its higher transmission capacity and associated adverse consequences including death. The reproductive number of coronavirus provides an estimate of the possible extent of the transmission. This study aims to provide a summary reproductive number of coronavirus based on available global level evidence.

Methods

A total of three databases were searched on September 15, 2020: PubMed, Web of Science, and Science Direct. The searches were conducted using a pre-specified search strategy to record studies reported the reproductive number of coronavirus from its inception in December 2019. It includes keywords of coronavirus and its reproductive number, which were combined using the Boolean operators (AND, OR). Based on the included studies, we estimated a summary reproductive number by using the meta-analysis. We used narrative synthesis to explain the results of the studies where the reproductive number was reported, however, were not possible to include in the meta-analysis because of the lack of data (mostly due to confidence interval was not reported).

Results

Total of 42 studies included in this review whereas 29 of them were included in the meta-analysis. The estimated summary reproductive number was 2.87 (95% CI, 2.39–3.44). We found evidence of very high heterogeneity (99.5%) of the reproductive number reported in the included studies. Our sub-group analysis was found the significant variations of reproductive number across the country for which it was estimated, method and model that were used to estimate the reproductive number, number of case that was considered to estimate the reproductive number, and the type of reproductive number that was estimated. The highest reproductive number was reported for the Diamond Princess Cruise Ship in Japan (14.8). In the country-level, the higher reproductive number was reported for France (R, 6.32, 95% CI, 5.72–6.99) following Germany (R, 6.07, 95% CI, 5.51–6.69) and Spain (R, 3.56, 95% CI, 1.62–7.82). The higher reproductive number was reported if it was estimated by using the Markov Chain Monte Carlo method (MCMC) method and the Epidemic curve model. We also reported significant heterogeneity of the type of reproductive number- a high-value reported if it was the time-dependent reproductive number.

Conclusion

The estimated summary reproductive number indicates an exponential increase of coronavirus infection in the coming days. Comprehensive policies and programs are important to reduce new infections as well as the associated adverse consequences including death.
Repurposing a microfluidic formulation device for automated DNA construction
Authors: Goyal Garima , Elsbree Nick , Fero Michael , Hillson Nathan J. , Linshiz Gregory
Published: November 2020

Microfluidic applications have expanded greatly over the past decade. For the most part, however, each microfluidics platform is developed with a specific task in mind, rather than as a general-purpose device with a wide-range of functionality. Here, we show how a microfluidic system, originally developed to investigate protein phase behavior, can be modified and repurposed for another application, namely DNA construction. We added new programable controllers to direct the flow of reagents across the chip. We designed the assembly of a combinatorial Golden Gate DNA library using TeselaGen DESIGN software and used the repurposed microfluidics platform to assemble the designed library from off-chip prepared DNA assembly pieces. Further experiments verified the sequences and function of the on-chip assembled DNA constructs.
Prognostic role of microRNA 182 and microRNA 18a in locally advanced triple negative breast cancer
Authors: Bajaj Rajat , Tripathi Rupal , Sridhar T. S. , Korlimarla Aruna , Choudhury Kumardeep Dutta , Suryavanshi Moushumi , Mehta Anurag , Doval Dinesh Chandra
Published: November 2020

Background

The study assessed the epigenetic regulation and the role of microRNA (miR) expression in locally advanced triple negative breast cancers (TNBC) and comparison with the clinico-pathological variables and survival.

Methods

Fifty patients of locally advanced TNBC during the period 2011–2013 were included. Expression level of test microRNA (miR-182 and miR-18a) was determined using Taqman quantitative Real time polymerase chain reaction (qRT-PCR) from formalin fixed paraffin embedded biopsy blocks. Clinical and demographic information and survival data was retrieved from the Hospital medical records.

Results

An improved clinical complete response (cCR) was observed in patients with age ≥ 45 years (80%), premenopausal status (70%), tumor size < 6 cms (80%), nodal status N0-N1 (95%) and grade II-III tumor (80%). A statistically significant correlation was observed on comparison of cCR with menopausal status (p-value 0.020), T category (p-value 0.018) and the clinical nodal status (p-value 0.003). pCR also correlated with clinical nodal status (p-value 0.008). Epigenetically, miR-18a under expression (< 8.84) was most commonly associated with tumor size < 6 cms (76.7%), clinical nodal status N0-N1 (90%), cCR (60%) and pCR (53.3%). A similar trend was observed with miR-182. Statistical significance was observed with T category (p-values 0.003 and 0.004), clinical nodal status (p-values 0.001 and 0.001), clinical response (p-values 0.002 and 0.002) and pathological response (p-values 0.007 and 0.006) with respect to miR-18a and miR-182, respectively. Also, the menopausal status significantly correlated with the miR-182 expression (p-value 0.009). miR-182 overexpression (≥ 6.32) was not observed in any of the postmenopausal patients. A univariate cox proportional hazard regression model also showed statistical interactions (p-values <0.004).

Conclusion

miR-182 and miR-18a overexpression correlates with worse clinical and pathological tumor characteristics in locally advanced TNBC and hence could be used to predict the outcomes and prognosis in these patients.
A human secretome library screen reveals a role for Peptidoglycan Recognition Protein 1 in Lyme borreliosis
Authors: Gupta Akash , Arora Gunjan , Rosen Connor E. , Kloos Zachary , Cao Yongguo , Cerny Jiri , Sajid Andaleeb , Hoornstra Dieuwertje , Golovchenko Maryna , Rudenko Natalie , Munderloh Ulrike , Hovius Joppe W. , Booth Carmen J. , Jacobs-Wagner Christine , Palm Noah W. , Ring Aaron M. , Fikrig Erol
Published: November 2020

Lyme disease, the most common vector-borne illness in North America, is caused by the spirocheteBorrelia burgdorferi. Infection begins in the skin following a tick bite and can spread to the hearts, joints, nervous system, and other organs. Diverse host responses influence the level ofB.burgdorferiinfection in mice and humans. Using a systems biology approach, we examined potential molecular interactions between human extracellular and secreted proteins andB.burgdorferi. A yeast display library expressing 1031 human extracellular proteins was probed against 36 isolates ofB.burgdorferi sensu lato. We found that human Peptidoglycan Recognition Protein 1 (PGLYRP1) interacted with the vast majority ofB.burgdorferiisolates. In subsequent experiments, we demonstrated that recombinant PGLYRP1 interacts with purifiedB.burgdorferipeptidoglycan and exhibits borreliacidal activity, suggesting that vertebrate hosts may use PGLYRP1 to identifyB.burgdorferi. We examinedB.burgdorferiinfection in mice lacking PGLYRP1 and observed an increased spirochete burden in the heart and joints, along with splenomegaly. Mice lacking PGLYRP1 also showed signs of immune dysregulation, including lower serum IgG levels and higher levels of IFNγ, CXCL9, and CXCL10.Taken together, our findings suggest that PGLYRP1 plays a role in the host’s response toB.burgdorferiand further demonstrate the utility of expansive yeast display screening in capturing biologically relevant interactions between spirochetes and their hosts.
DINAMIKA â€˜NGAJI ONLINEâ€™ RAMADHAN DI MASA PAGEBLUK COVID-19 PADA KOMUNITAS PESANTREN
Authors: Arifin Samsul
Published: November 2020

This paper reveals the dynamics of the changing therapeutic relationship of the kiai with students (santri) in learning (ngaji) from face-to-face to online models in the time of COVID-19. The research method is ethnographic-hermeneutic. In the face-to-face learning system, therapeutics occur because of the warm relationship by looking directly at the kiai's face which makes the students feel calm. In the â€œNgaji Onlineâ€ the therapeutic system switches to environmental settings that make students feel safe and comfortable. In the â€œNgaji Onlineâ€ system, the warmth of relationships begins to weaken. However, this weakness can be covered up because the spiritual relationship between the kiai and the students still feels strong. This spiritual relationship is the key to therapeutic for the Islamic boarding school.
KESENJANGAN KUALITAS LAYANAN PENDIDIKAN DI INDONESIA PADA MASA DARURAT COVID-19: TELAAH DEMOGRAFI ATAS IMPLEMENTASI KEBIJAKAN BELAJAR DARI RUMAH
Authors: Pratiwi Indah , Utama Bakti
Published: November 2020

One of the effects of the COVID-19 pandemic on the education sector in Indonesia is the closure of schools. To ensure education services continue, the government issued a policy of learning home (Belajar dari Rumah/BDR) through online/distance learning. This paper aims to describe the implementation of the BDR for learning quality. To that aim, we have conducted telephone interviews with school principals and teachers from frontier, outermost and remote regions (3T) and non-3T regions. By looking at demographics perspective, implementation of BDR has six variations are a) learning by interactive virtual classroom b) learning assignment by social media c) learning in teacher's or student's home d) learning by using TV/radio e) learning by â€˜mouth-to-mouthâ€™ messages and f) learning stopped. The variations generate different quality of learning and will produce an increasing education inequality in Indonesia.
PROFIL PENDUDUK TERKONFIRMASI POSITIF COVID-19 DAN MENINGGAL: KASUS INDONESIA DAN DKI JAKARTA
Authors: Hidayati Deny
Published: November 2020

This paper discusses the population that confirmed positive for COVID-19 and died in Indonesia and DKI Jakarta, which is epicentre of corona virus transmission in this country. The trend of population confirmed positive COVID-19 continues to increase and fluctuate every day, while the percentage of population deaths tends to decline. The paper using secondary data revealed that male residents were more vulnerable to COVID-19 than women. The number of male population confirmed positive corona virus is higher and the percentage of death is much higher. Covid-19 attacks all age groups, but the population is over 46 years, especially 60 years and above, more vulnerable than other age groups. Infants, toddlers and children who are detected positively have a low percentage, but the quantity is quite large. The population risk reduction policy for COVID-19 is indispensable for all residents with priority given to more vulnerable groups in Indonesia and DKI Jakarta.
PRODUKTIVITAS SELAMA WORK FROM HOME: SEBUAH ANALISIS PSIKOLOGI SOSIAL
Authors: Wahyu Agung Minto , Saâ€™id Mochammad
Published: November 2020

The spread of the COVID-19 pandemic requires each country to limit activities of its people outside the home by doing Work from Home (WFH). The purpose of this paper is to reveal the impact of WFH on worker productivity in the perspective of social psychology. The analysis shows that during WFH, worker productivity can increase due to the effects of social facilitation. Workers perceive the presence of others as triggers to increase their productivity. Conversely, workers' productivity can also decrease during working together with others because the presence of other people is perceived as a threat. On the other hand, job demands, distractors, and facilitators can activate the latent personality trait of an individual so that it manifests into a new work behavior during WFH. Strategies to maintain productivity is to use brainstorming, break down work teams into smaller, as well as the application of Nominal Group Technique
MEMPERSIAPKAN KETAHANAN KELUARGA SELAMA ADAPTASI KEBIASAAN BARU DI MASA PANDEMI COVID-19
Authors: Ramadhana Maulana Rezi
Published: November 2020

Changes in family dynamics during the isolation period of COVID-19 have an impact on family resilience in preparing for the adaptation of new habits in Indonesia. This study examines emotional reactions and family resilience, using family demographic groups, namely family type, parent's occupational type, and a residential area used as study variables. The sample came from 318 overseas student families who had reunited with families from 23 cities and districts in West Java Province. Simple frequency data analysis were used to present related situations. The results of the study showed that family type, family socioeconomic (parents' occupation), and the type of residential area of the family showed differences in positive emotions, negative emotions and were significant to family resilience during COVID-19 isolation. The implications of this study lead to the function of families in strengthening family resilience to prepare for the adaptation of new habits in Indonesia.
DAMPAK PANDEMI COVID-19 TERHADAP PHK DAN PENDAPATAN PEKERJA DI INDONESIA
Authors: Ngadi Ngadi , Meliana Ruth , Purba Yanti Astrelina
Published: November 2020

The larger-scale social restrictions policy to handling the COVID-19 pandemic had an impact on the socio-economic of the community including job sustainability and income of workers. This study analyzes the impact of the COVID-19 on worker layoffs and income in Indonesia. This research uses an accidental sampling through the online survey. The results showed that COVID-19 had an impact on layoffs and decreased income, especially during the social distancing. The result showed that layoffs of workers in Indonesia amounted to 15.6 percent.Â  Regarding income, about 31.0 percent of workers claim that their income has decreased by less than 50 percent and 8.6 percent of that has fallen above 50 percent. The government needs to conduct strict supervision of companies in each region. The role of the community is needed in overcoming existing problems by looking for new strategies that are utilizing technology and looking for new job opportunities, while still paying attention to health protocols.
DATA ACTIVISM AND COVID-19 IN INDONESIA
Authors: Nadzir Ibnu
Published: November 2020

The governmentâ€™s inability to provide information in relation to COVID-19 in Indonesia, has stimulated grassroots efforts from society to develop data activism. These are the kind of activism that proliferates from modern social media ecosystem and utilizes data as the core of their movement. The article proposes that there are at least three forms of activism differentiated based on the actors, their main sources of data, and characteristic. These forms of activisms are aimed to provide data and information that could help both government and society to better mitigate the impact of pandemic. While data activism provides some hope among other grim outlook of COVID-19 management in Indonesia, the questions on its impacts are still looming under the contested authorities of information in Indonesia.Â
PENANGGULANGAN COVID-19 DALAM KERANGKA TEORI KEPENDUDUKAN MALTHUS
Authors: Raharto Aswatini
Published: November 2020

This paper was not necessarily discussing COVID-19 as Malthus' positive check, but it examines the current efforts to overcome and control the COVID-19 pandemic as a preventive and positive check. COVID-19 gives credence to the Malthusian Theory of Population.Â  The key features of this model are that the preventive checks that should be carried out by men are not only limited to controlling the population through family planning but also to control the pressure on the existing resources. The two forces will act to restore equilibrium: preventive check and positive check. From the Malthusian theory, herd immunity in the time of COVID-19 regarded as a positive check. As Indonesia's home to more than 270 million population, the mortality rate likely uncontrollable. Thus herd immunity should not be chosen as a policy option.
DETERMINAN PERILAKU BERISIKO REMAJA TERKAIT SEKSUALITAS DI ERA GLOBALISASI: KASUS KOTA MEDAN
Authors: Fatoni Zainal , Situmorang Augustina
Published: November 2020

Adolescents play an essential role in development in the era of globalization, but they are also in a vulnerable period to do risky behaviors related to sexuality. This paper is based on a 2017 survey of 401 adolescents in Medan city to examine the determinants of risk behavior related to sexuality. The survey shows that 11% of respondents have high-risk behavior, 34% are moderate, and 55% are low. Pearsonâ€™s chi-square analysis found significant variables related to respondent characteristics, family background, peers, information technology, and non-sexual risky behaviors. Furthermore, the results of multivariate logistic regression showed the determinants of risky adolescent behaviors related to sexuality were influenced by eight factors: sex, age of adolescence, has brothers and sex (interaction), have peers who have had premarital sex, have homosexual friends, frequency of accessing the internet, have ever smoking, and have ever consumed drugs. This study recommends the need for policies/programs that provide information to adolescents and parents about sexuality and gender identity, pornography, as well as reproductive health in a comprehensive and up-to-date manner.
DAMPAK KEMISKINAN TERHADAP POLA MOBILITAS TENAGA KERJA ANTARSEKTOR DI INDONESIA
Authors: Pratiwi Evie Dian , Ashar Khusnul , Syafitri Wildan
Published: November 2020

Mobility can act as a stepping stone to get out of poverty. This research examines whether the effect of poverty encouraging or inhibiting the mobility of workers across sectors. By using data from the 2018 Indonesia National Labor Force Survey (Sakernas) that cover 8,869 respondents, this study applies multinomial regression models to analyse inter-sector mobility types among labors in Indonesia. The results show that low-income workers in the industrial and service sectors tend to have a 4.8% and 6.3% greater probability of transferring to the agricultural sector. However, agricultural workers that suffer from poverty choose to survive in the same sector due to the high cost of inter-sector mobility. Other findings show that older age and higher education level decreased the propensity to move across sectors. In the efforts to alleviate poverty, the role of the government is expected to be seen in two ways. Firstly, by facilitating workers to move into productive sectors, i.e. industrial and service sectors, and secondly, by increasing the productivity of the agricultural sector.
LINTASAN PENGHIDUPAN (LIVELIHOOD TRAJECTORIES) DAN MIGRASI LINGKUNGAN DI DELTA MAHAKAM
Authors: Rachmawati Laksmi , Latifa Ade
Published: November 2020

The studies of environmental migration are still limited in Indonesia. Within the limited literature in the Indonesian context, Research Center for Population LIPI has conducted studies on environmental migration in 2015-2016 and the abandonment of shrimp pond due to migration in 2013 in Delta Mahakam, East Kalimantan. Using Livelihood Trajectories (LT) approach, this paper aims to examine the peopleâ€™s adaptation in Delta Mahakam related to environmental migration. The LT approach gives more understanding of the adaptation process that leads to migration decision-making. By applying a qualitative approach using interviews and focus group discussion (FGD), data are collected related to the changes of landscape livelihood and the adaptation to respond to it.Â  The interviews and FGD conducted with farmers, fishers, aquaculture farmers who move or stay and with formal/informal leaders and patron. In the case of Delta Mahakam, migration becomes a strategy for adaptation. The decision to migrate is not an instant decision-making process but as a part of trajectories to sustain their livelihood.