bluuebunny/crossref_metadata_2025 huggingface dataset:
Diurnal variation of radar reflectivity factor during intense convective clouds over Indonesia
Authors: Yusnaini H , Marzuki
Published: June 2020

Intense convective clouds is represented by very high of clouds tops that produce heavy rainfall/intense convective precipitation. The vertical structure of intense convective clouds over Indonesia was investigated using radar reflectivity factor (dBZ) data from Tropical Rainfall Measuring Mission (TRMM) satellite-Precipitation Radar (PR) 2A25 product during 1998-2014. The vertical distribution of dBZ was classified into two convective cells following the classification proposed by some previous studies. The first type, Comulonimbus Tower (CbT) that contains Z threshold of 20 dBZ in 12 km altitude with at least 9 km depth and Intense Convective Clouds (ICC) that contains Z threshold of 30 and 41 dBZ at 8 and 3 km, respectively. The distribution of intense convective clouds is more frequently observed over land such as Sumatra, Kalimantan, Java and Irian Jaya than over ocean areas. To observe the pattern of vertical structure of intense convective clouds, the vertical profile of dBZ for several locations that represent land, coastal and ocean areas were analyzed. The land and coastal areas show similar vertical structure of intense convective. On seasonal basis, intense convective clouds are more frequently found during March, April and May (MAM) which coincided with the maximum of convective available potential energy (CAPE) value. Furthermore, on diurnal basis, intense convective clouds are significantly observed during 16-18 LT (local time) and 04-09 LT over mainland and ocean areas, respectively
Design of high efficiency active class E rectifier using PMOS switch for hybrid wireless power transfer
Authors: Alif Kurniawan Taufiq , Bagus Fauzan Dandy , Wibisono Gunawan
Published: June 2020

The wireless power transfer (WPT) circuits are very promising to conduct therapy in several conditions especially in neurological stimulation. In the WPT designs, a high efficiency rectification and a DC output regulation are performed simultaneously using active rectifier without the need of an additional regulating circuits. However, the significant ripple appeared at the DC output voltage waveform so that reducing the efficiency of the rectifier. This is due to the application of NMOS as a switching device, where the threshold voltage of NMOS is strongly influenced by the body bias voltage. In this paper, the design of the active class E rectifiers using PMOS switch produces the DC output voltage waveform with an average ripple over 0-100% duty cycle is 16.7%. With simple structure and compact size, this proposed active class E rectifier can be applied for the future Hybrid WPT applications especially in low power operations.
Detecting the burned area in southern Kalimantan by using the sentinel-1 polarimetric SAR and landsat-8 OLI optic
Authors: Prasasti I , Rahmi KIN , Nugroho JT , Sitorus J , Arief R , Triyono D , Suwarsono
Published: June 2020

Synthetic Aperture Radar (SAR) imageries data have turned out to be one of the essential sources for forest fire mapping, especially in tropical region since the smoke haze obstruct data acquisition by optical sensor. Despite these limitations, until now, the use of optical sensors still dominates in monitoring forest and land fires in the world. The Sentinel-1 satellites presently offer unreservedly accessible and freely available, world coverage and fast recurrent time (6-12 days), gives Sentinel-1 images the possibility to be broadly utilized for observing the Earth’s surface, including forest and land fire phenomenon. However, the use of sentinel-1 data for monitoring and mapping forest and land fires in the tropics of Indonesia, is still limited and has not been widely implemented. This study investigated the use of Sentinel-1, synergy with optical Landsat-8 OLI (Operational Land Imager) data, to identify the burned area, in the tropical region of Indonesia, during 2019 fire season. A pair of Landsat-8 OLI, collected before and after fires, has been used to delineate the boundaries of sample location of burned area. Then, the difference of reflectance and Normalized Burn Ratio were analyzed. A series of Sentinel-1 images, collected before and during/after fires, has been utilized to produce the backscatter values among images. Fire incident causes landcover changes from vegetated land to bareland. This changes can affect the reflectance detected from Landsat-8 OLI. This changes also influence the backscatter recognized from SAR sensor. Then analysis of SAR backscatter on the location of the burned area detected from Landsat-8 was performed. The synergy between SAR polarimetric and optical reflected data, creates a valuable tool for identifying and interpreting burned area following a fire event.
Microstrip rectangular with bended-slots antenna design for radar remote sensing application
Authors: Sirin Dinari N S , Rahardjo Eko T
Published: June 2020

The development of radar remote sensing applications in Indonesia is increasingly being used for environmental monitoring, rainfall estimation, earth, and coast observation, or even for disaster mitigation. The study in this paper is to carry out a compact and low profile design of a microstrip slot antenna for radar remote sensing applications, in the X-band frequency range. The proposed design is a rectangular microstrip antenna with bended-slots on the feed line sides. From the simulation, the result showed that the antenna has wide bandwidth 605 MHz. Thus, the antenna can be used for radar applications.
A simple paper-based color change label using plant extracts for Ammonia gas detection
Authors: Listyarini Arie , Fauzia Vivi , Imawan Cuk
Published: June 2020

Paper and plant extracts are materials that are cheap and easy to find everywhere, have great potential to be used as a portable, low-cost and biodegradable label for the application of chemical compounds detection. In this paper, we have explored potential methods for the label to detect ammonia gas, an indicator of meat spoilage, with the colorimetric principle. By immersing paper with plant extracts that are sensitive to ammonia, in this case, is anthocyanin from Ruellia simplex flower extract, the detection of ammonia at various concentrations can be achieved. Ammonia concentration used is 0; 0.005%; 0.025%; 0.1%, 0.25% and 0.5%. Color change images on the label when detection is scanned by a flatbed scanner. ImageJ software is used to quantify the color changes. Ammonia detection at various concentrations results in a color change from red to yellow on the paper label. Paper-based labels with discoloration that can be captured visually by the consumer’s eyes are considered as promising approaches to determine the freshness of meat.
Load alleviation of feather-inspired compliant airfoils for instantaneous flow control
Authors: Gamble Lawren L , Harvey Christina , Inman Daniel J
Published: June 2020

Birds morph their wing shape to adjust to changing environments through muscle-activated morphing of the skeletal structure and passive morphing of the flexible skin and feathers. The role of feather morphing has not been well studied and its impact on aerodynamics is largely unknown. Here we investigate the aero-structural response of a flexible airfoil, designed with biologically accurate structural and material data from feathers, and compared the results to an equivalent rigid airfoil. Two coupled aero-structural models are developed and validated to simulate the response of a bioinspired flexible airfoil across a range of aerodynamic flight conditions. We found that the bioinspired flexible airfoil maintained lift at Reynolds numbers below 1.5 × 105, within the avian flight regime, performing similarly to its rigid counterpart. At greater Reynolds numbers, the flexible airfoil alleviated the lift force and experienced trailing edge tip displacement. Principal component analysis identified that the Reynolds number dominated this passive shape change which induced a decambering effect, although the angle of attack was found to effect the location of maximum camber. These results imply that birds or aircraft that have tailored chordwise flexible wings will respond like rigid wings while operating at low speeds, but will passively unload large lift forces while operating at high speeds.
Lake area monitoring based on land surface temperature in the Tibetan Plateau from 2000 to 2018
Authors: Zhao Wei , Xiong Donghong , Wen Fengping , Wang Xiaodan
Published: June 2020

Lake area change in the Tibetan plateau is an important indicator for climate change assessment. To overcome the temporal inconsistency of optical remote sensing-based lake area detections, a land surface temperature (LST)-based detection scheme was proposed by utilizing the big difference between land and water surface temperatures. A trend test conducted by the Mann–Kendall (MK) method was successfully applied to investigate lake area variation from 2000 to 2018 with the use of the annual mean temperature information derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) LST daily product. A comparison with the monitoring results from Landsat images indicates the proposed method can provide spatial distributions of lake area change with high accuracy. More importantly, the temporal variation of annual mean LST provides a special way to detect the abrupt change year (ACY) in lake area.The ACYs of most lakes mainly occur from 2004 to 2012. For an individual lake, the ACY offers vital information about the lake area change process. In summary, this work demonstrates the good potential of the LST-based method for lake area monitoring and assessment.
A monocular wide-field vision system for geolocation with uncertainties in urban scenes
Authors: Arroyo Sebastián I , Bussi Ulises , Safar Félix , Oliva Damián
Published: June 2020

In engineering applications related to video surveillance, the use of monocular omnidirectional cameras would reduce costs and complications associated with infrastructure, installation, synchronization, maintenance and operation of multiple cameras. This makes omnidirectional cameras very useful for transport analysis, a key task of which is to accurately geolocate vehicles and/or pedestrians observed in an ample region. The problem of measuring on the plane was previously solved for monocular central perspective images. However, the problem of determining uncertainties in geolocalization using monocular omnidirectional images, has not been addressed. This problem is not trivial due to the complexity of the image formation models associated with these cameras. The contributions of this work are: (1) The geolocation problem is solved using omnidirectional monocular images through a Bayesian inference approach. (2) The calculation of Bayesian marginalization integrals is simplified through first-order approximations. (3) The accuracy of the estimated positions and uncertainties is shown through Monte Carlo simulations under realistic measurement conditions. (4) The method to geolocate a vehicle’s trajectory on a satellite map is applied in an urban setting.
F–actin-bundling sites are conserved in proteins with villin-type headpiece domains
Authors: George Sudeep P. , Esmaeilniakooshkghazi Amin , Roy Swati , Khurana Seema
Published: June 2020

Villin is a major actin-bundling protein that assembles the microvilli of intestinal and renal epithelial cells. Using the nuclear magnetic resonance structure of the isolated villin and advillin headpiece proteins and mutational analysis in full-length proteins, we identify the actin-bundling site in human villin and proteins with villin-type headpiece domain.
A Total Worker Health Approach to Skin Exposure Assessment: Experiences from the Firefighter Cancer Initiative
Authors: Caban-Martinez Alberto J , Hughes Jeff , Bator Christopher
Published: June 2020

Increasing scientific evidence suggests that addressing complex, wide-ranging concerns among worker populations should include the integration of traditional occupational safety and health with often siloed worksite wellness programs. The Total Worker Health (TWH) approach developed by the National Institute for Occupational Safety and Health can support skin cancer prevention efforts by integrating organizational-level policies, programs, and practices that strategically merge both skin protection from work-related safety and health hazards with promotion of skin illness prevention efforts. In the firefighter workforce, epidemiologic studies suggest an increased risk of skin cancer despite the use of personal protective equipment during fire incident response. Mechanisms for dermal absorption of carcinogenic compounds such as polycyclic aromatic hydrocarbons have given insight into how these hazardous chemicals can enter the skin and increase cancer risk. Mitigation of carcinogenic exposures requires a TWH approach that merges skin protection and promotion, routine surveillance, skin health assessment, worksite-based interventions, and regular evaluation of program activities. In this commentary, an example of a TWH approach is provided from the Firefighter Cancer Initiative (FCI), a transdisciplinary initiative focused at addressing excess burden of cancer in the firefighter workforce. The FCI builds on the TWH approach through the following components: (i) organizational leadership commitment; (ii) elimination of workplace hazards and promotion of worker well-being; (iii) engagement of workers in program design and delivery; (iv) ensuring confidentiality and privacy in program participation; and (v) integrating systems effectively. Occupational hygienists have strong potential to play a crucial role beyond traditional risk assessment, exposure assessment, and health protection that further includes skin health promotion and integration of related programs into a TWH framework.
PUMA: PANDA Using MicroRNA Associations
Authors: Kuijjer Marieke L , Fagny Maud , Marin Alessandro , Quackenbush John , Glass Kimberly
Published: June 2020

Motivation

Conventional methods to analyze genomic data do not make use of the interplay between multiple factors, such as between microRNAs (miRNAs) and the messenger RNA (mRNA) transcripts they regulate, and thereby often fail to identify the cellular processes that are unique to specific tissues. We developed PUMA (PANDA Using MicroRNA Associations), a computational tool that uses message passing to integrate a prior network of miRNA target predictions with target gene co-expression information to model genome-wide gene regulation by miRNAs. We applied PUMA to 38 tissues from the Genotype-Tissue Expression project, integrating RNA-Seq data with two different miRNA target predictions priors, built on predictions from TargetScan and miRanda, respectively. We found that while target predictions obtained from these two different resources are considerably different, PUMA captures similar tissue-specific miRNA–target regulatory interactions in the different network models. Furthermore, the tissue-specific functions of miRNAs we identified based on regulatory profiles (available at: https://kuijjer.shinyapps.io/puma_gtex/) are highly similar between networks modeled on the two target prediction resources. This indicates that PUMA consistently captures important tissue-specific miRNA regulatory processes. In addition, using PUMA we identified miRNAs regulating important tissue-specific processes that, when mutated, may result in disease development in the same tissue.

Availability and implementation

PUMA is available in C++, MATLAB and Python on GitHub (https://github.com/kuijjerlab and https://netzoo.github.io/).

Supplementary information

Supplementary data are available at Bioinformatics online.
Allowing mutations in maximal matches boosts genome compression performance
Authors: Liu Yuansheng , Wong Limsoon , Li Jinyan
Published: June 2020

Motivation

A maximal match between two genomes is a contiguous non-extendable sub-sequence common in the two genomes. DNA bases mutate very often from the genome of one individual to another. When a mutation occurs in a maximal match, it breaks the maximal match into shorter match segments. The coding cost using these broken segments for reference-based genome compression is much higher than that of using the maximal match which is allowed to contain mutations.

Results

We present memRGC, a novel reference-based genome compression algorithm that leverages mutation-containing matches (MCMs) for genome encoding. MemRGC detects maximal matches between two genomes using a coprime double-window k-mer sampling search scheme, the method then extends these matches to cover mismatches (mutations) and their neighbouring maximal matches to form long and MCMs. Experiments reveal that memRGC boosts the compression performance by an average of 27% in reference-based genome compression. MemRGC is also better than the best state-of-the-art methods on all of the benchmark datasets, sometimes better by 50%. Moreover, memRGC uses much less memory and de-compression resources, while providing comparable compression speed. These advantages are of significant benefits to genome data storage and transmission.

Availability and implementation

https://github.com/yuansliu/memRGC.

Supplementary information

Supplementary data are available at Bioinformatics online.
SOS: online probability estimation and generation of T-and B-cell receptors
Authors: Isacchini Giulio , Olivares Carlos , Nourmohammad Armita , Walczak Aleksandra M , Mora Thierry
Published: June 2020

Recent advances in modelling VDJ recombination and subsequent selection of T- and B-cell receptors provide useful tools to analyse and compare immune repertoires across time, individuals and tissues. A suite of tools—IGoR, OLGA and SONIA—have been publicly released to the community that allow for the inference of generative and selection models from high-throughput sequencing data. However, using these tools requires some scripting or command-line skills and familiarity with complex datasets. As a result, the application of the above models has not been available to a broad audience. In this application note, we fill this gap by presenting Simple OLGA & SONIA (SOS), a web-based interface where users with no coding skills can compute the generation and post-selection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones.

Availability and implementation

SOS is freely available to use at sites.google.com/view/statbiophysens/sos with source code at github.com/statbiophys/sos.
Regulation of the neuroendocrine axis in male rats by soy-based diets is independent of age and due specifically to isoflavone action†
Authors: Jeminiwa Bamidele O , Knight Rachel M , Braden Tim D , Cruz-espindola Crisanta , Boothe Dawn M , Akingbemi Benson T
Published: June 2020

Soy-based foods are consumed for their health beneficial effects, implying that the population is exposed to soy isoflavones in the diet. Herein, male rats at 21, 35, and 75 days of age were maintained either on a casein control diet, soybean meal (SBM), or control diet supplemented with daidzin and genistin (G + D) for 14 days. Feeding of SBM and G + D diets decreased testicular testosterone (T) secretion regardless of age. Altered androgen secretion was due to decreased (P < 0.05) Star and Hsd17β protein in the testes and was associated with increased (P < 0.05) Lhβ and Fshβ subunit protein expression in pituitary glands. Second, male rats were fed either a casein control diet, control diet + daidzin, control diet + genistin, or control diet + genistin + daidzin (G + D). Compared to control, feeding of all isoflavone-containing diets decreased (P < 0.05) testicular T concentrations, and more so in the G + D diet group. Interestingly, Esr1 and androgen receptor protein and pituitary Fshβ with Lhβ subunit protein were increased (P < 0.05) by feeding of genistin and G + D diets, but not the daidzin diet. However, daidzein and genistein both caused a concentration dependent inhibition (P < 0.05) of T secretion by Leydig cells in vitro with IC50 of 184 ηM and 36 ηM, respectively. Results demonstrated that altered testicular steroidogenic capacity and pituitary FSHβ and LHβ subunit expression due to soy-based diets result from specific actions by genistein and daidzein. Experiments to assess effects of isoflavone regulation of intratesticular androgen concentrations on male fertility are warranted.
Connecting plant evolutionary history and human well-being at Mt. Kilimanjaro, Tanzania
Authors: Molina-Venegas Rafael , Fischer Markus , Mollel Neduvoto Piniel , Hemp Andreas
Published: June 2020

Evolution is the source of all living organisms and hence the foundation for the ecosystem services that are directly supported by biodiversity. However, explicit connections between evolutionary history and human well-being are barely explored. Here, we focus on ethnobotanical data from Mt. Kilimanjaro (Tanzania) to identify significant associations between plant evolutionary lineages and six previously recognized usage guilds in the mountain (i.e. fodder, building material, fuelwood, food, ornamental/shading and traditional medicine), and further characterize the degree of phylogenetic overlap between the guilds using beta diversity metrics. In addition, we also explore how phylogenetic diversity of usage guilds varied along elevation and between natural and anthropized habitats. Our results suggest that the inhabitants of Mt. Kilimanjaro rely on multiple and deep lineages that specifically provide a certain type of service, supporting the notion that an increased number of lineages captures more current biodiversity benefits. However, we also found a few lineages that provided multiple benefits, indicating that particular efforts should be pursued in preserving individual multi-functional lineages of the phylogeny. Elevation was the most important factor explaining phylogenetic diversity of useful plants, whereas the effect of anthropogenic disturbance was comparatively weak. However, after controlling for the effect of elevation, a moderate negative effect of human disturbance was revealed, particularly for medicinal plants. Phylogenetic diversity of most guilds showed hump-shaped curves with elevation, revealing a major reservoir of useful plant lineages in the highly threatened montane forests of Mt. Kilimanjaro.
Maceration-Mediated Liquid–Liquid Extraction and Reverse-Phase High-Performance Liquid Chromatography-Based Pragmatic Analysis of Silybins
Authors: Hasany Syeda Mariam , Huma Rahila , Akram Sumia , Ashraf Rizwan , Mushtaq Muhammad
Published: June 2020

This study presents a pragmatic and easily scalable maceration-mediated liquid–liquid extraction (MMLLE) and reverse-phase high-performance liquid chromatography (RP-HPLC)-based determination of Silybins from plant material (Curcuma longa L.). The processing of calibration standards revealed that the RP-HPLC method was linear over a concentration range of 1–100 μg/mL with regression coefficient (R2) > 0.9950, limit of detection 0.02 μg/mL and limit of quantification <0.07 μg/mL. The optimum chromatographic conditions resolved Silybin A, Silybin B, Isosilybin A and Isosilybin B within 5 min of analysis time. The reproducible recovery rates of spiked flavonolignans (96.24–115.40%) from quality controls established the effectiveness of MMLLE procedure prior to HPLC determination. The real-time analysis revealed the presence of silybins in C. longa roots. The results further endorse that MMLLE prior to chromatographic determination may provide a more pragmatic analytical solution for the analysis/isolation of silybins.
Predicting mortality in hemodialysis patients using machine learning analysis
Authors: Garcia-Montemayor Victoria , Martin-Malo Alejandro , Barbieri Carlo , Bellocchio Francesco , Soriano Sagrario , Pendon-Ruiz de Mier Victoria , Molina Ignacio R , Aljama Pedro , Rodriguez Mariano
Published: June 2020

Background

Besides the classic logistic regression analysis, non-parametric methods based on machine learning techniques such as random forest are presently used to generate predictive models. The aim of this study was to evaluate random forest mortality prediction models in haemodialysis patients.

Methods

Data were acquired from incident haemodialysis patients between 1995 and 2015. Prediction of mortality at 6 months, 1 year and 2 years of haemodialysis was calculated using random forest and the accuracy was compared with logistic regression. Baseline data were constructed with the information obtained during the initial period of regular haemodialysis. Aiming to increase accuracy concerning baseline information of each patient, the period of time used to collect data was set at 30, 60 and 90 days after the first haemodialysis session.

Results

There were 1571 incident haemodialysis patients included. The mean age was 62.3 years and the average Charlson comorbidity index was 5.99. The mortality prediction models obtained by random forest appear to be adequate in terms of accuracy [area under the curve (AUC) 0.68–0.73] and superior to logistic regression models (ΔAUC 0.007–0.046). Results indicate that both random forest and logistic regression develop mortality prediction models using different variables.

Conclusions

Random forest is an adequate method, and superior to logistic regression, to generate mortality prediction models in haemodialysis patients.
Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon
Authors: Masuda Kanae , Yamamoto Eiji , Shirasawa Kenta , Onoue Noriyuki , Kono Atsushi , Ushijima Koichiro , Kubo Yasutaka , Tao Ryutaro , Henry Isabelle M , Akagi Takashi
Published: June 2020

Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.
Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes
Authors: Shah Abhijeet , Hoffman Joseph I , Schielzeth Holger
Published: June 2020

Eukaryotic organisms vary widely in genome size and much of this variation can be explained by differences in the abundance of repetitive elements. However, the phylogenetic distributions and turnover rates of repetitive elements are largely unknown, particularly for species with large genomes. We therefore used de novo repeat identification based on low coverage whole-genome sequencing to characterize the repeatomes of six species of gomphocerine grasshoppers, an insect clade characterized by unusually large and variable genome sizes. Genome sizes of the six species ranged from 8.4 to 14.0 pg DNA per haploid genome and thus include the second largest insect genome documented so far (with the largest being another acridid grasshopper). Estimated repeat content ranged from 79% to 96% and was strongly correlated with genome size. Averaged over species, these grasshopper repeatomes comprised significant amounts of DNA transposons (24%), LINE elements (21%), helitrons (13%), LTR retrotransposons (12%), and satellite DNA (8.5%). The contribution of satellite DNA was particularly variable (ranging from <1% to 33%) as was the contribution of helitrons (ranging from 7% to 20%). The age distribution of divergence within clusters was unimodal with peaks ∼4–6%. The phylogenetic distribution of repetitive elements was suggestive of an expansion of satellite DNA in the lineages leading to the two species with the largest genomes. Although speculative at this stage, we suggest that the expansion of satellite DNA could be secondary and might possibly have been favored by selection as a means of stabilizing greatly expanded genomes.
Genomic Signatures of Local Adaptation in Clam Shrimp (Eulimnadia texana) from Natural Vernal Pools
Authors: Baldwin-Brown James G , Long Anthony D
Published: June 2020

Vernal pools are unique in their isolation and the strong selection acting on their resident species. Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, small genomes, and obligate desiccated diapaused eggs. Clam shrimp are also androdioecious (sexes include males and hermaphrodites), and here we use population-scaled recombination rates to support the hypothesis that the heterogametic sex is recombination free in these shrimp. We collected short-read sequence data from pooled samples from different vernal pools to gain insights into local adaptation. We identify genomic regions in which some populations have allele frequencies that differ significantly from the metapopulation. BayPass (Gautier M. 2015. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201(4):1555–1579.) detected 19 such genomic regions showing an excess of population subdivision. These regions on average are 550 bp in size and had 2.5 genes within 5 kb of them. Genes located near these regions are involved in Malpighian tubule function and osmoregulation, an essential function in vernal pools. It is likely that salinity profiles vary between pools and over time, and variants at these genes are adapted to local salinity conditions.
Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora
Authors: Shrestha Bikash , Gilbert Lawrence E , Ruhlman Tracey A , Jansen Robert K
Published: June 2020

Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.
Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
Authors: Reddington Kate , Eccles David , O'Grady Justin , Drown Devin M , Hansen Lars Hestbjerg , Nielsen Tue Kjærgaard , Ducluzeau Anne-Lise , Leggett Richard M , Heavens Darren , Peel Ned , Snutch Terrance P , Bayega Anthony , Oikonomopoulos Spyridon , Ragoussis Jiannis , Barry Thomas , van der Helm Eric , Jolic Dino , Richardson Hollian , Jansen Hans , Tyson John R , Jain Miten , Brown Bonnie L
Published: June 2020

Background

Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad “aquascape” scale, and few if any have applied the newest nanopore technology.

Results

We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5–1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers.

Conclusions

Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.
Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data
Authors: Hafezqorani Saber , Yang Chen , Lo Theodora , Nip Ka Ming , Warren René L , Birol Inanc
Published: June 2020

Background

Compared with second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years owing to their relatively high affordability and portability compared with other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provide a cost-effective solution with ground truth. However, a nanopore sequence simulator targeting transcriptomic data is not available yet.

Findings

We introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-sequncing data. We comprehensively benchmarked Trans-NanoSim on direct RNA and complementary DNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore complementary DNA and direct RNA reads.

Conclusions

As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-sequencing data. Trans-NanoSim and its pre-trained models are freely accessible at https://github.com/bcgsc/NanoSim.
Measurement error as an explanation for the alcohol harm paradox: analysis of eight cohort studies
Authors: Peña Sebastián , Mäkelä Pia , Härkänen Tommi , Heliövaara Markku , Gunnar Teemu , Männistö Satu , Laatikainen Tiina , Vartiainen Erkki , Koskinen Seppo
Published: June 2020

Background

Despite reporting lower levels of alcohol consumption, people with lower socio-economic status (SES) experience greater alcohol-related harm. Whether differential biases in the measurement of alcohol use could explain this apparent paradox is unknown. Using alcohol biomarkers to account for measurement error, we examined whether differential exposure to alcohol could explain the socio-economic differences in alcohol mortality.

Methods

Participants from eight representative health surveys (n = 52 164, mean age 47.7 years) were linked to mortality data and followed up until December 2016. The primary outcome was alcohol-attributable mortality. We used income and education as proxies for SES. Exposures include self-reported alcohol use and four alcohol biomarkers [serum gamma-glutamyl transferase (available in all surveys), carbohydrate-deficient transferrin, alanine aminotransferase and aspartate aminotransferase (available in subsamples)]. We used shared frailty Cox proportional hazards to account for survey heterogeneity.

Results

During a mean follow-up of 20.3 years, totalling 1 056 844 person-years, there were 828 alcohol-attributable deaths. Lower SES was associated with higher alcohol mortality despite reporting lower alcohol use. Alcohol biomarkers were associated with alcohol mortality and improved the predictive ability when used in conjunction with self-reported alcohol use. Alcohol biomarkers explained a very small fraction of the socio-economic differences in alcohol mortality, since hazard ratios either slightly attenuated (percent attenuation range 1.0–12.1%) or increased.

Conclusions

Using alcohol biomarkers in addition to self-reported alcohol use did not explain the socio-economic differences in alcohol mortality. Differential bias in the measurement of alcohol use is not a likely explanation for the alcohol-harm paradox.
Combining the Runge Approximation and the Whitney Embedding Theorem in Hybrid Imaging
Authors: Alberti Giovanni S , Capdeboscq Yves
Published: June 2020

This paper addresses enforcing non-vanishing constraints for solutions to a 2nd-order elliptic partial differential equation by appropriate choices of boundary conditions. We show that, in dimension $d\geq 2$, under suitable regularity assumptions, the family of $2d$ solutions such that their Jacobian has maximal rank in the domain is both open and dense. The case of less regular coefficients is also addressed, together with other constraints, which are relevant for applications to recent hybrid imaging modalities. Our approach is based on the combination of the Runge approximation property and the Whitney projection argument [ 44]. The method is very general and can be used in other settings.
Envisioning an artificial intelligence documentation assistant for future primary care consultations: A co-design study with general practitioners
Authors: Kocaballi A Baki , Ijaz Kiran , Laranjo Liliana , Quiroz Juan C , Rezazadegan Dana , Tong Huong Ly , Willcock Simon , Berkovsky Shlomo , Coiera Enrico
Published: June 2020

Objective

The study sought to understand the potential roles of a future artificial intelligence (AI) documentation assistant in primary care consultations and to identify implications for doctors, patients, healthcare system, and technology design from the perspective of general practitioners.

Materials and Methods

Co-design workshops with general practitioners were conducted. The workshops focused on (1) understanding the current consultation context and identifying existing problems, (2) ideating future solutions to these problems, and (3) discussing future roles for AI in primary care. The workshop activities included affinity diagramming, brainwriting, and video prototyping methods. The workshops were audio-recorded and transcribed verbatim. Inductive thematic analysis of the transcripts of conversations was performed.

Results

Two researchers facilitated 3 co-design workshops with 16 general practitioners. Three main themes emerged: professional autonomy, human-AI collaboration, and new models of care. Major implications identified within these themes included (1) concerns with medico-legal aspects arising from constant recording and accessibility of full consultation records, (2) future consultations taking place out of the exam rooms in a distributed system involving empowered patients, (3) human conversation and empathy remaining the core tasks of doctors in any future AI-enabled consultations, and (4) questioning the current focus of AI initiatives on improved efficiency as opposed to patient care.

Conclusions

AI documentation assistants will likely to be integral to the future primary care consultations. However, these technologies will still need to be supervised by a human until strong evidence for reliable autonomous performance is available. Therefore, different human-AI collaboration models will need to be designed and evaluated to ensure patient safety, quality of care, doctor safety, and doctor autonomy.
Estimation of lifetime cumulative mortality risk of lung cancer by smoking status in Japan
Authors: Hori Megumi , Saito Eiko , Katanoda Kota , Tsugane Shoichiro
Published: June 2020

The main objective of this study was to estimate the cumulative mortality risk for lung cancer according to smoking status and exposure to secondhand smoke (SHS) in Japan. We applied a life-table method to estimate the cumulative risk. Estimated lifetime cumulative risk for 20-year-old non-smokers, former, and current smokers was 3.2%, 7.6%, and 14.9% for men and 1.9%, 5.6%, and 7.2% for women, respectively. For males, the estimated risk was 3.2% for non-smokers not exposed to SHS and 4.1% for non-smokers exposed to SHS. For females, the estimated risk was 1.9% for non-smokers not exposed to SHS and 2.4% for non-smokers exposed to SHS. Lifetime cumulative mortality risk differed greatly according to smoking status. Moreover, SHS exposure resulted in observable differences in lifetime mortality risk. This study may be useful for the development of tailored prevention programs.
A Collaborative Way of Knowing: Bridging Computational Communication Research and Grounded Theory Ethnography
Authors: Ophir Yotam , Walter Dror , Marchant Eleanor R
Published: June 2020

One of the great strengths of the field of communication is its interdisciplinarity. Yet this strength brings challenges, including rifts between diverse subfields. In this study, we illustrate the rich potential of collaborations across subfields. Specifically, we argue that due to often-overlooked epistemological similarities, unsupervised machine learning and grounded theory ethnography subfields are well-suited for an especially enriching collaboration. To demonstrate, a team of computational and ethnographic researchers together applied the analysis of topic model networks approach to ethnographic field notes. We illustrate how the inclusion of the ethnographer in the modeling stages, and of the computational researchers in the analysis stages, led to mutual reflexivity affecting every stage of the study, enabling profound reflections on the technical, conceptual, and theoretical pillars of both subfields. We conclude by discussing the potential future of such collaborative ways of knowing to open doors for cutting-edge interdisciplinary research for the new information era.
A gastric duplication cyst incidentally discovered during an obesity surgery for a 55-year-old female: a rare case report from Syria
Authors: Mansour Marah , Souliman Ola , Ismail Sawsan , Alsuliman Tamim , Souleiman Fadi
Published: June 2020

A gastric duplication cyst (GDC) is an uncommon gastrointestinal (GI) tract anomaly in adults. Nonspecific symptoms make it difficult to diagnose, while radiological examination might be helpful. However, the final diagnosis is made after eradication and histopathological study. Herein we report a case of an asymptomatic, incidentally diagnosed gastric duplication cyst discovered during laparoscopic sleeve gastrectomy in a 55-year-old female.
Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana
Authors: Raxwal Vivek Kumar , Ghosh Sourav , Singh Somya , Katiyar-Agarwal Surekha , Goel Shailendra , Jagannath Arun , Kumar Amar , Scaria Vinod , Agarwal Manu
Published: June 2020

Limited information is available on abiotic stress-mediated alterations of chromatin conformation influencing gene expression in plants. In order to characterize the effect of abiotic stresses on changes in chromatin conformation, we employed FAIRE-seq (formaldehyde-assisted isolation of regulatory element sequencing) and DNase-seq to isolate accessible regions of chromatin from Arabidopsis thaliana seedlings exposed to either heat, cold, salt, or drought stress. Approximately 25% of regions in the Arabidopsis genome were captured as open chromatin, the majority of which included promoters and exons. A large proportion of chromatin regions apparently did not change their conformation in response to any of the four stresses. Digital footprints present within these regions had differential enrichment of motifs for binding of 43 different transcription factors. Further, in contrast to drought and salt stress, both high and low temperature treatments resulted in increased accessibility of the chromatin. Also, pseudogenes attained increased chromatin accessibility in response to cold and drought stresses. The highly accessible and inaccessible chromatin regions of seedlings exposed to drought stress correlated with the Ser/Thr protein kinases (MLK1 and MLK2)-mediated reduction and increase in H3 phosphorylation (H3T3Ph), respectively. The presented results provide a deeper understanding of abiotic stress-mediated chromatin modulation in plants.
Gonorrhea and Chlamydia Specimen Positivity Rate by Polymerase Chain Reaction at a Regional Veteran Affairs Medical Center
Authors: Petersen Jeffrey M , Patel Sahil , Dalal Sharvari , Jhala Darshana
Published: June 2020

Objective

Sexually transmitted infections because of Neisseria gonorrhoeae (NG) and/or Chlamydia trachomatis (CT) remain a major public health problem. Although the literature describes the population-based epidemiology of CT/NG, it does not appear to contain reference points for the statistical analyses of specimen positivity rates by nucleic acid testing (NAT) with polymerase chain reaction (PCR) that would be collected by a laboratory following best laboratory and regulatory practice. For facilities that diagnose NG and CT by a real-time PCR assay, an understanding of the expected specimen positivity rate of gonorrhea and chlamydia would be helpful for monitoring the assay for quality assurance. Therefore, on behalf of the Michael J. Crescenz Veteran Affairs Medical Center (VAMC), we present this novel quality assurance study on its CT/NG specimen positivity rates conducted by NAT with PCR.

Methods

Quality assurance/improvement quarterly data from April 1, 2012 to September 30, 2019 were reviewed to obtain both the test volume of PCR for CT/NG and the number of positive test results at the VAMC to collate and perform statistical analyses. Testing had been performed using the Abbott m2000 RealTime System (Abbott Park, IL).

Results

A total of 22,709 PCR tests for CT/NG had been performed on the veteran population; of these, 502 tests were positive for NG and 744 were positive for CT. Quarterly percentage rates ranged from 1.67% to 5.30% for CT and from 1.00% to 3.25% for NG, with average rates of 3.35% and 2.22% for CT and NG, respectively.

Conclusion

The establishment of an expected rate of specimen positivity of CT/NG by NAT with PCR at the VAMC is a significant novel reference point in the quality assurance (QA) literature and provides a benchmark that aids tremendously in QA for the microbiology/molecular laboratory.