bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diurnal variation of radar reflectivity factor during intense convective clouds over Indonesia
Authors: Yusnaini H , Marzuki  
Published: June 2020

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
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

Abstract
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

Abstract

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

Abstract

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

Abstract

Summary
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

AbstractSoy-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 &lt; 0.05) Star and Hsd17β protein in the testes and was associated with increased (P &lt; 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 &lt; 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 &lt; 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 &lt; 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

AbstractEvolution 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

Abstract
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) &gt; 0.9950, limit of detection 0.02 μg/mL and limit of quantification &lt;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.