bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbon sequestration from bamboo biochar on the productivity of ultisols and soybean [Glycine max L.] plants
Authors: Maulana A , Prima S , Rezki D , Sukma V , Fitriani A , Herviyanti
Published: May 2021

Soil carbon is very important in food security, ecosystems, and environmental health, especially in the context of global climate change. This study was to determine the effect of carbon sequestration from bamboo biochar on increasing the productivity of marginal soils in the second planting season planted with soybean [Glycine max L.]. This study used a completely randomized design with 3 replications in 5 treatments: A = 0.0% [0g pot−1] B = 0.5% [173g pot−1]; C = 1.0% [348g pot−1]; D = 1.5% [520g pot−1] and E = 2.0 [693g pot−1] of bamboo biochar. The results showed that carbon sequestration from bamboo biochar had a significant effect on the chemical properties of Ultisols, such as increasing pH, available P, organic C, total N, CEC, and Ca-exch and could reduce Al-exch, by 0.90 units, 2.50 ppm P, 1.12% C, 0.13% N, 5.48; 1.79 and 0.88 cmolckg−1, compared to controls and increase in soybean growth and NPK nutrient uptake in stems and leaves [3.57g N, 2.61g P, 4.64g K], also in roots [0.93g N, 1.03g P, 0.94g K], compared to controls. Carbon sequestration from bamboo biochar with 2% application can increase the productivity of marginal soil [Ultisols] and soybean [Glycine max L.].
Activation of sub-bituminous coal with dolomite to improve chemical properties and palm oil growth on ultisols
Authors: Herviyanti H , Maulana A , Prasetyo T B , Darfis I , Hakim L , Ryswaldi R
Published: May 2021

Sub-bituminous coal [SC] activation with dolomite is the future technology in utilizing coal as an alternative organic material [Humic Substance]. This study aims to study the effect of SC activated with dolomite in improving the chemical properties of Ultisols and palm oil growth at the main-nursery stage [Elaeis guineensis Jacq.] In Dharmasraya. The experimental design was in Randomized Completely Block Design with three replications consisting of 6 treatments : A = 150g SC planting hole−1; B = 300g SC planting hole−1; C = 450g SC planting hole−1; D = 150g SC + 10% [15g] dolomite planting hole−1; E = 300g + 10% [30g] dolomite planting hole−1 and F = 450g SC + 10% [45g] dolomite planting hole−1. The results showed that the effect of activation on SC differs from those treatments without activation with dolomite. Effect of 450g SC activated with dolomite planting hole−1 is significant on the chemical properties of Ultisols, such as increasing in pH, available P, organic C, total N, CEC [Cation exchange capacity], and K, Ca, Exch-Mg, by 0.44 units, 1.33 ppm P, 0.44% C, 0.04% N, 0.25, 0.27, and 0.29 cmolckg−1, compared to 450g SC without activator and an increase in palm oil growth on height [12.33cm], stem diameter [0.84cm] and N, P, and K nutrient concentration from leaf of plant [0.014% N, 0.004% P, 0.002% K], compared to 450g SC without activator.
Comparative genomic of biosynthetic gene cluster of andrimid antibiotic from Serratia plymuthica UBCF_13
Authors: Fatiah R , Sulianyah I , Tjong D H , Jamsari J
Published: May 2021

Serratia plymuthica UBCF_13 was a promising bacterium to control plant pathogenic fungal. Availability of this bacterium genome and genome mining approaches has assisted to identify gene-encoded antibiotics. In this study, we identified the biosynthetic gene cluster (BGC) of andrimid and compared it with andrimid BGC from other bacterial strains and species. Andrimid is a hybrid non-ribosomal peptide-polyketide antibiotic that blocks the carboxyl-transfer reaction of bacterial acetyl-CoA carboxylase (ACC) and thereby inhibits fatty acid biosynthesis with submicromolar potency. Andrimid encoded by a gene cluster containing 20 genes, AdmA-T. Understanding the mechanism of synthesis of the non-ribosomal peptide (NRP) and polyketide assembly will assist the effort to manipulate production and increase efficacy of this antibiotic.
Simulated mutations in the geminivirus replicase gene using in-silico CRISPR / Cas9-based methods
Authors: Hidayati R , Nova B , Cania D , Runifah T , Tjong D H , Jamsari J
Published: May 2021

Geminivirus is one of the causes of losses in the agricultural sector. This virus infects many horticultural crops such as tomatoes, potatoes, eggplant, cucumbers, and chilies. All genes in geminivirus have an important and interrelated role in the success of infection. Replicase is a gene that is key in the replication of the viral genome in its host. The occurrence of mutations in this gene is thought to stop the virus from multiplying in the host. This will lead to the failure of the virus to infect the plant. To achieve this, an in-silico mutation simulation can be performed first. Mutations were simulated following the CRISPR / Cas9 method using Phyre2, ProFunc, CASTp, and Chimera software. This simulation succeeded in predicting that the CRISPR / Cas9 system on the replicase gene could inhibit viral replication. The success of this simulation will become a reference and consideration for CRISPR/Cas9 further research at the laboratory scale.
Traditional Fisherman Resilience Strategy to Coastal Pollution Pressure Impact of Tin Mining in Central Bangka District
Authors: Bidayani E , Reniati
Published: May 2021

This study aimed to analyze the income of traditional fishermen, the characteristics of individual traditional fishermen who have the ability to resilience, the factors that support the resilience of traditional fishermen, and the resilience strategies of traditional fishermen against the coastal pollution pressure from the impact of tin mining. This research used a survey method with a purposive sampling technique. The research was conducted in Bangka Tengah Regency, covering Sampur village, Pangkalan Baru sub-district and Baskara Bhakti village, Namang sub-district. The respondents in this study were traditional fishermen with more than 20 years of experience. Data collection methods in this study included primary data and secondary data. Primary data was collected using questionnaires, observation and documentation tools. Secondary data was collected through a literature study. The data was analyzed using a descriptive quantitative method. The result of the research showed that the average income of traditional fishermen is IDR 300,000 - IDR 800,000 per month. Fishermen have individual characteristics including: Insight, Independence, Relationships, Initiative, Creativity, Humor, and Morality. The factors that support the resilience of traditional fishermen are: individuals (the ability to overcome problems; family (family support); and Community (environmental support to deal with pressure). The strategy of traditional fishermen’s resilience to coastal pollution pressures due to tin mining is innovative and creative. So it is suggested that as an effort to empower traditional fishermen, the government can develop a capture fishery business into a larger business scale increase the income of traditional fishermen.
Genetic variation in the Asian seabass (Lates calcarifer Bloch, 1790) from Wallacea Region estimated using random amplified polymorphic DNA (RAPD) markers
Authors: Irmawati  , Malina Asmi Citra , Husain Aidah A.A. , Annisa Andi Rezky , Kadriah Ince Ayu Khaerana , Alimuddin Alimuddin
Published: May 2021

The Asian seabass (Lates calcarifer) is an important marine food fish in Southeast Asia. To facilitate a selective breeding program conducted in Indonesia, we genotyped 29 Asian seabass specimens collected from four wild populations in the Wallacea Region originating from coastal waters in two seaways: the Makassar Strait (Bulungan in North Kalimantan and Maros in South Sulawesi) and the Gulf of Bone (Siwa and Bone in South Sulawesi). We used four polymorphic markers with a random amplified polymorphic DNA (RAPD) method. A total of 43 alleles were detected at four loci across the four populations, four of which were shared by all the accessions while 39 were polymorphic. Of these 43 alleles, 34.88% were unique, with 46.67% in the Gulf of Bone and 53.33% in the Makassar Strait. Asian seabass within-population genetic distance was greater in Bone Bay than the Makassar Strait, and an ongoing speciation phenomenon is suspected. The greatest genetic distance (0.291) was between the Asian seabass populations from Bulungan, North Kalimantan and Cenranae River estuary, Bone Regency; the lowest (0.086) was between the Bulungan and Maros populations. In the phylogenetic analysis, Gulf of Bone and Makassar Strait specimens formed separate clades. Commercial scale cross-breeding between Asian seabass from Makassar Strait and the Gulf of Bone may produce highly adaptable seed. These results will be helpful in future Asian seabass breeding programs as well as for optimising management and conservation strategies for wild Asian seabass populations.
Papain Enzyme as Feed Additive for Grouper Cantang (Epinephelus fuscoguttatus-lanceolatus) and Silver Pompano (Triachonus blochii)
Authors: Rostika Rita , Iskandar Iskandar , Andriani Yuli , Purnama Mochammad Ichsan C. , Pratiwy Fittrie Meyllianawaty , Permana Rega
Published: May 2021

This research aims to observe growth and intestines condition of mariculture fish species, grouper cantang dan silver pompano which feed had been incorporated with papain enzyme (PE) containing papaya derived protease. The research was conducted in 2018 at The Floating Net Cages at Pangandaran Beach, Indonesia. A complete randomized design with five treatments and three repetitions was performed. The treatments involved were A (control ) B (1, 2.5% of PE added to feed), C (2.50% of PE added to feed), D (3.75% of PE added to feed), E (5.00% of PE added to feed). In addition, the research experiment if silver pompano with the same manner was conducted in 2020. The treatments were V (2% of PE added to feed), W (3% of PE added to feed), X (4% of PE added to feed), Y (5% of PE added to feed) and Z (6% of PE added to feed) for 2 months of observation time. The results showed that additional PE incorporation to feed could increase Average Daily Gain (ADG) and Feed Convertion Ratio (FCR) on fish. The addition of the papain enzyme dose in cantang grouper feed has a positive effect on the growth and intestinal conditions of the fish. At doses of 3.75% and 5% gave the best response to ADG (2.26 grams/day and 2.30 grams/day), FCR (1.41% and 1.40%) and SR (68% and 69%). The cantang grouper intestine which was given the addition of papain enzyme was 3.75% and 5%, the best conditions were the number of villi (52 and 53 pieces), the best length of the cantang grouper villi was in the 125% and 5% treatments, namely 539.3 and 524.5. Meanwhile the papain enzyme at a dose of 5% gave the best response to body weight, ADG (2.46 gram/day), SGR (0.83 %/day) and SR in silver pompano (100%).
Integrate of culture area for seaweed (Eucheuma cottonii) and fishing ground for Stripped Mullet (Mugil cephalus) in marine coastal waters
Authors: Musbir Musbir , Bohari Ridwan
Published: May 2021

Seaweed culture play role in human food, animal feed, and environmental quality. The intensively study of seaweed culture was conducted in many places. The need to assess seaweed production, fish catch and the water quality of the seaweed culture area was necessary. The present study investigates the integrated system for seaweed culture and fishing ground for Mugil cephalus in marine coastal waters area. The purpose of study was to assess the production of cultured seaweed (Eucheuma Cottonii) and caught Stripped Mullet (Mugil cephalus) in marine coastal waters. The study was conducted from October 2019 until March 2020 in southern marine coastal waters of Bulukumba Regency, South Sulawesi, Indonesia. The method of seaweed culture was longline with a rope length of 50 and the distance between rope stretches of 1 meter with the average number of rope stretches 50 stretches perunit. Stripped Mullet was caught using a surface gillnet 100 length, 2.5 m depth and 1,3/4 inch mesh size. The water quality such as water temperature, salinity, pH, brightness, current velocity was measured. The production of seaweed in this area during planting period between 40-45 days ranged 8.300-11.600 kg wet/ha and catch Stripped Mullet ranged 43-162 individuals/one day trip. The results of study suggest that a seaweed culture influence on the production of cultured seaweed and caught mullet in marine coastal waters. The water quality parameters during study were favorable for seaweed production grey mullet fish catching.
Management status of mud crab fisheries in selected areas of FMA 713, East Kalimantan, Indonesia using the Indonesian Ecosystem Approach to Fisheries Management (EAFM) Assessment Methodology
Authors: Syahdan Muhammad , Rosadi Erwin , Nursalam  , Dewi Ira Puspita , Anshary Ananda Fitrian
Published: May 2021

The selected study area in Fisheries Management Area (FMA) 713 in Kartanegara District, East Kalimantan Province, Indonesia has extensive mangrove forests with suitable habitat for mud crabs (Scylla sp.), a valuable fisheries resource. Concerns have been raised regarding reported declines in the abundance of mud crabs and in the condition of their mangrove habitat. To evaluate the management status of the mud crab fishery in this area, an assessment was carried out using the Indonesian Ecosystem Approach to Fisheries Management (EAFM) methodology. The 25 indicators assessed represent 6 domains: Fisheries Resources, Habitat and Ecosystems, Fishing Technology, Social, Economic, and Institutional. The flag model technique was applied using multi-criteria analysis through an expansion of the composite index. The results indicate that the overall management status of mud crab fisheries in Kutai Kartanegara District was in the Moderate class (on a scale of Poor, Insufficient, Moderate, Good, Excellent). Indicators in the Habitat and Ecosystems, Fishing Technology, and Institutional Domains highlighted areas of concern where improvements are needed. The Fisheries Resources Domain aggregate status (moderate) indicated that wild mud crab stocks were still reasonably abundant and reliable, supporting the moderate status in the Social and Economic Domains, which relate to the welfare of fishing communities. The Institutional Domain status was in the poor category. Good governance measures to improve the Institutional Domain indicators have the potential to strengthen the other domains, in particular the Habitat and Ecosystem Domain and the Fishing Technology Domain, and to improve the overall EAFM status of the mud crab fishery in the future.
Plankton’s abundance and its implications for Sardinella lemuru catch in Prigi waters
Authors: Sartimbul Aida , Trishnayana Egha , Rohadi Erfan , Muslihah Nurul , Lutfi Oktiyas M , Iranawati Feni , Harlyan Ledhyane Ika , Wulandari Erawati , Sambah A B
Published: May 2021

Sardinella lemuru is well known as a dominant fish in Bali Strait. However, since 2010 the stocks have collapsed. Surprisingly, at the end of 2019 it was caught very abundantly in Prigi waters, Trenggalek, reaching 56.42% of the production by volume and 39.44% in value. The reason for this abundance is thought to be the abundant availability of food in nature. This study aimed to analyse the abundance of plankton in relation to the abundance of S. lemuru in Prigi waters at the end of November 2019. A total of 100 S. lemuru samples were caught using a purse seiner, while marine plankton were collected using a 20μm plankton net with a vertical method at 5 sampling sites in S. lemuru fishing grounds in Prigi waters. The morphology, morphometric and meristic characters of the S. lemuru specimens were analysed, as well as the gut contents. Plankton samples collected from the sea and S. lemuru guts were identified and their abundance analysed. The S. lemuru samples had a mean total length (TL) of 16.47 ± 0.19 cm. The plankton from the seawater consists of 52.8% zooplankton and 47.2% phytoplankton, consisting of 21 genera of phytoplankton and 12 genera of zooplankton. Actinocyclus dominated the phytoplankton group with an abundance of 14,098 ind/m3, while the zooplankton group was dominated by Acartia with an abundance of 15,592 ind/m3. Correlation analysis shows the value of the correlation coefficient between phytoplankton in the waters and the S. lemuru was r = 0.920 with a determination coefficient of 84.9%. The abundance of S. S. lemuru in November 2019 was due to the abundant availability of food in the fishing area, when phytoplankton is the main food choice for S. lemuru.
Chiral glass of charged DNA rods, cavity loops
Authors: Kang Kyongok
Published: May 2021

Recently, the collective phase behaviors of charged DNA-viruses (rods) are explored in various low ionic strengths, where much slowing down relaxations are observed in equilibrium. These phases are distinguished by crossing the critical ionic strength, where the salt-dependent effective microscopic dynamics are important with non-monotonic multi-phase boundaries. This is also interested in terms of phase transition and replica symmetry breaking (RSB), realized by the divergence of relaxation time and the exponent power of correlation lengths in dynamic disorderorder transitions. RSB occurs as the result of many-body interactions of randomized orientations. Here, in this paper, one of the chiral mesophases, the X-pattern is highlighted for its long-time metastable state consisting of cavity loops bounded within the planar nematic, as a new type of a glass, noted as a chiral glass. The chiral glass is discussed in terms of the divergences for relaxations in the characteristic time as well the inverse of an optical pitch length, which are analyzed in the long-time-lapsed orientation textures via image-time correlations. The outcome highlights interesting aspects of charge effect in the ‘twist’ elasticity energy for optimizing the long-ranged repulsive electrostatic interactions among charged DNA rods.
Image segmentation for neuroscience: lymphatics
Authors: Tabassum N , Wang J , Ferguson M , Herz J , Dong M , Louveau A , Kipnis J , Acton S T
Published: May 2021

A recent discovery in neuroscience prompts the need for innovation in image analysis. Neuroscientists have discovered the existence of meningeal lymphatic vessels in the brain and have shown their importance in preventing cognitive decline in mouse models of Alzheimer’s disease. With age, lymphatic vessels narrow and poorly drain cerebrospinal fluid, leading to plaque accumulation, a marker for Alzheimer’s disease. The detection of vessel boundaries and width are performed by hand in current practice and thereby suffer from high error rates and potential observer bias. The existing vessel segmentation methods are dependent on user-defined initialization, which is time-consuming and difficult to achieve in practice due to high amounts of background clutter and noise. This work proposes a level set segmentation method featuring hierarchical matting, LyMPhi, to predetermine foreground and background regions. The level set force field is modulated by the foreground information computed by matting, while also constraining the segmentation contour to be smooth. Segmentation output from this method has a higher overall Dice coefficient and boundary F1-score compared to that of competing algorithms. The algorithms are tested on real and synthetic data generated by our novel shape deformation based approach. LyMPhi is also shown to be more stable under different initial conditions as compared to existing level set segmentation methods. Finally, statistical analysis on manual segmentation is performed to prove the variation and disagreement between three annotators.
Queer Comics
Authors: Councilor KC
Published: May 2021

Queer comics have been a staple of LGBTQIA+ culture, from independent and underground comics beginning in the late 1960s to web comics in the current digital age. Comics are a uniquely queer art form, as comics scholar Hillary Chute has argued, consistently marginalized in the art world. Queer comics have also principally been produced by and for queer audiences, with mainstream recognition not being their primary goal. This marginalization has, in some sense, been a benefit, as these comics have not been captive to the pressures of capitalist aesthetics. This makes queer comics a rich historical archive for understanding queer life and queer communities. Collections of queer comics from the late 1960s and onward have recently been published, making large archives of work widely available. The Queer Zine Archive Project online also houses a large volume of underground and self-published material.

There are some affordances inherent to the medium of comics which make it a distinctly powerful medium for queer self-expression and representation. In comics, the passage of time is represented through the space of the page, which makes complex expressions of queer temporality possible. The form is also quite intimate, particularly hand-drawn comics, which retain their original form rather than being translated into type. The reader plays a significant role in the construction of meaning in comics, as what happens between panels in the “gutter” (and is thus not pictured) is as much a part of the story as what is pictured within the panels. In addition to the value of reading queer stories in comic form, incorporating making comics and other creative practices into pedagogy is a powerful way to engage in queer worldmaking.
Schooling and Equity in Israel
Authors: Feniger Yariv , Shavit Yossi , Caller Shir
Published: May 2021

Education in Israel is compulsory and free, from the age of three to the end of secondary school (12th grade). Compulsory education culminates in matriculation examinations that serve as the main criterion for enrollment in higher education. Although Israel is geographically small, and ethnic and religious subpopulations live in close proximity to one another, they are highly segregated both residentially and in schools. The Jewish and Arab school sectors are almost completely separate. Most Arab students study in Arab state schools, where the language of instruction is Arabic and the staff are Arab. Jewish students study in state, state religious, or independent ultra-Orthodox schools. The high degree of economic inequality in Israel is reflected in educational inequality, which is the highest among the countries participating in the 2018 Programme for International Student Assessment (PISA). Inequalities between social strata are affected in part by the economic circumstances of families in early childhood. Inequality in educational achievement is particularly evident between Jews and Arabs but it is also prominent within each of these two societies. The public educational system is centralized and curricula are standardized, but religious Jewish groups enjoy considerable organizational and curricular autonomy. Arab state schools, in contrast, do not enjoy similar autonomy. Rapid expansion of higher education has contributed to a dramatic increase in graduation rates in all social categories but large gaps remain, especially along ethnoreligious lines, in graduation rates, fields of study, and quality of institutions attended.
The State of Higher Education in the Arab World
Authors: Qasem Islam
Published: May 2021

The mid-20th century marked the birth of higher education systems in the majority of the 22 Arabic-speaking countries. Driven by post-independence nationalism, ruling elites deemed education, including higher education, as a crucial part of nation-state building, next to the development of the army, bureaucracy, and economy. With government funding, new public universities were established throughout the region. Enrollment steadily increased as governments expanded access to higher education through lax admission and free or highly subsidized admission, and often guaranteeing employment for university graduates in the public sector. By the end of the 20th century, higher education became widely accessible in most Arab countries, but decades of neglect have led to a crisis in quality and research. Academic quality has deteriorated under the weight of decades of neglect from overcrowded classrooms, outdated curriculum, poor pedagogy, underpaid faculty, lack of quality mechanisms, strapped budget to limited autonomy. No more encouraging is the universities’ role as a center of knowledge discovery and innovation, given their lack of adequate qualified human and necessary physical resources. The low performance of public universities on the global ranking systems and the high unemployment rate among university graduates sums up the Arab higher education system’s inauspicious condition.

During the last two decades, governments enacted various reform measures. To relieve overcrowded public universities and reduce public finance burden, countries in the region authorized private higher education. Consequently, the number of private universities has mushroomed, many of which are for-profit and exclusively focused on teaching. However, a shortage of cash and limited freedom to manage academic and administrative affairs continue to beset most public institutions. Some countries have made incremental changes, such as introduced measures to increase equity, endorsed new admission policies, and established accreditation and quality assurance bodies. The Gulf countries undertook far-reaching measures to transform the system. Cushioned by oil and gas revenues and a relatively small population, the six Gulf countries have invested considerably in upgrading public universities’ infrastructure, hiring faculty and administrative staff from abroad, and developing a research infrastructure including establishing new research-oriented universities.

Consequently, the Arab higher education landscape has become increasingly diversified and with growing differences among countries. To compare the Arab countries on their current state of their higher education system, the countries are ranked on an index composed of three key aspects: access to higher education (gross enrollment ratio), equity (gross enrollment ratio for female), and publication intensity (citable documents per million inhabitants). The ranking shows the Gulf countries vying for the top spots. At the low end of the rank are countries which have been conflict-ridden or poverty-stricken.
The Impact of Surgical Procedures During Septorhinoplasty on the Intraoperative Pain Response
Authors: Ince Bilsev , Zuhour Moath , Yusifov Merve , Erol Atilla , Dadaci Mehmet
Published: May 2021

Background

During septorhinoplasty, many different surgical procedures are employed to bring the nose to the desired shape and solve breathing complaints. As a matter of course, intraoperative pain response occurs due to these procedures.

Objectives

With this study, the authors aimed to evaluate the intraoperative pain formed during septorhinoplasty surgery with numerical values and to determine which stage of surgery is more painful.

Methods

Between April 2019 and March 2020, a total of 30 female patients who were planned to undergo septorhinoplasty were included in this prospective study. Standard anesthesia and analgesia were applied to all patients. During surgery, state entropy measure was utilized to evaluate the depth of anesthesia, and Surgical Pleth Index was employed to evaluate the response of the central nervous system to pain “nociception.”

Results

The age of the patients ranged from 18 to 42 years (average, 25.3 ± 6.1 years). The average value of state entropy recorded during the surgery for all patients was found to be 45.43 ± 5.37. The mean beginning Surgical Pleth Index value recoded from all of the patients was 23.4 ± 8.84 compared with the beginning value; the values recorded during periost dissection, lateral osteotomy, and lower turbinate lateralization were statistically significantly higher (P < 0.005).

Conclusions

Although sufficient depth of anesthesia and standard protocol of analgesia were applied, pain response was found to be significantly higher at some procedures during septorhinoplasty. The authors think that increasing the depth of anesthesia during these procedures will increase the comfort of this operation by inhibiting pain response.

Level of Evidence: 4
Males perceive honest information from female released sex pheromone in a moth
Authors: Gonzalez-Karlsson Adrea , Golov Yftach , Steinitz Hadass , Moncaz Aviad , Halon Eyal , Horowitz A Rami , Goldenberg Inna , Gurka Roi , Liberzon Alexander , Soroker Victoria , Jurenka Russell , Harari Ally R
Published: May 2021

There is accumulating evidence that male insects advertise their quality to conspecific females through pheromones. However, most studies of female released sex pheromone assume information transfer regarding merely the species of the female and her mating status. We show that more information is conveyed through the female sex pheromone, positioning it as an honest sexual trait. We demonstrate that females in bad physical conditions (small, starved, or old) lay significantly fewer eggs than females in good conditions (large, fed, or young). The ratio of components in the sex pheromone blend in gland extracts of the female pink bollworm moths provided honest information on most of the phenotypic conditions tested, whereas the pheromone amount in the glands provided an honest signal of quality for extreme phenotypes only. Moreover, males used the information conveyed by the female pheromone to choose their mates, approaching females that signaled higher reproductive potential. In addition, when simulating the female effect, using the synthetic pheromone blend that represents higher quality females (0.6:0.4 ZZ:ZE), more males were attracted to this blend than to the blend representing the population mean (0.5:0.5 ZZ:ZE). Both, female advertisement for males and the male choosiness, suggest that pheromones have evolved as sexual traits under directional, sexual selection. We suggest that the pheromone blend may serve as a multicomponent signal whereby each component adds information concerning the current condition of the female, and all are necessary to elicit a mate searching response.
Natural noise affects conspecific signal detection and territorial defense behaviors in songbirds
Authors: Reed Veronica A , Toth Cory A , Wardle Ryan N , Gomes Dylan G E , Barber Jesse R , Francis Clinton D
Published: May 2021

Recent research suggests that anthropogenic noise can substantially alter animal behavior. Although there are many sources of natural background noise, the relative influence of these sounds on behavior has received much less attention. Using landscape-scale playbacks of rushing rivers and crashing ocean surf, we investigated how habitat appropriate natural noise alters territorial defense behaviors in lazuli buntings (Passerina amoena) occupying riparian areas and spotted towhees (Pipilo maculatus) in riparian and coastal areas when exposed to simulated intruder song. We also incorporated naturally occurring cicada noise as an acoustic source influencing lazuli bunting behavior. Both songbird species possess songs that share substantial spectral overlap with low-frequency, water-generated noise, and lazuli bunting song shares an additional high-frequency overlap with cicada calls. Thus, there is potential for background acoustic conditions to mask conspecific signals. We found that detection and discrimination of conspecific playback occurred more slowly for both species as background sound levels increased. Lazuli buntings also exhibited complex flight behavior in noise, suggesting they respond differently depending on the amplitude and type of background noise (with versus without cicada calls). Our results suggest natural noise can impair territorial defense behaviors in songbirds, highlighting natural soundscapes as an under-appreciated axis of the environment.
LSTM-PHV: prediction of human-virus protein–protein interactions by LSTM with word2vec
Authors: Tsukiyama Sho , Hasan Md Mehedi , Fujii Satoshi , Kurata Hiroyuki
Published: May 2021

Viral infection involves a large number of protein–protein interactions (PPIs) between human and virus. The PPIs range from the initial binding of viral coat proteins to host membrane receptors to the hijacking of host transcription machinery. However, few interspecies PPIs have been identified, because experimental methods including mass spectrometry are time-consuming and expensive, and molecular dynamic simulation is limited only to the proteins whose 3D structures are solved. Sequence-based machine learning methods are expected to overcome these problems. We have first developed the LSTM model with word2vec to predict PPIs between human and virus, named LSTM-PHV, by using amino acid sequences alone. The LSTM-PHV effectively learnt the training data with a highly imbalanced ratio of positive to negative samples and achieved AUCs of 0.976 and 0.973 and accuracies of 0.984 and 0.985 on the training and independent datasets, respectively. In predicting PPIs between human and unknown or new virus, the LSTM-PHV learned greatly outperformed the existing state-of-the-art PPI predictors. Interestingly, learning of only sequence contexts as words is sufficient for PPI prediction. Use of uniform manifold approximation and projection demonstrated that the LSTM-PHV clearly distinguished the positive PPI samples from the negative ones. We presented the LSTM-PHV online web server and support data that are freely available at http://kurata35.bio.kyutech.ac.jp/LSTM-PHV.
Pupal colour plasticity in the butterfly Catopsilia pomona (Lepidoptera: Pieridae)
Authors: Yumnam Tarunkishwor , Banerjee Birupaksha , Kodandaramaiah Ullasa
Published: May 2021

Pupal colour plasticity (PCP) in many lepidopterans can be adaptive by helping pupae match their background colours. Studies on PCP, most of which have been laboratory-based, have largely used human assessment of colour to categorize pupae as green or brown. This binary categorization limits the understanding of finer pupal colour variations and their function. We conducted a study of PCP in the butterfly Catopsilia pomona by comparing laboratory-reared and wild populations. Considering pupal colour as a continuous variable, we showed that a large proportion of the pupae matched the colours of their substrates, with leaf-borne pupae tending to be greener and off-leaf pupae browner. Pupal colour also responded to the leaf substrate’s finer colour variations, highlighting the importance of treating pupal colour as a continuous variable. Compared to the wild population, the laboratory population had more green pupae on off-leaf substrates. Our study thus illustrates that caution should be used when extrapolating the results from laboratory-based studies to the natural world. In leaf-borne wild pupae, pupation position on the leaf, the thickness of the midrib where pupation occurred and the leaf’s length influenced the pupal colour. Our study underscores the need for further research on PCP as a background-matching strategy in light of predation.
RP11-51O6.1 sponges miR-206 to accelerate colorectal cancer carcinogenesis and metastasis through upregulating YAP1
Authors: Zhu Xiaojian , Zhu Jinfeng , Tan Ting , Bu Fanqin , Zhao Jiefeng , Luo Chen , Luo Hongliang
Published: May 2021

Long non-coding RNAs (lncRNAs) have been characterized by playing a crucial role in tumorigenesis. However, the detail biological function and clinical importance of lncRNAs in colorectal cancer (CRC) are unclear and have attracted different levels of in-depth research. In this context, we explored the differentially expressed profiles of lncRNAs in six CRC tissues and three adjacent non-tumor tissues from RNA-sequencing (RNA-seq) study and noted a lncRNA, RP11-51O6.1, which is markedly overexpressed in CRC tissues, particularly in aggressive cases. Impressively, an elevated RP11-51O6.1 level was highly correlated with poor prognosis in clinical patients. Functional analyses revealed that RP11-51O6.1 could promote cell proliferation in vitro and in vivo. Furthermore, we reported that RP11-51O6.1 enhances cell migration and invasion in vitro. Mechanistic studies (Bioinformatics binding site analyses, the Luciferase reporter, Ago2 immunoprecipitation, the RNA pull-down, immunofluorescence colocalization, rescued assays and western blotting) implicated that RP11-51O6.1 could regulate YAP1 expression by competitively sponging miR-206 and blocking its activity in promoting CRC progression. Conclusively, our findings identify a novel RP11-51O6.1/miR-206/YAP1 regulatory axis that participates in CRC progression and development, suggesting RP11-51O6.1 is an exploitable biomarker and appealing therapeutic target in treating CRC.
Cross-Diagnosis Structural Correlates of Autistic-Like Social Communication Differences
Authors: Kushki Azadeh , Cardy Robyn E , Panahandeh Sina , Malihi Mahan , Hammill Christopher , Brian Jessica , Iaboni Alana , Taylor Margot J , Schachar Russell , Crosbie Jennifer , Arnold Paul , Kelley Elizabeth , Ayub Muhammad , Nicolson Robert , Georgiades Stelios , Lerch Jason P , Anagnostou Evdokia
Published: May 2021

Social communication differences are seen in autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and obsessive–compulsive disorder (OCD), but the brain mechanisms contributing to these differences remain largely unknown. To address this gap, we used a data-driven and diagnosis-agnostic approach to discover brain correlates of social communication differences in ASD, ADHD, and OCD, and subgroups of individuals who share similar patterns of brain-behavior associations. A machine learning pipeline (regression clustering) was used to discover the pattern of association between structural brain measures (volume, surface area, and cortical thickness) and social communication abilities. Participants (n = 416) included children with a diagnosis of ASD (n = 192, age = 12.0[5.6], 19% female), ADHD (n = 109, age = 11.1[4.1], 18% female), or OCD (n = 50, age = 12.3[4.2], 42% female), and typically developing controls (n = 65, age = 11.6[7.1], 48% female). The analyses revealed (1) associations with social communication abilities in distributed cortical and subcortical networks implicated in social behaviors, language, attention, memory, and executive functions, and (2) three data-driven, diagnosis-agnostic subgroups based on the patterns of association in the above networks. Our results suggest that different brain networks may contribute to social communication differences in subgroups that are not diagnosis-specific.
Alcohol Availability and Alcohol-Attributable Mortality: Economic Implications following a Change in Sales Policy
Authors: Stoppel Relika
Published: May 2021

It is commonly known that irresponsible alcohol use can have adverse effects. For some people, it results in health problems, for others in productivity loss, and some experience the worst possible outcome of alcohol misuse – death. This paper estimates the effect of reduced alcohol sales hours on alcohol-attributable mortality (AAM) in Estonia. Using novel mortality data from 1997 to 2015, this paper analyzes the effect of alcohol sales policies at both the county level and the country level. By applying the difference-in-differences method and the ARIMA model, this paper finds that the alcohol sales policy reduced AAM to between 1.710 and 2.401 deaths per 100,000 per month, which equals a reduction of 31% to 40% in AAM deaths. These findings suggest that individuals who are the most at risk of dying from alcohol-attributable causes of death benefit remarkably from reduced alcohol availability (JEL codes: I12, I18, and H75).
Rotavirus Vaccination Likely to Be Cost Saving to Society in the United States
Authors: Newall Anthony T , Leong Robert Neil , Reyes Josephine F , Curns Aaron T , Rudd Jessica , Tate Jacqueline , Macartney Kristine , Parashar Umesh
Published: May 2021

Background

Following the introduction of rotavirus immunization in 2006 in the United States, there were substantial declines in the domestic rotavirus disease burden. In this study, we assess the value for money achieved by the program in the decade following vaccine introduction.

Methods

We applied an age-specific, static, multicohort compartmental model to examine the impact and cost-effectiveness of the US rotavirus immunization program in children <5 years of age using healthcare utilization data from 2001 to 2015 inclusive. We calculated the incremental cost-effectiveness ratio (ICER) per quality-adjusted life year (QALY) gained from both a healthcare system and societal perspective.

Results

Declines in healthcare use associated with the rotavirus and acute gastroenteritis occurred from 2006 and continued to grow before stabilizing from 2010 through 2011. From 2011 to 2015, an estimated annual average of approximately 118 000 hospitalizations, 86 000 emergency department presentations, and 460 000 outpatient and physician office visits were prevented. From a societal perspective during this same period, the program was estimated to be cost saving in the base case model and in >90% of probabilistic sensitivity analysis simulations and from a healthcare system perspective >98% of simulations found an ICER below $100 000 per QALY gained.

Conclusions

After the program stabilized, we found the rotavirus immunization in the United States was likely to have been cost saving to society. The greater than expected healthcare and productivity savings reflect the success of the rotavirus immunization program in the United States.
The European Biological Variation Study (EuBIVAS): Biological Variation Data for Coagulation Markers Estimated by a Bayesian Model
Authors: Aarsand Aasne K , Kristoffersen Ann Helen , Sandberg Sverre , Støve Bård , Coşkun Abdurrahman , Fernandez-Calle Pilar , Díaz-Garzón Jorge , Guerra Elena , Ceriotti Ferruccio , Jonker Niels , Røraas Thomas , Carobene Anna
Published: May 2021

Background

For biological variation (BV) data to be safely used, data must be reliable and relevant to the population in which they are applied. We used samples from the European Biological Variation Study (EuBIVAS) to determine BV of coagulation markers by a Bayesian model robust to extreme observations and used the derived within-participant BV estimates [CVP(i)] to assess the applicability of the BV estimates in clinical practice.

Method

Plasma samples were drawn from 92 healthy individuals for 10 consecutive weeks at 6 European laboratories and analyzed in duplicate for activated partial thromboplastin time (APTT), prothrombin time (PT), fibrinogen, D-dimer, antithrombin (AT), protein C, protein S free, and factor VIII (FVIII). A Bayesian model with Student t likelihoods for samples and replicates was applied to derive CVP(i) and predicted BV estimates with 95% credibility intervals.

Results

For all markers except D-dimer, CVP(i) were homogeneously distributed in the overall study population or in subgroups. Mean within-subject estimates (CVI) were <5% for APTT, PT, AT, and protein S free, <10% for protein C and FVIII, and <12% for fibrinogen. For APTT, protein C, and protein S free, estimates were significantly lower in men than in women ≤50 years.

Conclusion

For most coagulation markers, a common CVI estimate for men and women is applicable, whereas for APTT, protein C, and protein S free, sex-specific reference change values should be applied. The use of a Bayesian model to deliver individual CVP(i) allows for improved interpretation and application of the data.
Evolutionary engineering reveals amino acid substitutions in Ato2 and Ato3 that allow improved growth ofSaccharomyces cerevisiaeon lactic acid
Authors: Baldi Nicolò , de Valk Sophie Claire , Sousa-Silva Maria , Casal Margarida , Soares-Silva Isabel , Mans Robert
Published: May 2021

In Saccharomyces cerevisiae, the complete set of proteins involved in transport of lactic acid across the cell membrane has not been determined. In this study, we aimed to identify transport proteins not previously described to be involved in lactic acid transport via a combination of directed evolution, whole-genome resequencing and reverse engineering. Evolution of a strain lacking all known lactic acid transporters on lactate led to the discovery of mutated Ato2 and Ato3 as two novel lactic acid transport proteins. When compared to previously identified S. cerevisiae genes involved in lactic acid transport, expression of ATO3T284C was able to facilitate the highest growth rate (0.15 ± 0.01 h-1) on this carbon source. A comparison between (evolved) sequences and 3D models of the transport proteins showed that most of the identified mutations resulted in a widening of the narrowest hydrophobic constriction of the anion channel. We hypothesize that this observation, sometimes in combination with an increased binding affinity of lactic acid to the sites adjacent to this constriction, are responsible for the improved lactic acid transport in the evolved proteins.
Study on the strategy of multimodal transportation of medical aid materials for public health emergencies: a case study basing on COVID-19
Authors: Ning Tao , Duan Xiaodong , An Lu
Published: May 2021

The emergency response to sudden public health incident often encounters problems such as the long distance between the medical material supply node and the demand point or the destruction of key roads, which makes it difficult to transport materials directly to the disaster area by vehicles in time. Helicopters are increasingly being used to transport critical medical emergency resources, but it is not easy to distribute medical supplies through helicopter in large-scale public health incidents. In order to solve the above problems, a two-stage combined transportation method for medical supplies based on clustering is proposed in this paper. In the first stage, the quantum bacterial foraging (QBF) algorithm is used to select emergency transit points and divide the medical assistance points. In view of the imbalance of remaining capacity in QBF division, an improved division method (quantum bacterial foraging with capacity constraints (QBFwCC)) is proposed and a ‘helicopter–vehicle’ medical material combined transportation network structure is constructed in consideration of capacity constraints. In the second stage, a transportation route optimization model based on clustering is established to determine the specific transportation route from the emergency transit point to the medical assistance point. The performance of the method proposed in the paper was analyzed through experimental COVID-19 simulation and compared between QBF and QBFwCC. The results show that the method not only achieves the goal of optimization, but also effectively reduces the number of vehicles.
Novel phase-locked loop-based resonant frequency tracking control for linear reciprocating compressor
Authors: Wang Liqiang , Yu Xiaofan , Lei Meizhen , Yin Xiuxing
Published: May 2021

The paper presents a novel phase-locked loop (PLL)-based resonant frequency tracking method for linear compressors with oscillatory motions. The proposed method achieves the phase-locked control between two signals by using PLL, which includes a multiplier, and a low-pass filter to obtain the phase signal difference. Consequently, based on the phase signal difference, the electrical frequency of the power supply can be adjusted through a PI (proportional-derivative) regulator such that the phase signal difference converges to 90° and the linear compressor works under the resonant frequency conditions. The analytical expression of the resonant frequency condition is proposed for the linear compressor. Then, the detailed design and procedure of the proposed method are presented. The designed method and the resonant frequency characteristics are verified by using the simulation experiment. The simulated results demonstrate that the proposed algorithm has faster response speed and higher convergence accuracy to step load change in comparison with the other commonly used algorithms.