bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effectiveness of rhizosphere bacteria in inducing the resistance of maize to downy mildew, Peronosclerospora philipinensis
Authors: Djaenuddin N , Azrai M , Kuswinanti T , Patandjengi B 
Published: July 2021

Abstract
The aim of study was to determine the efficacy of bacterial isolates from the rhizosphere in influencing the resistance of maize to downy mildew by measuring the accumulated concentration of salicylic acid. Treatments were based on a fully randomized 2-factor design with 3 levels of; factor I (bacteria) 3 levels (b0 = no bacteria, b1 = Bacillus paramycoides Ga-3, b2 = B. cereus Si-4) and factor II (salicylic acid) 2 levels (as0 = 0 g/L and as1 = 2 g/L). The research was carried out at the greenhouse and plant pathology laboratory, Indonesian Cereal Research Institute (ICERI), from March to July 2020. Each treatment combination was tested on three varieties of maize, namely Anoman, Bima20, and Bima3. Hence there were 18 treatment combinations. Furthermore, the results showed that rhizosphere bacteria and salicylic acid could control downy mildew in maize. In the case of the Bima20 variety, the combined treatment of B. paramycoides Ga3 + salicylic acid had the lowest incidence of disease at 13%. Meanwhile, treatment of B. cereus Si4 + salicylic acid in the Bima3 variety had the lowest incidence of disease by 26%. Considering the results, the enrichment of salicylic acid content was highest at 9.6 ppm on maize which was applied with the rhizosphere bacterium B. paramycoides Ga3 + salicylic acid.
The effect of biochar corn cobs and rice husks on the chemical properties of vertisol from Kupang Regency of East Nusa Tenggara
Authors: Masria  , Salli Maria Klara , Tang Basry Yadi , Syarifuddin Magfira 
Published: July 2021

Abstract
This study aims to determine the effect of corn cobs and rice husk biochar on Vertisol chemical properties from Kupang Regency, East Nusa Tenggara. This study used a completely randomized design with two factors and three replications. The first factor is the type of biochar which consists of biochar of corn cobs and rice husks. The second factor is the dose of biochar (% soil weight), consisting of 4 levels: 1.5%, 3%, 4.5%, and 6%, and incubated for two months. Chemical properties observed in this study included pH, C-organic, and soil cation exchange capacity (CEC). The results showed that giving biochar of corn cobs and rice husks did not significantly affect changes in soil chemical properties.
The effect of fertilization and variety on maize productivity in two tillage systems in North Sumatra
Authors: Girsang S S , Manurung E D , Parhusip D 
Published: July 2021

AbstractMaize is the second crucial food crop commodity that has great potential to develop in North Sumatra. The study’s objective is to determine maize production is influenced by fertilization and varieties under two tillage systems. The experiment is conducted in Batu Mamak Village, Juhar Sub-District, Karo District period March-August 2019. The three factorial experiments are tillage systems (non-tillage and conventional), fertilization (soil test kid (STK), site-specific nutrient management (PuJS), and farmers practice (FFP), and variety (Bima 2, Bima 20, JH-27, Nasa-29, NK-22, P23). Each treatment is replicated four times using a randomized complete block design with a plot size is 25 m2. The result showed that a non-tillage system with the PuJS increased grain yield by 1.1% and 21.3% compared to PuJS and FFP on the tillage system, respectively. The existing variety was still dominant compared to the newly introduced types supported by total dry matter, harvest index, and 100 grains. Bulk density was inversely related to all components was inversely associated with Ksat (infiltration). The application of organic fertilizers with a non-tillage system can increase Ksat and grain yield and provide benefits to farmers of IDR22,778,591 with a B/C ratio of 1.36.
Isolation and identification of fungi associated with natural forest land and post-mining areas of PT. Vale Indonesia: Preliminary study
Authors: Jufri S W , Iswanto  , Larekeng S H , Arif A 
Published: July 2021

Abstract
This study aimed to determine the types of fungi that can provide information on microbes associated with the post-mining forest land area of PT. Vale Indonesia. This study used a descriptive method by recording and describing the phenomena obtained. Sampling in the field was done by taking 500 g of soil/point (with three replications). Soil samples were taken around the roots or rhizosphere areas with 10 - 30 cm depth in natural and reclamation forest areas. Isolation of microbial growth was conducted by using the dilution technique. The purification of the obtained isolates was carried out by inoculation in PDA media with the point method, then incubated for ± 5 days at 27°C, and their growth was observed. Characterization of microscopic fungi isolates was identified based on the characteristics of the morphological structures. Based on preliminary research results of fungi soil samples originating from reclamation and natural forest areas, 11 rhizosphere fungi isolates were obtained. The fungi colonies’ color at the top and bottom had various colors and different textures. Greenish and whitish colors dominated the colony color, but some isolates had white, brown, cream, gray, yellowish, whitish, greenish colors, and some had spots. Colony texture was dominated by velvet, but some isolates had the texture of fine cotton and coarse cotton, presumably Aspergillus niger, Aspergillus sp, Fusarium oxysporum, Pénicillium sp., Trichoderma harzianum, and Trichoderma viride. This research will be continued to ascertain the type and function of each isolate.
Development of an inhibitory drilling mud to reduce environmental pollution
Authors: Dvoynikov M V , Rozentsvet A V , Morov V P 
Published: July 2021

Abstract
During the drilling of oil and gas wells, drilling fluids are used to transport the drilled cuttings to the surface. The most commonly used drilling fluids are water-based with the addition of various polymers. Such mud systems are used not only for transporting cuttings, but also for drilling in unstable formations. When drilling clay rocks, they are hydrated and then dispersed, which leads to various accidents. Therefore, there is a need for the correct selection of the composition of the drilling fluid with high inhibitory properties. Since polymer solutions contain a large number of toxic chemical reagents, in order to reduce harm to the outside world, it is necessary to select a solution that performs all the necessary functions, but with a smaller amount of toxic chemical reagents. This paper discusses modern drilling fluids that are currently used in production, as well as developed new compositions of more environmentally friendly fluids.
Snakes of the Volga basin in the Red Data Books of Differnt Levels
Authors: Klenina A A , Bakiev A G 
Published: July 2021

Abstract
Currently, 11 species of snakes are reliably known to be found in the Volga River basin. Vipera renardi has been assigned the Vulnerable (VU) category on the IUCN Red List of Threatened Species. The authors analyze the representation of snakes in the Volga basin in the latest editions of the Red Data Book (RDB) of the Republic of Kazakhstan, the RDB of the Russian Federation and the RDBs of Russian Oblasts, which are fully or partially related to the Volga basin. The species Hierophis caspius is included in the list of protected species in the RDB of Kazakhstan in the interfluve of the Volga and the Urals. The RDB of the Russian Federation considers rare and threatened three ophidiofauna species of the Volga basin: Eryx jaculus, Eryx miliaris, and Elaphe sauromates. Coronella austriaca is the most listed species in the Red Data Books of the constituent entities of Russia in the Volga Basin (35 Red Data Books); it is widespread but rare. The RDB of the Republic of Kalmykia protects the world’s northernmost population of Eryx jaculus. The RDBs of the Republic of Bashkortostan and Samara Oblast protect the world’s northernmost populations of Natrix tessellata, the RDB of Tatarstan protects the world’s northernmost population of Vipera renardi. The RDB of Volgograd Oblast protects the world’s northernmost population of Hierophis caspius, and the RDB of Samara Oblast – the northernmost population of Elaphe dione in Europe. Anthropogenic transformation of habitats, traffic-related deaths and actual killing of snakes are the main limiting factors in the RDBs. The authors believe that an effective measure of conservation is the creation of protected areas in the habitats of species, and, first of all, the preservation of winter brumation sites.
Profiting From Pablo: Victimhood and Commercialism in A Global Society
Authors: Goyes David Rodríguez , Franko Katja 
Published: July 2021

Abstract
Collective memory of atrocities is a fractured and disputed terrain. In this article, we empirically explore the complex process of translating violent events that took place in Medellín during the 1980s and 1990s into collective memory. It examines the conflict between Medellín inhabitants’ (in)ability to overcome trauma and shape their collective identity and the power of global media representations, exemplified by popular TV shows such as Narcos, to impose their narratives and consequently shape the present nature of the city. Drawing on original empirical material, consisting of ethnographic observations and interviews with residents of Medellín, including victims of narco-violence, this paper examines processes of memory commodification and its consequences on the global recognition of victimhood.
New insights into the diversity, taxonomy and history of the fern genusTrichomanes(Hymenophyllaceae, Polypodiidae), with a focus on Africa and the western Indian Ocean
Authors: Dubuisson Jean-Yves , Péchon Timothée Le , Hennequin Sabine , Rouhan Germinal , Salino Alexandre , Deblauwe Vincent , Droissart Vincent , Tuomisto Hanna , Lehtonen Samuli , Ebihara Atsushi 
Published: July 2021

AbstractThe filmy fern genus Trichomanes mainly comprises Neotropical species and a few taxa in Africa and the western Indian Ocean. The aim of this study is to infer the phylogenetic placement of all five Afro-Malagasy taxa in the genus and to investigate their history via an expanded and dated phylogenetic analysis including 39 species representing over half the diversity of the genus. The results support the monophyly of Trichomanes including all the sampled species attributed to the genus, but also suggest the inclusion of the species Abrodictyum cellulosum, revealing a morphological diversity of the genus greater than what was traditionally recognized, and highlighting the importance of the campanulate sorus as a generic diagnostic character. To accommodate those new phylogenetic results and morphological investigations, we describe a new subgenus Afrotrichomanes grouping the Afro-Malagasy taxa (except T. crenatum). The dated history of the genus among the trichomanoids suggests at least two origins for the Palaeotropical species. A recent Cainozoic colonization from the Neotropics towards Africa gave rise to the West African taxon T. crenatum, and a possible Mesozoic vicariance event gave rise to subgenus Afrotrichomanes. The low species diversity of the genus in the Afro-Malagasy region is discussed.
The Value of Medical Registries and Observational Studies Early in Pandemics: The Coronavirus Disease 2019 (COVID-19) Experience
Authors: Albhaisi Somaya , Wenzel Richard P 
Published: July 2021

Abstract
Whereas randomized clinical trials remain the gold standard for evaluating new therapies for infections, we argue that registries and observational studies early in the coronavirus disease 2019 (COVID-19) pandemic provided invaluable understanding of the natural history and preliminary data on risk factors and possible treatments. We review the data from the current pandemic, the history of registries in general, and their value in public health emergencies. Lessons from these experiences should be incorporated into rigorous planning for the next pandemic.
An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern
Authors: Morris C Paul , Luo Chun Huai , Amadi Adannaya , Schwartz Matthew , Gallagher Nicholas , Ray Stuart C , Pekosz Andrew , Mostafa Heba H 
Published: July 2021

Abstract

Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concerning for enhanced transmission, evasion of immune responses, or associated with severe disease have motivated the global increase in genomic surveillance. In the current study, large-scale whole-genome sequencing was performed between November 2020 and the end of March 2021 to provide a phylodynamic analysis of circulating variants over time. In addition, we compared the viral genomic features of March 2020 and March 2021.

Methods
A total of 1600 complete SARS-CoV-2 genomes were analyzed. Genomic analysis was associated with laboratory diagnostic volumes and positivity rates, in addition to an analysis of the association of selected variants of concern/variants of interest with disease severity and outcomes. Our real-time surveillance features a cohort of specimens from patients who tested positive for SARS-CoV-2 after completion of vaccination.

Results
Our data showed genomic diversity over time that was not limited to the spike sequence. A significant increase in the B.1.1.7 lineage (alpha variant) in March 2021 as well as a transient circulation of regional variants that carried both the concerning S: E484K and S: P681H substitutions were noted. Lineage B.1.243 was significantly associated with intensive care unit admission and mortality. Genomes recovered from fully vaccinated individuals represented the predominant lineages circulating at specimen collection time, and people with those infections recovered with no hospitalizations.

Conclusions
Our results emphasize the importance of genomic surveillance coupled with laboratory, clinical, and metadata analysis for a better understanding of the dynamics of viral spread and evolution.
Fully automated identification of cephalometric landmarks for upper airway assessment using cascaded convolutional neural networks
Authors: Yoon Hyun-Joo , Kim Dong-Ryul , Gwon Eunseo , Kim Namkug , Baek Seung-Hak , Ahn Hyo-Won , Kim Kyung-A , Kim Su-Jung 
Published: July 2021

SummaryObjectivesThe aim of the study was to evaluate the accuracy of a cascaded two-stage convolutional neural network (CNN) model in detecting upper airway (UA) soft tissue landmarks in comparison with the skeletal landmarks on the lateral cephalometric images.Materials and methodsThe dataset contained 600 lateral cephalograms of adult orthodontic patients, and the ground-truth positions of 16 landmarks (7 skeletal and 9 UA landmarks) were obtained from 500 learning dataset. We trained a UNet with EfficientNetB0 model through the region of interest-centred circular segmentation labelling process. Mean distance errors (MDEs, mm) of the CNN algorithm was compared with those from human examiners. Successful detection rates (SDRs, per cent) assessed within 1–4 mm precision ranges were compared between skeletal and UA landmarks.ResultsThe proposed model achieved MDEs of 0.80 ± 0.55 mm for skeletal landmarks and 1.78 ± 1.21 mm for UA landmarks. The mean SDRs for UA landmarks were 72.22 per cent for 2 mm range, and 92.78 per cent for 4 mm range, contrasted with those for skeletal landmarks amounting to 93.43 and 98.71 per cent, respectively. As compared with mean interexaminer difference, however, this model showed higher detection accuracies for geometrically constructed UA landmarks on the nasopharynx (AD2 and Ss), while lower accuracies for anatomically located UA landmarks on the tongue (Td) and soft palate (Sb and St).ConclusionThe proposed CNN model suggests the availability of an automated cephalometric UA assessment to be integrated with dentoskeletal and facial analysis.
Chi-Dependent Intramolecular Recombination in Escherichia coli
Authors: Friedman-Ohana Rachel , Karunker Iris , Cohen Amikam 
Published: July 2021

Abstract
Homologous recombination in Escherichia coli is enhanced by a cis-acting octamer sequence named Chi (5′-GCTGGTGG-3′) that interacts with RecBCD. To gain insight into the mechanism of Chi-enhanced recombination, we recruited an experimental system that permits physical monitoring of intramolecular recombination by linear substrates released by in vivo restriction from infecting chimera phage. Recombination of the released substrates depended on recA, recBCD and cis-acting Chi octamers. Recombination proficiency was lowered by a xonA mutation and by mutations that inactivated the RuvABC and RecG resolution enzymes. Activity of Chi sites was influenced by their locations and by the number of Chi octamers at each site. A single Chi site stimulated recombination, but a combination of Chi sites on the two homologs was synergistic. These data suggest a role for Chi at both ends of the linear substrate. Chi was lost in all recombinational exchanges stimulated by a single Chi site. Exchanges in substrates with Chi sites on both homologs occurred in the interval between the sites as well as in the flanking interval. These observations suggest that the generation of circular products by intramolecular recombination involves Chi-dependent processing of one end by RecBCD and pairing of the processed end with its duplex homolog.
Genetic Analysis of Chloroplast c-Type Cytochrome Assembly in Chlamydomonas reinhardtii: One Chloroplast Locus and at Least Four Nuclear Loci Are Required for Heme Attachment
Authors: Xie Zhiyi , Culler Duane , Dreyfuss Beth Welty , Kuras Richard , Wollman Francis-Andre , Girard-Bascou Jacqueline , Merchant Sabeeha 
Published: July 2021

Abstract
Chloroplasts contain up to two c-type cytochromes, membrane-anchored cytochrome f and soluble cytochrome c6. To elucidate the post-translational events required for their assembly, acetate-requiring mutants of Chlamydomonas reinhardtii that have combined deficiencies in both plastid-encoded cytochrome f and nucleus-encoded cytochrome c6 have been identified and analyzed. For strains ct34 and ct59, where the phenotype displays uniparental inheritance, the mutations were localized to the chloroplast ccsA gene, which was shown previously to be required for heme attachment to chloroplast apocytochromes. The mutations in another eight strains were localized to the nuclear genome. Complementation tests of these strains plus three previously identified strains of the same phenotype (ac206, F18, and F2D8) indicate that the 11 ccs strains define four nuclear loci, CCS1–CCS4. We conclude that the products of the CCS1–CCS4 loci are not required for translocation or processing of the preproteins but, like CcsA, they are required for the heme attachment step during assembly of both holocytochrome f and holocytochrome c6. The ccsA gene is transcribed in each of the nuclear mutants, but its protein product is absent in ccs1 mutants, and it appears to be degradation susceptible in ccs3 and ccs4 strains. We suggest that Ccs1 may be associated with CcsA in a multisubunit “holocytochrome c assembly complex,” and we hypothesize that the products of the other CCS loci may correspond to other subunits.
The tumorous-head-1 Locus Affects Bristle Number of the Drosophila melanogaster Cuticle
Authors: Packert G , Kuhn D T 
Published: July 2021

Abstract
The tuh-1 maternal effect locus contains two naturally occurring isoalleles, tuh-1h and tuh-1g. Until recently there has been no possibility to distinguish between the tuh-1h and the tuh-1g maternal effects other than evaluating their effect on the Bithorax-Complex (BX-C) Abdominal B (Abd-B) mutant tuh-3. However, in this report we identify a bristle phenotype associated with the tuh-1 locus that has very interesting evolutionary implications. Females homozygous for tuh-1h always produce adult offspring with more bristles than females homozygous or heterozygous for tuh-1g. The effect is global. Increased bristle number occurs in the head, the thorax, and the anterior and posterior abdomen. Females totally deficient for the tuh-1 gene produce offspring with high bristle number. Thus, the bristle phenotype results from the absence of the maternally contributed tuh-1g factor. Genetic evidence shows that the bristle phenotype is caused by the tuh-1 locus and that tuh-1h is completely recessive to tuh-1g. The tuh-1 locus is located at the euchromatin-β-heterochromatin junction near the centromere of the X chromosome and deficiency analysis places the locus between the lethal genes extra organs (eo) and lethal B20 (lB20). The variance in bristle number attributable to the tuh-1 locus in nature is approximately 10.1%, an indication that the bristle phenotype is most likely a neutral, pleiotrophic side effect of tuh-1.
Higher Frequency of Concerted Evolutionary Events in Rodents Than in Man at the Polyubiquitin Gene VNTR Locus
Authors: Nenoi Mitsuru , Mita Kazuei , Ichimura Sachiko , Kawano Akihiro 
Published: July 2021

Abstract
The polyubiquitin gene is an evolutionarily conserved eukaryotic gene, encoding tandemly repeated multiple ubiquitins, and is considered to be subject to concerted evolution. Here, we present the nucleotide sequences of new alleles of the polyubiquitin gene UbC in humans and CHUB2 in Chinese hamster, which encode a different number of ubiquitin units from those of previously reported genes. And we analyze the concerted evolution of these genes on the basis of their orthologous relationship. That the mean of the synonymous sequence difference Ks, which is defined as the number of synonymous substitution relative to the total number of synonymous sites, within the UbC and CHUB2 genes (0.192 ± 0.096) is significantly less than Ks between these genes (0.602 ± 0.057) provides direct evidence for concerted evolution. Moreover, it also appears that concerted evolutionary events have been much more frequent in CHUB2 than in UbC, because Ks within CHUB2 (0.022 ± 0.018) is much less than that within UbC (0.362 ± 0.192). By a numerical simulation, postulating that the major mechanism of concerted evolution in polyubiquitin genes is unequal crossing over, we estimated the frequency of concerted evolutionary events of CHUB2 at 3.3 × 10−5 per year and that of UbC at no more than 5.0 × 10−7 per year.