bluuebunny/crossref_metadata_2025 huggingface dataset:
Urinary incontinence and the impact on migrant individuals with intellectual disability
Authors: Kelly Anne Marie , Keenan Paul
Published: October 2021

Enhancing and enriching the health and wellbeing of migrant individuals with intellectual disability is essential in our diverse society. The needs of this population can be substantial, but unfortunately migrant individuals with intellectual disability face many challenges, from accessing health services, cultural complexities, financial difficulties, and language barriers, to lack of knowledge on the availability of particular services. Although a common condition, urinary incontinence remains a taboo subject and many individuals do not seek intervention even though it impacts on all aspects of their life. The migrant individual who has an intellectual disability may be unable to understand information that is provided, unable to gain knowledge, access educational material to promote continence and manage incontinence. This article considers what is known on the subject of urinary incontinence for an individual with intellectual disability from the migrant community in Ireland.
Examining the challenges of hospital discharge for patients with a urinary catheter
Authors: Cheekooree Blair , Casey Sean , Clayton Hayley , Hambling Elaine , Tomlinson Caroline
Published: October 2021

Background:

Patient discharge between acute and secondary care will be viewed differently based on the stakeholder groups involved. Examining these different perceptions may help improve the discharge process and the patient journey from hospital to home.

Aims:

To determine the perceptions of community and hospital nursing staff regarding the challenges that exist with the general hospital discharge process for patients with a urinary catheter.

Methods:

A survey was created and sent to a wide range of acute and community nurses and the subscriber list of Journal of Community Nursing, Journal of General Practice Nursing and Wound Care Today.

Findings:

Compared with hospital staff, the opinions of community staff were more negative around the discharge process and post-discharge care and materials.

Conclusions:

Results of this survey provide insight into the perceptions of nursing staff into general patient discharge for those with a urinary catheter and help identify the challenges that exist on the patient journey from hospital to home.
Modeling Age at Menstrual Onset and Developing Menarcheal Life Table
Authors: Singh Brijesh P.
Published: October 2021

Population scientists are generally developing mathematical models/techniques in demography and trying to provide brief explanation of extensive data sets. The prime objective of the present paper is to suggest a probability model to illustrate the distribution of female’s age at first menstrual onset. Menarcheal age distribution is used to evaluate risk associated to reproductive issues and may be used as a demographic indicator of female fecundity. The suitability of the model suggested is tested with the real data sets. Parameters of the model have been estimated through least square estimation technique. It is observed that older female’s age at menarche is somewhat higher than the younger female’s age at menarche. Also, a life table for menarcheal age using a probability model has been constructed. This life table will enable providing the expected duration of getting menarche for a girl of a particular age.
Agarwood formation in Aquilaria beccariana and Aquilaria microcarpa in response to inoculation of newly isolated fungi from Brunei Darussalam
Authors: MOHAMMAD YUMNI HAZIQAH , Shivanand Pooja , Metali Faizah , Taha Hussein , MATUSSIN NUR BAZILAH AFIFAH , ABDUL-HALIM ABDUL MUIZZ AL-AZIM , MOHAIMIN ABDUL ZUL’ADLY
Published: October 2021

Abstract. Mohammad YH, Shivanand P, Metali F, Taha H, Matussin NBA, Abdul-Halim AMA, Mohaimin AZ. 2021. Agarwood formation in Aquilaria beccariana and Aquilaria microcarpa in response to inoculation of newly isolated fungi from Brunei Darussalam. Biodiversitas 22: 4131-4138. Aquilaria is an important agarwood-producing tree, but naturally occurring agarwood is rare. Artificial induction method is the most commonly used to produce agarwood in a short time. Out of the 21 species of Aquilaria, Brunei Darussalam houses two species that produce high quality agarwood, namely Aquilaria beccariana and A. microcarpa. The aims of this study are to artificially induce agarwood formation using eight different induction treatments: six fungal inoculant treatments with two control treatments, and to isolate and identify fungal strains from naturally infected agarwood tree using DNA barcoding. Agarwood formation was observed at four different time intervals i.e. 1, 3, 6 and 9 months of post-inoculation. Results exhibited that the area and the total length of discoloration zone were significantly greater at 6 and 9 months of incubation period. Induction treatment did not significantly affect the area and the total length of discoloration. FTIR analysis revealed that two aromatic compounds (C – H and C – C stretching) were detected at the wavelength ranges of 3000 – 2800 cm-1, and 1500 – 1400 cm-1 respectively, and OH group was detected at 3600 – 3400 cm-1.  Nine fungal strains from Aspergillus, Fusarium, Mucor and Trichosporon were isolated and identified from a naturally infected agarwood, and the last two fungi (Mucor and Trichosporon) were never been previously reported.
Screening of chitinase-producing rhizosphere actinomycetes and their genetic diversity
Authors: Wahyudi Aris Tri , FITHRIANSYAH NAUFAL GHAZI , AMRI MUHAMMAD FAIZ , PRIYANTO JEPRI AGUNG , NAWANGSIH ABDJAD ASIH
Published: October 2021

Abstract. Wahyudi AT, Fitriansyah NG, Amri MF, Priyanto JA, Nawangsih AA. 2021. Screening of chitinase-producing rhizosphere actinomycetes and their genetic diversity. Biodiversitas 22: 4186-4192. Soil microbial community, especially rhizosphere actinomycetes, plays an important role in protecting plants from phytopathogenic fungi by producing various agroactive compounds, including mycolytic enzymes particularly chitinase. The objective of this study was to investigate chitinase activity and analyze the diversity of family 19 chitinase genes of actinomycetes isolated from maize and soybean rhizosphere. Of fivety actinimycetes, Seventeen isolates exhibited chitinolytic activities and formed a hydrolytic zone around the colony with chitinolytic index ranging from 0.49±0.01 to 2.15±0.69, qualitatively tested in 0.3% chitin agar medium. Six selected isolates (ARJ 36, ARJ 81, ARJ 15, ARK 17, ARK 143, ARK 103) showed chitinase activities ranging from 0.157±0.04 to 0.440±0.09 U/mL, based on chitinolytic index. The production of chitinase was confirmed by the presence of family 19 chitinase encoding genes from Streptomyces sp. Some conserved regions and essential amino acid residues were also detected. This study suggests that chitinolytic actinomycetes isolated from maize and soybean rhizosphere can be studied further as biological control candidates for controlling phytopathogenic fungi.
Identification of dragon fruit (Selenicereus) species in Mekong Delta based on DNA barcode sequences
Authors: Huy Tran Gia , Men Tran Thanh , Thi Nguyen Pham Anh , KHANG DO TAN
Published: October 2021

Abstract. Huy TG, Men TT, Thi NPA, Khang DT. 2021. Identification of dragon fruit (Selenicereus) species in Mekong Delta based on DNA barcode sequences. Biodiversitas 22: 4216-4222. Selenicereus species is one of the valuable fruiting plants in Vietnam due to its properties, e.g., rich nutrition and medicine activity. Eight DNA barcodes applied to the discrimination power of dragon fruit species in the Mekong delta. Total DNA extracted from fresh roots and the loci of interest were amplified and sequenced. DNA sequences were aligned and determined variable regions. The findings revealed that four loci, including matK, rbcL, rpoC1, and atpF-H reached high PCR yield and specificity compared to those in ycf1b, psbK-I, and ITS. The atpF-H was the most variable region due to the number of single nucleotide polymorphisms (SNPs) and indel mutations, whereas rpoC1 was the least one. Based on sequence characteristics, each locus only discriminated some of the Selenicereus monacanthus from Southern Horticultural Research Institute identified by combining three loci, atpF-H, matK, and rbcL. The results elucidated the close genetic relationship between Mekong delta dragon fruits and National Center for Biotechnology Information (NCBI) database. Furthermore, this finding generated a DNA barcode database of ten dragon fruit accessions and suggested that multiple loci in the chloroplast genome should be a reliable solution for identifying this highly commercial fruiting plant.
Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia
Authors: FATIMAH Fatimah , Rahayu Rahayu , Wiwoho Jamal , Firdaus Sunny Ummul , Pujiyono Pujiyono , Marimin Marimin , Ariyanto Dwi Priyo , Pramono Ahmad
Published: October 2021

Abstract. Rahayu, Fatimah, Wiwoho J, Firdaus SU, Pujiyono, Marimin, Arianto DP, Pramono A. 2021. Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia. Biodiversitas 22: 4223-4235. As a repository of a gene pool, eucalypts germplasm enriches biodiversity, maintains ecosystem sustainability, and aids in conservation. Therefore, this study aims to analyze the genetic diversity of eucalypts (Corymbia and Eucalyptus) for the development of germplasm conservation in Forest Area with the Special Purpose (KHDTK) Bromo Forest, Karanganyar, Indonesia. In this study, 14 simple sequence repeat (SSR) markers were used to assess the genetic diversity among 20 accessions (Corymbia and 5 Eucalyptus species) from Central and West Java. Subsequently, the genetic parameters were measured and a phylogenetic tree was constructed. The result showed that the SSR markers have high variability, although they belong to different genera. Furthermore, the genetic diversity showed 49 alleles with an average of 3 alleles per locus, while the polymorphism information content (PIC) values were 0.55. There were 4 SSR markers (EMBRA13, EMBRA8, EMCRC11, and EMBRA2) with high PIC value, while the gene diversity (He) of Corymbia and 5 Eucalyptus showed a low level of genetic diversity. The genetic relationship and population structure were divided into genera Corymbia and Eucalyptus. For further application, the eucalypt cultivated in the KHDTK Bromo Forest can contribute as a reference set and 14 SSR markers as a potential marker in combination with morphological characterization to generate a database for germplasm management and conservation.
Detection of infectious bronchitis-like virus isolated from psittacines at breeding facilities
Authors: Suryaman Ganita Kurniasih , Soejoedono Retno Damajanti , Poetri Okti Nadia , Setiyono Agus , HANDHARYANI EKOWATI
Published: October 2021

Abstract. Suryaman GK, Soejoedono RD, Poetri ON, Setiyono A, Handharyani E. 2021. Detection of infectious bronchitis-like virus isolated from psittacines at breeding facilities. Biodiversitas 22: 4261-4265. Captive breeding of parrots has been carried out in Indonesia to fulfill market demand for pets and support conservation efforts. However, there is limited information about Infectious Bronchitis Virus (IBV) in captive parrots. Therefore, this study examines IBV virus in psittacines and observes the pathological changes in inoculated chicken embryos. Cloacal swabs were obtained from 31 psittacine birds consisting of 15 sulfur-crested cockatoos (Cacatua sulphurea), 10 palm cockatoos (Probosciger aterrimus), two blue and yellow macaws (Ara ararauna), two green-winged macaws (Ara chloropterus), and two scarlet macaws (Ara macao). Swabs were also injected for 9 days to obtain specific pathogen-free (SPF) embryonated chicken eggs, and allantoic fluids were collected after 7 days. The residual cloacal swabs and allantoic fluid samples were tested for IBV by reverse transcription polymerase chain reaction (RT-PCR) targeting spike 1 glycoprotein (S1) and nucleoprotein (N) gene by primer set XCE2+/XCE2- and IBVN+/IBVN-, while the harvested inoculated embryos were examined for histopathological lesions by hematoxylin-eosin staining. Three and one allantoic fluid of C. sulphurea and P. aterrimus respectively were found positive for IBV by primer set IBVN+IBVN-. However, there was no significant difference in the inoculated embryo's gross anatomy, and the slight histopathological changes observed were not caused by the virus. Therefore, it is unclear whether the IB-like virus causes clinical disease manifestation in both Psittacine species or the chicken embryo. This is the first study carried out on IB-like viruses for both species.
Ethnobotanical study of medicinal plants used by local communities in Sekerak Subdistrict, Aceh Tamiang, Indonesia
Authors: Navia Zidni Ilman , Suwardi Adi Bejo , Baihaqi Baihaqi
Published: October 2021

Abstract. Navia ZI, Suwardi AB, Baihaqi. 2021. Ethnobotanical study of medicinal plants used by local communities in Sekerak Subdistrict, Aceh Tamiang, Indonesia. Biodiversitas 22: 4273-4281. Local communities in Aceh Tamiang have gained a wealth of medicinal knowledge through practice and experience in their long-term battles with the disease. However, because of a lack of written records and rapid economic development, their traditional medicinal knowledge is under threat. This study investigated medicinal plants and related traditional knowledge of local communities in the Sekerak subdistrict, Aceh Taming, Indonesia. Field surveys, plant collections, and interviews with communities were used in this study. The Snowball Sampling technique was used to select 60 informants for the interviews. A total of 46 medicinal plant species belonging to 40 genera and 26 families were used for medicinal purposes by local communities to treat 28 different diseases. The itch, swelling, cough, and nosebleed were the most commonly treated. With a use-value index of 0.98, Tagetes erecta was the most commonly used medicinal plant by local communities. In addition, local communities identified the leaf (50%) as the most widely used plant part and oral administration (65%) as the most common method of administering traditional medicine. Elders have more knowledge of medicinal plants than younger generations, indicating that traditional knowledge is eroding across generations. However, initiatives to promote and conserve medicinal plants must be improved, particularly among the younger generation. This is required to ensure the availability of medicinal plants and the preservation of traditional knowledge in the future.
Genetic diversity of phenol hydroxylase-encoding genes among wastewater sludge bacteria
Authors: TAN WATUMESA AGUSTINA , KUSUMA FEDHO
Published: October 2021

Abstract. Tan WA, Kusuma F. 2021. Genetic diversity of phenol hydroxylase-encoding genes among wastewater sludge bacteria. Biodiversitas 22: 4291-4297. Phenol is a toxic aromatic compound that is used in various industries. In this study, we explore the molecular diversity of bacterial genes that encode for phenol hydroxylase, a key enzyme for phenol degradation, within sludge samples collected from the aeration and microbial recovery tank of an automotive wastewater treatment system. Partial phenol hydroxylase-encoding gene (600 bp) was amplified from the total DNA of each tank using a degenerate primer pair and cloned to construct a gene library. A total of 37 and 38 clones were obtained from the aeration and microbial recovery tank, respectively. The clones were sequenced and compared to GenBank database using BLASTX, followed by neighbor joining-based phylogenetic analysis using MEGA7. A majority of the clones recovered from both tanks belonged to Betaproteobacteria, which have been reported as phenol degraders with various metabolic activities and lifestyles. The clones are grouped into eight clusters. Six clusters were present in both the aeration and microbial recovery tank, and one unique cluster was identified in each tank. This indicated that diverse microbial communities play a role in phenol-containing wastewater treatment. They may have changed throughout the process as the surrounding chemical compositions differed and a variety of metabolic roles surfaced.
Reproductive biology of Vatica venulosa Blume (Dipterocarpaceae)
Authors: Widjaya Aulia Hasan , Latifah Dian , HARDWICK KATE A. , Suhartanto M. Rahmad , Palupi Endah Retno
Published: October 2021

Abstract. Widjaya AH, Latifah D, Hardwick KA, Suhartanto MR, Palupi ER. 2021. Reproductive biology of Vatica venulosa Blume (Dipterocarpaceae). Biodiversitas 22: 4327-4337. Vatica venulosa Blume is categorized as Critically Endangered A1c ver 2.3, according to the IUCN Red List. A study of the reproductive biology of V. venulosa Blume was carried out in August 2019-February 2020 at the Research Center for Plant Conservation and Botanic Gardens, Bogor, Indonesia. The research observed flower morphology, flower development, type of pollination, fruit and seed structures. V. venulosa is categorized as having a sub-annual flowering pattern. The flowering phenology of V. venulosa from flower bud emergence until fruit senescence takes about 6 months. The flower is hermaphroditic, with position of the pistil is higher/longer than the stamen; and pollen was released prior to stigma being receptive (protandrous). V. venulosa is a cross-pollinated plant, the flower visitors are insect nymphs of Thrips sp. (Thysanoptera: Thripidae), which are white and 1-1.5 mm in size. The percentage of blooming flowers was 32.3-37.9%, fruit set 10.9 %-12.6%. Seed physiological maturity  is reached at the age of 101±3-106±3 days after the flowers bloom when the wings are yellow green or green orange in color. V. venulosa seed is a non endospermous seed, and the cotyledons are composed mainly of small clumps of starch, being 42.5% carbohydrate.
Species identification and prevalence of gastrointestinal helminths in Indonesian native chickens, and its impact on egg production
Authors: Zalizar Lili , WINAYA ARIS , Malik Abdul , Widodo Wahyu , Suyatno Suyatno , Anggraini Apriliana Devi
Published: October 2021

Abstract. Zalizar L, Winaya A, Malik A, Widodo W, Suyatno, Anggraini AD. 2021. Species identification and prevalence of gastrointestinal helminths in Indonesian native chickens, and its impact on egg production. Biodiversitas 22: 4363-4369. Gastrointestinal parasite (GIP) infection is a severe problem of local chicken production, such as poultry and egg. Hence, the proper strategy to control the parasite invasion should be implemented regarding chicken productivity performance. Moreover, the existing environment is also essential in supporting chicken production. The study's objective was to determine the prevalence rate of the gastrointestinal helminths in four strains of Indonesian native chicken viz. Ranupane, Lokal Putih, Wareng, and Lurik, and the impact of the chicken egg production. A total of 280 chickens which were evaluated consisting of 70 birds from each strain, were tested for the prevalence of helminths eggs in a sample of feces and the effect on hen day production (HDP). The results showed that the percentage rates of infected chicken with helminths reached 56.43%, and the number of eggs per gram (EPG) in all four strains was considered moderate (115 EPG of feces). At the same time, the average of HDP per the four strains at 7 to 12 months was about 34.36-45.80%, which was in a normal range. The majority of helminths species found in examined native chicken were Ascaridia galli, Heterakis gallinarum, Raillietina spp., and Capillaria spp. The prevalence of GIP helminths did not negatively affect egg production in all four strains of chicken by moderately tolerant infections, and the HDP of chickens was normal.
Isolation, identification, and characterization of phosphate solubilizing bacteria, Paenibacillus sp., from the soil of Danum Valley Tropical Rainforest, Sabah, Malaysia
Authors: Lindang Herman Umbau , SUBBIAH VIJAY KUMAR , Rodrigues Kenneth Fransic , Budiman Cahyo
Published: October 2021

While phosphorus (P) is a vital element for the plant to grow, only 0.1% of the phosphate soil is directly to be uptake by plants. Consequently, P fertilizer, which is mostly taken from unrenewable resources of phosphate rock, is practically added into the croplands. Nevertheless, as the demand for this fertilizer kept increasing, the availability of resources and environmental issues are currently raising wide concerns. Alternatively, soil phosphate solubilizing bacteria (PSB) is promising to be further developed as a biofertilizer to increase the availability of P elements for plants. This study aims to screen and characterize novel PSB from the tropical rainforest soil. The soil samples were collected from the Danum Valley tropical rainforest, Sabah. Phosphatase solubilizing bacteria were then screened using the NBRIP Agar selective media. The screening results yielded five colonies, designated as PSB1, PSB2, PSB3, PSB4, and PSB5, displaying halos, with an average diameter of 10mm. Further, 16s rRNA gene sequence analysis using BLASTn suggested that PSB1, PSB2, PSB3, PSB4, and PSB5 were designated as Bacillus sp. PSB01, Pseudomonas oryzyhabitans PSB02, Staphylococcus pasteuri PSB03, Paenibacillus sp. PSB04, and Staphylococcus pasteuri PSB05, respectively. Interestingly, the Paenibacillus group is a promising biofertilizer and is currently used in the global agriculture industry. Accordingly, Paenibacillus sp. PSB04 was then selected for further characterization using Gram staining and observed under scanning electron microscope (SEM). The Gram staining revealed that Paenibacillus sp. PSB04 is a Gram-negative bacterium with a rod shape, which is in good agreement with the SEM result. The specific phosphatase activity of the extracellular fraction of this bacterium was 7378.12 U mg-1 which is the highest activity compared to previous studies. This study provides an early insight into an excellent phosphate solubilizing bacterium for the agriculture industry obtained from Danum Valley.
Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia
Authors: Zulfahmi Zulfahmi , Parjanto Parjanto , Purwanto Edi , Yunus Ahmad
Published: October 2021

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.
A snapshot on composition and distribution of fish larvae across the North Atlantic Ocean
Authors: Harith Mohd Nasarudin , O'Donnell Cieran , JOHNSTON GRAHAM , Power Anne Marie
Published: October 2021

Abstract. Harith MN, O’ Donnell C, Johnston G, Power AM. 2021. A snapshot on composition and distribution of fish larvae across the North Atlantic Ocean. Biodiversitas 22: 4496-4504. This study aims to describe the composition and distribution patterns of fish larvae communities across the North Atlantic Ocean. Several cruises were involved in the effort to collect the fish larvae samples. The sampling took place on the east side of the North Atlantic Ocean, towards the mid-Atlantic Ocean, and on the west side of the North Atlantic Ocean, near the eddies approaching Flemish Cap. A total of 9522 fish larvae were collected and identified from these surveys. These larvae came from 79 taxa and 29 families. Referring to the total abundance, considering all the sampled stations, Atlantic mackerel (Scomber scombrus) was the most abundant species (38.82% of the total fish larvae abundance), followed by blue whiting (Micromesistius poutassou) (15.9%). Referring to the Multi-dimensional scaling (MDS) ordination plots, two major stations clusters separate the on-shelf and off-shelf stations supported by SIMPER analysis. This study provides a snapshot of larval fish concentrations and assembly structure, but current knowledge suggests that the distribution of larval fish assemblages will be highly spatially variable, more research into plume front dynamics and their effects on the region's biota is needed to predict and understand changes.
Changes in landscape ecology between nature reserve and palm oil plantation in West Java, Indonesia based on the observations of macrofungal population
Authors: Arko Putut , Sudirman Lisdar , Qayim Ibnul
Published: October 2021

Abstract. Arko PF, Sudirman LI, Qayim I. 2021. Changes in landscape ecology between nature reserve and palm oil plantation in West Java, Indonesia based on the observations of macrofungal population. Biodiversitas 22: 4526-4537. As the biggest tropical country in Southeast Asia with the third-largest forest, Indonesia has limited data on macrofungal diversity. The limitation of the data is due to the lack of study on macrofungi in high biodiversity locations such as Dungus Iwul Nature Reserve (CADI). The purpose of this study was to determine and analyze the population of macrofungal species caused by the conversion in landscape structure (fragmentation and land-use change) that occurred in CADI patch and oil palm plantation of PT Perkebunan Nusantara VIII (PTPN) matrix, Cigelung, West Java. The sampling method used was opportunistic sampling assisted by line intercept. The macrofungal identification was based on morphological characters. The analysis of community ecology was performed in R programme. The results showed that macrofungal population and diversity in CADI were the highest, followed by PTPN planted in 2004 and planted in 2003, with a significant difference among the three study locations. The community dominance index shows the opposite, with the highest in PTPN 2003 and the lowest in CADI. These results showed changes in macrofungal population and diversity from the conversion in landscape structure. There were eleven indicator species in CADI, two species in PTPN 2003, and five species in PTPN 2004.
Exploration of vitamin B12-producing bacteria from Indonesia Eutrophic Lake: A new strategy to improve microalgae biomass production
Authors: Sitoresmi Prabaningtyas , ARDYATI TRI , SUHARJONO SUHARJONO , RETNANINGDYAH CATUR
Published: October 2021

Abstract. Prabaningtyas S, Ardyati T, Suharjono, Retnaningdyah C. 2021. Exploration of vitamin B12-producing bacteria from Indonesia Eutrophic Lake: A new strategy to improve microalgae biomass production. Biodiversitas 22: 4538-4544. Biofuel producing autotrophs and heterotrophs organisms are mostly found in freshwaters such as lakes. Preliminary research showed that Ranu Grati has a high diversity of microalgae and bacteria. Microalgae are known as one source of biofuels due to the high content of lipid. The growth of microalgae is strongly influenced by vitamin B12, which is synthesized by bacteria. The role of vitamin B12 in the metabolism of algae is mainly as a co-enzyme for vitamin B12-dependent methionine synthase. The purpose of this research was to observe the bacterial diversity based on NGS analysis, to explore vitamin B12 produced by bacteria from Ranu Grati lake, and also to identify the highest potency of vitamin B12-producing bacteria based on 16S rRNA gene sequencing. The study was carried out by taking a water sample at a depth of 50 cm at five stations. Isolation of total bacterial DNA was carried out using FastDNA Spin Kit for Soil. The metagenomic method of Next Generation Sequencing (NGS) was used as an initial study of bacterial diversity. Vitamin B12-producing bacteria was isolated using PYBG agar (phytone peptone, trypticase peptone, lab-lemco powder, bacto yeast extract, glucose, agar). Isolated bacteria were screened for production of vitamin B12. The potential isolates were identified base on 16S rRNA gene sequence similarity. The results of the metagenomic study showed that the genus of potential bacteria producing vitamin B12 included Bacillus, Pseudomonas, Propionibacterium, Enterobacter, Escherichia, Acinetobacter, and Flavobacterium. The results of screening with PYBG media obtained 30 isolates of vitamin B12 producing bacteria. Ten efficient vitamin B12-producing isolates were identified as Lysinibacillus fusiformis (isolate G2V1), Bacillus cereus group (isolate G2V25, G2V24, G2V13, G2V9, G2V8), Alcaligenes faecalis (isolate G2V22), Delftia acidovorans (isolate G2V14A) and the genus Delftia (isolate G2V19). The isolate G2V1 (Lysinibacillus fusiformis) was the highest producer of vitamin B12 which was able to produce 33,783 ug/mL of vitamin B12 at 4 days incubation time.
Improving SCOBY starter using co-culture of tapai and bakery yeast
Authors: Urbahillah Aurora , Jayus Jay , NURHAYATI NURHAYATI
Published: October 2021

Abstract. Urbahillah A, Jayus J, Nurhayati N. 2021. Improving SCOBY starter using co-culture of tapai and bakery yeast. Biodiversitas 22: 4617-4624. Kombucha is a beverage fermented by a symbiotic bacteria and yeast known as SCOBY (Symbiotic Culture of Bacteria and Yeast). Bacteria and yeast contribute to the formation of organic acids, aroma, taste, and flavor of kombucha. The commercial yeasts used in Indonesian are baker’s yeast and tapai yeast. This study was conducted to develop SCOBYco-culture with tapai yeast and baker’s yeast and evaluate its activity. The ingredients for the kombucha were cascara, water, and sugar, which were fermented with three formula starter, i.e. original SCOBY 10% w/v (SN), co-culture SCOBY 10% w/v with 0.1% w/v of baker’s yeast (SNR), and co-culture SCOBY 10% w/v with tapai yeast 0.1% w/v (SNT). The starter activity were determined based on the OD (Optical Density) value. Yeast screening was carried out on the dominant starter population. Furthermore, morphologically yeast was identified based on colony type, color, and shape of cell. Then yeast was identified by their fermentation profile using API 20C Aux Kit. Isolate A showed white colony with convex elevation and the cell was round-shaped. Colony of isolate B and isolate C were creamy in color and oval cell shaped. The API results revealed that the first isolate was identified as Candida famata, second isolate was as Candida krusei, and the third isolate was as Candida magnoliae. Three types of fungi were found from SCOBY, namely Mucor sp., Trichoderma sp., and Fusarium sp. Mucor sp. has non-septate hyphae, and round black spores. Trichoderma sp. has septate hyphae, greenish-white spores, and the conidia have the shape of globose to ellipsoidal Fusarium sp. has a mold with septate hyphae, yellowish-white colonies, and the conidia have the shape of obovoid. Bacteria, yeast, and mold present in the medium form a powerful symbiosis for produce metabolite.
Short Communication: Proportion faunal assemblages of carnivorous mammals in geoecological districts of Mordovia, Russia
Authors: Andreychev Alexey
Published: October 2021

Abstract. Andreychev A. 2021. Short Communication: Proportion faunal assemblages of carnivorous mammals in geoecological districts of Mordovia, Russia. Biodiversitas 22: 4625-4632. In the forest-steppe area, carnivorous mammals are represented by species of different faunistic assemblages. This circumstance makes the study region a priority since the species of which faunistic assemblages prevail is of interest. Fifteen carnivorous species have been identified in the territory of Mordovia. Among them, the family Mustelidae predominates in terms of the number of species. The species are found in all geoecological districts, but their distribution is uneven. The most notable species in the region are located in coniferous and broad-leaved forests (40%) and species widely distributed in several natural areas (40%). 13% of the total number of noted species belong to the taiga fauna types. The steppe type of fauna is represented by only 7% of the total number of recorded species. For each geoecological region, the fauna features are given, and a list of rare and exciting species is given. The forest-steppe zone to which Mordovia belongs is compared by the fauna of carnivorous mammals with other regions from three typical faunal assemblages.
Inner shell excitation by strong field laser rescattering: optimal laser conditions for high energy recollision
Authors: Kelley L. , Germain Z. , Jones E. C. , Milliken D. , Walker Barry C.
Published: October 2021

We address the challenge of finding the optimal laser intensity and
wavelength to drive high-energy, strong field rescattering and report
the maximum yields of K-shell and

L

I

-shell hole creation. Surprisingly,
our results show laser-driven rescattering is able to create inner
shell holes in all atoms from lithium to uranium with the interaction
spanning from the deep IR to x-ray free electron laser sources. The
calculated peak rescattering follows a simple scaling with the atomic
number and laser wavelength. The results show it is possible to
describe the ideal laser intensity and wavelength for general
high-energy laser rescattering processes.
Computational image enhancement of multimode fibre-based holographic endo-microscopy: harnessing the muddy modes
Authors: Tučková Tereza , Šiler Martin , Boonzajer Flaes Dirk E. , Jákl Petr , Turtaev Sergey , Krátký Stanislav , Heintzmann Rainer , Uhlířová Hana , Čižmár Tomáš
Published: October 2021

In imaging geometries, which employ wavefront-shaping to control the light transport through a multi-mode optical fibre (MMF), this terminal hair-thin optical component acts as a minimally invasive objective lens, enabling high resolution laser-scanning fluorescence microscopy inside living tissues at depths hardly accessible by any other light-based technique. Even in the most advanced systems, the diffraction-limited foci scanning the object across the focal plane are contaminated by a stray optical signal carrying typically few tens of % of the total optical power. The stray illumination takes the shape of a randomised but reproducible speckle, and is unique for each position of the focus. We experimentally demonstrate that the performance of imaging a fluorescent object can be significantly improved, when resulting images are computationally post-processed, utilising records of intensities of all speckle-contaminated foci used in the imaging procedure. We present two algorithms based on a regularised iterative inversion and regularised direct pseudo-inversion respectively which lead to enhancement of the image contrast and resolution.
Design and comprehensive analysis of an ultra-fast fractional-order temporal differentiator based on a plasmonic Bragg grating microring resonator
Authors: Ahmadpour Afshin , Habibzadeh-Sharif Amir , Bahrami-Chenaghlou Faezeh
Published: October 2021

This paper presents the design and comprehensive analysis of an ultra-fast fractional-order temporal differentiator (DIFF) based on a plasmonic inner-wall Bragg grating microring resonator (BG-MRR). Due to the ring radius of 1.1 µm and the strong confinement of the surface plasmon polaritons in the plasmonic waveguide with very small cross-section, the overall footprint of the DIFF circuit is significantly small (approximately 4 × 2.5 µm2). By changing the coupling regimes of the microring resonator, a broad range for the differentiation order α, i.e., 0.7–1.7 and a wide 3 dB bandwidth of 3.1 THz [24.8 nm] for α = 0.7 and 3.9 THz [31.2 nm] for α = 1.7 have been realized. Comparing the outputs of the BG-MRR-based DIFF with the corresponding mathematical DIFF indicates that deviations for α > 1 are significantly larger than those of α < 1. Therefore, a fractional-order temporal DIFF circuit based on plasmonic cascaded BG-MRR has been proposed for α > 1.
Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces
Authors: Chen Xinzhong , Yao Ziheng , Stanciu Stefan G. , Basov D. N. , Hillenbrand Rainer , Liu Mengkun
Published: October 2021

The scattering-type scanning near-field optical microscope (s-SNOM) has emerged as a powerful tool for resolving nanoscale inhomogeneities in laterally heterogeneous samples. However, most analytical models used to predict the scattering near-field signals are assuming homogenous landscapes (bulk materials), resulting in inconsistencies when applied to samples with more complex configurations. In this work, we combine the point-dipole model (PDM) to the finite-element method (FEM) to account for the lateral and vertical heterogeneities while keeping the computation time manageable. Full images, spectra, or hyperspectral line profiles can be simulated by calculating the self-consistent dipole radiation demodulated at higher harmonics of the tip oscillation, mimicking real experimental procedures. Using this formalism, we clarify several important yet puzzling experimental observations in near-field images on samples with rich typography and complex material compositions, heterostructures of two-dimensional material flakes, and plasmonic antennas. The developed method serves as a basis for future investigations of nano-systems with nontrivial topography.
Feedback-assisted transmission matrix measurement of a multimode fiber in a referenceless system
Authors: Wang Zhengyang , Wu Daixuan , Huang Guoqiang , Luo Jiawei , Ye Bolin , Li Zhaohui , Shen Yuecheng
Published: October 2021

Recent development in wavefront shaping shows the promise to employ multimode fibers (MMFs) to deliver images in endoscopy. In these applications, retrieving the transmission matrix (TM) of the MMF is especially important. Among existing non-holographic approaches, feedback-based wavefront shaping requires a large number of measurements, while directly measuring the TM can be easily trapped into local optimums if the constraints are insufficient. To reduce the required number of measurements, we combine the concepts of these two approaches and develop a scheme termed feedback-assisted TM measurements. We show that under such a hybrid scheme, less than

3

N

intensity measurements are sufficient to accurately retrieve one row of the TM that contains

N

unknown complex elements. As a proof of concept, we experimentally demonstrated retrieving multiple rows of the TM of an MMF using the proposed scheme with high fidelity. In particular, a single focus and dual foci through the MMF with enhancements larger than 75% of the theoretical values were reported.
School to go: Neues Lernen im Social-Media-Stil
Authors: Eckle Jannick , Jungfleisch Anne , Stattkus Daniel , Zarvić Novica , Knopf Julia , Thomas Oliver
Published: October 2021

Mit dem pandemiebedingten ersten Lockdown im März 2020 hat das digitale Lernen einen enormen Aufschwung erfahren. Mit der Initiative „School to go“ wird in Zeiten bundesweiter Schulschließungen ein relevanter Beitrag zur digitalen Bildung für Schülerinnen und Schüler, Eltern, Lehrkräfte und die interessierte Öffentlichkeit geleistet. Auf der gleichnamigen Plattform (www.schooltogo.de) werden digitale Lernangebote für Kinder, Jugendliche sowie junge Erwachsene gebündelt. Ferner finden sich dort Blogbeiträge zu Trendthemen der digitalen Bildung: Wie können digitale und didaktisch motivierte Raumkonzepte zu einem verbesserten Lernen beitragen und welche Bedeutung hat Gamification für die Lernmotivation der Schülerinnen und Schüler? Derzeit befinden sich auf „School to go“ bereits über 1000 innovative Lernformate (Stand Mai 2021) für verschiedene Fächer, die sich an Schülerinnen und Schüler aller Alters- und Jahrgangsstufen richten. Der vorliegende Beitrag zeigt, wie neues Lernen im Zeitalter der Digitalisierung gelingt und wie hierbei Didaktik und Wirtschaftsinformatik in Einklang gebracht werden können, um nachhaltige Lernerlebnisse zu ermöglichen.
Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts
Authors: Huang Yi , Chattopadhyay Ishanu
Published: October 2021

The spread of a communicable disease is a complex spatio-temporal process shaped by the specific transmission mechanism, and diverse factors including the behavior, socio-economic and demographic properties of the host population. While the key factors shaping transmission of influenza and COVID-19 are beginning to be broadly understood, making precise forecasts on case count and mortality is still difficult. In this study we introduce the concept of a universal geospatial risk phenotype of individual US counties facilitating flu-like transmission mechanisms. We call this the Universal Influenza-like Transmission (UnIT) score, which is computed as an information-theoretic divergence of the local incidence time series from an high-risk process of epidemic initiation, inferred from almost a decade of flu season incidence data gleaned from the diagnostic history of nearly a third of the US population. Despite being computed from the past seasonal flu incidence records, the UnIT score emerges as the dominant factor explaining incidence trends for the COVID-19 pandemic over putative demographic and socio-economic factors. The predictive ability of the UnIT score is further demonstrated via county-specific weekly case count forecasts which consistently outperform the state of the art models throughout the time-line of the COVID-19 pandemic. This study demonstrates that knowledge of past epidemics may be used to chart the course of future ones, if transmission mechanisms are broadly similar, despite distinct disease processes and causative pathogens.
Systematic review of the scrub typhus treatment landscape: Assessing the feasibility of an individual participant-level data (IPD) platform
Authors: Saraswati Kartika , Maguire Brittany J. , McLean Alistair R. D. , Singh-Phulgenda Sauman , Ngu Roland C. , Newton Paul N. , Day Nicholas P. J. , Guérin Philippe J.
Published: October 2021

Background

Scrub typhus is an acute febrile illness caused by intracellular bacteria from the genus Orientia. It is estimated that one billion people are at risk, with one million cases annually mainly affecting rural areas in Asia-Oceania. Relative to its burden, scrub typhus is understudied, and treatment recommendations vary with poor evidence base. These knowledge gaps could be addressed by establishing an individual participant-level data (IPD) platform, which would enable pooled, more detailed and statistically powered analyses to be conducted. This study aims to assess the characteristics of scrub typhus treatment studies and explore the feasibility and potential value of developing a scrub typhus IPD platform to address unanswered research questions.

Methodology/principal findings

We conducted a systematic literature review looking for prospective scrub typhus clinical treatment studies published from 1998 to 2020. Six electronic databases (Ovid Embase, Ovid Medline, Ovid Global Health, Cochrane Library, Scopus, Global Index Medicus), ClinicalTrials.gov, and WHO ICTRP were searched. We extracted data on study design, treatment tested, patient characteristics, diagnostic methods, geographical location, outcome measures, and statistical methodology.

Among 3,100 articles screened, 127 were included in the analysis. 12,079 participants from 12 countries were enrolled in the identified studies. ELISA, PCR, and eschar presence were the most commonly used diagnostic methods. Doxycycline, azithromycin, and chloramphenicol were the most commonly administered antibiotics. Mortality, complications, adverse events, and clinical response were assessed in most studies. There was substantial heterogeneity in the diagnostic methods used, treatment administered (including dosing and duration), and outcome assessed across studies. There were few interventional studies and limited data collected on specific groups such as children and pregnant women.

Conclusions/significance

There were a limited number of interventional trials, highlighting that scrub typhus remains a neglected disease. The heterogeneous nature of the available data reflects the absence of consensus in treatment and research methodologies and poses a significant barrier to aggregating information across available published data without access to the underlying IPD. There is likely to be a substantial amount of data available to address knowledge gaps. Therefore, there is value for an IPD platform that will facilitate pooling and harmonisation of currently scattered data and enable in-depth investigation of priority research questions that can, ultimately, inform clinical practice and improve health outcomes for scrub typhus patients.