bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity and species composition of ants at coffee agroforestry systems in East Java, Indonesia: Effect of habitat condition and landscape composition
Authors: MUHAMMAD FAIZ NASHIRUDDIN , RIZALI AKHMAD , RAHARDJO BAMBANG TRI
Published: August 2022

Abstract. Muhammad FN, Rizali A, Rahardjo BT. 2022. Diversity and species composition of ants at coffee agroforestry systems in East Java, Indonesia: Effect of habitat condition and landscape composition. Biodiversitas 23: 3313-3321. Habitat condition and landscape composition are the main factors that shape biodiversity in agroecosystems. However, information on the effect of habitat conditions and landscape composition on biodiversity in agroforestry systems is lacking. Agroforestry systems possess habitats that are characterized by a high diversity of vegetation, that can support biodiversity both on the field or landscape scale. This research aimed to study the diversity and species composition of ants in coffee (Coffea spp.) agroforestry systems, and to investigate the effects of habitat conditions and landscape composition on ant communities. Field research was conducted in twelve coffee agroforestry systems in East Java, Indonesia. Ants were sampled with the fogging method for canopy ants and pitfall traps for ground-dwelling ants in 40 m x 30 m plots. In each location, habitat conditions aspects (such as cultural technique and tree age) were identified by interviews with farmers and vegetation observation. Meanwhile, landscape composition was characterized by ground checking and mapping the land-use type within a 500 m radius from plot centers. This research recorded 35 species and 4,622 individuals of ants from all coffee plantations. Dolichoderus thoracicus was the most dominant canopy ant, while Pheidole sp.2 was the most dominant ground-dwelling ant in all plantations. Based on the GLM analysis, different responses were found between canopy and ground-dwelling ants in relation to habitat conditions and landscape composition. Canopy and ground-dwelling ants were affected by habitat conditions (such as tree age and canopy cover). The species composition of ground-dwelling ants was also affected by habitat conditions. In conclusion, habitats in coffee plantations can affect ant communities with ground-dwelling ants being more sensitive than canopy ants. Meanwhile, landscape composition can affect the species richness of all ants and not affect each stratum (canopy and ground-dwelling ants).
Effectiveness of Dyella japonica and Enterobacter cloacae as biofertilizers to increase maize (Zea mays) production on andisol soil
Authors: SEMBIRING MARIANI , SABRINA TENGKU
Published: August 2022

Abstract. Sembiring M, Sabrina T. 2022. Effectiveness of Dyella japonica and Enterobacter cloacae as biofertilizers to increase maize (Zea mays) production on andisol soil. Biodiversitas 23: 3338-3343. Nitrogen is a very important nutrient in plant growth because it is one of the constituents of plant cells. The availability of nitrogen nutrients in the soil is very low, and this is because nitrogen is easily leached and easy to evaporate. Application of N-fixing microbes is one way to increase the availability of nitrogen in the soil. This study aims to utilize nitrogen-fixing microbes to increase nutrient uptake, production, and efficiency of urea fertilization. The study used a factorial randomized block design (RBD) consisting of Factor I, namely biofertilizer consisting of 4 treatments, namely without the application of bacteria (N0), Dyella japonica 5g (N1), Enterobacter cloacae 5g (N2) and D. japonica 2.5g + E. cloacae 2.5g (N3). Factor II is urea fertilizer with 5 levels U0 = No urea fertilizer, U1 = 1.25 g, U2 = 2.50 g, U3 = 3.75g and U4 = 5g. Parameters observed were plant height observed in weeks I-VIII, plant nitrogen (N) uptake (mg/plant), phosphorus (P) uptake (mg/plant), potassium (K) uptake (mg/plant), and plant production (g). Sampling of plants for analysis of nutrient uptake was carried out at the end of the vegetative period, namely the 8th week, while for plant production parameters, plant samples were taken at the 12th week. The results showed that the applications of nitrogen-fixing bacteria could increase N uptake up to 89.35%, P uptake up to 79.57%, K uptake up to 48.81%, and crop production increase up to 49.76%. The applications of nitrogen-fixing microbes can streamline the use of urea fertilizer by up to 50%. In general, the best treatment is the applications of D. japonica and E. cloacae plus 2.5g urea (N3U2).
Local ecological knowledge of coffee agroforestry farmers on earthworms and their relation to soil quality in East Java (Indonesia)
Authors: MARDIANI MILA OKTAVIA , KUSUMAWATI IRMA ARDI , PURNAMASARI EKA , PRAYOGO CAHYO , VAN NOORDWIJK MEINE , HAIRIAH KURNIATUN
Published: August 2022

Abstract. Mardiani MO, Kusumawati IA, Purnamasari E, Prayogo C, van Noordwijk V, Hairiah K. 2022. Local ecological knowledge of coffee agroforestry farmers on earthworms and their relation to soil quality in East Java (Indonesia). Biodiversitas 23: 3344-3354. Farmers manage their land-based on their understanding of biotic and abiotic factors, including soils, and how these factors affect crop growth and productivity. Their local ecological knowledge (LEK) is built upon intergenerational transfer and can use concepts that don’t directly match those of current science-based ecological knowledge. We explored farmer LEK related to soil organic matter management and earthworms in coffee-based agroforestry systems on volcanic slopes in East Java (Indonesia) by in-depth interviews with key informants and by surveying the concurrence of respondents, stratified by gender and age, with resulting statements. The term used in the local language for earthworms (‘cacing tanah’) included a range of species. According to 22% (n=48) of farmers, small earthworms (probably Pontoscolex corethrurus) are harmful to coffee trees because they eat the roots. Also, 54% (n=48) of farmers thought earthworms that eat soil cause a decrease in soil volume. However, according to the farmers, large earthworms (reddish-brown) can fertilize the soil by leaving their casts on the soil surface. Such worms are often found in coffee agroforestry systems. Farmers have little explicit knowledge of the activities of earthworms and their relation with litter as a source of food. Farmer knowledge of ecosystem services provided by earthworms can enrich current scientific literature and trigger a two-way dialogue.
Freshwater gastropod community in South Konawe District, Southeast Sulawesi, Indonesia
Authors: OETAMA DEDY , PURNAMA MUHAMMAD FAJAR
Published: August 2022

Abstract. Oetama D, Purnama MF. 2022. Freshwater gastropod community in South Konawe District, Southeast Sulawesi, Indonesia. Biodiversitas 23: 3364-3372. The freshwater gastropod population in South Konawe District, Southeast Sulawesi, Indonesia, consists of aquatic and terrestrial snail communities. This resource (gastropod) is an ecological and economic potential that needs to be maintained and utilized optimally and sustainably. This research was conducted in April-July 2021 and aimed to determine the ecological index of the inland gastropod community in the South Konawe District. The sampling location was determined qualitatively using the purposive sampling method and a simple random sampling technique (Quantitative based). Gastropod samples were collected manually (hand picking) with a paralon pipe (3.5 inches), Sieve (1 mm), and Gloves. The total gastropods obtained at 33 sampling locations in this district were 2635 individuals. The inland gastropods comprised 19 genera and 33 species spread over 9 families, namely Achantinidae, Ampullariidae, Ariophantidae, Lymnaeidae, Neritidae, Pachychilidae, Planorbidae, Thiaridae, and Viviparidae. The average abundance of gastropods reached 79.85 ind./m2 and the abundance of gastropod species ranged from 0.58-13.48 ind./m2. Overall, the analysis of gastropod ecology index showed a stable condition, where the diversity of gastropod species was categorized as high (H'= 3.03), moderate evenness (E= 0.87), and high species richness (R= 4.06). There were no dominant species (C= 0.08) and the gastropod distribution showed a clustered pattern (Ip= 0.02). These ecological index values indicated that the gastropod community in the inland waters of South Konawe District was in a stable condition. Although the gastropod community in the inland waters of the South Konawe District simultaneously has the same area as the invasive gastropod from the family Thiaridae, namely Melanoides tuberculata (O.F.Müller, 1774) and Tarebia granifera (Lamarck, 1816).
Application of Lactobacillus inoculant from various rice paddy (Oryza sativa) to total mixed ration silage microbial composition
Authors: WAHYUDI AHMAD , HENDRANINGSIH LISTIARI , SUTAWI SUTAWI , SISKAWARDANI DEVI DWI
Published: August 2022

Abstract. Wahyudi A, Hendraningsih L, Sutawi S, Siskawardani DD. 2022. Application of Lactobacillus inoculant from various rice paddy (Oryza sativa) to total mixed ration silage microbial composition. Biodiversitas 23: xxxx. Evaluation of microorganisms profile of total mixed ration (TMR) silage inoculated with lactic acid bacteria (LAB) from local rice paddy (Oryza sativa L.) in tropical climate was analyzed to solve the feed management system. This study aimed to compare the effect of local LAB inoculants with commercial strain Lactobacillus plantarum FCC 123 on microorganisms composition of TMR silage in small-scale silage preparation. LAB was isolated from whole crop rice (w) and rice straw (s). Local rice paddy was planted in field around the University of Muhammadiyah Malang, East Java Province, Indonesia. Four rice paddy varieties: Membramo (M), Ciherang (C), Rajalele (R), and Impari (I) were utilized for isolation of LAB. Then, LAB was selected and purified in lactobacilli deMan Rogosa sharp agar (MRSA) and partially stored in dimethyl sulfoxide (DMSO) at -30°C as microbial stock. These selected LAB was used as inoculants at room temperature for 30 days TMR silage incubation. Completely randomized design (CRD) with 6 treatments (T0: TMR without fermentation, T1: TMR silage without inoculants, T2: TMR silage with L. plantarum FCC 123, T3: TMR with Local LAB Cs, T4: TMR silage with local LAB Mw, T5: TMR silage with local LAB Rs) were applied. Microorganism composition of LAB, aerobic bacteria, coliforms, clostridia, and mold was measured as experiment parameters. This research showed that LAB could be isolated and identified from all local paddy rice, both whole crop and straw. The implementation of local LAB on ensilage TMR was not significantly different from commercial L. plantarum FCC 123. Both local and commercial strains increased LAB population and suppressed harmful microbes (coliform, aerobic bacteria, and mold). The LAB isolates from local paddy rice could well act as an inoculant for TMR silage preparation in tropical climate.
Establishing breeding house of superior sandalwood in Gunung Sewu, Indonesia: preserving the 27 selected genotypes grafted onto two types of rootstocks
Authors: RATNANINGRUM YENI W.N. , FARIDAH ENY , UTAMA ILHAM N.S. , PRASTYO BAMBANG
Published: August 2022

Abstract. Ratnaningrum YWN, Faridah E, Utama INS, Prastyo B. 2022. Establishing breeding house of superior sandalwood in Gunung Sewu, Indonesia: preserving the 27 selected genotypes grafted onto two types of rootstocks. Biodiversitas 23: 3488-3497. Developing methods for vegetative propagation of sandalwood (Santalum album Linn.) is important for the mass production of selected genotypes. Previous research has selected the superior genotypes of sandalwood in Gunung Sewu based on seed production, crossing-ability, santalol content and/or the rare alleles characters. This study estimates the grafting compatibility of 27 selected genotypes of sandalwood, which are grafted onto two types of rootstock. In the peak rainy season in February 2021, scions were picked from the 27 genotypes originating from four landraces (Imogiri, Bejiharjo, Bleberan and Petir) in Gunung Sewu. Scions were then grafted onto two types of rootstock using the top-cleft technique. The first rootstock type is the 8 months old seedlings of the red-big-flower sandalwood variant planted in a polybag (Type 1); while the second one is the root-suckers that emerged from horizontal roots (Type 2). Results revealed Petir genotypes as the most surviving scions (100% in Type 2 and 75% in Type 1 rootstock), followed by those originating from Imogiri. All four genotypes originating from Petir (Pt1, Pt2, Pt3 and Pt4) achieved the highest scores in most of the parameters observed. The Type 2 rootstock survived more grafts (57%)  compared to those of Type 1 (49%). The number of shoots and the height increment of grafting showed significant differences. The top-cleft grafting technique is considered effective in conserving the superior genotypes of sandalwood and to provide a copy of those genotypes for materials of the crossing units. The use of Petir and Imogiri genotypes as the scions, and the red-big flower variant root-suckers as the rootstocks, are highly recommended for the best grafting success.
Genetic diversity of Burmese grape (Baccaurea ramiflora Lour.) cultivars and Ha Chau cultivar identification based on DNA barcodes
Authors: KHANG DODO TAN , HUY TRAN GIA , THI NGUYEN PHAM ANH , QUYEN DOAN THI HONG , NHU NGUYEN THI BICH , MEN TRAN THANH , DUNG TRAN NHAN
Published: August 2022

Abstract. Khang DT, Huy TG, Thi NPA, Quyen DTH, Nhu NTB, Binh BN, Men TT, Dung TN. 2022. Genetic diversity of Burmese grape (Baccaurea ramifloraLour.) cultivars and Ha Chau cultivar identification based on DNA barcodes. Biodiversitas 23: 3513-3520. Burmese grape (Baccaurea ramiflora Lour.) is an underutilized fruit tree in the Mekong Delta and has the potential for food sources as well as landscape plants,especially Ha Chau cultivar. It has been considered an indigenous plant in Can Tho city, Vietnam with specific taste. However, their genetic diversity, utilization,and identification have not been dealt with in-depth. This study aimed to characterize genetic diversity among the five cultivars of Burmese grape in the Mekong Delta and to distinguish Ha Chau from other cultivars based on DNA barcodes, namely matK, rbcL, ycf1b, rpoC1, psbK-I, atpF-H,and ITS. DNA of twelve individuals belong to five Burmese grape cultivars was extracted prior to further amplification and sequencing. Sequences were analyzed to detect variable sites and the phylogenetic tree was constructed by the Maximum Likelihood method. Based on substitution sites and indel mutations, the plastid intergenic spacer atpF-H and ycf1b gene reflected the genetic diversity in five Burmese grape cultivars. Moreover, these sequences were valuable DNA barcodes for discrimination of Ha Chau cultivar. In combination of four markers (rbcL, rpoC1, ycf1b, and psbK-I) for phylogenetic construction, our finding revealed that Ha Chau cultivar is closely related to Red cultivar with highly supported bootstrap value of 89%. Such data could be applied for reliable identification of Ha Chau cultivar from other B. ramiflora cultivars in plant authentication.
Cytogenetic study of five species of medicinal plants from Maha Sarakham Province, Thailand
Authors: SAENSOUK PIYAPORN , SAEN-IN NATKAMON , SAENSOUK SURAPON
Published: August 2022

Abstract. Saensouk S, Saen-in N, Saensouk P. 2022. Cytogenetic study of five species of medicinal plants from Maha Sarakham Province, Thailand. Biodiversitas 23: 3593-3603. The cytogenetic study of five species of medicinal plants, namely Butomopsis latifolia (D. Don) Kunth, Iris domestica (L.) Goldblatt & Mabb., Limnocharis flava (L.) Buchenau, Murdannia loriformis (Hassk.) R.S. Rao & Kammathy, and Pontederia hastata L. from Maha Sarakham Province, northeastern Thailand was conducted. This study aimed to investigate the chromosome numbers, fundamental number (NF), karyotype forms, and perform ideogram analysis of the five species. The cytogenetic characteristics, including the chromosome number, karyology (fundamental number (NF), karyotype formula), symmetrical karyotype, chromosome size, relative length (RL), centromeric indexes (CI), and ideograms of B. latifolia (D. Don) Kunthwere studied for the first time. The chromosome numbers of five medicinal plant species were reported as 2n = 14 (B. latifolia (D. Don) Kunth)- 80 (I. domestica (L.) Goldblatt & Mabb.). Moreover, the NF had 28 (B. latifolia (D. Don) Kunth) - 80 (Iris domestica). Two species (M. loriformis(Hassk.) R.S. Rao & Kammathyand P. hastata L.) were recognized as having symmetrical karyotypes. Three species, namely B. latifolia (D. Don) Kunth, Iris domestica, and L. flava(L.) Buchenau were reported as having asymmetrical karyotypes. Chromosomes of large size (L), chromosomes of medium size (M), and chromosomes of small size (S) were observed. Ideograms of five species were provided in this study. The NF, RL, CI, chromosome size, and ideograms of all species were reported for the first time in this study. The karyotype formulae of the five species, except the karyotype formula of P. hastata L., differed from those previously studied. The cytogenetic data of the five species in this study can be used for identification.
Distribution of invasive alien plant species, Bellucia pentamera, in forest conservation of oil palm plantation, West Sumatra, Indonesia
Authors: SOLFIYENI SOLFIYENI , MUKHTAR ERIZAL , SYAMSUARDI SYAMSUARDI , CHAIRUL CHAIRUL
Published: August 2022

Abstract. Solfiyeni, Mukhtar E, Syamsuardi, Chairul. 2022. Distribution of invasive alien plant species, Bellucia pentamera, in forest conservation of oil palm plantation, West Sumatra, Indonesia. Biodiversitas 23: 3667-3674. Bellucia pentamera has been found in disturbed forests across Indonesia, but little is known about how it spreads under its tree canopy. The spread of the invasive plant B. pentamera in the PT KSI conservation forest area was investigated. The goal of this research is to study B. pentamera's strategy for exploiting forest gaps horizontally and vertically on degraded forest vegetation invaded by B. pentamera at various degrees of invasion. An Unmanned Aerial Vehicle (UAV) and direct field mapping are used for the mapping approach. Aerial photographs revealed 40 B. pentamera trees and 32 non-B. pentamera trees in forest areas with varying degrees of B. pentamera invasion (based on the ratio of B. pentamera non-B. pentamera: dense and loose). Bellucia pentamera trees were distributed evenly in a large gap and randomly in a small gap/space between the canopy, whereas sapling and seedling B. pentamera trees were distributed in groups, uniformly and randomly, according to microhabitat conditions under the canopy of B. pentamera and non-tree trees. Bellucia pentamera seedlings and saplings were detected under the parent tree's canopy rather than in the canopy gaps. Different responses were seen in seedlings, saplings, and juvenile stages concerning the explanatory factors investigated and between the two stands. The purpose of the study was to determine the factors that influence the distribution of the B. pentamera species in conservation forest areas with different compositions of existence, both vertically and horizontally, using drones and direct measurements in the field.
Leaf anatomical characters variation of Strobilanthes s.l. from Sumatra, Indonesia and its taxonomic implications
Authors: SURATMAN SURATMAN , SURANTO SURANTO , MUZZAZINAH MUZZAZINAH , PURNOMO PURNOMO
Published: August 2022

Abstract. Suratman, Suranto, Muzzazinah, Purnomo. 2022. Leaf anatomical characters variation of Strobilanthes s.l. from Sumatra, Indonesia and its taxonomic implications. Biodiversitas 23: 3705-3720. The objective of this study was to evaluate leaf anatomical character variation among species of Strobilanthes s.l. from Sumatra. A total of 35 species from four genera previously recognized within the subtribe Strobilanthineae (Strobilanthes, Hemigraphis, Sericocalyx, Semnostachya) were used for leaf paradermal section observations. A total of seventeen leaf anatomical characters consisting of ten quantitative and seven qualitative characters were selected for leaf anatomical comparison. The quantitative and qualitative character analysis showed great variability in the majority of tested leaf anatomical characters. This result indicates the large diversity of leaf anatomical characters occurs among species of Strobilanthes s.l. A similarity dendrogram among species of Strobilanthes s.l. based leaf anatomical character data revealed two major clusters. The first cluster consists of eleven species with regular epidermal cell shape and straight cell wall with a similarity coefficient of 0.67. The second cluster consists of twenty four species that differed from species in the first cluster due to their irregular epidermal cell shape and undulate anticlinal cell wall with a similarity coefficient of 0.59. This study indicates that leaf anatomical characters are valuable taxonomic features in taxa delimitation at the species level. The results of this study also support earlier works through molecular studies that all members of the Strobilanthinae then accepted as Strobilanthes s.l. group which could not be easily split into smaller component genera.
Short Communication: Analysis of detected metabolites compounds from the crude extract of Rimau Gerga Lebong oranges fruit (Citrus reticulata ‘RGL’) using LC-QTOF-MS/MS
Authors: YUNITA ELVIRA , KURNIATI TRI , ROSA FEBY LILIA , MELATI PUTJHA , LESTARI NOVRIANTIKA
Published: August 2022

Abstract.Yunita E, Kurniati T, Rosa FL, Melati P, LestariN. 2022. Short Communication: Analysis of detected metabolites compounds from the crude extract of Rimau Gerga Lebong orangesfruit (Citrus reticulata ‘RGL’) using LC-QTOF-MS/MS. Biodiversitas 23: 3778-3783. Rimau Gerga Lebong (RGL) oranges are the leading commodity in Bengkulu Province. However, the content of bioactive compounds in RGL oranges has not been widely reported. This study aims to identify the flavonoid, alkaloids, and tannins from the ethanol extract of RGL oranges. The results of further identification will be used as a reference in further research on molecular docking in various biological activities. Chemical compounds were identified using qualitative tandem liquid chromatography quadrupole time of flight mass spectrometry (LC-QTOF-MS/MS). The measurement of vitamin C levels was carried out using High-Performance Liquid Chromatography (HPLC). The results showed 25 identified compounds, consisting of 6 compounds belonging to the alkaloid group, 17 from the flavonoid group, and 2 from the tannin group. The alkaloid group compounds were 2?, 3?, 6exo-trihydroxy nortopane, 2?, 3?-dihydroxy nortopane, isosalsolin,3?-dihydrocadambine, chelidimerine, and oleracein D. The compounds from identified flavonoid group were chebuloside, neokurarinol, rutinoside, flavonone, glucoside, licochalcone, viscumneoside, and pinnatifinoside. The identified tannins are corilagin and moracin. These compounds that have been identified have biological activity potential as antioxidants, anti-asthma, anti-dementia, and anticancer. The vitamin C content of the ethanol extract of RGL oranges was 0.02±0.0001%. This vitamin C supports the antioxidant activity of RGL orange.
Characteristic of the material deposits, microclimate profile, epiphyte abundance, and bacteria populations in the above-ground ecosystem of oil palm
Authors: PRADIKO IPUT , FARRASATI RANA , RAHUTOMO SUROSO , SAPALINA FADILLA , PANE RIZKI DESIKA PUTRI , HIDAYAT FANDI , GINTING EKO NOVIANDI
Published: August 2022

Abstract. Pradiko I, Farrasati R, Rahutomo S, Sapalina F, Pane RDP, Hidayat F, Ginting EN. 2022. The physical, chemical, and biological characteristics of microhabitats inside oil palm trunk axils in North Sumatra, Indonesia. Biodiversitas 23: 3793-3807. Above-ground ecosystems (AGE) components in oil palm plantations consist of epiphytic plants and fauna in microhabitat within the axil of pruned fronds. This research aimed to identify the characteristics of microhabitat, including microclimate profile, physical and chemical properties of the material deposit, epiphyte abundance, and microbe population. The study sites were located in the eastern and western regions of North Sumatra. Furthermore, vertical observations were taken on oil palm trunks at the height of 20, 100, 150, 200, and 300 cm. The study indicated that the microclimate, nutrients content, physical properties of the material deposit, and bacterial populations in the trunk axils of oil palm in the eastern differed from the western region. There was no obvious pattern in the microclimate profile for individual oil palms. However, there was a change in N, C-organic, and C/N ratios with the increasing height of microhabitat sites. In terms of abundance, Nephrolepis bisserata and Vittaria ensiformis epiphytes were more dominant in the upper and bottom trunk, respectively. The microhabitat at the bottom trunk had a denser bacterial population, negatively correlated with N, C-organic, C/N ratio, Mg, and pH.
“She starts to be her old self again”: familial reflections on pre- and post-onset identity in people with Alzheimer’s and behavioural-variant frontotemporal dementia
Authors: Harris Sophia A. , Baird Amee , Harris Celia B.
Published: August 2022

We investigated perceptions of identity in Alzheimer’s disease and behavioural-variant frontotemporal dementia. We asked family members of people with dementia to describe them before and after onset of the disease, comparing across type (Alzheimer’s disease versus behavioural-variant frontotemporal dementia) and time period. Family members’ perceptions of people with dementia changed over time. Compared with Alzheimer’s disease, behavioural-variant frontotemporal dementia was perceived to cause greater disruption to identity and more often associated with negative moral traits. We found a relationship between assessments of moral character and perceived self-continuity. Our data revealed different ways family members navigate stability and change in the identity of their loved ones with dementia.
Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness
Authors: Heitzman-Breen Nora , Ciupe Stanca M.
Published: August 2022

The relationship between transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the amount of virus present in the proximity of a susceptible host is not understood. Here, we developed a within-host and aerosol mathematical model and used it to determine the relationship between viral kinetics in the upper respiratory track, viral kinetics in the aerosols, and new transmissions in golden hamsters challenged with SARS-CoV-2. We determined that infectious virus shedding early in infection correlates with transmission events, shedding of infectious virus diminishes late in the infection, and high viral RNA levels late in the infection are a poor indicator of transmission. We further showed that viral infectiousness increases in a density dependent manner with viral RNA and that their relative ratio is time-dependent. Such information is useful for designing interventions.
PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases
Authors: Giacalone David , Yap Rochelle E. , Ecker Alwyn M. V. , Tan Shumin
Published: August 2022

The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function.
Neuromuscular denervation and deafferentation but not motor neuron death are disease features in the Smn2B/- mouse model of SMA
Authors: Carlini Maria J. , Triplett Marina K. , Pellizzoni Livio
Published: August 2022

Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by loss of motor neurons and skeletal muscle atrophy which is caused by ubiquitous deficiency in the survival motor neuron (SMN) protein. Several cellular defects contribute to sensory-motor circuit pathology in SMA mice, but the underlying mechanisms have often been studied in one mouse model without validation in other available models. Here, we used Smn2B/- mice to investigate specific behavioral, morphological, and functional aspects of SMA pathology that we previously characterized in the SMNΔ7 model. Smn2B/- SMA mice on a pure FVB/N background display deficits in body weight gain and muscle strength with onset in the second postnatal week and median survival of 19 days. Morphological analysis revealed severe loss of proprioceptive synapses on the soma of motor neurons and prominent denervation of neuromuscular junctions (NMJs) in axial but not distal muscles. In contrast, no evidence of cell death emerged from analysis of several distinct pools of lumbar motor neurons known to be lost in the disease. Moreover, SMA motor neurons from Smn2B/- mice showed robust nuclear accumulation of p53 but lack of phosphorylation of serine 18 at its amino-terminal, which selectively marks degenerating motor neurons in the SMNΔ7 mouse model. These results indicate that NMJ denervation and deafferentation, but not motor neuron death, are conserved features of SMA pathology in Smn2B/- mice.
What is the scope of teaching and training of undergraduate students and trainees in point of care testing in United Kingdom universities and hospital laboratories?
Authors: Peters Lee , Sergio Da Silva Ana , Newton Philip Mark
Published: August 2022

Point of care testing (POCT) is an analytical test performed by a healthcare professional outside of a conventional laboratory. The global POCT market was valued at US$ 23.16 billion in 2016 and is forecasted to grow to US$ 36.96 billion in 2021. This upward trend for POCT has increased workload for pathology departments who manage POCT. This research aims to characterize and analyse the teaching and training of POCT at United Kingdom (UK) universities on Institute of Biomedical Science (IBMS) accredited biomedical science degrees, and at UK hospital laboratories. A freedom of information (FOI) request was sent in 2018 to all 52 UK universities with an accredited IBMS Biomedical science degree to request information on teaching of POCT, with a 100% response rate. Further FOI requests were sent to all National Health Service (NHS) hospital pathology departments in the UK, regarding POCT training provided to trainee Biomedical scientists, with a 97% response rate. Twelve of the degrees contained no POCT teaching, with a further 9 having no specific POCT teaching. Sixty-six laboratories confirmed that there was no POCT training. The university teaching hours varied between 0 and 35 hours. The median time spent teaching POCT at university was 2 hours. The laboratory teaching hours varied between 0 and 450 hours The median time spent teaching POCT in hospital laboratories was 3 hours. A content analysis of the learning outcomes provided by 29 universities showed that only 61% (84/137) were measurable and 26% (36/137) of the learning outcomes used action verbs that have previously been listed to be avoided in learning outcome writing. Only 9% (13/137) of outcomes specifically described POCT, with 8 of these being measurable. The findings demonstrate that although this is a commonly required skill for biomedical scientists, there is a clear lack of POCT teaching and training in the UK. To meet the new Quality Assurance Agency for Higher Education (QAA) guidelines, but most importantly to ensure the workforce is fit for the needs of the current healthcare system, the quality and quantity of POCT teaching and training needs to improve.
Chronotropic incompetence in end-stage liver disease
Authors: Główczyńska Renata , Borodzicz-Jażdżyk Sonia , Peller Michał , Raszeja-Wyszomirska Joanna , Milkiewicz Piotr , Zieniewicz Krzysztof , Opolski Grzegorz
Published: August 2022

Background

Cirrhosis causes alterations in the cardiovascular and autonomic nervous systems and leads to cirrhotic cardiomyopathy (CCM). CCM is defined as cardiac dysfunction characterized by an impaired systolic responsiveness to stress or exercise, and/or impaired diastolic function, as well as electrophysiological abnormalities, including chronotropic incompetence (CI), in the absence of other known cardiac disease. CI is a common feature of autonomic neuropathy in cirrhosis. The aim of the study is to assess the role of cardiac exercise stress test in the diagnosis of CCM.

Methods

The analysis included 160 end-stage liver disease (ESLD) patients who underwent a cardiac exercise stress test prior to the orthotopic liver transplantation. CI was defined as the inability to achieve the heart rate reserve (HRR). Pertaining to the therapy with beta-blockers: 80% of HRR was achieved in patients not taking beta-blockers and 62% in patients taking beta-blockers.

Results

In the analyzed population, 68.8% of patients met the criteria for CI. CI was more frequent in the more severe ESLD (with a higher MELD score and in a higher Child-Pugh class). In comparison to the viral hepatitis and other etiologies of ESLD, patients with alcoholic cirrhosis had a significantly lower rest heart rate (HR), lower maximal HR, lower median achieved percentage of maximal predicted HR (MPHR), a smaller percentage of patients achieved ≥ 85% of MPHR and a lower heart rate reserve. No significant relationship between the survival of OLT recipients and presence of chronotropic incompetence regarding to class of Child-Pugh scale, MELD score and etiology of ESLD were found.

Conclusions

The prevalence of CI is higher among liver transplant candidates than previously described. The altered chronotropic response may differ in regard to the severity of liver disease correlating with both the Child-Pugh and MELD scores, however CI does not seem to influence the long-term survival post OLT. Exercise stress test is a reliable, safe and useful tool for the diagnosis of CCM in liver transplant candidates and should be included in the standard cardiovascular assessment prior to OLT.
Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019–2022
Authors: Sharif Nadim , Alzahrani Khalid J. , Ahmed Shamsun Nahar , Khan Afsana , Banjer Hamsa Jameel , Alzahrani Fuad M. , Parvez Anowar Khasru , Dey Shuvra Kanti
Published: August 2022

In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient information to reduce the health burden of the pandemic. This study focused to conduct worldwide genomic surveillance. About 7.6 million genomic data were analyzed during 2019 to 2022. Multiple sequence alignment was conducted by using maximum likelihood method. Clade GK (52%) was the most predominant followed by GRY (12%), GRA (11%), GR (8%), GH (7%), G (6%), GV (3%), and O (1%), respectively. VOC Delta (66%) was the most prevalent variant followed by VOC Alpha (18%), VOC Omicron (13%), VOC Gamma (2%) and VOC Beta (1%), respectively. The frequency of point mutations including E484K, N501Y, N439K, and L452R at spike protein has increased 10%-92%. Evolutionary rate of the variants was 23.7 substitution per site per year. Substitution mutations E484K and N501Y had significant correlation with cases (r = .45, r = .23), fatalities (r = .15, r = .44) and growth rate R0 (r = .28, r = .54). This study will help to understand the genomic diversity, evolution and the impact of the variants on the outcome of the COVID-19 pandemic.
Validation of a graphic test to quantitatively assess the dominant hand dexterity
Authors: Angelucci Alessandra , Tettamanti Andrea , Sarasso Elisabetta , Filippi Massimo , Aliverti Andrea , Scarlato Marina
Published: August 2022

Dexterity dysfunction is a key feature of disability in many neurological and non-neurological diseases. The Nine-Hole Peg Test (NHPT) is the most used test to assess hand dexterity in clinical practice but presents limitations. A new graphic test to enhance objective evaluation of the of the dominant hand dexterity is proposed. The task consists in drawing a continuous line in paths composed by a part with multiple orthogonal changes of direction (‘meander’), and a second part derived from the Archimedean spiral (‘spiral’). The test was validated in 200 healthy controls and 93 neurological patients. 48 patients performed also the NHPT. Several parameters were analyzed, among which total time, total length, number of touches and number of crossings. Healthy subjects display statistically significant differences with respect to pathological subjects in the case of total time, number of touches, and number of crossings (p<0.001), but not in the case of total length (p = 0.27) needed to complete the second sheet. Moreover, healthy controls display a learning effect, the time needed to complete the second sheet was significantly lower than for the first sheet (p<0.001), and an inverse correlation with age was observed (r = 0.56, p<0.001). The comparison between the NHPT and the new test showed a strong positive correlation (r = 0.71, p<0.001) whereas touches and crossing a weak positive one (r = 0.35, p = 0.01). The new test distinguishes between a slow but precise performance and a fast but imprecise performance, thus providing additional information with respect to NHPT.
Could ultrasound midwifery training increase antenatal detection of congenital anomalies in Ghana?
Authors: Abdul-Mumin Alhassan , Rotkis Lauren N. , Gumanga Solomon , Fay Emily E. , Denno Donna M.
Published: August 2022

Background

As part of World Health Organization (WHO) 2016 updated antenatal care (ANC) guidelines routine ultrasonography is recommended, including to detect congenital anomalies. The Ghana Health Service (GHS) developed an in-service midwifery ultrasound training course in 2017, which includes fetal anomaly detection. Training rollout has been very limited. We sought to determine proportions of anomalies among neonates presenting to Tamale Teaching Hospital (TTH) that should be prenatally detectable by course-trained midwives in order to determine training program potential utility.

Methods

We analyzed data from a registry of neonates admitted to TTH with congenital anomaly diagnoses in 2016. We classified ultrasonographic detectability of anomalies at ≤13 and 14–23 weeks gestation, based on GHS course content and literature review. Secondary analysis included 2011–2015 retrospective chart review data.

Results

Eighty-five neonates with congenital anomalies were admitted to TTH in 2016. Seventy-three (86%) mothers received ≥1 ANC visit; 47 (55%) had at least one prenatal ultrasound, but only three (6%) were interpreted as abnormal. Sixteen (19%) and 26 (31%) of the anomalies should be readily detectable by course-trained midwives at ≤13 and 14–23 weeks gestation, respectively. When the 161 anomalies from 2011–2015 were also analyzed, 52 (21%) and 105 (43%) should be readily detectable at ≤13 and 14–23 weeks gestation, respectively. “Optimal conditions” (state-of-the-art equipment by ultrasonography-trained physicians) should readily identify 53 (22%) and 115 (47%) of the anomalies at ≤13 and 14–23 weeks gestation, respectively.

Conclusion

Training Ghanaian midwives could substantially increase second trimester anomaly detection, potentially at proportions nearing highly resourced settings. Our data also highlight the need for refinement of the WHO antenatal ultrasonography recommendation for a scan before 24 weeks gestation for multiple purposes. Gestational dating accuracy requires first trimester scanning while fetal anomaly detection is more accurate during second trimester. Further specification will enhance guideline utility.
Early pregnancy body mass index and gestational weight gain: A mediating or moderating factor for short stature and risk of gestational diabetes mellitus?
Authors: Yong Heng Yaw , Mohd Shariff Zalilah , Mohd Yusof Barakatun Nisak , Rejali Zulida , Tee Yvonne Yee Siang , Bindels Jacques , van der Beek Eline M.
Published: August 2022

This study examined the association between height and the risk of Gestational Diabetes Mellitus (GDM), and whether this association was mediated or moderated by early pregnancy body mass index (BMI) and gestational weight gain (GWG) that are known independent risk factors for GDM. Data of a retrospective cohort of pregnant women (N = 1,945) were extracted from antenatal clinic cards. The cut-off values of height in relation to risk of GDM were identified using receiver operating characteristic analysis and four categories of height were derived: < 150 cm, 150–155 cm, 156–160 cm, and > 160cm. Mediation analysis was performed using the Preacher and Hayes bootstrapping method while the moderation effect was tested with multiple regression analysis with interaction terms. Although there was no mediation effect of BMI and GWG on the association between height and risk of GDM, both factors moderated this association with a significant association between shorter height and risk of GDM was observed in overweight / obese women (height < 150 cm: AOR = 1.41, 95% CI = 1.03–2.44; height 156–160 cm: AOR = 1.48, 95% CI = 1.03–2.14). Overweight / obese women with height < 150 cm and excessive GWG at the end of the second trimester (AOR = 2.25, 95% CI = 1.45–4.17) had significantly higher risk of GDM than those without these factors. Short stature (< 150 cm) was significantly associated with GDM risk among OW/OB women with excessive gestational weight gain at the end of second trimester. This finding underscores the importance of maintaining a healthy BMI during reproductive age and gaining weight in recommended range during pregnancy.
Analysis of mobility level of COVID-19 patients undergoing mechanical ventilation support: A single center, retrospective cohort study
Authors: Nawa Ricardo Kenji , Serpa Neto Ary , Lazarin Ana Carolina , da Silva Ana Kelen , Nascimento Camila , Midega Thais Dias , Caserta Eid Raquel Afonso , Corrêa Thiago Domingos , Timenetsky Karina Tavares
Published: August 2022

Background

Severe coronavirus disease 2019 (COVID-19) patients frequently require mechanical ventilation (MV) and undergo prolonged periods of bed rest with restriction of activities during the intensive care unit (ICU) stay. Our aim was to address the degree of mobilization in critically ill patients with COVID-19 undergoing to MV support.

Methods

Retrospective single-center cohort study. We analyzed patients’ mobility level, through the Perme ICU Mobility Score (Perme Score) of COVID-19 patients admitted to the ICU. The Perme Mobility Index (PMI) was calculated [PMI = ΔPerme Score (ICU discharge–ICU admission)/ICU length of stay], and patients were categorized as “improved” (PMI > 0) or “not improved” (PMI ≤ 0). Comparisons were performed with stratification according to the use of MV support.

Results

From February 2020, to February 2021, 1,297 patients with COVID-19 were admitted to the ICU and assessed for eligibility. Out of those, 949 patients were included in the study [524 (55.2%) were classified as “improved” and 425 (44.8%) as “not improved”], and 396 (41.7%) received MV during ICU stay. The overall rate of patients out of bed and able to walk ≥ 30 meters at ICU discharge were, respectively, 526 (63.3%) and 170 (20.5%). After adjusting for confounders, independent predictors of improvement of mobility level were frailty (OR: 0.52; 95% CI: 0.29–0.94; p = 0.03); SAPS III Score (OR: 0.75; 95% CI: 0.57–0.99; p = 0.04); SOFA Score (OR: 0.58; 95% CI: 0.43–0.78; p < 0.001); use of MV after the first hour of ICU admission (OR: 0.41; 95% CI: 0.17–0.99; p = 0.04); tracheostomy (OR: 0.54; 95% CI: 0.30–0.95; p = 0.03); use of extracorporeal membrane oxygenation (OR: 0.21; 95% CI: 0.05–0.8; p = 0.03); neuromuscular blockade (OR: 0.53; 95% CI: 0.3–0.95; p = 0.03); a higher Perme Score at admission (OR: 0.35; 95% CI: 0.28–0.43; p < 0.001); palliative care (OR: 0.05; 95% CI: 0.01–0.16; p < 0.001); and a longer ICU stay (OR: 0.79; 95% CI: 0.61–0.97; p = 0.04) were associated with a lower chance of mobility improvement, while non-invasive ventilation within the first hour of ICU admission and after the first hour of ICU admission (OR: 2.45; 95% CI: 1.59–3.81; p < 0.001) and (OR: 2.25; 95% CI: 1.56–3.26; p < 0.001), respectively; and vasopressor use (OR: 2.39; 95% CI: 1.07–5.5; p = 0.03) were associated with a higher chance of mobility improvement.

Conclusion

The use of MV reduced mobility status in less than half of critically ill COVID-19 patients.