High Speed Crop and Weed Identification in Lettuce Fields for Precision Weeding.

Precision weeding can significantly reduce or even eliminate the use of herbicides in farming. To achieve high-precision, individual targeting of weeds, high-speed, low-cost plant identification is essential. Our system using the red, green, and near-infrared reflectance, combined with a size differentiation method, is used to identify crops and weeds in lettuce fields. Illumination is provided by LED arrays at 525, 650, and 850 nm, and images are captured in a single-shot using a modified RGB camera. A kinematic stereo method is utilised to compensate for parallax error in images and provide accurate location data of plants. The system was verified in field trials across three lettuce fields at varying growth stages from 0.5 to 10 km/h. In-field results showed weed and crop identification rates of 56% and 69%, respectively. Post-trial processing resulted in average weed and crop identifications of 81% and 88%, respectively.

First evaluation of the population structure, genetic diversity and landscape connectivity of the Endangered Arabian tahr.

The Arabian tahr (Arabitragus jayakari) occurs only in the mountains of northern Oman and the United Arab Emirates. The species is classified as Endangered due to its small declining population. In this study, we combined genetic and landscape ecology techniques in order to inform landscape scale conservation and genetic management of Arabian tahr. Using 540 base pairs of mitochondrial control region in a dataset of 53 samples, we found eight haplotypes, which fell into two haplogroups. Population genetic analysis using a panel of 14 microsatellite loci also showed a weak, but significant division. Analyses of landscape connectivity supported the genetic results showing poor connectivity between populations in the far south of the study area and those in the north. The most likely location of corridors connecting Arabian tahr populations were identified. Many corridors between tahr populations are impeded by multi-lane highways and restoration of these connections is required to maintain population viability of Arabian tahr. Owing to limited genetic samples outside of Wadi Sareen, further sampling is needed to elucidate both mtDNA and the nuclear structure of Arabian tahr more fully. Our study provides a toolkit that may be used for future genetic and connectivity monitoring of the Arabian tahr population.

Demographic and conservation genomic assessment of the threatened marbled teal (Marmaronetta angustirostris).

Genetic assessment of species that have experienced dramatic population declines provides critical information that is instrumental for the design of conservation recovery programs. Here, we use different sources of molecular data (mtDNA and ddRAD-seq) to evaluate the genetic status of wild and captive populations of marbled teal (Marmaronetta angustirostris), a duck species classified as critically endangered in Spain and near threatened at a global scale. First, we determined the evolutionary and demographic trajectories of the wild population from Spain and the currently much larger population from Iraq, which is also the documented source of European zoo stocks. Second, we evaluated the suitability of the different captive populations for ongoing restocking programs in Spain and assessed their potential impact on the genetic composition of wild populations. Populations from Spain and Iraq were assigned to distinct genetic clusters, albeit with an overall low level of genetic differentiation, in line with their recent divergence (<8000 years ago) and lack of phylogeographic structure in the species. Demogenomic inferences revealed that the two populations have experienced parallel demographic trajectories, with a marked bottleneck during the last glacial period followed by a sudden demographic expansion and stability since the onset of the Holocene. The wild population from Spain presented high levels of inbreeding, but we found no evidence of recent genetic bottlenecks compatible with the human-driven decline of the species during the past century. The captive populations from the two Spanish centers involved in restocking programs showed genetic introgression from European zoos; however, we found limited evidence of introgression from the zoo genetic stock into the wild population from Spain, suggesting captive-bred birds have limited breeding success in the wild. Our study illustrates how ex situ conservation programs should consider the genetic distinctiveness of populations when establishing breeding stocks and highlights the importance of genetically assessing captive populations prior to reinforcement actions.

Introduction of Aedes aegypti mosquitoes carrying wAlbB Wolbachia sharply decreases dengue incidence in disease hotspots.

Partial replacement of resident Aedes aegypti mosquitoes with introduced mosquitoes carrying certain strains of inherited Wolbachia symbionts can result in transmission blocking of dengue and other viruses of public health importance. Wolbachia strain wAlbB is an effective transmission blocker and stable at high temperatures, making it particularly suitable for hot tropical climates. Following trial field releases in Malaysia, releases using wAlbB Ae. aegypti have become operationalized by the Malaysian health authorities. We report here on an average reduction in dengue fever of 62.4% (confidence intervals 50-71%) in 20 releases sites when compared to 76 control sites in high-rise residential areas. Importantly the level of dengue reduction increased with Wolbachia frequency, with 75.8% reduction (61-87%) estimated at 100% Wolbachia frequency. These findings indicate large impacts of wAlbB Wolbachia invasions on dengue fever incidence in an operational setting, with incidence expected to further decrease as wider areas are invaded.

Factors associated with COVID-19 brought-in deaths: A data-linkage comparative cross-sectional study.

BACKGROUND: The phenomenon of Coronavirus disease 2019 (COVID-19) brought-in-dead (BID), i.e., COVID-19 deaths occurring outside hospital settings, suggests missed opportunities for life-saving care. However, much is still unknown with regards to its potential determinants. The present study aimed to examine the factors associated with COVID-19 BID by integrating new variables from multiple databases. METHODS: This multi-database comparative cross-sectional study examined COVID-19 in-patient deaths (IPD) and COVID-19 BID (n = 244 in each group) in Selangor, Malaysia. BID cases, IPD cases, and their sociodemographic, clinical, and health behaviour factors were identified from the COVID-19 mortality investigation reports submitted to the Selangor State Health Department between 14 February 2022 and 31 March 2023. Data linkage was used to connect three open-source databases-GitHub-MOH, Socioeconomic Data and Applications Center, and OpenStreetMap-and identify health infrastructure and geospatial factors. The groups were compared using chi-square tests, independent t-tests, and logistic regression analyses to identify factors associated with COVID-19 BID. RESULTS: The COVID-19 IPD and BID cases were comparable. After adjusting for confounders, non-Malaysian nationality (AOR: 3.765, 95% CI: 1.163, 12.190), obesity (AOR: 5.272, 95% CI: 1.131, 24.567), not seeking treatment while unwell (AOR: 5.385, 95% CI: 3.157, 9.186), and a higher percentage of COVID-19-dedicated beds occupied on the date of death (AOR: 1.165, 95% CI: 1.078, 1.259) were associated with increased odds of COVID-19 BID. On the other hand, being married (AOR: 0.396, 95% CI: 0.158, 0.997) and the interaction between the percentage of COVID-19-dedicated beds occupied and the percentage of ventilators in use (AOR: 0.996, 95% CI: 0.994, 0.999) emerged as protective factors. CONCLUSION: These findings indicated that certain groups have higher odds of COVID-19 BID and thus, require closer monitoring. Considering that COVID-19 BID is influenced by various elements beyond clinical factors, intensifying public health initiatives and multi-organisational collaboration is necessary to address this issue.

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease.

The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.

Phylogeographical analysis shows the need to protect the wild yaks' last refuge in Nepal.

The wild yak Bos mutus was believed to be regionally extinct in Nepal for decades until our team documented two individuals from Upper Humla, north-western Nepal, in 2014. The International Union for Conservation of Nature (IUCN) seeks further evidence for the conclusive confirmation of that sighting. We conducted line transects and opportunistic sign surveys in the potential wild yak habitats of Humla, Dolpa, and Mustang districts between 2015 and 2017 and collected genetic samples (present and historic) of wild and domestic yaks Bos grunniens. We also sighted another wild yak in Upper Humla in 2015. Phylogenetic and haplotype network analyses based on mitochondrial D-loop sequences (~450 bp) revealed that wild yaks in Humla share the haplotype with wild yaks from the north-western region of the Qinghai-Tibetan Plateau in China. While hybridization with domestic yaks is a major long-term threat, illegal hunting for meat and trophy put the very small populations of wild yaks in Nepal at risk. Our study indicates that the unprotected habitat of Upper Humla is the last refuge for wild yaks in Nepal. We recommend wild yak conservation efforts in the country to focus on Upper Humla by (i) assigning a formal status of protected area to the region, (ii) raising awareness in the local communities for wild yak conservation, and (iii) providing support for adaptation of herding practice and pastureland use to ensure the viability of the population.

Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA.

The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching and fragmentation. Here, we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186 bp and cytochrome b 487 bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared with the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126, cytochrome b 0.0528) and high F ST statistics (D-loop 0.725, cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.

Comorbidities and clinical features related to severe outcomes among COVID-19 cases in Selangor, Malaysia.

BACKGROUND: Pre-existing comorbidities can predict severe disease requiring intensive care unit (ICU) admission among COVID-19 cases. We compared comorbidities, clinical features and other predictive factors between COVID-19 patients requiring ICU admission for intubation/mechanical ventilation and all other COVID-19 cases in Selangor, Malaysia. METHOD: Field data collected during the COVID-19 outbreak in Selangor, Malaysia, up to 13 April 2020 were used, comprising socio-demographic characteristics, comorbidities and presenting symptoms of COVID-19 cases. ICU admission was determined from medical records. Multiple logistic regression analysis was performed to identify factors associated with ICU admission requiring intubation/mechanical ventilation among COVID-19 cases. RESULTS: A total of 1287 COVID-19-positive cases were included for analysis. The most common comorbidities were hypertension (15.5%) and diabetes (11.0%). More than one third of cases presented with fever (43.8%) or cough (37.1%). Of the 25 cases that required intubation/mechanical ventilation, 68.0% had hypertension, 88.0% had fever, 40.0% had dyspnoea and 44.0% were lethargic. Multivariate regression showed that cases that required intubation/mechanical ventilation had significantly higher odds of being older (aged 360 years) [adjusted odds ratio (aOR) = 3.9] and having hypertension (aOR = 5.7), fever (aOR = 9.8), dyspnoea (aOR = 9.6) or lethargy (aOR = 7.9) than cases that did not require intubation/mechanical ventilation. CONCLUSION: The COVID-19 cases in Selangor, Malaysia requiring intubation/mechanical ventilation were significantly older, with a higher proportion of hypertension and symptoms of fever, dyspnoea and lethargy. These risk factors have been reported previously for severe COVID-19 cases, and highlight the role that ageing and underlying comorbidities play in severe outcomes to respiratory disease.

Characterization of Sodium Channel Mutations in the Dengue Vector Mosquitoes Aedes aegypti and Aedes albopictus within the Context of Ongoing Wolbachia Releases in Kuala Lumpur, Malaysia.

Specific sodium channel gene mutations confer target site resistance to pyrethroid insecticides in mosquitoes and other insects. In Aedes mosquito species, multiple mutations that contribute to resistance vary in their importance around the world. Here, we characterize voltage sensitive sodium channel (Vssc) mutations in populations of Aedesaegypti from Kuala Lumpur, Malaysia, and look at their persistence in populations affected by ongoing Wolbachia releases (a dengue control measure). We also describe a Vssc mutation in Aedesalbopictus (F1534L) found for the first time in Malaysia. We show that there are three predominant Vssc haplotypes in Aedesaegypti in this region, which all persist with regular backcrossing, thereby maintaining the original genetic composition of the populations. We identify changes in genotype frequency in closed populations of Ae. aegypti maintained for multiple generations in laboratory culture, suggesting different fitness costs associated with the genotypes, some of which may be associated with the sex of the mosquito. Following population replacement of Ae. aegypti by Wolbachia in the target area, however, we find that the Vssc mutations have persisted at pre-release levels. Mosquitoes in two genotype classes demonstrate a type I pyrethroid resistance advantage over wildtype mosquitoes when exposed to 0.25% permethrin. This resistance advantage is even more pronounced with a type II pyrethroid, deltamethrin (0.03%). The results point to the importance of these mutations in pyrethroid resistance in mosquito populations and the need for regular backcrossing with male mosquitoes from the field to maintain similarity of genetic background and population integrity during Wolbachia releases.

Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration.

The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35-SNP-marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild-living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species.

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.