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ItemMovement and ranging behaviour of long-nosed potoroos (Potorous tridactylus) in south-west Victoria, Australia(CSIRO Publishing, 2023)Context. A comprehensive understanding of movements and space use can underpin the effective management of threatened species. GPS dataloggers can collect large amounts of high-quality movement data, and recent advances in statistical approaches allow for robust estimates of home range size to be generated. Until recently, technological and practical constraints have generally restricted the collection of movement data via GPS dataloggers to larger species. However, reductions in the size and weight of GPS dataloggers now allow for this technology to be applied to smaller species. Aims. The aim of this study was to describe the home range and movement patterns of a nationally vulnerable, native Australian ground-dwelling mammal, the long-nosed potoroo (Potorous tridactylus), in south-west Victoria, mainland Australia. Methods. We attached GPS dataloggers to 40 long-nosed potoroos between 2020 and 2022 and estimated home range size using dynamic Brownian Bridge movement models. We evaluated the influence of physiological factors such as body mass and sex on home range size and described patterns of home range overlap between and within sexes. Key results. Mean home range sizes were estimated to be 13.73 ha (95% CI: 10.9–16.6) and 6.67 ha (95% CI: 5.49–7.85) for males and females respectively. Home range size scaled with body mass in males but not females, and ranges were largely overlapping – although there was some evidence of intrasexual spatial partitioning of core range areas in females. Conclusions. Ours is the first application of GPS dataloggers to this species, and our home range estimates are over twice as large as other reported estimates for mainland Australia. Long-nosed potoroos may range across larger areas than previously predicted on mainland Australia. Implications. This knowledge may be used to optimise the management of long-nosed potoroo populations before and after fire – a key threatening process for this species. Our study highlights the value of integrating GPS dataloggers and robust home range estimators when describing the movement ecology of a population.
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ItemSurficial sediment data along the shoreface and inner continental shelf of western Victoria, Australia(ELSEVIER, 2022-12)A comprehensive dataset of 138 surficial sediment samples retrieved from the shallow marine waters of six secondary compartments off the western coast of Victoria, Australia, is presented. Samples were collected between October 2018 and November 2020 at water depths ranging from four to 55 m using Shipek and Van Veen grabs. Sampling design targeted unconsolidated areas of the seafloor based on bathymetric and seafloor habitat data. Retrieved sediments were subsampled and subject to grain size analysis using a combination of dry sieving and laser diffraction methods, carbonate and organic matter content determination via Loss-on-Ignition, colour description using a Munsell chart, and roundness analysis using microscopic photography. This dataset, the most comprehensive surficial shallow water sedimentary record of the Otway Shelf, serves as a benchmark to understand sediment dynamics and conectivity along the coast, and can be used in environmental and engineering studies to support a range of management decisions.
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ItemSoil Bacterial Community May Offer Solutions for Ginger Cultivation(AMER SOC MICROBIOLOGY, 2022-09-13)The Taitung region is one of Taiwan's main sites for ginger agriculture. Due to issues with disease and nutrients, farmers cannot use continuous cropping techniques on ginger, meaning that the ginger industry is constantly searching for new land. Continuous cropping increases the risk of infection by Pythium myriotylum and Ralstonia solanacearum, which cause soft rot disease and bacterial wilt, respectively. In addition, fertilizer additives, which are commonly used to increase trace elements in the soil, cannot restore the soil when it is undergoing continuous cropping on ginger, even when there has been no observable decrease in trace elements in the soil. Recent studies about soil microbiome manipulation and the application of microorganisms have shown that plant-associated microbes have the ability to improve plant growth and facilitate sustainable agriculture, but studies of this kind still need to be carried out on ginger cultivation. Therefore, in this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S rRNA region to investigate microbe compositions in ginger soil to identify the difference between ginger soil with and without disease. Later, to investigate the influence of the well-known biocontrol agent B. velezensis and the fungicide Etridiazole on soil microbes and ginger productivity, we designed an experiment that collected the soil samples according to the different periods of ginger cultivation to examine the microbial community dynamics in the rhizome and bulk soil. We demonstrated that B. velezensis is beneficial to ginger reproduction. In accordance with our results, we suggest that B. velezensis may influence the plant's growth by adjusting its soil microbial composition. Etridiazole, on the other hand, may have some side effects on the ginger or beneficial bacteria in the soils that inhibit ginger reproduction. IMPORTANCE Pythium myriotylum and Ralstonia solanacearum cause soft rot disease and bacterial wilt, respectively. In this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S rRNA region to investigate microbe compositions in healthy and diseased ginger soil and find out the influence of the well-known biocontrol agent B. velezensis and the fungicide Etridiazole on soil microbes and ginger productivity. These results demonstrated that B. velezensis benefits ginger reproduction and may influence the soil bacterial composition, while Etridiazole may have some side effects on the ginger or beneficial bacteria in the soils. The interactions among ginger, biocontrol agents, and fungicides need to be further investigated.
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ItemAssessing clinical trial failure risk factors and reasons in gastric cancer(BMC, 2022-11-30)BACKGROUND: Gastric cancer is one of the leading cancer-related death causes. Enormous efforts have been focused on this field in these years. However, clinical trial failure is becoming a massive obstacle for researchers to apply their research results for clinical use. This study aimed to analyze the reasons behind clinical failures and identify potential risk factors of clinical trial failures. METHODS: On December, 1, 2021, we queried ClinicalTrials.gov for gastric cancer listed in phase II/III. We included trials specifying their interests in "stomach cancer", "Stomach Neoplasms", "Gastric Cancer", "Gastric Neoplasms", "Gastric Carcinoma", "Stomach Carcinoma", "Gastroesophageal Junction Cancer". Exclude criteria are: (1) Trials that start prior to 01/01/2007 and start after 12/01/2020; (2) Trials with "not yet recruiting", "suspended", "withdrawn", or "unknown" status; (3) Trials do not provide an anticipated accrual number or a start date. RESULTS: A total of 567 trials are included. 10.2% of these trials are failed. 16 (2.82%) were terminated for good reasons, and 42 (7.41%) were terminated for bad reasons. Multi-centre (P-value = 0.088) and anticipated accrual (P-value = 0.099) are potential risk factors for clinical failures in the simple logistic regression model. After considering the interaction between multi-centre and anticipated accrual, the odds ratio of anticipated accrual is 0.60 (P-value = 0.009) in single centre trials. In multi-centre trials, the odds ratio of anticipated accrual is 0.72 (P-value = 0.025). The primary reason for gastric cancer trial terminations is recruitment failure. CONCLUSION: The rate that trials terminated in gastric cancer has decreased compared to previous studies. Comparing to other types of oncology trials, poor accrual continues to be the predominant reason, followed by business or sponsor reasons. Single-center trials with smaller anticipated accrual number are more likely to be terminated which may resulted by limited resources invested to the trial. Single-center design exacerbated the difficulty of participant recruitment. Future studies need to continue tracking the rate of trial termination across oncology and whether the reasons behind them have changed.
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ItemBlood biochemical parameters of Murrah buffalo (Bubalus bubalis) reared in the high salinity area of Bangladesh.(ScopeMed, 2022-12)OBJECTIVES: The study's goal was to determine the impacts of drinking saline water on the biochemical parameters of Murrah buffalo. MATERIALS AND METHODS: Twenty Murrah buffalo of both sexes, ranging in age from 6 months to 11 years, were randomly selected. 10 ml of blood samples were collected from each buffalo and processed to separate serums. The supplied drinking water and feed samples were also collected. Blood parameters-glucose, alanine-aminotransferase (ALT), aspartate-aminotransferase (AST), creatinine, urea, uric acid, magnesium, phosphorous, calcium, zinc, potassium, sodium, and chloride-were analyzed. Different clinical manifestations of selected buffalo were also recorded. RESULTS: The buffaloes with skin lesions had higher serum concentrations of AST, creatinine, zinc, sodium, and chloride compared to another group. Significant age effects were found for serum concentrations of glucose (p < 0.05), creatinine (p < 0.01), uric acid (p < 0.001), phosphorus (p < 0.05), and potassium (p < 0.05). No significant age and gender effects were found for AST, ALT, urea, magnesium, calcium, zinc, sodium, and chloride. The serum concentration of creatinine was higher in female buffaloes, whereas the uric acid concentration was lower in female buffaloes compared to males. CONCLUSION: The blood parameters that were measured and remained within reference ranges show that Murrah buffaloes can adapt to saline water with little to no impairment to their liver and renal functions. The differences in the ages and sexes of the animals within the study groups highlight that mature female buffaloes suffer more from skin disorders and attempt to adjust to exotic conditions by changing the functioning of their liver and kidney.
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ItemNo Preview AvailableConsistency of Planck, ACT, and SPT constraints on magnetically assisted recombination and forecasts for future experiments(AMER PHYSICAL SOC, 2022-01-11)
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ItemNo Preview AvailableHints of early dark energy in Planck, SPT, and ACT data: New physics or systematics?(American Physical Society (APS), 2022-08-15)
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ItemNo Preview AvailableActionable secondary findings following exome sequencing of 836 non-obstructive azoospermia cases and their value in patient management(OXFORD UNIV PRESS, 2022-05-10)STUDY QUESTION: What is the load, distribution and added clinical value of secondary findings (SFs) identified in exome sequencing (ES) of patients with non-obstructive azoospermia (NOA)? SUMMARY ANSWER: One in 28 NOA cases carried an identifiable, medically actionable SF. WHAT IS KNOWN ALREADY: In addition to molecular diagnostics, ES allows assessment of clinically actionable disease-related gene variants that are not connected to the patient's primary diagnosis, but the knowledge of which may allow the prevention, delay or amelioration of late-onset monogenic conditions. Data on SFs in specific clinical patient groups, including reproductive failure, are currently limited. STUDY DESIGN, SIZE, DURATION: The study group was a retrospective cohort of patients with NOA recruited in 10 clinics across six countries and formed in the framework of the international GEMINI (The GEnetics of Male INfertility Initiative) study. PARTICIPANTS/MATERIALS, SETTING, METHODS: ES data of 836 patients with NOA were exploited to analyze SFs in 85 genes recommended by the American College of Medical Genetics and Genomics (ACMG), Geisinger's MyCode, and Clinical Genome Resource. The identified 6374 exonic variants were annotated with ANNOVAR and filtered for allele frequency, retaining 1381 rare or novel missense and loss-of-function variants. After automatic assessment of pathogenicity with ClinVar and InterVar, 87 variants were manually curated. The final list of confident disease-causing SFs was communicated to the corresponding GEMINI centers. When patient consent had been given, available family health history and non-andrological medical data were retrospectively assessed. MAIN RESULTS AND THE ROLE OF CHANCE: We found a 3.6% total frequency of SFs, 3.3% from the 59 ACMG SF v2.0 genes. One in 70 patients carried SFs in genes linked to familial cancer syndromes, whereas 1 in 60 cases was predisposed to congenital heart disease or other cardiovascular conditions. Retrospective assessment confirmed clinico-molecular diagnoses in several cases. Notably, 37% (11/30) of patients with SFs carried variants in genes linked to male infertility in mice, suggesting that some SFs may have a co-contributing role in spermatogenic impairment. Further studies are needed to determine whether these observations represent chance findings or the profile of SFs in NOA patients is indeed different from the general population. LIMITATIONS, REASONS FOR CAUTION: One limitation of our cohort was the low proportion of non-Caucasian ethnicities (9%). Additionally, as comprehensive clinical data were not available retrospectively for all men with SFs, we were not able to confirm a clinico-molecular diagnosis and assess the penetrance of the specific variants. WIDER IMPLICATIONS OF THE FINDINGS: For the first time, this study analyzed medically actionable SFs in men with spermatogenic failure. With the evolving process to incorporate ES into routine andrology practice for molecular diagnostic purposes, additional assessment of SFs can inform about future significant health concerns for infertility patients. Timely detection of SFs and respective genetic counseling will broaden options for disease prevention and early treatment, as well as inform choices and opportunities regarding family planning. A notable fraction of SFs was detected in genes implicated in maintaining genome integrity, essential in both mitosis and meiosis. Thus, potential genetic pleiotropy may exist between certain adult-onset monogenic diseases and NOA. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the Estonian Research Council grants IUT34-12 and PRG1021 (M.L. and M.P.); National Institutes of Health of the United States of America grant R01HD078641 (D.F.C., K.I.A. and P.N.S.); National Institutes of Health of the United States of America grant P50HD096723 (D.F.C. and P.N.S.); National Health and Medical Research Council of Australia grant APP1120356 (M.K.O'B., D.F.C. and K.I.A.); Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Ciência, Tecnologia e Inovação grant POCI-01-0145-FEDER-007274 (A.M.L., F.C. and J.G.) and FCT: IF/01262/2014 (A.M.L.). J.G. was partially funded by FCT/Ministério da Ciência, Tecnologia e Ensino Superior (MCTES), through the Centre for Toxicogenomics and Human Health-ToxOmics (grants UID/BIM/00009/2016 and UIDB/00009/2020). M.L.E. is a consultant for, and holds stock in, Roman, Sandstone, Dadi, Hannah, Underdog and has received funding from NIH/NICHD. Co-authors L.K., K.L., L.N., K.I.A., P.N.S., J.G., F.C., D.M.-M., K.A., K.A.J., M.K.O'B., A.M.L., D.F.C., M.P. and M.L. declare no conflict of interest. TRIAL REGISTRATION NUMBER: N/A.
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ItemNo Preview AvailableOptimal Interruption of P. vivax Malaria Transmission Using Mass Drug Administration(SPRINGER, 2023-06-01)Plasmodium vivax is the most geographically widespread malaria-causing parasite resulting in significant associated global morbidity and mortality. One of the factors driving this widespread phenomenon is the ability of the parasites to remain dormant in the liver. Known as 'hypnozoites', they reside in the liver following an initial exposure, before activating later to cause further infections, referred to as 'relapses'. As around 79-96% of infections are attributed to relapses from activating hypnozoites, we expect it will be highly impactful to apply treatment to target the hypnozoite reservoir (i.e. the collection of dormant parasites) to eliminate P. vivax. Treatment with radical cure, for example tafenoquine or primaquine, to target the hypnozoite reservoir is a potential tool to control and/or eliminate P. vivax. We have developed a deterministic multiscale mathematical model as a system of integro-differential equations that captures the complex dynamics of P. vivax hypnozoites and the effect of hypnozoite relapse on disease transmission. Here, we use our multiscale model to study the anticipated effect of radical cure treatment administered via a mass drug administration (MDA) program. We implement multiple rounds of MDA with a fixed interval between rounds, starting from different steady-state disease prevalences. We then construct an optimisation model with three different objective functions motivated on a public health basis to obtain the optimal MDA interval. We also incorporate mosquito seasonality in our model to study its effect on the optimal treatment regime. We find that the effect of MDA interventions is temporary and depends on the pre-intervention disease prevalence (and choice of model parameters) as well as the number of MDA rounds under consideration. The optimal interval between MDA rounds also depends on the objective (combinations of expected intervention outcomes). We find radical cure alone may not be enough to lead to P. vivax elimination under our mathematical model (and choice of model parameters) since the prevalence of infection eventually returns to pre-MDA levels.