Miracle-dz/UniFAR-FTUs huggingface dataset:
Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals

Documenting and predicting spatial connections arising from planktonic larval dispersal in marine species remains a formidable challenge. Biophysical dispersal models using simulations based on biological attributes and physical oceanography are attractive predictive tools. Here we evaluate how such simulated long-distance multigenerational connections align with spatial genetic data for two common coral species (Acropora tenuis and Acropora millepora) from the Great Barrier Reef (GBR), Australia. We focus on signatures of asymmetric dispersal and evaluate concordance using coalescent genetic simulations, directions of inferred gene flow, and spatial eigenvector modelling. The strongest matches rely on asymmetric north to south connections, consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality. For A. tenuis and A. millepora, northern and central reefs have been important sources to downstream southern reefs over the recent evolutionary past, yet endemic diversity of southern reefs also suggests substantial recruitment of local progeny.
Translating surveillance data into incidence estimates

Monitoring a population for a disease requires the hosts to be sampled and tested for the pathogen. This results in sampling series from which to estimate the disease incidence, i.e. the proportion of hosts infected. Existing estimation methods assume that disease incidence is not changing between monitoring rounds, resulting in underestimation of the disease incidence. In this paper we develop an incidence estimation model accounting for epidemic growth with monitoring rounds sampling varying incidence. We also show how to accommodate the asymptomatic period characteristic to most diseases. For practical use, we produce an approximation of the model, which is subsequently shown accurate for relevant epidemic and sampling parameters. Both the approximation and the full model are applied to stochastic spatial simulations of epidemics. The results prove their consistency for a very wide range of situations.
Saliency Guided Subdivision for Single-View Mesh Reconstruction

In this paper, we present a novel deep architecture to recover a 3D shape in triangular mesh from a single image based on mesh deformation. Most existing deformationbased methods produce uniform mesh predictions by repeatedly applying global subdivision but fail to require the highlighted details due to the memory limits. To address this problem, we propose a novel saliency guided subdivision method to achieve the trade-off between detail generation and memory consumption. Instead of using local geometric cues such as curvature, we introduce a global point-based saliency voting operation to guide the adaptive mesh subdivision and deformation explicitly. Moreover, we propose the oriented chamfer loss to mitigate the mesh self-intersection problem in subdivision. We further make our network configurable and explore the best structure combination. Extensive experiments show that our method can both produce visually pleasing results with fine details and achieve better performance compared to other state-of-the-art methods.
Analysis of Virological, Histological and Clinical Features of Hepatitis Delta Virus Infection in Southeastern Turkey

Ad dress for Cor res pon den ce: Mehmet Suat Yalçın MD, Aksaray University Training and Research Hospital, Clinic of Gastroenterology, Aksaray, Turkey Phone: +90 530 575 74 96 E-mail: drsuat02@hotmail.com ORCID ID: orcid.org/0000-0003-1054-1882 Re cei ved: 13.04. 2018 Ac cep ted: 13.06. 2018 ©Copyright 2018 by Viral Hepatitis Society / Viral Hepatitis Journal published by Galenos Publishing House. ABSTRACT ÖZ
Allometric models for estimation of aboveground biomass of Gmelina arborea Roxb. in pulpwood plantations of Bangladesh

Gmelina arborea Roxb. is a fast-growing, deciduous tree species native to Bangladesh. It has been widely planted since 1992 for commercial production of pulpwood in hilly areas of Bangladesh. The purpose of this study was to derive well-fitting allometric models for estimation of aboveground biomass, and carbon and nutrient (nitrogen, phosphorus and potassium) stocks in G. arborea to ensure sustainable production and management of this species. Eight linear models with 64 regression equations were tested for estimation of aboveground biomass, carbon and nutrient stocks in different parts (leaves, branches, bark and stem) of the plant. The best-fitting allometric models were selected in accordance with various relevant statistical criteria.
Effects of Plant Age and Nitrogen Fertilization on Nitrate Accumulation and Postharvest Nitrite Accumulation in Fresh Spinach1

Leaves of spinach (Spinacia oleracea L.) from N fertilized and unfertilized plots were harvested at different stages of maturity, and analyzed for nitrate and nitrite at harvest and after storage at 10°C for 5, 10 or 15 days. Leaf nitrate-N increased with time in plants sidedressed with 340 kg N/ha, but decreased in unfertilized spinach. Leaves harvested at market maturity accumulated 5-fold more nitrite-N when held at 10°C for 15 days than immature leaves. N fertilization increased nitrate accumulation at harvest, and nitrite accumulation after 15 days at 10°C.
Soybean Response to Dicamba: A Meta-Analysis

Abstract A meta-analysis of 11 previously published field studies was conducted with the objectives being to (1) estimate the no observable effects dose (NOED) for dicamba on susceptible soybean; (2) evaluate available evidence for hormesis, or increased soybean yield in response to low doses of dicamba; (3) estimate the dose of dicamba likely to cause measurable soybean yield loss under field conditions; and (4) quantify the relationship between visible injury symptoms and soybean yield loss. All studies that included visible injury data (N=7) reported injury symptoms at the lowest nonzero dicamba dose applied (as low as 0.03 g ae ha-1), and therefore a NOED could not be estimated from the existing peerreviewed literature. Based on statistical tests for hormesis, there is insufficient evidence to support any claim of increased soybean yield at low dicamba doses. Future research should include a range of dicamba doses lower than 0.03 g ha-1 to estimate a NOED and determine whether a hormesis effect is possible at or below dicamba doses that cause visible injury symptoms. Soybean is more susceptible to dicamba when exposed at flowering (R1 to R2 stage) compared with vegetative stages (V1 to V7). A dicamba dose of 0.9 g ha-1 (95% CI=0.08 to 1.7) at the flowering stage was estimated to cause 5% soybean yield loss. When exposed at vegetative stages, dicamba doses that cause less than 30% visible injury symptoms (95% CI=23 to 49%) appear unlikely to cause greater than 5% soybean yield loss; however, if soybean is exposed at flowering, visible injury symptoms greater than 12% (95% CI=8 to 16%) are likely to be associated with at least 5% soybean yield loss. Nomenclature: Dicamba; soybean, Glycine max (L.) Merr.
Growth Performance of Milkfish (Chanoschanos) Fed Plant-Based Diets

The high cost of fish feeds is the biggest problem in milkfish production caused by the protein from the expensive fish meal. Looking for an alternative from the agricultural commodities is imperative. This paper evaluates the nutritive composition of plant-based formulated feeds utilizing breadnut, breadfruit and banana peelings and their effects on the growth performance (weight gain and length increased) and, survival rate of milkfish. Results showed that the three formulated feeds have lower protein levels (19.9, 19.6, 20.35) but with extensively higher fat contents (24.4, 15.72, 10.75) than the commercial feed (27.1%, 4%). The samples’ growth responses have no significant difference (p < 0.05) among the four feeds. Thus, the plant-based formulated feeds have the potential to contribute to the growth of milkfish comparable to the commercial feed. Further, the agricultural products used in the formulations are feasible for the replacement of fishmeal and must be promoted for utilization in feed production.
Variability Characterization of the Olive Species Regarding Virgin Olive Oil Aroma Compounds by Multivariate Analysis of GC Data

Virgin olive oil is characterized by its unique aroma, which is synthesized when olive fruits are crushed during the industrial process used for oil production. The genetic variability of the major volatile compounds comprising the oil aroma was studied in a representative sample of olive cultivars from the World Olive Germplasm Collection (IFAPA, Cordoba, Spain). The analytical data demonstrated that a high degree of variabil- ity for the content of volatile compounds is found in the olive species and that most of the volatile compounds found in the oils were synthetized by the enzymes included in the so-called lipoxygenase pathway. The use of multivariate analysis to identify cultivars is particularly interesting in terms of volatile composition and deduced organoleptic qual- ity. It can be used for identification of old olive cultivars that give rise to oils with a high organoleptic quality and in parent selection for olive breeding programs.
Dealing with partially observed covariates in propensity score analysis of observational data

Observational data, such as electronic health records, are a valuable source of information for researchers seeking to answer health-related questions. Since treatment allocation is not typically randomised in studies using observational data, there is confounding systematic differences in the characteristics of patients in different treatment groups. Propensity score analysis (PSA) can be used to handle confounding by modelling the probability of being allocated to a particular treatment, based on patient characteristics. However, a common issue in analyses of observational data is missing data. In general, not dealing appropriately with missing data can lead to loss of efficiency and biased estimates of the treatment effect. Furthermore, having partially observed covariate data can complicate the estimation of the propensity score. The missingness pattern approach (MPA) has been proposed to handle partially observed covariate data in PSA. One key objective of my thesis is to understand when the approach is appropriate, by exploring its underlying assumptions. I began by comparing different statements of the MPA's underlying assumptions given in the literature. I considered the plausibility of the MPA's assumptions in simple scenarios, finding that they are separate to the conventional classification of missingness mechanisms. I used d-separation (a rule for testing conditional independence statements) with single world intervention graphs, representing a variety of scenarios, in order to develop guidance for when the assumptions seem plausible. I also explored the connection between using the MPA and using missing indicators in the context of PSA, finding that the use of missing indicators is a simplification of the MPA. I extended this work to outcome regression, mathematically proving that using missing indicators is valid under the MPA's assumptions as well as an additional simplifying assumption. I also conducted simulation studies to assess bias when using missing indicators to handle partially observed covariate data in outcome regression.
First Record of the Interstitial AnnelidPharyngocirrus uchidai (Annelida: Saccocirridae)from Korea, Confirmed byTopotypic DNA Barcoding Data from Japan

The marine interstitial annelid Pharyngocirrus uchidai (Sasaki, 1981) has been only known from Japan. In this study, we report the occurrence of P. uchidai for the first time in four localities along the eastern coast of Korea: Bukmyeon, Gamchu, Gase, and Oeongchi. Species identification was confirmed by comparison of DNA barcoding sequences with morphological examination from the type locality, Oshoro, Japan. We generated a total of 25 sequences of a partial segment (580 bp) of the cytochrome c oxidase subunit I gene (COI), representing five specimens from each locality. Maximum intra-specific variation was 1.2% in terms of Kimura two-parameter (K2P) distance, observed between two individuals each from Gamchu (i.e., between two specimens from the single locality), Gamchu and Oeongchi, Gamchu and Oshoro, and Oeongchi and Oshoro. On the other hand, an identical haplotype was found in all the five localities, substantiating our species identification for the Korean populations. Inter-specific K2P distance between P. uchidai and an unidentified Saccocirrus sp. from Canada (based on public database entries) was 22.4-23.4%.
Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

How age-associated decline of immune function leads to increased cancer incidence is poorly understood. Here, we have characterized the cellular composition of the γδ T cell pool in peripheral lymph nodes (pLNs) upon ageing. We found that ageing has minimal cell-intrinsic effects on function and global gene expression of γδ T cells, and TCRγδ diversity remained stable. However, ageing altered TCRδ chain usage and clonal structure of γδ T cell subsets. Importantly, IL-17-producing γδ17 T cells dominated the γδ T cell pool of aged mice - mainly due to the selective expansion of Vγ6+ γδ17 T cells and augmented γδ17-polarisation of Vγ4+ T cells. Expansion of the γδ17 T cell compartment was supported by increased Interleukin-7 expression in the T cell zone of old mice. In a Lewis lung cancer model, pro-tumourigenic Vγ6+γδ17 T cells were exclusively activated in the tumour-draining LN and their infiltration into the tumour correlated with increased tumour size in aged mice. Thus, upon ageing, substantial compositional changes of γδ T cell pool in a dysregulated pLN microenvironment promote tumour growth.
Plant growth responses to vesicular-arbuscular mycorrhiza. XV: Influence of soil pH on the symbiotic efficiency of different endophytes

Nine vesicular‐arbuscular mycorrhizal endophytes were assessed for their infectivity and ability to improve the growth of alpine strawberry seedlings in sterilized, low‐phosphate soils (4 and 8 mg kg−1 NaHCO3‐soluble P), limed to different pHs. At pH 4, Glomus clarum greatly stimulated plant growth, but the other endophytes except Gigaspora margarita and Glomus fasciculatum‘E3’ had little or no effect. The most efficient endophytes at pH 5 were E3, Acaulospora laevis and G. clarum. The largest plants were those growing at pH 7 and inoculated with Glomus epigaeum; A. laevis and G. clarum were ineffective at this pH. The most effective endophytes at pH 6 and 7 were G. epigaeum, Glomus mosseae, E3, Glomus caledonium and Gigaspora heterogama, although results varied slightly between soils. Most endophytes infected well at all pHs, even where they did not enhance plant growth. In studies of this nature plant growth is affected by different pHs, soil P levels and the inoculum used. Nevertheless these data show clearly that different endophytes vary enormously in their symbiotic effectiveness at different soil pHs. The practical implications of these results are discussed.
Risk management in Norwegian avalanche rescue operations

Avalanche incidents commonly take place in adverse environmental conditions, and the expected survival time of avalanche victims is short. These situations require an immediate rescue response, which may pose a serious challenge to the safety of both rescuers and avalanche victims. Historically, the Norwegian rescue service has experienced few serious accidents, but undesirable incidents where rescuers are dangerously exposed in avalanche runout zones seem more frequent. Risk management in the avalanche rescue service is multifaceted, influenced by its multi-organizational structure. Individuals acting in this socio-technical rescue system are easily caught between two imperatives: saving lives and staying alive. The aim of risk management is to maintain equilibrium in rescue commitment. This project analysed whether the Norwegian avalanche rescue system is correctly balanced to withstand the extra load of common risk influencing factors in rescue operations. Aim: The fundamental aim of this thesis was to contribute to new knowledge on factors that are important for risk management and performance in the Norwegian avalanche rescue service. Methods: Mixed methods research was applied to answer the specific research questions. This implied multiple research activities in a combination of quantitative and qualitative methodologies. Study number 1 was a retrospective study to characterize Norwegian avalanche incidents and rescue response (Paper I). A comprehensive study comprising avalanche rescue statistics, cross-case analysis, factor analysis and risk modelling was conducted to gain insight into avalanche rescue performance (Paper II). In a phenomenological study to explore the concept of overcommitment, nine air ambulance crews from five bases took part in focus group interviews (Papers III and IV). Lastly, a systemic safety analysis was conducted in two separate seminars, supported by the insight of six experts in Norwegian avalanche rescue operations (Paper V). The thesis itself is a cross-paper synthesis of results. Results: The studies returned results which contribute to justified beliefs about patient and rescuer safety in Norwegian avalanche rescue operations. Conclusion: A synthesis of results from the various studies indicates that the Norwegian rescue service is vulnerable to common risk sources in rescue operations, affecting the safety of both rescuers and patients. The avalanche rescue system could benefit from a focus on the integrity of already established safety barriers. This implies an interorganizational effort to identify and reach common goals and system requirements. This thesis may serve as input to discussions on risk acceptance levels in the rescue service, the applicability and validity of control algorithms in rescue management and how to adjust the degree of commitment in various rescue missions.
CORRELATION BETWEEN AGE, WEIGHT AND BODY MEASURES AT FIRST PREGNANCY OF NELLORE HEIFERS

T he objective of this study was to characterize and correlate weight, body condition and morphometric measurements with the beginning of the reproductive life in heifers of the Nellore breed. To determine the age of first pregnancy, 56 heifers of the Nellore breed were exposed to bulls. The females were evaluated for weight, body condition and body measurements every two months, from 16 to 32 months of age. The body measurements were: withers height, rump height, body length, head length, rump length, ear length, distance between ribs, distance from dorsal spine to belly, distance from ground to belly, head width, rump width, distance between ischiums, ear width, cannon bone perimeter, tail implantation perimeter, and thoracic perimeter. The results show that the animals had an average weight of 334±39 kg and an average age of 29±3 months at first pregnancy. The morphometric measurements of withers height, rump height, body length, rump length, head width, rump width, width between ischiums, tail implantation perimeter and thoracic perimeter were significantly greater in the pregnant animals. Can conclude from these results that a relationship between morphometric measurements and the first pregnancy in Nel l ore heifers.
RHEUMATOID ARTHRITIS-INCREASED GENE EXPRESSIONS IN MUSCLE ATROPHY ARE RESTORED BACK TO CONTROL AS A RESPONSE TO ACUTE RESISTANCE EXERCISE

This study had as objective to analyze the acute effects of resistance exercise (RE) on the mRNA levels of the following genes (MyoD, myogenin, IGF-1, atrogin-1, MuRF-1, and myostatin) in rheumatoid arthritis (experimental arthritis). Therefore, 26 females rats were randomly allocated into four groups, control (CT, n=7), exercise (Ex, n=6), rheumatoid arthritis (RA, n=6) and RA with exercise (RAEx, n=7). Met-BSA was injected into the tibiotarsal joint in the RA and RAEx groups. After 15 days from injection, the animals were submitted to an acute bout of RE and six hours post protocol the animals were euthanized. We evaluated the joint thickness, inflammation score, cross-sectional area (CSA) of gastrocnemius muscle fibers and mRNA expression of the IGF-1, MyoD, myogenin, myostatin, MuRF-1, atrogin-1 and GAPDH. It was observed that the joint thickness and score strongly increased in arthritic rats (p <0.001) while the CSA decreased (p ? 0.05). Increased mRNA levels of IGF-1 (2.0 fold), myostatin (4.5 fold), atrogin-1 (2.5 fold), MyoD (3.7-fold) and myogenin (5 fold) were observed in muscle of arthritic rats. The mRNA expression of myostatin, atrogin-1, MyoD and myogenin decreased in the RAEx group. In this way, we can conclude that experimental arthritis-increased gene expressions in muscle atrophy (myostatin, atrogin-1, MyoD and myogenin) are restored back to control as a response to acute RE.
The Effect of Forkhead Box Class O1, Mammalian Target of Rapamycin Complex 1, Survivin, and Interleukin-17 on the Degree of Acne Vulgaris Based on Serum Levels

BACKGROUND: Acne vulgaris (AV) is a health problem that is routinely found throughout the world and has an impact on the quality of life of sufferers. Several studies have shown that forkhead box Class O1 (FoxO1), the mammalian target of rapamycin complex 1 (mTORC1), survivin, and interleukin-17 (IL-17) play a role in the pathogenesis of multifactorial AV. AIM: The study aims to determine the relationship between serum levels of FoxO1, mTORC1, survivin, and IL-17 with the severity of AV. METHODS: This is observational research with cross-sectional design. Samples from venous blood sufferers of AV mild, moderate, and severe, each of 20 people were colected. Classification of AV was based on the criteria of Lehmann et al. Examination of serum levels of FoxO1, mTORC1, survivin, and IL-17 using the ELISA technique was done. The statistical test used was the ANOVA test and the Kruskal–Wallis test. RESULTS: The results showed that average levels of FoxO1 decreased with increasing degree of severity of AV. An average increase in mTORC1, survivin, IL-17 levels with an increase in the severity of AV was found. Statistical test results showed a significant correlation of FoxO1, mTORC1, survivin levels, and the severity of AV (p 0.05). CONCLUSION: This study concluded that FoxO1 levels decrease at increasing severity. Conversely, levels of mTORC1, survivin, and IL-17 increase with increasing degrees of the severity of AV.
Evolution of placentotrophy: using viviparous sharks as a model to understand vertebrate placental evolution

Reproducing sharks must provide their offspring with an adequate supply of nutrients to complete embryonic development. In oviparous (egg-laying) sharks, offspring develop outside the mother, and all the nutrients required for embryonic growth are contained in the egg yolk. Conversely, in viviparous (live-bearing) sharks, embryonic development is completed inside the mother, providing offspring with the opportunity to receive supplementary embryonic nourishment, known as matrotrophy. Viviparous sharks exhibit nearly all forms of matrotrophy known in vertebrates, including a yolk-sac placenta, which involves several significant ontogenetic modifications to fetal and maternal tissues. The selective pressures that have driven the evolution of complex placentas in some shark species, but not in others, are unresolved. Herein we review the mechanisms of reproductive allocation and placental diversity in sharks, and consider the application of both adaptive and conflict hypotheses for the evolution of placental nutrient provisioning. Both have likely played roles in placental evolution in sharks, perhaps at different times in evolutionary history. Finally, we recommend sharks as an outstanding model system to investigate the evolution of placentas and mechanisms for fetal nutrition during pregnancy in vertebrates.