Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Abstract The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein‐coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16‐trnQ, ycf1, ndhF‐rpl32, petN‐psbM, and rpl32‐trnL, and they may be suitable for the development of robust, authentic, and cost‐effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co‐occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.
Health-Related Quality-of-Life and Associated Factors Among Post-Partum Women in Arba Minch Town

Background It is generally accepted that pregnancy and childbirth are natural physiological processes. However, these significantly affect the quality of mothers’ lives. Little is known about the level of quality-of-life and associated factors among postpartum women in Ethiopia, particularly in the study area. Methods A community-based cross-sectional study was conducted among 409 randomly selected post-partum women who were living in Arba Minch town. Systematic random sampling was employed to select the study participants. The standard quality-of-life assessment tool which is known as the short-form SF 36 tool was used to assess health-related quality-of-life. The logistic regression model was used to identify associated factors. Statistically significant variables at a p-value<0.25 in the bi-variable analysis were candidate variables for multi-variable analysis and statistical significance which was declared at a p-value<0.05. Results Among the study participants, 255 (62.3%) had lower level health-related quality-of-life (HRQoL). About 46.2% of the study participants had lower physical HRQoL and about 79% of the study participants had lower mental HRQoL. The overall mean score of HRQoL was 45.15 (±8.13). Factors associated with lower overall HRQoL were age group 17–24 years (AOR=2.73, 95% CI=1.22–6.10), no formal education [AOR 2.02, 95% CI (1.05–3.89)], and cesarean delivery (AOR=0.49, 95% CI=0.24–0.97). A factor associated with lower physical HRQoL was cesarean delivery (AOR=0.34, 95% CI=0.13–0.88). Factors associated with lower mental HRQoL were age group 17–24 (AOR=3.37, 95% CI=1.60–7.04), not receiving antenatal care (AOR=3.65, 95% CI=1.45–9.16), and having postpartum depression (AOR=2.27, 95% CI=1.30–3.93). Conclusion The results suggest that the majority of post-partum women had a lower HRQoL, particularly women’s mental health was compromised. In this study, a suggestion is made that the respective bodies need to give particular attention to mothers during the post-partum period to prevent poor quality-of-life.
A Monte Carlo Platform for Characterization of X-Ray Radiation Dose in CT Imaging

Background: Computed tomography (CT) is currently known as a versatile imaging tool in the clinic used for almost all types of cancers. The major issue of CT is the health risk, belonging to X-ray radiation exposure. Concerning this, Monte Carlo (MC) simulation is recognized as a key computational technique for estimating and optimizing radiation dose. CT simulation with MCNP/MCNPX MC code has an inherent problem due to the lack of a fan-beam shaped source model. This limitation increases the run time and highly decreases the number of photons passing the body or phantom. Recently, a beta version of MCNP code called MCNP-FBSM (Fan-Beam Source Model) has been developed to pave the simulation way of CT imaging procedure, removing the need of the collimator. This is a new code, which needs to be validated in all aspects. Objective: In this work, we aimed to develop and validate an efficient computational platform based on modified MCNP-FBSM for CT dosimetry purposes. Material and Methods: In this experimental study, a setup is carried out to measure CTDI100 in air and standard dosimetry phantoms. The accuracy of the developed MC CT simulator results has been widely benchmarked through comparison with our measured data, UK’s National Health Service’s reports (known as ImPACT), manufacturer’s data, and other published results. Results: The minimum and maximum observed mean differences of our simulation results and other above-mentioned data were the 1.5%, and 9.79%, respectively. Conclusion: The developed FBSM MC computational platform is a beneficial tool for CT dosimetry.
An index for measuring functional extension and evenness in trait space

Abstract Most existing functional diversity indices focus on a single facet of functional diversity. Although these indices are useful for quantifying specific aspects of functional diversity, they often present some conceptual or practical limitations in estimating functional diversity. Here, we present a new functional extension and evenness (FEE) index that encompasses two important aspects of functional diversity. This new index is based on the straightforward notion that a community has high diversity when its species are distant from each other in trait space. The index quantifies functional diversity by evaluating the overall extension of species traits and the interspecific differences of a species assemblage in trait space. The concept of minimum spanning tree (MST) of points was adopted to obtain the essential distribution properties for a species assembly in trait space. We combined the total length of MST branches (extension) and the variation of branch lengths (evenness) into a raw FEE0 metric and then translated FEE0 to a species richness‐independent FEE index using a null model approach. We assessed the properties of FEE and used multiple approaches to evaluate its performance. The results show that the FEE index performs well in quantifying functional diversity and presents the following desired properties: (a) It allows a fair comparison of functional diversity across different species richness levels; (b) it preserves the essence of single‐facet indices while overcoming some of their limitations; (c) it standardizes comparisons among communities by taking into consideration the trait space of the shared species pool; and (d) it has the potential to distinguish among different community assembly processes. With these attributes, we suggest that the FEE index is a promising metric to inform biodiversity conservation policy and management, especially in applications at large spatial and/or temporal scales.
Challenges and opportunities for comparative studies of survival rates: An example with male pinnipeds

Abstract Survival rates are a central component of life‐history strategies of large vertebrate species. However, comparative studies seldom investigate interspecific variation in survival rates with respect to other life‐history traits, especially for males. The lack of such studies could be due to the challenges associated with obtaining reliable datasets, incorporating information on the 0–1 probability scale, or dealing with several types of measurement error in life‐history traits, which can be a computationally intensive process that is often absent in comparative studies. We present a quantitative approach using a Bayesian phylogenetically controlled regression with the flexibility to incorporate uncertainty in estimated survival rates and quantitative life‐history traits while considering genetic similarity among species and uncertainty in relatedness. As with any comparative analysis, our approach makes several assumptions regarding the generalizability and comparability of empirical data from separate studies. Our model is versatile in that it can be applied to any species group of interest and include any life‐history traits as covariates. We used an unbiased simulation framework to provide “proof of concept” for our model and applied a slightly richer model to a real data example for pinnipeds. Pinnipeds are an excellent taxonomic group for comparative analysis, but survival rate data are scarce. Our work elucidates the challenges associated with addressing important questions related to broader ecological life‐history patterns and how survival–reproduction trade‐offs might shape evolutionary histories of extant taxa. Specifically, we underscore the importance of having high‐quality estimates of age‐specific survival rates and information on other life‐history traits that reasonably characterize a species for accurately comparing across species.
Ecological genetics of Juglans nigra: Differences in early growth patterns of natural populations

Abstract Many boreal and temperate forest tree species distributed across large geographic ranges are composed of populations adapted to the climate they inhabit. Forestry provenance studies and common gardens provide evidence of local adaptation to climate when associations between fitness traits and the populations' home climates are observed. Most studies that evaluate tree height as a fitness trait do so at a specific point in time. In this study, we elucidate differences in early growth patterns in black walnut (Juglans nigra L.) populations by modeling height growth from seed up to age 11. The data comprise tree height measurements between ages 2 and 11 for 52 natural populations of black walnut collected through its geographic range and planted in one or more of 3 common gardens. We use the Chapman–Richards growth model in a mixed effects framework and test whether populations differ in growth patterns by incorporating populations' home climate into the model. In addition, we evaluate differences in populations' absolute growth and relative growth based on the fitted model. Models indicated that populations from warmer climates had the highest cumulative growth through time, with differences in average tree height between populations from home climates with a mean annual temperature (MAT) of 13°C and of 7°C estimated to be as high as 80% at age 3. Populations from warmer climates were also estimated to have higher and earlier maximum absolute growth rate than populations from colder climates. In addition, populations from warm climates were predicted to have higher relative growth rates at any given tree size. Results indicate that natural selection may shape early growth patterns of populations within a tree species, suggesting that fast early growth rates are likely selected for in relatively mild environments where competition rather than tolerance to environmental stressors becomes the dominant selection pressure.
Studies on relationship between milk yield and skin thickness of dairy animals

The aim of the present investigation was to examine the relationship between skin thickness and milk yield. The experiment was conducted at Livestock Farm Complex, C.V. Sc. & A.H. , ANDUAT Ayodhya, Ram Newaj Singh Dairy Farm, Kumarganj, Ayodhya (UP) and Gorakhnath Singh Dairy, Baijnathpur Gorakhpur (UP) as per availability of lactating animals (Murrah buffalo, Gir and Sahiwal cows) which was 32 animals of each breed. A total of 96 dairy animals were studied in this experiment in which 32 Murrah buffaloes, 32 Sahiwal cows and 32 Gir cows ranging from first to fourth lactation periods. The dairy animals were selected on daily milk yield and total milk yield were recorded from the records over an average period of 120 days of lactation length. The skin thickness was measured from seven sites or regions namely neck, chest, abdomen, rump, hind quarter, udder and flank of each animal. The result shows that, in Murrah buffaloes the highest average DMY was 8.16 ± 0.52, 8.62 ± 0.55, 8.29 ± 0.78, 8.15 ± 0.55, 8.69 ± 0.77 and 7.86 ± 0.39 litres by animals under thin skin thickness of neck, chest, abdomen, hind quarter, udder and flank regions respectively. In Sahiwal cows, it was observed that the highest average DMY was 7.26 ± 0.31, 7.47 ± 0.65, 7.63 ± 0.48, and 7.69 ± 0.76 litres by animals under low skin thickness of neck, chest, abdomen and udder regions respectively. Where as in Gir cows it was observed that the highest average DMY was 6.23 ± 0.46, 6.06+0.41, 5.96 ± 0.51, 5.06 ± 0.36 and 6.03 ± 0.65 litres by animals under low skin thickness of neck, abdomen, hind quarter, udder and flank regions respectively. However, it was also observed that all the Murrah buffaloes, Sahiwal and Gir cows having thick skin of different regions were found to produce lowest milk yield per day. Least square analysis showed that the relation between DMY and skin thickness of thin, moderate and thick in different regions was found to be statistically non-significant except in flank regions where different types of skin thickness found significant (p<0.01). Further it was observed TMY and type of skin thickness in different regions were not found significant (p<0.01) except udder and abdomen regions where thick skin TMY were found to be statistically highly significant (p<0.01). It may be concluded that, the udder skin thickness was minimum followed by that in ascending order in the neck, chest, abdomen, hindquarter, flank and rump regions of the animals. Further it was evident that Murrah buffalo, Sahiwal and Gir cows under their skin thickness were found to produce more milk, while moderate skin thickness produced more milk and then thick skin thickness produced milk.
Comparison of adductor canal block with femoral nerve block for post-operative pain relief after bilateral total knee arthroplasty: A non-randomised controlled trial

Background and Aims: Pain perception and pain threshold vary from one individual to another and also differ in the right and left limbs leading to an inter-cerebral pain variability bias and inter-patient pain variability bias. To date, data comparing adductor canal block (ACB) with femoral nerve block (FNB) in the same patient who underwent bilateral total knee arthroplasty (TKA) remain limited. Methods: We performed a prospective, non-randomised, controlled study. Patients scheduled for bilateral TKA with central neuraxial anaesthesia received every 12-hourly intermittent boluses of 15 mL of ropivacaine 0.5% in two different peripheral nerve blocks (ACB and FNB) in either of the lower limbs postoperatively. The primary outcome was to assess postoperative VAS score, and the secondary outcomes were muscle strength of the quadriceps muscle and degree of flexion at the knee joint. Results: Among the 80 patients assessed for eligibility, 72 patients were enroled, and 69 were included in the final analysis. VAS scores after the two blocks during rest at 30 minutes, 6 hours, 12 hours and 48 hours post-operatively had no significant difference. VAS scores during rest at 24 hours and on doing exercise at 24 hours and 48 hours showed a significant difference. Quadriceps muscle strength and degree of flexion of knee at 24 hours and 48 hours post-operatively did show a significant difference in favour of the ACB over FNB. Conclusion: ACB provides equivalent analgesia in comparison with FNB at rest and during passive exercise up to 48 hours post-operatively. ACB significantly preserved motor power of quadriceps muscles when compared with FNB with no added complications.
Contributions of Pre and Postmorbid Nondominant Language Interventions to Coactivation of L1-L2 Lexical Representations: A Case Study of Persian-English Bilingual Stroke-Induced Aphasic Patients

The current study sought to bring into light the important functions of pre and postmorbid nondominant language interventions and aphasia patients’ level of L1-L2 proficiency considering the productive dimension of vocabulary knowledge affected by intertrial tasks. Two Persian-English bilingual cases with anomia and different levels of postmorbid L2 proficiency were subjected to a treatment of English naming to find the contribution of English naming improvement to Persian naming. Both cases were given the therapeutic language intervention to enhance their naming performance of English lexical items and to find out whether it could be generalized to Persian equivalents.Data obtained from the 2 participants were analyzed using semantic naming tests, and the responses were validated through time-series analysis. Statistical findings suggested that participant 1, who had a higher L2 proficiency, exhibited higher performance than participant 2 throughout 5 consecutive trials, once they had received phonemic cues after semantic ones. Concerning within-language impacts, treated items exhibited a considerable improvement. The treated items and repeated untreated ones improved concerning cross-language impacts.
The complete mitochondrial genome of the peppermint shrimp Lysmata wurdemanni (Decapoda: Lysmatidae)

Abstract In this study, the complete 16,979 bp mitochondrial genome of Lysmata wurdemanni (Gibbes, 1850) was determined from a specimen collected from Apalachee Bay, U.S. The mitogenome contains 37 genes, and consists of 32.33% A, 35.01% T, 19.55% C, and 13.10% G, with a total G + C content of 32.65%. A maximum likelihood phylogenetic tree based on mitochondrial protein-coding genes suggested L. wurdemanni is clustered with Lysmata vittata and Lysmata amboinensis, based on available mitochondrial sequences of relatives. These data are useful in determining phylogenetic relationships between Lysmatidae and Thoridae. The sequenced mitochondrial genome may also assist in understanding evolutionary distinctions and breeding strategies in hermaphroditic species.
Time to SARS-CoV-2 PCR Clearance in Immunocompromising Conditions: Is Test-Based Removal From Isolation Necessary in Severely Immunocompromised Individuals?

Abstract To determine the association between immunosuppression and time to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) clearance, we studied 3758 adults retested following initial SARS-CoV-2 infection. Cox proportional hazards models demonstrated delayed PCR clearance with older age, multiple comorbidities, and solid organ transplant but not by degree of immunocompromise. These findings challenge current retesting practices.
Assessment of Radioactivity Contents and Radiological Effects of Marble, Granite, and Ceramic Used in Alexandria City, Egypt

Article history: Received: 30th Jan. 2021 Accepted: 5th Apr. 2021 The main aims of the present study are to analyze and internationally comparing the radioactivity contents of (Ra, Th, and K) in marbles, granites, and product and raw materials of ceramics utilized in different construction purposes in Alexandria city, additionally, the associated radiological hazard indices have been assessed. Measurements have been performed by using high-resolution gamma rays spectrometer equipped with (HPGe) detector. The mean levels of the radioactivity of (Ra, Th, and K) in marbles were 26.87, 4.30 and 19.13 Bqkg; respectively, and in granites were 42.90, 58.40, and 933.36 Bqkg;respectively, while in ceramic were 47.73, 66.09, and 385.59 BqKg; respectively. Results of ceramic raw materials showed the highest levels for Ra and Th as16307.46, and1738.69Bqkgboth are recorded in zirconium, while the highest of K as 1760.62 Bqkg in feldspar. Radiological hazards were assessed by radium equivalent activity, external and internal radiation hazard indices as well as the annual effective dose. The maximum values of indices were observed in Baltic Brown granite samples to be 425.92Bqkg, 1.15, and 1, 48 for radium equivalent, external and internal hazard indices; respectively. The observed highest external effective doses in marble, granite and ceramic were 396.53, 2109.81 , and 1495. 06μSvy;respectively. From the obtained results is clear that granite may pose health risks as well, additional regulating the amount of zircon adding to ceramic industries is highly required.
Small‐scale genetic structure and mating patterns in an extensive sessile oak forest (Quercus petraea (Matt.) Liebl.)

Abstract Oaks (Quercus) are major components of temperate forest ecosystems in the Northern Hemisphere where they form intermediate or climax communities. Sessile oak (Quercus petraea) forests represent the climax vegetation in eastern Germany and western Poland. Here, sessile oak forms pure stands or occurs intermixed with Scots Pine (Pinus sylvestris). A large body of research is available on gene flow, reproduction dynamics, and genetic structure in fragmented landscapes and mixed populations. At the same time, our knowledge regarding large, contiguous, and monospecific populations is considerably less well developed. Our study is an attempt to further develop our understanding of the reproduction ecology of sessile oak as an ecologically and economically important forest tree by analyzing mating patterns and genetic structure within adult trees and seedlings originating from one or two reproduction events in an extensive, naturally regenerating sessile oak forest. We detected positive spatial genetic structure up to 30 meters between adult trees and up to 40 meters between seedlings. Seed dispersal distances averaged 8.4 meters. Pollen dispersal distances averaged 22.6 meters. In both cases, the largest proportion of the dispersal occurred over short distances. Dispersal over longer distances was more common for pollen but also appeared regularly for seeds. The reproductive success of individual trees was highly skewed. Only 41 percent of all adult trees produced any offspring while the majority did not participate in reproduction. Among those trees that contributed to the analyzed seedling sample, 80 percent contributed 1–3 gametes. Only 20 percent of all parent trees contributed four or more gametes. However, these relatively few most fertile trees contributed 51 percent of all gametes within the seedling sample. Vitality and growth differed significantly between reproducing and nonreproducing adult trees with reproducing trees being more vital and vigorous than nonreproducing individuals. Our study demonstrates that extensive, apparently homogenous oak forests are far from uniform on the genetic level. On the contrary, they form highly complex mosaics of remarkably small local neighborhoods. This counterbalances the levelling effect of long‐distance dispersal and may increase the species’ adaptive potential. Incorporating these dynamics in the management, conservation, and restoration of oak forests can support the conservation of forest genetic diversity and assist those forests in coping with environmental change.