Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-cultural adaptation and psychometric evaluation of the Yoruba version of Oswestry disability index

Introduction Low Back Pain is a common public health problem worsened by maladaptive beliefs and incongruent back pain behaviour. It is imperative to develop outcome measures to assess these beliefs among patients with chronic LBP. This study aimed to cross-culturally adapt and determine the psychometric properties of the Yoruba version of the ODI (ODI-Y). Methods The ODI-Y was cross-culturally adapted following the process involving forward translation, synthesis, backward translation, expert review, and pilot testing. One hundred and thirty-six patients with chronic LBP took part in the validation of the ODI-Y; 86 of these individuals took part in the test-retest reliability (within 1-week interval) of the translated instrument. Internal consistency and test-retest reliability of the ODI-Y were determined using the Cronbach’s alpha and intra-class correlation. Other psychometric properties explored included the factor structure and fit, convergent validity, standard error of measurement and the minimal detectable change. Results The mean age of the respondents was 50.5±10.6years. The ODI-Y showed a high internal consistency, with a Cronbach’s alpha (α) of 0.81. Test-retest of the Yoruba version of the ODI within 1-week interval yielded an Intra-Class Correlation coefficient of 0.89. The ODI-Y yielded a two-factor structure which accounted for 51.7% of the variance but showed poor fit. Convergent of ODI-Y with the visual analogue scale was moderate (r=0.30; p=0.00). The standard error of measurement and minimal detectable change of the ODI-Y were 2.0 and 5.5. Conclusions The ODI was adapted into the Yoruba language and proved to have a good factor structure and psychometric properties that replicated the results of other obtainable versions. We recommend it for use among Yoruba speaking patients with low-back pain.
The root-associated microbiome and agricultural nitrogen use efficiency

Agricultural nitrogen (N) waste is a serious problem that causes many environmental issues. Plant roots and microorganisms work in synchrony; roots exude carbon which fuels the metabolism of microorganisms, and microbes in turn increase N availability near the root that both plants and microbes can use. There is mounting interest in taking advantage of this interaction to better couple N availability with crop demand. This thesis explores questions regarding how plant roots and agricultural management interact to affect the root microbiome, with implications for soil N retention. We compared two cropping systems at the Marsden experimental farm: conventional (two-year rotation, inorganic fertilization) and diversified (four-year rotation, manure inputs). Chapter 2 investigates how maize development and agricultural management interact to shape the root-associated community. We used next-generation amplicon sequencing to assess the prokaryotic and fungal communities at four points in maize development corresponding to high or low predicted plant N demand in both cropping systems. We found that prokaryotic and fungal communities follow different patterns of assembly in relation to maize development. Additionally, roots in the diversified system hosted a bacterial community better suited to complex C decomposition at a period of high predicted N demand, implicating better coupling of N mineralization in the soil to plant demand. Chapter 3 examines competition between arbuscular mycorrhizal fungi (AMF), symbionts that help roots absorb nutrients from the soil, and ammonia-oxidizing (AO) bacteria and archaea (AOB, AOA), which mediate ammonium conversion to nitrate. Competition between these groups for ammonium may reduce AO abundance and hence nitrate leaching from soil. We used quantitative PCR to assess the abundances of AOB
Effect of timing of postweaning xylanase supplementation on growth performance, nutrient digestibility, and fecal microbial composition in weanling pigs

Abstract: Effect of timing of xylanase supplementation to weanling pigs and its effect on growth performance, nutrient digestibility, and fecal microbiota was investigated. A total of 128 weanling pigs [(Hampshire × Duroc) × (Yorkshire × Landrace); 6.2 ± 0.6 kg body weight (BW); weaning age: 21 d] were assigned to four treatments, with eight replicate pens and four pigs per pen. Treatments were a combination of two dietary treatments (without or with xylanase) in two periods; (period 1, days 0–14) and period 2 (days 14–42): xylanase–xylanase, xylanase–control, control–xylanase, and control–control. Fecal microbiota diversity and apparent total tract digestibility (ATTD) were determined. From days 0–14, pigs had lower (P < 0.01) BW, average daily gain (ADG), and feed efficiency when xylanase was included in the diets. The final BW (P < 0.05) and overall ADG (P < 0.02) at day 42 were greater when xylanase was supplemented from day 14 compared with supplementation from day 0. The apparent ileal digestibility and ATTD of dry matter, gross energy, nitrogen, and phosphorus were increased (P < 0.05) by xylanase. Xylanase significantly decreased (P < 0.05) the relative abundance of Veillonella spp. and tended (P = 0.08) to decrease the relative abundance of Megasphaera spp. in period 2 compared with the non-supplemented group.
The Medicinal Role of Centella asiatica and Its Applications in the Dahi: A Research Review

Thankuni, scientifically known as Centella asiatica is a ground creeper and whole plant is used for medicinal purpose. The leaf juice is used as a good health tonic and also gives relief from hypertension, CNS and gastrointestinal diseases. Thankuni extract is incorporated with dahi to improve the medicinal value. These properties have been ascribing to the active principles viz., Asiatic acid, Asiaticoside, madecassic acid, and madecassocide. These are pentacyclic triterpenes, found to display venous insufficiency, various vein and wound healing properties.
Effects of inbreeding on performance traits in Karan Fries crossbred cattle

Present study includes the effect of inbreeding on expected genetic gain and estimation of regression with respect to first lactation production, reproduction and lifetime traits in Karan Fries crossbred cattle maintained at ICAR-NDRI, Karnal. Out of total, only 36.97% were found to be inbred with an average inbreeding coefficient 3.68%. Overall least squares mean for reproduction traits (days) AFC, SP, DP and CI were 1020.41 ± 5.49, 141.42± 3.86, 74.54 ± 2.04 and 421.20 ± 3.81 respectively. For production traits (kg) were 305MY, LL, LTMY, FY and SNFY were 3169.15 ± 37.87, 353.25 ± 4.18, 3686.10 ± 55.10, 266.19 ± 4.66 and 127.81 ± 2.26 respectively and lifetime traits like LTMY and stayability were 14588.47 ± 486.09 (kg) and 2444.69 ± 41.26 (days) respectively. Among reproduction traits (days), AFC increased by +3.70, DP +3.66 and CI +68.44 however SP decreased by -0.85 d and production traits (kg), 305MY decreased by -10.2 TMY -16.09, LL -1.23 d, 305FY -1.75, 305SNFY - 0.26, LTMY 202.02 and stayability -17.37 days per unit increase in the inbreeding coefficient. Although there was no inbreeding depression in any of the traits except AFC. The expected genetic gain of AFC increased two folds in IBL2 (Fx >5%) as compared to IBL1 (Fx<5) group that is not desirable, so in future, to maintain the optimum genetic gain we should keep inbreeding at optimum level and so more precise pedigree recording and planned mating strategies should be adopted to avoid inbreeding depression in next generation.
Breadth of the thermal response captures individual and geographic variation in temperature‐dependent sex determination

Population‐scale responses of key ecological traits to local environmental conditions provide insight into their adaptive potential. In species with temperature‐dependent sex determination (TSD), short‐term, individual developmental responses to the incubation environment have long‐term consequences for populations. We took a model‐based approach to study within‐ and among‐population variation in the physiological components of TSD in 12 populations of painted turtles (Chrysemys picta). We used laboratory and field incubation data to quantify variation in thermal reaction norms at both population and clutch scales, focusing on the pivotal temperature that produces a 1:1 sex ratio (P) and the transitional range of incubation temperatures (TRTs) that produce mixed sex ratios. Defying theoretical expectations, among‐population variation in P was not convincingly explained by geography or local thermal conditions. However, within some populations, P varied by >5°C at the clutch scale, indicating that the temperature sensitivity of gonadal differentiation can vary substantially among individual nesting females. In addition, the TRT was wider at lower latitudes, suggesting responsiveness to local incubation conditions. Our results provide a potential explanation for discrepancies observed between constant‐temperature experimental results and outcomes of fluctuating incubation conditions experienced in natural nests, exposing important knowledge gaps in our understanding of local adaptation in TSD and identifying shortcomings of traditional laboratory studies. Understanding individual variation and the timing of gonadal differentiation is likely to be far more useful in understanding local adaptation than previously acknowledged. A free Plain Language Summary can be found within the Supporting Information of this article.
Biocultural Species Enhancement in the Archaeological Site of Tzintzuntzan, the “Place of Hummingbirds”

Biocultural species enhancement within archaeological sites is particularly challenging because restoration goals and the preservation of cultural assets need to be met simultaneously. Biocultural restoration aims to reestablish the ecological components while preserving or restoring the cultural components of the site, as well as the relationships between them. Biocultural species enhancement is one component of these efforts. Biocultural species enhancement within archaeologically protected sites can establish multiple connections among nature and culture; yet, it can be complicated by the need to preserve the archaeological remains. Tzintzuntzan, in the State of Michoacan, Mexico, holds the remains of the capital of the Tarascan empire. Due to ecological degradation of Tzintzuntzan’s landscape, hummingbirds are seldom seen within the archeological site. As part of a project that aims to restore habitat components for hummingbirds within the Tzintzuntzan Archaeological Site, we established patches of the native Salvia fulgens (Mexican red sage). Initially, potted S. fulgens plants were temporarily placed within the study site to test the feasibility of attracting hummingbirds by providing feeding resources. Five hummingbird species were recorded using the sage pots, with Cynanthus latirostris (Broad-billed hummingbird) being the most frequent. Results of this study show that at least 37 flowers per patch are needed to attract C. latirostris. A permanent S. fulgens plantation was established to provide this habitat at Tzintzuntzan.
Out of the blue: Phototropins of the leaf vascular bundle sheath mediate the regulation of leaf hydraulic conductance by blue light

The Arabidopsis leaf veins bundle sheath cells (BSCs) – a selective barrier to water and solutes entering the mesophyll – increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs’ expression of PHOT1 and PHOT2, and the known blue-light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs’ phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5phot2-1, and aha2-4 was lower than that of the WT. BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light – ineffective in the phot1-5 mutant – acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts’ water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance. One-Sentence summary Blue light regulates the leaf hydraulic conductance via the bundle-sheath cells’ blue light PHOT receptors which, via an autonomous signaling pathway, activate the BSCs’ AHA2 H+-pump.
Site‐Specific Load‐Induced Expansion of Sca‐1+Prrx1+ and Sca‐1−Prrx1+ Cells in Adult Mouse Long Bone Is Attenuated With Age

Aging is associated with significant bone loss and increased fracture risk, which has been attributed to a diminished response to anabolic mechanical loading. In adults, skeletal progenitors proliferate and differentiate into bone‐forming osteoblasts in response to increasing mechanical stimuli, though the effects of aging on this response are not well‐understood. Here we show that both adult and aged mice exhibit load‐induced periosteal bone formation, though the response is significantly attenuated with age. We also show that the acute response of adult bone to loading involves expansion of Sca‐1+Prrx1+ and Sca‐1−Prrx1+ cells in the periosteum. On the endosteal surface, loading enhances proliferation of both these cell populations, though the response is delayed by 2 days relative to the periosteal surface. In contrast to the periosteum and endosteum, the marrow does not exhibit increased proliferation of Sca‐1+Prrx1+ cells, but only of Sca‐1−Prrx1+ cells, underscoring fundamental differences in how the stem cell niche in distinct bone envelopes respond to mechanical stimuli. Notably, the proliferative response to loading is absent in aged bone even though there are similar baseline numbers of Prrx1 + cells in the periosteum and endosteum, suggesting that the proliferative capacity of progenitors is attenuated with age, and proliferation of the Sca‐1+Prrx1+ population is critical for load‐induced periosteal bone formation. These findings provide a basis for the development of novel therapeutics targeting these cell populations to enhance osteogenesis for overcoming age‐related bone loss. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
Kinetic Inference Resolves Epigenetic Mechanism of Drug Resistance in Melanoma

We resolved a mechanism connecting tumor epigenetic plasticity with non-genetic adaptive resistance to therapy, with MAPK inhibition of BRAF-mutant melanomas providing the model. These cancer cells undergo multiple, reversible drug-induced cell-state transitions, ultimately yielding a drug-resistant mesenchymal-like phenotype. A kinetic series of transcriptome and epigenome data, collected over two months of drug treatment and release, revealed changing levels of thousands of genes and extensive chromatin remodeling. However, a 3-step computational algorithm greatly simplified the interpretation of these changes, and revealed that the whole adaptive process was controlled by a gene module activated within just three days of treatment, with RelA driving chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes. These findings were confirmed across several patient-derived cell lines and in melanoma patients under MAPK inhibitor treatment. Co-targeting BRAF and histone-modifying enzymes arrests adaptive transitions towards drug tolerance in epigenetically plastic melanoma cells and may be exploited therapeutically.
Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application to Listeria monocytogenes

Automatic de novo identification of the main regulons of a bacterium from genome and transcriptome data remains a challenge. To address this task, we propose a statistical model of promoter DNA sequences that can use information on exact positions of the transcription start sites and condition-dependent expression profiles. Two main novelties are to allow overlaps between motif occurrences and to incorporate covariates summarising expression profiles (e.g. coordinates in projection spaces or hierarchical clustering trees). All parameters are estimated using a dedicated trans-dimensional Markov chain Monte Carlo algorithm that adjusts, simultaneously, for many motifs and many expression covariates: the width and palindromic properties of the corresponding position-weight matrices, the number of parameters to describe position with respect to the transcription start site, and the choice of relevant expression covariates. A data-set of transcription start sites and expression profiles available for the Listeria monocytogenes is analysed. The results validate the approach and provide a new global view of the transcription regulatory network of this important model food-borne pathogen. A previously unreported motif that may play an important role in the regulation of growth was found in promoter regions of ribosomal protein genes.
An Integrated Pipeline for Combining in vitro Data and Mathematical Models Using a Bayesian Parameter Inference Approach to Characterize Spatio-temporal Chemokine Gradient Formation

All protective and pathogenic immune and inflammatory responses rely heavily on leukocyte migration and localization. Chemokines are secreted chemoattractants that orchestrate the positioning and migration of leukocytes through concentration gradients. The mechanisms underlying chemokine gradient establishment and control include physical as well as biological phenomena. Mathematical models offer the potential to both understand this complexity and suggest interventions to modulate immune function. Constructing models that have powerful predictive capability relies on experimental data to estimate model parameters accurately, but even with a reductionist approach most experiments include multiple cell types, competing interdependent processes and considerable uncertainty. Therefore, we propose the use of reduced modeling and experimental frameworks in complement, to minimize the number of parameters to be estimated. We present a Bayesian optimization framework that accounts for advection and diffusion of a chemokine surrogate and the chemokine CCL19, transport processes that are known to contribute to the establishment of spatio-temporal chemokine gradients. Three examples are provided that demonstrate the estimation of the governing parameters as well as the underlying uncertainty. This study demonstrates how a synergistic approach between experimental and computational modeling benefits from the Bayesian approach to provide a robust analysis of chemokine transport. It provides a building block for a larger research effort to gain holistic insight and generate novel and testable hypotheses in chemokine biology and leukocyte trafficking.
Co‐occurrence patterns and morphological similarity of semiaquatic insects (Hemiptera: Gerromorpha) in streams of Eastern Amazonia

1. To understand how the semiaquatic bug communities are shaped, it was first verified whether there was a pattern of co‐occurrence between species. It was subsequently tested whether the pattern found was related to environmental variables. Lastly, it was verified whether morphological divergence between species was present in the morphological and functional traits selected.
Effects of Captivity and Season on the Gut Microbiota of the Brown Frog (Rana dybowskii)

The gut microbiota of amphibians is affected by exogenous and endogenous factors. We performed a comprehensive analysis using high-throughput sequencing technology and functional predictions and observed general changes in the gut microbiota of frogs in different growth stages, seasons, and growth environments. There were no significant differences in microbial richness and diversity between juvenile and adult wild frogs, between the summer and autumn groups of captive frogs, or between wild and captive frogs. There were significant differences in the gut microbiota community structure of Rana dybowskii between the summer and autumn groups of captive frogs and between wild and captive R. dybowskii, whereas the differences between juvenile and adult wild frogs were not significant. The dominant gut bacterial phyla in frogs from both captive and wild environments included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Linear discriminant effect size (LEfSe) analysis showed that Bacteroidetes and Firmicutes were significantly enriched in captive and wild R. dybowskii, respectively linear discriminant analysis (LDA > 4). The core operational taxonomical units (OTUs) that were found in >90% of all frogs tested encompassed 15 core OTUs. The captive frogs exhibited 15 core OTUs in addition to the above overall core microbiota, whereas the wild frogs exhibited 19 core OTUs in addition to the above overall core microbiota. Predictions made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that eleven KEGG pathways, such as infectious diseases, immune system diseases, metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, metabolism of terpenoids and polyketides, neurodegenerative diseases, and transport and catabolism, were enriched in captive frogs. The relative abundance of several red-leg-syndrome-related pathogens increased significantly in captive frogs compared with that in wild frogs. To our knowledge, this is the first study on the effects of individual seasons and captivity on the gut microbiota of frogs.
Detection of Mycobacterium bovis in whey, by multiplex polymerase chain reaction (PCR) and bacteriological culture

The objective of this study was to detect the presence of Mycobacterium bovis (M. bovis) in whey. A total of 233 cow milk samples were analyzed together with 26 tank milk samples that came from dairy herds of several states of the Mexican Republic (Queretaro, San Luis Potosi, Guanajuato, Hidalgo, Coahuila). DNA was obtained from whey and used for polymerase chain reaction-multiplex (PCR-M). Tuberculosis complex was first identified through the detection of gene RD1. Positive samples were subjected to a second PCR-M with the primers for gene RD9 to identify M. bovis. Samples were bacteriologically cultured using conventional techniques for the isolation of mycobacteria. Cohen’s Kappa test (k) and Pearson’s Chi2 were carried out for statistical analysis. A 150 bp amplification product of the RD1 region was obtained, which corresponds to the tuberculosis complex, in 34/233 (14.59%) of the individual milk samples and in 4/26 (15.38%) of the tank milk samples. PCR-M with primer RD9, of the 34 individual samples and the 4 tank milk samples, gave an amplification product of 200 pb, which is the expected product for M. bovis. By bacteriological culture, six isolates were obtained; four in individual whey samples and two from tank milk samples, which were then classified by biochemical tests as M. bovis. The concordance between RD1, RD9 PCR-M and bacteriological culture was low, but there was a significant difference between diagnostic techniques with a P = 0.000. The results showed the potential of the PCR-M as a confirmatory test for the diagnosis of tuberculosis in cattle, as well as the advantage of using whey samples, that may be a possible source of infection for the herd and/or humans. Key words: Bovine tuberculosis, whey, polymerase chain reaction-multiplex (PCR-M), RD1, RD9, milk, isolation.