Miracle-dz/UniFAR-FTUs huggingface dataset:
GENETIC RELATIONSHIPS AMONG SIX MANGO (Mangifera indica L.) CULTIVARS USING RAPD MARKERS

Mango (Mangifera indica L.) is considered as one of the oldest cultivated trees in the world. Six elite mango cultivars namely, Alphonse, Ewais, Hindi khassa, Keitt, Langra and Zebda were screened using Randomly Amplified Polymorphic DNA (RAPD) genetic markers with ten random primers (12 - mer) of arbitrary sequence. The obtained results showed that, the six tested mango cultivars in this study were varied at the DNA level. A total number of 130 fragments were visualized among the investigated cultivars, including 125 polymorphic fragments. Number of produced fragments were ranged from six (A1 primer) to 18 (A9 primer) among the six cultivars. Polymorphism levels were differed from one primer to the other. The ten primers showed 83 specific molecular markers which discriminated each cultivar from the others. The highest similarity index (0.600) was recorded between Ewais and Hindi khassa cultivars, while the lowest similarity index (0.220) was observed between Ewais and Langra cultivars.
Functional Analysis of the Contribution of HIF-1alpha Proline 402 to the Interaction with VHL

Hypoxia-inducible factor 1 alpha (HIF-1α) is involved in transcription of hypoxia-inducible genes. In normoxia, it binds von Hippel-Lindau (VHL) resulting in ubiquitin-proteasome degradation. This requires hydroxylation at prolines 564 (P564) or 402 (P402) within the oxygen-dependent degradation (ODD) domain. P402 hydroxylation only occurs at higher oxygen concentrations. Its specific contribution to the HIF-1α-VHL interaction is unknown. It was hypothesized that loss of P402 in normoxia will dampen the HIF-1α-VHL interaction. HAtagged ODD constructs (WT, P402A, P564G, and P402A/P564G) were generated. FLAG-VHL co-immunoprecipitation was lower for P402A compared to WT. In vitro ubiquitination decreased with P402 mutation when P564 was also mutated. Cycloheximide chase analysis showed that P402 loss had no significant effect on ODD half-life. These results indicate a secondary role for P402 in the HIF-1alpha-VHL interaction. Elucidating the details of P402’s role in the interaction of HIF-1alpha with VHL will enhance the understanding of mammalian oxygen sensing and ubiquitin-proteasome pathways.
Investigation of valproic acid-associated oxidative stress and hepatotoxicity

A serious adverse reaction of valproic acid (VPA), a widely used anti-epileptic, is a rare but potentially fatal hepatotoxicity affecting mostly children under 2 years of age with developmental delay and who are on V P A polytherapy. The mechanism of the hepatotoxicity remains unknown. This thesis describes in vivo and in vitro studies to examine the hypothesis that V P A increases oxidative stress in rats that in turn is associated with liver toxicity. 15-F 2 t Isoprostaglandin (15-F 2 tlsoP), a free-radical catalyzed, lipid peroxidation breakdown product of arachidonic acid, was measured as an indicator of oxidative stress. Our findings showed a dose-dependent elevation in plasma and liver 15-F 2 t lsoP with plasma concentration-time profiles similar to that of the drug in rats given a single high dose of V P A . This increase in 15F 2 t lsoP did not involve cytochrome P450-mediated biotransformation even though rats treated with both phenobarbital (PB) and V P A resulted in greater levels of 15-F 2 t lsoP compared to rats treated with only V P A . These results prompted further mechanistic studies in rats to establish an association between V P A glucuronidation and 15-F 2 t lsoP levels. V P A glucuronidation, the major V P A biotransformation pathway, correlated with 15-F 2 t lsoP formation. Levels of both 15F 2 t lsoP and VPA-1-O-acyl glucuronide (VPA-G) were elevated by P B and reduced by inhibitors of VPA-glucuronidation in rats after a single dose of V P A . The fluorinated analogue of V P A (afluoro-VPA), which was a poor substrate for glucuronidation, did not elevate 15-F 2 t lsoP levels. To determine whether there was a temporal relationship between VPA-associated oxidative stress and hepatotoxicity, rats were given high daily doses of V P A for 14 days. V P A elevated levels of 15-F 2 ,lsoP prior to the onset of hepatic necrosis and steatosis. An in vitro model using primary cultured rat hepatocytes also demonstrated that V P A induces oxidative stress as measured by elevated levels of 15-F 2 t lsoP and 2',7'-dichlorofluorescein (DCF). In hepatocytes with reduced levels of glutathione, these oxidative stress biomarkers were further elevated, and
Physio-morphological analysis of rapeseed-mustardcultivars

Seven cultivars of rapeseed-mustard, viz. IGC-01 and Pusa Gaurav of Brassica carinata, Jagannath, Kranti, Rohini and TERI (0E) M21-Swarna of Brassica juncea and Hyola PAC-401 of Brassica napus, were evaluated in a randomized complete block design field experiment. Shoot length per plant, leaf number per plant, leaf area index, fresh weight per plant, dry weight per plant and net assimilation rate were studied at 45 and 60 days after sowing to assess their growth performance. Carbonic anhydrase activity, nitrate reductase activity and leaf NPK content were estimated at above stages. At maturity, pod number per plant, seed number per pod, 1000-seed weight, seed yield, oil percentage and oil yield as well as fatty acid composition of oil were estimated. The data revealed the overall superiority of Hyola PAC-401, which produced highest yield of seed and oil. It was followed by TERI (0E) M21-Swarna, which showed parity with Rohini. In comparison, Kranti performed poorly. It was also confirmed that the oil of Hyola PAC-401 and TERI (OE) M21-Swarna, was almost free from erucic acid and could, be preferred for human consumption.
Effect of Binding Agents on Quality Characteristics of Mushroom Based Sausage Analogue

Effect of binding agents (carrageenan, soy protein concentrate, casein and xanthan gum) at different concentrations on quality characteristics and nutritional properties of mushroom based sausage analogues made with 5% saturated fat was studied. Significant improvement in textural properties (purge loss and emulsion stability) was observed in samples made with carrageenan as binding agent (P < 0.5). Compression and springiness values also corroborated the same. Sausage samples with xanthan gum were rated as second best after carrageenan samples in terms of textural properties by objective evaluation but subjective evaluation by panelists rated the product as sticky. With carrageenan concentration at 0.8%, purge loss and cook loss of analogue sausages decreased by 59.63 and 55.55% respectively, while yield and emulsion stability improved by 37.62 and 67.49%, respectively, as compared to control. Sausages with SPC and casein were found to be unacceptable by subjective as well as objective evaluation. Practical Applications The concept of utilization of fat replacement additives to improve the quality characteristics of low fat meat sausages has been extended to mushroom based sausage analogues made with added fat. This will lead to development of mushroom based sausages as meat analogues and this study would further open research for utilization of mushrooms and fungal mycelia for meat replacement. Soya has been in use for years as a meat replacer and with studies in this area would open scope for utilization of mushroom for the same purpose and also for new product development from mushrooms. This would also cater to the large vegetarian population and also to the growing vegan population across the globe.
A deep learning-based method for reducing residual motion effects in diffusion parameter estimation

Purpose : Conventional motion correction techniques for diffusion MRI can introduce motion level– dependent bias in derived metrics. To address this challenge, a deep learning-based technique is developed to minimize such residual motion effects. Methods : The data-rejection approach is adopted in which motion-corrupted data are discarded before model fitting. A deep learning-based parameter estimation algorithm, using hierarchical convolutional neural network (H-CNN), is combined with a procedure of motion assessment and corrupted volume rejection. The method has been designed to overcome limitations of existing methods of this kind that produce parameter estimation whose quality depends strongly on the proportion of the data discarded. Evaluation experiments are conducted for estimation of diffusion kurtosis and diffusion tensor derived measures at both individual and group levels. The performance is compared to robust approach of iteratively reweighted linear least squares (IRLLS) after motion correction with and without outlier replacement. Results : Compared to IRLLS, the H-CNN-based technique is minimally sensitive to motion effects, as tested at severe motion levels when 70%-90% of the data are rejected, and when random motion is present, showing stable performance independent of the numbers and schemes of data rejection. A further test on dataset from children with attention deficit hyperactivity disorder demonstrates the technique can potentially ameliorate spurious group-level difference due to head motion. Conclusion : This method shows great potential for reducing residual motion effects in motion-corrupted DWI data, bringing benefits that include reduced bias in derived metrics in individual scans and reduced motion-level dependent bias in population studies employing diffusion MRI
Diosmin attenuates schizophrenia-like behavior, oxidative stress, and acetylcholinesterase activity in mice.

Objectives Diosmin (DSM), commonly isolated from various plants, is a citrus nutrient that has been shown to increase intracellular antioxidant capacity and assuage symptoms associated with neurological disorders. Deficiency in the antioxidant system has been implicated in the pathogenesis of schizophrenia. The use of antioxidants as neuroprotectants to suppress schizophrenia pathology is increasingly being sought. Hence, this study investigated the effects of DSM on schizophrenia-like behavior and the underlying changes in biomarkers of oxidative stress and acetylcholinesterase (AChE) activity in mice. Methods The acute antipsychotic effect of DSM (25, 50, and 100 mg/kg, intraperitoneally [i.p.]), haloperidol (1 mg/kg, i.p.), and risperidone (RIS) (0.5 mg/kg, i.p.) was investigated on stereotyped behaviors induced by apomorphine (2 mg/kg, i.p.) and ketamine (10 mg/kg, i.p.). The effect of DSM on ketamine-induced hyperlocomotion, immobility enhancement, and its woodblock cataleptogenic potential was evaluated. Also, the subacute antipsychotic potential of DSM was assessed following intraperitoneal injection of DSM (25-100 mg/kg, i.p.) alone and in combination with ketamine (20 mg/kg, i.p.) for 10 days. The behaviors of the animals were assessed in the open-field, Y-maze, and forced swim tests. Brains of the animals were afterward processed for spectrophotometric assay of oxidative stress and AChE contents. Results DSM (25, 50, and 100 mg/kg) attenuated apormorphine-induced stereotypy and devoid of cataleptogenic effect. DSM and RIS reversed acute and subacute ketamine-induced schizophrenia-like behaviors. Disomin alone increased cognitive function and reduced despair-like phenotype. Furthermore, DSM increased superoxide dismutase and glutathione and decreased malondialdehyde and AChE levels in naïve and ketamine schizophrenic mice. Conclusions DSM prevents schizophrenia-like behavior, attenuates oxidative stress, and AChE activity in naïve and ketamine schizophrenic mice.
CRISPR–Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes

Abstract Current clinical approaches for mutation discovery are based on short sequence reads (100–300 bp) of exons and flanking splice sites targeted by multigene panels or whole exomes. Short-read sequencing is highly accurate for detection of single nucleotide variants, small indels and simple copy number differences but is of limited use for identifying complex insertions and deletions and other structural rearrangements. We used CRISPR-Cas9 to excise complete BRCA1 and BRCA2 genomic regions from lymphoblast cells of patients with breast cancer, then sequenced these regions with long reads (>10 000 bp) to fully characterise all non-coding regions for structural variation. In a family severely affected with early-onset bilateral breast cancer and with negative (normal) results by gene panel and exome sequencing, we identified an intronic SINE-VNTR-Alu retrotransposon insertion that led to the creation of a pseudoexon in the BRCA1 message and introduced a premature truncation. This combination of CRISPR–Cas9 excision and long-read sequencing reveals a class of complex, damaging and otherwise cryptic mutations that may be particularly frequent in tumour suppressor genes replete with intronic repeats.
An affordance perspective of team collaboration and enforced working from home during COVID-19

ABSTRACT COVID-19 has caused unprecedented challenges to our lives. Many governments have forced people to stay at home, leading to a radical shift from on-site to virtual collaboration for many knowledge workers. Existing remote working literature does not provide a thorough explanation of government-enforced working from home situations. Using an affordance lens, this study explores the sudden and enforced issues that COVID-19 has presented, and the technological means knowledge workers use to achieve their team collaboration goals. We interviewed 29 knowledge workers about their experiences of being required to work from home and introduced the term “enforced work from home”. This paper contributes to the affordance theory by providing an understanding of the substitution of affordances for team collaboration during COVID-19. The shifting of affordances results in positive and negative effects on team collaboration as various affordances of technology were perceived and actualised to sustain “business as usual”.
Are buyers of forest ecosystem services willing to consider distributional impacts of payments to local suppliers? Results from a choice experiment in Antananarivo, Madagascar

SUMMARY A controversial issue in the debate on payments for ecosystem services (PESs) is whether distributional goals should be considered in the design of such schemes. We contribute to this debate by analysing the preferences of citizens of Antananarivo (Madagascar) as potential buyers of forest ecosystem services from a developing country. We conducted a choice experiment to investigate citizens’ willingness to pay to conserve the endemic spiny forests in southwest Madagascar and their preferences for including distributional goals in the design of a PES scheme aimed at spiny forest conservation. We found that respondents were willing to pay for forest conservation and preferred a PES scheme in which the poorest households in a community would receive the largest share of payments over a scheme in which every household would receive the same share, which, in turn, they preferred over a PES scheme in which they would have no information about its distributional impact. In comparing these results with those of a similar survey in a developed country (in Cottbus, Germany), we find that the preference ranking regarding distributional impacts is identical. However, citizens in Cottbus attach greater importance to the consideration of distributive goals in PESs than citizens in Antananarivo.
Technical note: Interpolated Pareto surface similarity metrics for multi-criteria optimization in radiation therapy.

PURPOSE There is a strong clinical need to evaluate different multi-criteria optimization (MCO) algorithms, including inverse optimization sampling algorithms and machine learning-based predictions. This study aims to develop and compare several interpolated Pareto surface similarity metrics. METHODS AND MATERIALS The first metric is the root-mean-square error (RMSE) evaluated between vertices on the interpolated surfaces, augmented by intra-simplex sampling of the barycentric coordinates of the surfaces' simplicial complexes. The second metric is the average projected distance (APD), which evaluates the displacements between the vertices and computes their projections along the mean displacement. The third metric is the average nearest-point distance (ANPD), which numerically integrates point-to-simplex distances over the sampled simplices of the interpolated surfaces. These metrics were compared by their convergence rates, the times required to achieve convergence, and their representation of the underlying surface interpolations. For analysis, several interpolated Pareto surface pairs were constructed abstractly, with one pair from a nasopharyngeal treatment planning case using MCO. RESULTS Convergence within 1% is typically achieved at approximately 50 and 80 samples per barycentric dimension for the RMSE and the ANPD, respectively. Calculation requires approximately 1 millisecond and 10 milliseconds to achieve convergence for the RMSE and the ANPD in two dimensions, respectively, while the APD always requires less than 1 millisecond. These time costs are much higher in higher dimensions for just the RMSE and ANPD. The APD values more closely approximated the ANPD limits than the RMSE limits. CONCLUSION The ANPD's formulation and generality make it likely more meaningful than the RMSE and APD for representing the similarity between the underlying interpolated surfaces rather than the sampling points on the surfaces. However, in situations requiring high-speed evaluations, the APD may be more desirable due to its speed, independence from a subjectively chosen sampling rate, and similarity to the ANPD limits.
A pairwise pseudo‐likelihood approach for left‐truncated and interval‐censored data under the Cox model

Left truncation commonly occurs in many areas, and many methods have been proposed in the literature for the analysis of various types of left‐truncated failure time data. For the situation, a common approach is to conduct the analysis conditional on truncation times, and the method is relatively simple but may not be efficient. In this paper, we discuss regression analysis of such data arising from the proportional hazards model that also suffer interval censoring. For the problem, a pairwise pseudo‐likelihood approach is proposed that aims to recover some missing information in the conditional methods. The resulting estimator is shown to be consistent and asymptotically normal. A simulation study is conducted to assess the performance of the proposed method and suggests that it works well in practical situations and is indeed more efficient than the existing method. The approach is also applied to a set of real data arising from an AIDS cohort study.
Zebrafish as an Animal Model for Ocular Toxicity Testing: A Review of Ocular Anatomy and Functional Assays

Xenobiotics make their way into organisms from diverse sources including diet, medication, and pollution. Our understanding of ocular toxicities from xenobiotics in humans, livestock, and wildlife is growing thanks to laboratory animal models. Anatomy and physiology are conserved among vertebrate eyes, and studies with common mammalian preclinical species (rodent, dog) can predict human ocular toxicity. However, since the eye is susceptible to toxicities that may not involve a histological correlate, and these species rely heavily on smell and hearing to navigate their world, discovering visual deficits can be challenging with traditional animal models. Alternative models capable of identifying functional impacts on vision and requiring minimal amounts of chemical are valuable assets to toxicology. Human and zebrafish eyes are anatomically and functionally similar, and it has been reported that several common human ocular toxicants cause comparable toxicity in zebrafish. Vision develops rapidly in zebrafish; the tiny larvae rely on visual cues as early as 4 days, and behavioral responses to those cues can be monitored in high-throughput fashion. This article describes the comparative anatomy of the zebrafish eye, the notable differences from the mammalian eye, and presents practical applications of this underutilized model for assessment of ocular toxicity.
Spatial and temporal shift in the factors affecting the population dynamics of Calanus copepods in the North Sea

The swap in abundance between two Calanus species in the North Sea during the 1980s constitutes a quintessential example of regime shift, with important ecosystemic and economic repercussions because these copepods constitute a major component of the diet of larval and juvenile cods. It is hypothesized that this transition was driven by gradual changes in primary productivity, the North Atlantic Oscillation (NAO) and sea surface temperatures (SST), and yet how these factors contribute to the population dynamics of these two species and the overall regime shift remains unclear. Here, we combine a highly resolved and spatially structured longitudinal dataset with population dynamics theory‐based models to obtain a thorough and more detailed description of populations’ responses to the regime shift observed in the North Sea. Our analyses highlight that this transition exhibits a clear spatial structure and involved a decoupling between the dynamics of Calanus finmarchicus and the NAO in western regions and between Calanus helgolandicus and SST in the eastern regions of the North Sea. Consequently, the observed switch in abundance between these species reflects the interaction between species‐specific attributes, a well‐defined spatial structure with a marked east–west axis and a decoupling between the ecological drivers and Calanus population dynamics following the shift. Succinctly, we suspect that higher water temperatures have favored C. helgolandicus and resulted in restrictive conditions for C. finmarchicus, eventually overshadowing the effects of NAO detected in historical records. Overall, our study illustrates how population dynamics theory can be successfully employed to disentangle the complex and multifactorial nature of a regime shift in response to gradually changing environmental conditions.
Impacts of water stress, environment and rootstock on the diurnal behaviour of stem water potential and leaf conductance in pistachio (Pistacia vera L.).

Little information is available on the diurnal behaviour of water potential and leaf conductance on pistachio trees despite their relevance to fine tune irrigation strategies. Mature pistachio trees were subject to simultaneous measurements of stem water potential (Ψ x ) and leaf conductance (g l ) during the day, at three important periods of the irrigation season. Trees were grown on three different rootstocks and water regimes. An initial baseline relating Ψ x to air vapor pressure deficit (VPD) is presented for irrigation scheduling in pistachio. Ψ x was closely correlated with VPD but with a different fit according to the degree of water stress. No evidence of the variation of Ψ x in relation to the phenology of the tree was observed. Furthermore, midday Ψ x showed more accuracy to indicate a situation of water stress than predawn water potential. Under well irrigated conditions, g l was positively correlated with VPD during stage II of growth reaching its peak when VPD reached its maximum value (around 4 kPa). This behaviour changed during stage III of fruit growth suggesting a reliance of stomatal behaviour to the phenological stage independently to the tree water status. The levels of water stress reached were translated in a slow recovery of tree water status and leaf conductance (more than 40 days). Regarding rootstocks, P. integerrima showed little adaptation to water shortage compared to the two other rootstocks under the studied conditions.