Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of fire severity and salvage logging traffic on regeneration and early growth of aspen suckers in north-central Alberta

Density and growth of trembling aspen (Populus tremuloides Michx.) were measured in the first two years following wildfire to determine the effects of: 1) fire severity and 2) salvage logging damage on sucker regeneration. Results indicate that stand leaf area was not affected by fire severity, although the greatest number of suckers was produced following high severity burns. In contrast, plots with the highest level of machine disturbance in the salvage-logging study had 60% fewer suckers compared to the non-trafficked plots. These suckers tended to be smaller and had less leaf area than the non-trafficked plots, resulting in a stand leaf area reduction of up to 75%. This suggests that salvage logging could have a negative impact on the future growth and productivity of regenerating aspen stands. Key words: trembling aspen, regeneration, suckering, leaf area, wildfire, fire severity, salvage logging, machine traffic
Influence of Conditions of Maize Starch Enzymatic Hydrolysis on Physicochemical Properties of Glucose Syrups

Amylose complexed with lipid is more resistant to the attack of amylolytic enzymes than the free polysaccharide. The susceptibility of amylose-lipid complexes (AML) present in maize starch to enzymatic digestion still remains obscure, although the enzymatic hydrolysis of AML with defined composition, prepared from amylose and selected lipids, was an objective of several research projects. Therefore our studies were aimed at elucidation of AML properties and their relationship with features of maize starch hydrolysates, particularly with respect to the character of a lipolytic enzyme, additionally used for saccharification, apart from the glucoamylase. Differential scanning calorimetry (DSC) measurements revealed that treatment of maize starch with suitable α-amylase preparation resulted in significant degradation of AML. More pronounced cleavage of AML can be also achieved by using both amylolytic and lipolytic enzymes for starch saccharification. The lysophospholipase appeared to be particularly active towards AML when used with glucoamylase. The common application of these enzymes brought about an enhanced glucose yield and filtration rate, and better color and transparency of the final product.
Nutrient utilization by caterpillars of the generalist beet armyworm, Spodoptera exigua

Abstract Beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), caterpillars are destructive crop pests responsible for considerable annual economic losses. These generalist herbivores are challenged with a diversity of dietary choices that can impact their survival, development and fecundity. In the present study, dietary choices of S. exigua caterpillars, based on the protein to digestible carbohydrate (P : C) ratio of the food, and the impact of nutritionally unbalanced foods on caterpillar performance are assessed. In choice experiments, individual third‐instar caterpillars are offered simultaneously a P‐biased and a C‐biased food until pupation. Caterpillars feed nonrandomly and select a slightly P‐biased diet (22P : 20C). In no‐choice experiments, second instar caterpillars are reared until pupation on diets ranging in P : C ratio from extremely P‐ to extremely C‐biased. High mortality and delayed development are observed on the C‐rich, P‐poor diets, highlighting the potential deleterious effects of excess carbohydrates and the importance of protein for growth and development. Diet‐dependent differences in pupal weight or pupal lipid reserves are not observed. This contrasts with closely‐related Spodoptera species where pupal mass and lipid stores increase on C‐rich, P‐poor diets. On the extremely P‐biased diet, performance is similar to that of individuals reared on the self‐selected diet, suggesting that these caterpillars may efficiently be deaminating excess amino acids to generate carbon skeletons, which are shunted into lipid biosynthesis. Spodoptera exigua caterpillars exhibit flexible and efficient pre‐ingestive nutrient intake regulation and post‐ingestive utilization, allowing these generalist feeders to cope with the heterogeneous diets they may encounter.
Rapid monitoring of health services utilization following a shift in coverage from brand name to biosimilar drugs in British Columbia—An interim report

We explored changes in health services utilization associated with the Biosimilars Initiative introduced in British Columbia on May 27, 2019. To maintain drug coverage, the policy requires users of originator infliximab or etanercept to transition to biosimilar versions. We present a three‐month interim analysis of this initiative.
A Snapshot of RTI Implementation a Decade Later: New Picture, Same Story

Response to intervention (RTI) has evolved from its first decade of implementation. Because states guide and regulate policy and practice at the state and local education agency levels, it is important to understand their critical role in RTI implementation. A systematic review of all 50 state education agency websites was conducted to provide an updated “snapshot” of states’ interpretation of RTI a decade after IDEA regulations were finalized. Findings revealed substantive progress towards developing approaches to systematic supports to students, with a major trend in adoption of multi-tiered system of support (MTSS) models. Findings also documented continued variation in how states are communicating about tiered systems on such matters as the roles of tiered systems in schoolwide prevention frameworks, meeting special education requirements, and aligning multiple systems within schools. Implications for special education services for students with learning disabilities are discussed.
Polyphenol profile and content in wild and cultivated Cynara cardunculus L.

The species Cynara cardunculus L. is native to the Mediterranean Basin, where its commercial production makes a significant contribution to the agricultural economy. It contains phenolic acids and flavones, which play an important role in diet, because of their beneficial effects on human health, and in industrial processing, due to the browning phenomenon. The quantitative and qualitative profile of these compounds is affected by different factors, such as genotype, environmental conditions, crop management and processing procedures. As a consequence, these are relevant for defining the quality of the product. Therefore, our aim was to review the main factors that influence polyphenol biosynthesis and degradation in C. cardunculus. From available data in literature, the genetic background appears to be the main factor, followed by environmental effects. However, crop management also could be a valuable tool to enhance the polyphenol content. C. cardunculus also provides substantial quantities of polyphenol-rich by-products, which could be considered as a natural source of health-promoting compounds and an added value for the farming business.
The effect of multiple simulation parameters on MM/PBSA performance for binding affinity prediction of CB1 cannabinoid receptor agonists and antagonists

Both the inactive‐ and active‐state CB1 receptor crystal structures have now been solved, allowing their application in various structure‐based drug design methods. One potential method utilizing these crystal structures is the Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) method of predicting relative binding free
Phosphorus uptake by arbuscular mycorrhizal hyphae does not increase when the host plant grows under atmospheric CO2 enrichment.

• We conducted an experiment to test whether phosphorus (P) uptake by mycorrhizal hyphae could be enhanced by growing the host plant under [CO2 ] enrichment and whether any response to [CO2 ] was dependent on C source-sink relationships. • Plant C assimilation, mass allocation, growth and P uptake were measured in pea (Pisum sativum) plants inoculated with 0, 1 or 5% of a mixture of three Glomus spp. Intra- and extra-radical mycorrhizal development was followed and hyphal 33 P uptake from a root-exclusion compartment was measured. • Total P and 33 P content measurements indicated that root, not hyphal, P uptake was increased by elevated [CO2 ] in the mycorrhizal treatments and that hyphal P uptake was actually reduced by elevated [CO2 ] after 57 d. Neither intra- nor extraradical mycorrhizal development was related to this response. • Plant and fungal measurements suggested positive interactions in plant growth and P uptake only when C source-sink relationships were balanced; high C source (enhanced assimilation at elevated [CO2 ]) and high C sink (increasing mycorrhizal development). The results also indicated that enhanced plant C supply does not alter growth or function of arbuscular mycorrhizal fungi.
The Effects of Genetic Transformation of Tomato with Antisense Phospholipase D cDNA on the Quality Characteristics of Fruits and Their Processed Products

Abstract The physico-chemical characteristics of tomato juice and sauce, prepared from transgenic tomato fruits (Lycopersicon esculentum Mill, var. Celebrity) transformed with an antisense phospholipase D (PLD) cDNA construct, were evaluated. The antisense transformation resulted in a 30–40% reduction of PLD activity in ripe fruits. The transgenic fruits were firmer, possessed better red color, and flavor. The juice and sauce preparations from transgenic fruits showed improved red color, lycopene content, Brookfield viscosity, and increased levels of major flavor volatiles such as hexenal. The dry matter and ash contents, as well as the precipitate weight ratio (PPT) of the transgenic fruit products were significantly higher when compared to the products from control fruits. The vitamin C content of the transgenic fruits was also higher as compared to the control fruits. The results suggest that a reduction in PLD activity may lead to increased membrane stability and preservation of membrane compartmentalization that can have positive quality impacts in transgenic fruits and their products.
Historical and current distribution, population size and possible migration routes of the Blue Swallow Hirundo atrocaerulea in Africa

Summary The Blue Swallow Hirundo atrocaerulea is restricted to sub-Saharan Africa, its population size previously estimated at fewer than 1,500 pairs, and is classified as Vulnerable. A better understanding of its current distributional range, population size, protection status and migration routes would improve our ability to conserve the species and the grassland and wetland habitat on which it depends. We now estimate that the Blue Swallow population in the 1850s may have numbered between 1,560 and 2,300 pairs. Based on an assessment of available data, we now estimate the total current Blue Swallow population at 1,006 pairs or 2,012 individuals, an estimated 36–56% decline over the last 150 years. There may be three separate Blue Swallow sub-populations and seven separate migratory routes between their breeding and non-breeding grounds. The Blue Swallow’s range in South Africa and Swaziland has contracted by 74%. The majority of Blue Swallows occupy unprotected areas on their non-breeding grounds in the Democratic Republic of the Congo, Uganda and Kenya. The Blue Swallow population in Africa will continue to decline unless the causes of reduction in Blue Swallow habitat quantity and quality can be stopped and sufficient and additional habitat set aside to sustain viable Blue Swallow populations throughout their range.
Overall clinical outcomes of Descemet membrane endothelial keratoplasty in 600 consecutive eyes: A large retrospective case series

Purpose: To analyze the overall clinical outcomes of Descemet membrane endothelial keratoplasty (DMEK) in 600 consecutive cases. Methods: Retrospective, consecutive interventional case series operated by a single surgeon. Six hundred consecutive eyes of 524 patients with endothelial dysfunctions of different etiologies scheduled for DMEK were included in this study. All donor tissues were prepared by the operating surgeon during the procedure, using McCarey Kaufman medium or Cornisol-preserved cornea with endothelial cell density (ECD) of ≥2500 cells/mm2. Indications, postoperative best spectacle-corrected visual acuity (BSCVA), ECD, endothelial cell loss (ECL), and complications were analyzed postoperatively between 3 months and 2 years. Results: The commonest indication was post-cataract corneal edema/bullous keratopathy in 262 (43.7%) eyes followed by Fuchs' endothelial corneal dystrophy 218 (36.3%). Vision affected comorbidities were present in 91 (15.2%) eyes. In phakic eyes with cataract (222; 37%), DMEK was combined with cataract surgery (Triple-DMEK). BSCVA of ≥20/25 was achieved in 41.0%, 46.4%, 49.2%, and 48.7% of eyes at 3, 6, 12, and 24 months, respectively and stabilized at 6 months (P = 0.54). Mean ECD decreased from 2884 ± 178 cells/mm2 (n = 600) before surgery to 2223 ± 321 (n = 597), 2099 ± 354 (n = 524), 1918 ± 373 (n = 374), and 1772 ± 439 cells/mm2 (n = 158) at 3, 6, 12, and 24 months respectively. The corresponding mean ECL was 22.9 ± 11.4%, 27.2 ± 12.4%, 33.5 ± 13.0%, and 38.6 ± 14.3%, respectively (P < 0.05 for all-time points). The commonest complication was DM detachment in 59 (9.8%) eyes of which 23 (3.8%) eyes required rebubbling. Three (0.5%) eyes had primary graft failure. Endothelial rejection occurred in 7 (1.2%) eyes until the last follow-up. Conclusion: DMEK is a safe and effective procedure in different types of endothelial diseases with encouraging surgical and clinical outcomes. Complications are less and ECL percentage up to 2 years is acceptable.
High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D

Significance Adoptive T cell therapy (ACT) is an experimental cancer immunotherapy with partial clinical responses (∼20%). A mechanistic understanding of T cell receptors (TCR) isolated from tumors and defining the biochemical attributes associated with tumor elimination may improve the ACT success rate. Here, we studied a successful case of ACT targeting HLA-C–restricted KRAS-G12D neoantigens. Through biochemical, structural, and cellular approaches, we define how these TCRs recognized their neoantigens. Key findings were that these TCRs were of higher affinity than most tumor-specific TCRs identified to date and these TCRs were specific for two distinct neoantigens. Whether these are general features of successful ACT remains to be seen, but this approach may serve as a basis for future rational improvement of ACT. Complete cancer regression occurs in a subset of patients following adoptive T cell therapy (ACT) of ex vivo expanded tumor-infiltrating lymphocytes (TILs). However, the low success rate presents a great challenge to broader clinical application. To provide insight into TIL-based immunotherapy, we studied a successful case of ACT where regression was observed against tumors carrying the hotspot mutation G12D in the KRAS oncogene. Four T cell receptors (TCRs) made up the TIL infusion and recognized two KRAS-G12D neoantigens, a nonamer and a decamer, all restricted by human leukocyte antigen (HLA) C*08:02. Three of them (TCR9a, 9b, and 9c) were nonamer-specific, while one was decamer-specific (TCR10). We show that only mutant G12D but not the wild-type peptides stabilized HLA-C*08:02 due to the formation of a critical anchor salt bridge to HLA-C. Therapeutic TCRs exhibited high affinities, ranging from nanomolar to low micromolar. Intriguingly, TCR binding affinities to HLA-C inversely correlated with their persistence in vivo, suggesting the importance of antigenic affinity in the function of therapeutic T cells. Crystal structures of TCR–HLA-C complexes revealed that TCR9a to 9c recognized G12D nonamer with multiple conserved contacts through shared CDR2β and CDR3α. This allowed CDR3β variation to confer different affinities via a variable HLA-C contact, generating an oligoclonal response. TCR10 recognized an induced and distinct G12D decamer conformation. Thus, this successful case of ACT included oligoclonal TCRs of high affinity recognizing distinct conformations of neoantigens. Our study revealed the potential of a structural approach to inform clinical efforts in targeting KRAS-G12D tumors by immunotherapy and has general implications for T cell-based immunotherapies.
Entecavir+tenofovir vs. lamivudine/telbivudine+adefovir in chronic hepatitis B patients with prior suboptimal response

Background/Aims Suboptimal responses to lamivudine or telbivudine plus adefovir (LAM/LdT+ADV) rescue therapy are common in patients with LAM-resistant hepatitis B virus (HBV) infections. We compared patients switched to entecavir plus tenofovir (ETV+TDF) to those maintained on LAM/LdT+ADV. Methods This prospective randomized controlled trial examined 91 patients whose serum HBV DNA levels were greater than 60 IU/mL after at least 24 weeks of treatment with LAM/LdT+ADV for LAM-resistant HBV. Patients were randomized to receive a new treatment (ETV+TDF, n=45) or maintained on the same treatment (LAM/LdT+ADV, n=46) for 48 weeks. Patients with baseline ADV resistance were excluded. Results Compared to LAM/LdT+ADV group, ETV+TDF group had more patients with a virologic response (42/45 [93.33%] vs. 3/46 [6.52%], P<0.001) and had a greater mean reduction in serum HBV DNA level from baseline (-4.16 vs. -0.37 log10 IU/mL, P<0.001). Multivariate analysis indicated that high baseline HBV DNA level (P=0.005) and LAM/LdT+ADV maintenance therapy (P=0.001) were negatively associated with virologic response. At week 48, additional ADV- or ETV-associated mutations were cleared in ETV+TDF group, but such mutations were present in 4.3% of patients in LAM/LdT+ADV group (P=0.106). The two groups had similar rates of adverse events. Conclusions ETV+TDF combination treatment led to a significantly higher rate of virologic response compared to LAM/LdT+ADV combination treatment in patients with LAM-resistant HBV who had suboptimal responses to LAM/LdT+ADV regardless of HBV genotypic resistance profile (NCT01597934).
Starch-lipid composites in plain set yogurt

Summary Starch-lipid composites (SLC) were used to replace milk solids in yogurt mixes. The effects of the SLC on the yogurt fermentations and rheology were studied. The rate of fermentation was evaluated by the change of pH during the fermentation of yogurt. The syneresis of yogurt was observed over 3 weeks of storage. Small amplitude oscillatory shear flow measurements of the storage modulus, the loss modulus, and the loss tangent were obtained using a vane geometry. Yogurt mixes with milk solids partially replaced by SLC fermented at a similar rate than as with no milk solids replaced. Initial viscosity was higher for yogurt mixes with higher levels of SLC. The higher initial viscosity did not affect the gel structure. The addition of SLC above a level of 3% strengthened the gel and resulted in no syneresis for yogurt samples stored for 3 weeks at 4 °C.
HLA-A gene variation modulates residual function of the pancreatic β-cells in children with type 1 diabetes.

AIM OF THE STUDY The study aimed to analyze an association between the HLA-A gene variation and a risk of type 1 diabetes development and to evaluate the association of HLA class I and class II alleles with β-cell destruction. MATERIAL AND METHODS A group of 108 children with type 1 diabetes were genotyped in HLA-A, -DRB1, and -DQB1 genes using hybridization with oligonu-cleotides probes. Plasma C-peptide concentration was assessed by radioimmunoassay method. RESULTS No differences in allele HLA-A distribution between type 1 diabetes patients and healthy individuals were found. Among "low C-peptide"(< 0.28 pmol/ml) individuals, the frequency of HLA-A*02 allele was 41.3%, whereas only one HLA-A*26 allele was detected in this group (0.7%). Conversely, among "high C-peptide"( 0.28 pmol/ml) probands the prevalence of A*02 allele was 19.7% (Pc = 0.008, OR = 1.4, 95% CI: 1.2-1.7) and A*26 10.5 % (Pc < 0.007, OR = 0.15, 95% CI: 0.02-0.9). Genotype analysis showed that A*02/*02 and A*02/X children were more likely to have "low" C-peptide at the onset compared to those with non-A*02/non-A*02 genotype (p = 0.008, OR = 1.6, 95% CI: 1.3-2.0 and p = 0.015, OR = 1.4, 95% CI: 1.1-1.9, respectively). A02 phenotype individuals had lower median C-peptide (0.17 pmol/ml) than non-A02 patients (0.26 pmol/ml, p = 0.008). Median C-peptide was higher in the A26-positive group comparing to A26-negative (0.40 and 0.20, respectively, p = 0.04). No association between HLA class II and C-peptide levels was observed. CONCLUSIONS HLA-A alleles are not associated with disease development nevertheless strongly influence a residual pancreatic β-cell function. The results suggest a different role of HLA class I and class II in type 1 diabetes pathogenesis.
Vulnerability Zone of Glaucoma Progression in Combined Wide-field Optical Coherence Tomography Event-based Progression Analysis

Purpose To investigate the spatial characteristics and patterns of structural progression using the combined retinal nerve fiber layer (RNFL) and ganglion cell–inner plexiform layer event-based progression analysis feature provided by the Guided Progression Analysis (GPA) software of spectral-domain optical coherence tomography. Methods In this retrospective observational study, we evaluated 89 patients with open-angle glaucoma showing clinically confirmed structural progression within a minimum follow-up period of 3 years. For each eye, the RNFL and ganglion cell–inner plexiform layer GPA data were extracted from serial spectral-domain optical coherence tomography (HD-OCT 4000, Carl Zeiss Meditec, Inc., Dublin, CA) data from 2012 to 2017 (available in commercial report). A combined wide-field GPA map was merged using vascular landmark-guided superimposition of RNFL and ganglion cell–inner plexiform layer GPA event-based progression maps onto the RNFL image (resulting in the GPA PanoMaps: proposed in this study). The pattern of progressive structural changes was evaluated by comparing the baseline combined wide-field OCT deviation maps (PanoMap deviation maps: available in commercial report) and GPA PanoMaps at the time the first progression was detected and the GPA PanoMaps at the last follow-up. Spatial characteristics and patterns of glaucoma structural progression on GPA PanoMaps were evaluated. Results Progressive structural progression was detected most frequently at the macular vulnerability zone (MVZ), with the peripapillary and macular progression being well-correlated spatially. Compared with the baseline structural change on PanoMap, the progressive structural changes extended toward the fovea at both the peripapillary and macular areas. A spatial difference was observed between the areas where structural damage was frequently found on PanoMap (peripapillary inferoinferior sector and macular MVZ) and areas where progression was frequently found on GPA PanoMap (peripapillary and macular MVZ). Conclusions The patterns of progressive glaucomatous structural changes in both the peripapillary and macular areas were confirmed on the combined wide-field GPA map (GPA PanoMap). An analysis of the progression pattern using the GPA PanoMap facilitates the understanding of the spatial relation between the peripapillary and macular areas in glaucoma.