Miracle-dz/UniFAR-FTUs huggingface dataset:
The Alpha-1-Antitrypsin Promoter Improves the Efficacy of an AAV Vector for the Treatment of MNGIE.

MNGIE (mitochondrial neurogastrointestinal encephalomyopathy) is a devastating disease caused by mutations in TYMP, which encodes thymidine phosphorylase (TP). In MNGIE patients, TP dysfunction results in systemic thymidine and deoxyuridine overload, which interferes with mitochondrial DNA replication. Preclinical studies have shown that gene therapy using a lentiviral vector targeted to hematopoietic stem cells or an adeno-associated vector (AAV) transcriptionally targeted to liver are feasible approaches to treat MNGIE. Here, we studied the effect of various promoters (thyroxine-binding globulin [TBG], phosphoglycerate kinase [PGK], hybrid liver-specific promoter [HLP], and alpha-1-antitrypsin [AAT]) and DNA configuration (single stranded or self complementary) on expression of the TYMP transgene in the AAV8 serotype in a murine model of MNGIE. All vectors restored liver TP activity and normalized nucleoside homeostasis in mice. However, the liver-specific promoters TBG, HLP, and AAT were more effective than the constitutive PGK promoter, and the self-complementary DNA configuration did not provide any therapeutic advantage over the single-stranded configuration. Among all constructs, only AAV-AAT was effective in all mice treated at the lowest dose (5 × 1010 vector genomes/kg). As use of the AAT promoter will likely minimize the dose needed to achieve clinical efficacy as compared to the other promoters tested, we propose using the AAT promoter in the vector eventually designed for clinical use.
The complete chloroplast genome of Scutellaria indica var. coccinea (Lamiaceae), an endemic taxon in Korea

Abstract Scutellaria indica var. coccinea (Lamiaceae) is an endemic taxon in Jeju Island, Korea. We present the complete chloroplast genome sequence of S. indica var. coccinea. Its genome size is 151,956 bp in length comprising a large single copy of 83,951 bp, a small single copy of 17,539 bp, and a pair of inverted repeats measuring 25,233 bp. The complete genome contains 115 genes including 80 protein-coding genes, four rRNAs, and 31 tRNAs. Phylogenetic analysis of this species with 10 published chloroplast genomes in Lamiaceae showed that S. insignis is a sister to S. indica var. coccinea.
Does Genetic Engineering Influence the Nutritional Value of Plums? Case Study on Two conventional and One Genetically Engineered Plum Fruits

Plums are low-calorie fruits with a low glycaemic index score. Prunus domestica L. is one of the tree fruits threatened by Plum pox potyvirus (PPV), a quarantine disease that causes fruit loss to plums and other stone fruits. HoneySweet is a plum tree created to be resistant to this virus. Beside genetical determinations, chemical composition and nutritional value are important for a future acceptance in the cultivation of this type of fruit trees. Two conventional (Renclod Althan and Stanley) and one genetically engineered (HoneySweet) plum fruits were evaluated for the nutritional value determination. The analyzed samples showed nutritionally valuable features. HoneySweet variety had a balanced content of individual carbohydrates. The total lipid content had values quite close to the HoneySweet and Stanley varieties, far superior to Renclod Althan variety. HoneySweet transgenic plum had the highest total protein content. Also, HoneySweet variety is distinguished by a balanced protein and lipid content. By comparing the three analyzed varieties from the perspective of the most important physic-chemical nutrients (carbohydrates, proteins and lipids), the highest nutritional value was registered in Stanley variety, closely followed by HoneySweet, and then by Reine Claude d’Althan.
Phenotypic and genetic divergence in reed frogs across a mosaic hybrid zone on São Tomé Island

Although naturally heterogeneous environments can lead to mosaic hybrid zones, human-induced habitat fragmentation can also lead to environmental heterogeneity and hybridization. Here we quantify phenotypic and molecular divergence across a reed frog mosaic hybrid zone on São Tomé Island as a first step towards understanding the consequences of hybridization across this heterogeneous landscape. The São Tomé giant reed frog (Hyperolius thomensis) is strongly tied to cool, wet, forest habitats whereas the distribution of Moller’s reed frog (H. molleri) spans cool, wet, forests to warm, dry, disturbed habitats. Correspondingly, hybridization is concentrated in the more forested, cool, wet sites relative to non-forested, warmer, drier habitats. Four of six sites with hybrid frogs are artificial water bodies near the forest edge, indicating that both breeding habitat and broader scale environmental variation are probably important for understanding interspecific interactions and the extent of hybridization in this system. Phenotypic variation (body size and ventral coloration) largely tracks genetic and environmental variation across the hybrid zone with larger and more pigmented frogs occurring in forested, cool, wet habitats. Understanding whether human-induced changes in habitat break down reproductive barriers will be essential for conservation management of the less abundant, forest-associated H. thomensis in the face of rampant hybridization.
Short-Term High-NaCl Dietary Intake Changes Leukocyte Expression of VLA-4, LFA-1, and Mac-1 Integrins in Both Healthy Humans and Sprague-Dawley Rats: A Comparative Study

This study is aimed at assessing the effects of a short-term high-salt (HS) diet on the peripheral blood leukocyte (PBL) activation status in healthy rats and young human individuals. Distribution of PBL subpopulations and surface expression of integrins were determined using flow cytometry in 36 men and women on a 7-day low-salt diet (<3.2 g salt/day) immediately followed by a 7-day HS diet (~14 g salt/day) or in Sprague-Dawley (SD) rats (n = 24) on a 0.4% NaCl diet (aLS group) or a 4% NaCl diet (aHS group) for 7 days. The aHS group presented with an increased frequency of granulocytes, while the frequency of lymphocytes was reduced. Although in humans HS diet reduced the expression of CD11b(act) integrin on lymphocytes, the frequency of CD11b(act)-bearing cells among all PBL subsets was increased. The aHS group of rats exhibited increased expression of total CD11b/c in granulocytes and CD3 lymphocytes. The expression of CD11a was significantly reduced in all PBL subsets from human subjects and increased in the aHS group. CD49d expression on all PBL subsets was significantly decreased in both humans and rats. In human subjects, we found reduced frequencies of intermediate monocytes accompanied by a reciprocal increase in classical monocytes. Present results suggest that a short-term HS diet can alter leukocytes' activation status and promote vascular low-grade inflammation.
Effect of Leaf Quality on Herbivory of Three Atlantic Forest Species

The present study evaluated the relationship between herbivory and leaf quality of three abundant tree species (Cupania oblongifolia Mart., Siparuna guianensis Aubl. and Xylopia sericea St. Hill.) in the understory of a eucalyptus plantation and an adjacent Atlantic Rainforest fragment. Herbivory differed among species, since X. sericea was less attacked, while C. oblongifolia and S. guianensis were more. The species showed similar herbivory patterns between the investigated areas (eucalyptus plantation versus forest), although X. sericea showed higher herbivory rates in the forest fragment. Fiber values (NDF, CEL and LIG) varied significantly among the species, being lower in S. guianensis. X. sericea, the species with the highest C/N ratio, higher concentrations of total phenols, smaller leaf area and higher trichome density, showed the lowest leaf herbivory rates, corroborating the hypothesis that herbivory is lower in species with lower nutritional quality and a greater set of leaf defense features.
The first contribution to karyotyping of the Australian allodapine bee Exoneura robusta

The Australian allodapine bee, Exoneura robusta, is an important pollinator of native flowering plants in Australian wet forests. In this study, the karyotype of E. robusta is illustrated and described using an air-drying technique. The metaphase analysis of the females revealed a diploid chromosome number of 26 (2n = 26). We then discuss parameters affecting the quality of chromosomal spreads including humidity which is not included or examined in existing insect karyotyping protocols. It is further discussed that this might be a reason why current bee chromosomal preparation protocols cannot be easily adapted to different bee species.
Light-sheet engineering using the Field Synthesis theorem

Recent advances in light-sheet microscopy have enabled sensitive imaging with high spatiotemporal resolution. However, the creation of thin light-sheets for high axial resolution is challenging, as the thickness of the sheet, field of view and confinement of the excitation need to be carefully balanced. Some of the thinnest light-sheets created so far have found little practical use as they excite too much out-of-focus fluorescence. In contrast, the most commonly used light-sheet for subcellular imaging, the square lattice, has excellent excitation confinement at the cost of lower axial resolving power. Here we leverage the recently discovered Field Synthesis theorem to create light-sheets where thickness and illumination confinement can be continuously tuned. Explicitly, we scan a line beam across a portion of an annulus mask on the back focal plane of the illumination objective, which we call C-light-sheets. We experimentally characterize these light-sheets and demonstrate their application on biological samples.
Interleaving of oxygenized intrusions into the Baltic Sea redoxcline

Semi‐enclosed marginal seas like the Baltic Sea are often characterized by permanently anoxic deep layers, and may therefore serve as important model systems to study the causes and consequences of the predicted global expansion of oxygen minimum zones. Here, we focus on the role of lateral intrusions in maintaining the “hypoxic transition zone” (HTZ) of the Baltic Sea, which characterizes the quasi‐permanent hypoxic region located between the oxygenized surface layer and the sulfidic deep‐water region. Based on long‐term deployments of an autonomous profiling system in the central Baltic Sea, we show that oxic mid‐water intrusions are ubiquitous features, providing the most important oxygen source for the HTZ, and largely control the vertical and lateral extent of the hypoxic areas. An oxygen budget for the HTZ suggests that oxygen turnover in the HTZ is, to first order, determined by a long‐term balance between sedimentary oxygen demand and oxygen import by intrusions. The downward mixing of oxygen into the HTZ is generally non‐negligible but unlikely to provide a first‐order contribution to the HTZ oxygen budget. On the long‐term average, mid‐water intrusions were shown to inject 30–60 Gmol of oxygen per year into the deep‐water region below the permanent halocline. This is approximately one order of magnitude larger than the average amount of oxygen imported during the massive deep‐water inflow events (Major Baltic Inflows) that occur on an approximately decadal time scale, highlighting the HTZ as a hotspot for biogeochemical turnover.
Maximizing Productivity of Lohmann Chickens by Feeding Diets Inclusion Different Levels of Moringa oleifera Leaf Powder as a Safe Feed Additive

The purpose of the present study was to investigate the effect of inclusion graded levels of Moringa oleifera leaf powder (MOLP) as a safe feed additive on productive performance, some blood parameters, egg quality traits and egg cholesterol contents of Lohamnn chicken. A total number of 150 hens, aging 20 weeks were randomly allocated in a completely randomized design to 5 dietary treatments, in each three replicates (n=10) and their initial mean body weight ranged from 1501.0 to 1530.0 g (±7.01), where each 2 birds were placed in one cage. The control group was fed a corn-soybean meal based diet and the other experimental groups were fed on control diet supplemented with 0.5%, 1.0%, 1.5% and 2.0% MOLP. The results revealed that laying performance statistically (P≤0.05) improved due to the addition of MOLP as compared to the control group. Furthermore, FCR recorded the best values for groups fed MOLP, which displayed relatively high performance. However, inclusion of MOLP in diets improved both egg shell thickness and yolk color. In addition, egg cholesterol contents significantly (P≤0.05) decreased due to increasing levels of MOLP in diets. Obliviously, health status as judged by measuring some blood constituents, showed decreases (P≤0.05) of lipid profile and Corticosterone concentration, while level of HDL and protein profile significantly (P≤0.05) increased due to the addition of MOLP in the diets. Clearly, it can be recommended that the incorporating of MOLP in Lohmann chickens diets could enhance their productive performance and improve physiological status.
Study of Some Factors Affected on Dry Seed Yield and its Components of Common Bean (Phaseolus vulgaris L.)

This experiment was suggested to study the beneficial effects of some levels of NPK fertilizers i.e. (0, 50, 75 and 100%) from NPK recommendation for common bean with humic acid (HA) on plant growth, dry seed yield and its components, quality and seeds chemical composition of common bean(Phaseolus vulgaris L.) cvs. Nebraska and Bronco. All experiments were achieved at the Experimental Farm of Kaha Research Farm, Horticulture Research Institute, Agriculture Research Center (ARC), Qaliobia Governorate, Egypt, during the two successive summer seasons of 2013 and 2014. The results showed that adding humic acid (HA) to common bean plantswith the level of 50% from NPK recommendation gave the highest values of vegetative growth, total dry seed yield and its chemical composition with cv. Nebraska or also cv. Bronco which cultivated under these study for the purpose of dry seed production. This treatment also led to save 50% of NPK fertilizers for common bean requirements. For that, it can be recommended that fertilization of common bean plants for the purpose of dry seed production by 50% from common bean NPK recommendation plus humic acid (HA) to obtain significant highest dry seed yield with best quality and at the same time save 50% from mineral fertilizer recommendation of common bean.
Response of Some Egyptian Cotton Cultivars to Foliar Spray by Some Microelements

Two field experiments were conducted on the Farm of Agricultural Research and Experiment Center, Faculty of Agriculture Moshtohor, Benha University, Toukh Directorate, Kalubia Governorate, Egypt, during the two successive seasons of 2015 and 2016 to study the effect of foliar spray by eight micronutrient treatments, i.e. without application (control), Zn, Mn, Fe, Zn + Mn, Zn + Fe, Mn + Fe and Zn + Mn + Fe on growth, yield components and yield as well as fiber quality properties for the two Egyptian cotton (Gossypium barbadense, L.) verities, i.e. Giza 86 and Giza 88. The experimental design was split plot design in four replications. The obvious results of this investigation can be summarized as follows: Significant differences were detected for all growth, yield components and yield as well as fiber properties of cotton among the two Egyptian cotton cultivars during 2015 and 2016 seasons. Giza 86 cultivar significantly surpassed Giza 88 cultivar and gave the greatest mean values of plant height, No. of sympodial branches/plant, No. of open bolls/plant, seed cotton yield/plant, boll weight, lint %, lint cotton yield/plant, seed index, seed cotton yield/fed, lint cotton yield/fed, fiber elongation %, micronaire value, fiber maturity ratio and fiber reflectance in the both seasons. While, Giza 88 recorded the highest mean values of upper half mean length, length uniformity index, fiber strength and fiber yellowness degree in the two seasons. Data revealed that the differences between the studied eight microelements treatments on growth, yield components and yield as well as fiber properties of cotton during 2015 and 2016 seasons were significant except, fiber reflectance and fiber yellowness degree were not significant. The application of combined of Zn + Mn + Fe treatment gave significantly the greatest mean values of plant height, No. of sympodial branches/plant, No. of open bolls/plant, seed cotton yield/plant, boll weight, lint %, lint cotton yield/plant, seed index, seed cotton yield/fed, lint cotton yield/fed, upper half mean length, length uniformity index, fiber strength, fiber elongation %, micronaire value and fiber maturity ratio in the both seasons. Planting Giza 86 which foliar spray by mixed Zn + Mn + Fe treatment significantly recorded the highest mean values of No. of open bolls/plant, seed cotton yield/plant, boll weight, lint cotton yield/plant, seed cotton yield/fed, lint cotton yield/fed and fiber maturity ratio in the first and second seasons. Meanwhile, planting Giza 88 under the same micronutrients application surpassed the other combinations in upper half mean length, length uniformity index and fiber strength during the both seasons.
Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics

In bottom-up discovery proteomics, target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control. Despite unquestionable statistical foundations, this method has drawbacks, including its hitherto unknown intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinter-preted. This article provides evidence that TDC has become less reliable as the accuracy of modern mass spectrometers improved. We therefore propose to replace TDC by a totally different method to control the FDR at spectrum, peptide and protein levels, while benefiting from the theoretical guarantees of the Benjamini-Hochberg framework. As this method is simpler to use, faster to compute and more stable than TDC, we argue that it is better adapted to the standardization and throughput constraints of current proteomic platforms.
Effect of Transplanting Dates, Cultivars and Irrigation Regimes on Microclimate and Yield of Rice

Agricultural productivity is influenced mainly by cultural practices followed and prevailing weather conditions. Rice is the predominant cereal crop in east India including the state of West Bengal. The total cultivated area of rice in India is 43.2 million ha and the country produced 110.2 million tons of rice in 2016-17. West Bengal is the largest rice producing state in India. Almost half of its arable land is under rice cultivation. In the fiscal year 2016, the state produced about 15.75 million tonnes of rice over 5.46 million hectare cultivable area (Anonymous, 2019). Rice requires a mean temperature range of 17 to 33 °C and solar radiation range of 300 to 600 calories cm-2 day-1 in its growing areas and seasons. Rice is a water loving plant requiring a heavy rainfall of 125 cm during its vegetative period and an annual rainfall of 100-200 cm (Prasada Rao, 2008). To improve production it is imperative to understand the weather at both macro and micro-levels as weather directly influences the crop growth Effect of Transplanting Dates, Cultivars and Irrigation Regimes on Microclimate and Yield of Rice
Neural Mechanisms for Executive Control of Speed-Accuracy Tradeoff

The balance of speed with accuracy requires error detection and performance adaptation. To date, neural concomitants of these processes have been investigated only with noninvasive measures. To provide the first neurophysiological description, macaque monkeys performed visual search under cued speed accuracy tradeoff (SAT). Monkeys changed SAT emphasis immediately after a cued switch while neuron discharges were sampled in medial frontal cortex area supplementary eye field (SEF). A multiplicity of SEF neurons signaled production of choice errors and timing errors. Modulation of SEF activity after choice errors predicted production of un-rewarded corrective saccades. Modulation of activity after timing errors signaled reward prediction error. Adaptation of performance during SAT of visual search was accomplished through pronounced changes in neural state from before search array presentation until after reward delivery. These results contextualize previous findings using noninvasive measures, complement neurophysiological findings in visuomotor structures, endorse the role of medial frontal cortex as a critic relative to the actor instantiated in visuomotor structures, and extend our understanding of the distributed neural mechanisms of SAT. HIGHLIGHTS Medial frontal cortex enables post-error adjustment during SAT Choice and timing errors were signaled by partially overlapping neural pools Medial frontal cortex can proactively modulate visuomotor processes Medial frontal cortex is to visuomotor circuits as critic to actor
Nutritional composition of some jute genotypes as vegetables

ABSTRACT Jute (Corchorus sp.) is consumed as a leafy vegetable in many parts of the world. There is little information on nutritional composition of cultivated jute species and their wild relatives. To determine nutritional components of jute leaf, 3 C. capsularis L. , germplasm, ‘Merha red’, ‘Merha green’, ‘Birol red’, a C. olitorius L. , ‘Accession-3840ʹ, and ‘BJRI deshi pat shak-1ʹ and ‘BINA pat shak-1ʹ were examined, with the latter 2 as controls. In most cases, the four wild species contained more vitamins and minerals, and had more surviving plants per unit area, compared with controls. The highest percent protein and ash, highest leaf area, and most leaves per plant, were in the controls. The desired biochemical properties with high heritability and genetic advance can likely be transmitted from wild germplasm to cultivated C. capsularis species through crossing, but evaluation in other agro-climatic regions is needed to determine the efficacy of wild germplasm as donor parent.