Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of three strategies for the management of Meloidogyne arenaria on carrot in Mexico using Pochonia chlamydosporia var. mexicana under greenhouse conditions

ABSTRACT Three control strategies for management of Meloidogyne arenaria were evaluated on carrot under greenhouse conditions. The control strategies tested were: i) incorporation of fresh broccoli; ii) carbofuran (Furadan®); and iii) Pochonia chlamydosporia var. mexicana, isolate Pcp21. Each strategy was evaluated separately and in combination (16 treatment combinations), each with three replicates. The experiment was done between February and April 2014 and repeated over the same time period in 2015. Each replicate experimental unit consisted of a 1 kg pot filled with tyndallised soil, to which broccoli, fungus and carbofuran were added according to treatment. Carrot seeds were sown into each pot and inoculated with M. arenaria eggs according to treatment. Pots were then maintained in the glasshouse for 12 weeks at 25 ± 5°C. After this time the fresh root weight, root length, percent reduction in root galling, P. chlamydosporia var. mexicana colony forming units (CFU)/g of soil, and CFU/g root were all measured. Results showed that isolate Pcp21 of P. chlamydosporia var. mexicana significantly reduced root galling percentage by 50 and 78% in 2014 and 2015, respectively. Application of the fungus in combination with broccoli or carbofuran also reduced root galling. The number of CFU/ g of soil or root remained the same over the 12 weeks of the experiment. This isolate of P. chlamydosporia significantly reduced damage caused by M. arenaria on carrot and is a promising agent for management of this nematode.
The development and potential of spinal cord stem and progenitor cells

Spinal cord injury (SCI) is an incurable condition, which is mainly due to the highly limited regenerative potential of the adult spinal cord. The discovery of ependymal cells as the source of spinal cord stem cells raises hopes for the development of new therapies, while cell transplantations for SCI also provide promising means for potential treatments. However, curing SCI has been proven difficult as the potential of these progenitors and ependymal stem cells is still understudied. Moreover, the development of the spinal cord is a key factor influencing the regenerative potential of neural stem/progenitor stem cells, but the link between the development of spinal cord progenitors and adult spinal cord regeneration has been largely overlooked. By using different transgenic mouse lines and biomedical techniques, we studied the neural progenitors and stem cells during spinal cord development, after SCI and after cell transplantation in this thesis. FoxJ1 is traditionally regarded as a transcription factor involved in ciliogenesis and a specific marker for ependymal cells. In Paper I, however, we discovered that FoxJ1 is transiently expressed in neuronal and glial progenitors, which will further give rise to subsets of interneurons, two subsets of astrocytes and all ependymal cells. FoxJ1 is required for the maintenance of stemness of the progenitors during development and the stem cell potential during adulthood. After SCI, FoxJ1 is required for the normal stem cell potential, proliferation and migration of ependymal cells to promote regeneration. After the early developmental stage, in Paper II, we observed that the stem cell potential is fully confined to ependymal cells from P10 in mice, and the potential of self-renewal and oligodendrocytic differentiation decreases over time. Juvenile ependymal cells have higher stem cell potential after SCI than adult ones, but their contribution to the glial scar formation in vivo is lesion sizeand age-dependent. We found that the resident astrocytes and stromal derived pericytes show higher regenerative potential at the juvenile stage, and ependymal cells serve as a backup regeneration candidate after SCI. Clinically in the adult spinal cord, the transplantation of bulbar olfactory ensheathing cell (bOEC) has shown significant functional recovery in SCI patients, but the mechanisms are not elucidated. In Paper III, we found that after SCI, bOEC transplantation increases the proliferation and self-renewal potential of ependymal cells. The transplantation of bOECs promotes higher astrocytic differentiation of ependymal cells but reduces the axonal growth inhibitors after SCI. The microenvironment of the injured spinal cord is enriched after bOEC transplantation in terms of less axonal growth inhibitor, a higher level of neurotrophic factors and better neuronal survival. Unexpectedly, we found newborn neurons after SCI with bOEC transplantation, challenging the current central stream theory that there is no neurogenesis after
Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Winemakers have long used copper as a fungicide on grapevine. However, the potential of copper to accumulate on soil and affect the biota poses a challenge to achieving sustainable agriculture. One recently developed option is the use of biocontrol agents to replace or complement traditional methods. In the present study, a field experiment was conducted in South Africa in which the leaves in two blocks of a vineyard were periodically treated with either copper sulphate or sprayed with Lactobacillus plantarum MW-1 as a biocontrol agent. This study evaluated the impact of the two treatments on the bacterial and fungal communities as they changed during the growing season. To do this, NGS was combined with quantitative strain-specific and community qPCRs. The results revealed the progression of the microbial communities throughout the season and how the different treatments affected the microbiota. Bacteria appeared to be relatively stable at the different time points, with the only taxa that systematically changed between treatments being Lactobacillaceae, which included reads from the biocontrol agent. Cells of Lactobacillus plantarum MW-1 were only detected on treated leaves using strain-specific qPCR, with its amount spanning from 103to 105cells/leaves. Conversely the fungal community was largely shaped by a succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the number of ITS copies was also comparable. In this regards, the two treatments seemed to affect the microbial community similarly, revealing the potential of this biocontrol strain as a promising alternative among sustainable fungicide treatments, although further investigation is required.
Dietary crude palm oil supplementation improves egg quality and modulates tissue and yolk vitamin E concentrations of laying hen

Crude palm oil (CPO) is a valuable energy supplement for poultry diets and a rich source of vitamin A and E. Data on the effect of vitamin E tocotrienol in CPO on laying hen metabolism are limited. The present study examined the effects of dietary CPO supplementation on the performance and tissue distribution of vitamin E in laying hens and on egg quality. In total, 144 49-week old Hysex Brown hens were allocated randomly into four groups (36 per group), in single cages, and received corn–soybean basal diet supplemented with either lard at 20 g/kg (control), or CPO at 20 (CPO1), 30 (CPO2) or 40 g/kg (CPO3). Egg quality, hen performance, egg yolk cholesterol and hen tissue concentrations of vitamin E were examined. Dietary supplementation with CPO increased the egg yolk colour, egg and yolk weight compared with the control group, but not specific gravity, albumen quality, albumen weight and shell weight. Importantly, CPO supplementation significantly decreased egg yolk cholesterol concentrations (lowest level in the CPO3 group) and enhanced (P < 0.05) the total vitamin E tocopherols in CPO1 and total tocotrienols in CPO2 and CPO3. Hens fed on CPO3 had the lowest total tocopherol concentrations in their egg yolk and adipose tissue, but the highest tocotrienol in their plasma, egg yolk and adipose tissue. In addition, dietary CPO supplementation resulted in the highest deposition of tocotrienol in the hen’s adipose tissue compared with in the egg yolk, or hen’s liver and plasma. In conclusion, dietary supplementation with CPO improved the egg yolk weight and yolk colour, while it reduced the total cholesterol concentration and resulted in more vitamin E in the egg and hen’s adipose tissue, with increased concentrations of α-tocopherol, α-tocotrienol and γ-tocotrienol.
Cell-Based Assays for Evaluation of Autophagy in Cancers

Autophagy is a cellular mechanism that degrades damaged organelles and misfolded proteins to maintain cellular homeostasis. Autophagy in cancers is drawing increasing attentions due to its multifaceted roles in cancer development, progression, and treatment. There are several key autophagy effectors that are being extensively studied to understand the role of autophagy in cancer as well as their potential value as predictive and/or prognostic biomarkers and therapeutic target. These include ATG4A, ATG4B, Beclin-I, p62, LC3A, LC3B, LC3C, and LAMP. While having its own sophisticated pathway, autophagy has been reported to associate with multiple oncogenic pathways such as NF-kB, mTOR, and PI3K signaling. This chapter aims to provide a detailed protocol for researchers to investigate the role of autophagy using in vitro cell line as model. Here, we demonstrate several techniques including Western blot (WB), immunofluorescence (IF), and small-interfering RNA (siRNA) knockdown using colorectal cancer cell lines as samples. This chapter provides information to researchers especially those in their early- and mid-career to plan and design their experiments to study the autophagy events in their area of interests.
Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

Non-genetic factors can cause individual cells to fluctuate substantially in gene expression levels over time. Yet it remains unclear whether these fluctuations can persist for much longer than the time for a single cell division. Current methods for measuring gene expression in single cells mostly rely on single time point measurements, making the time of a fluctuation of gene expression or cellular memory difficult to measure. Here, we report a method combining Luria and Delbrück’s fluctuation analysis with population-based RNA sequencing (MemorySeq) for identifying genes transcriptome-wide whose fluctuations persist for several cell divisions. MemorySeq revealed multiple gene modules that express together in rare cells within otherwise homogeneous clonal populations. Further, we found that these rare cell subpopulations are associated with biologically distinct behaviors in multiple different cancer cell lines, for example, the ability to proliferate in the face of anti-cancer therapeutics. The identification of non-genetic, multigenerational fluctuations has the potential to reveal new forms of biological memory at the level of single cells and suggests that non-genetic heritability of cellular state may be a quantitative property.
Labeling via Feature Valuation

Chomsky (2015: 9) proposes that English T differs from Italian T in that it is so weak that it cannot label an output syntactic object derived by the application of Merge. Interestingly enough, Chomsky (2015: 10) also proposes that English T can be strengthened sufficiently by a Spec-Head relation to serve as a label for an unlabeled syntactic object. In this paper, we propose a new manner of labelingby means of which the label of {T, v*P} is determined without recourse to Spec-Head relations. More specifically, we argue that the valuation of the φ feature strengthens both English weak T and universally weak R. Given Boeckx's (2011) analysis of feature composition for parametric variation, the difference in licensing of pro-drop phenomena―subjectless finite sentences― between, for example, English and Italian follows from our proposal.
Reframing the Debate Surrounding the Yield Gap between Organic and Conventional Farming

In this article, we review the literature regarding the yield gap between organic and conventional agriculture and then reflect on the corresponding debate on whether or not organic farming can feed the world. We analyze the current framework and highlight the need to reframe the yield gap debate away from “Can organic feed the world? ” towards the more pragmatic question, “How can organic agriculture contribute to feeding the world? ”. Furthermore, we challenge the benchmarks that are used in present yield comparison studies, as they are based on fundamentally distinct paradigms of the respective farming methods, and then come up with a novel model to better understand the nature of yield gaps and the benchmarks that they are premised on. We thus conclude that, by establishing appropriate benchmarks, re-prioritizing research needs, and focusing on transforming natural resources rather than inputs, organic systems can raise their yields and play an ever-greater role in global sustainable agriculture and food production in the future.
The Striking Flower-in-Flower Phenotype of Arabidopsis thaliana Nossen (No-0) is Caused by a Novel LEAFY Allele

Summary The transition to reproduction is a crucial step in the life cycle of any organism. In Arabidopsis thaliana the establishment of reproductive growth can be divided into two phases: In the first phase, cauline leaves with axillary meristems are formed and internode elongation begins. In the second phase, lateral meristems develop into flowers with defined organs. Floral shoots are usually determinate and suppress the development of lateral shoots. Here, we describe a Ds transposon insertion mutant in the Nossen (No-0) accession with severe defects in floral development and flower morphology. The most striking aspect is the outgrowth of stems from the axillary bracts of the primary flower carrying terminal secondary flowers. Therefore, we named this mutant flower-in-flower (fif). However, the insertion of the transposon in the annotated gene is not responsible for the fif phenotype. By means of classical and genome sequencing-based mapping, the mutation responsible for the fif phenotype was found to be in the LEAFY (LFY) gene. The mutation, a G-to-A exchange in the second exon of LFY, creates a novel lfy allele and causes a cysteine-to-tyrosine exchange in the α1-helix of the LFY DNA-binding domain. Whereas subcellular localization and homomerization are not affected, the DNA-binding of LFYFIF is abolished. We propose that the amino acid exchange interferes with the cooperative binding of LFY to its target DNA. To generate the strong fif phenotype, LFYFIF may act dominant-negatively by either forming non-binding LFY/LFYFIF heteromers or by titrating out the interaction partners, required for LFY function as transcription factor. Significant Statement: The fif phenotype of Arabidopsis thaliana No-0 is caused by a novel allele of the LEAFY gene
Antibacterial Activity of Crude Aronia melanocarpa (Black Chokeberry) Extracts against Bacillus cereus, Staphylococcus aureus, Cronobacter sakazakii, and Salmonella Enteritidis in Various Dairy Foods: Preliminary Study

In this study, the antibacterial activity of Aronia melanocarpa (black chokeberry) ethanol extract against Bacillus cereus, Staphylococcus aureus, Cronobacter sakazakii, and Salmonella Enteritidis was investigated using the spot-on-lawn assay. The results showed that this extract exhibited antibacterial activities against Bacillus cereus (complete inhibition) and Staphylococcus aureus (partial inhibition), but did not inhibit the growth of Cronobacter sakazakii and Salmonella Enteritidis. This study shows that the Aronia melanocarpa (black chokeberry) ethanol extract was more effective against Gram-positive bacteria than Gramnegative bacteria. Hence, it is suggested that Aronia melanocarpa could be a useful food supplement, and could be utilized as a naturally derived additive for maintaining the safety of various dairy products. Furthermore, future research should be conducted to examine the possibility of using such products as functional ingredients for improving the antioxidative and anti-inflammatory activities of food products.
Determinants of productivity of farmland in Imo State

The study analysed the determinants of productivity of farmland in Imo State, Nigeria. Primary data were collected using a set of structured questionnaires from 60 food crop farmers who were selected through purposive and random sampling techniques. Data were analysed using descriptive statistics and econometric tools. The results showed that majority of the respondents were young in their active years, with a mean age of 45 years, married, mostly females, had mean level education of 8 years and mostly farming as their major occupation. The results also showed that the food crop farmers had adequate labour force of a mean 7 persons per household and cultivated an average farm size of 1.06 hectares. The result of the productivity of farmland was 4.03, which showed high productivity. From the results also, the exponential function is the lead equation. The study concluded that farmlands in Imo state are productive and are determined by farm size, location, distance, quantity of fertilizer used, type of soil and duration of tenancy. The study advocated for food crop farmers to form a cooperative to enable them pool their resources together for gaining larger farmlands, fertilizer and other farm inputs. Keywords: Farmland, Determinants, Productivity, Imo state.
Relationship between cash transfer programmes and school outcomes in Africa and Latin America: A systematic review

Poverty is popularly believed to be a hindrance to schooling for children from poor households. To overcome this obstacle, cash transfers have been used to support and promote their access to education. This review assesses the effect of some cash transfers programmes in Africa and Latin America on children’s educational outcomes. A systematic search for relevant studies was conducted online through google scholar. Inclusion criteria were met by ten studies- 5 in Africa and 5 in Latin America. Eight studies used a quantitative approach, while two adopted a mixed-methods technique. The included studies used different study designs, and their outcomes showed that both Conditional Cash Transfers (CCTs) and Unconditional Cash Transfers (UCTs) have positive effects on school outcomes. Some results showed strong evidence, others showed weak evidence while others showed limited evidence. Cash transfer programmes offer disadvantaged children the opportunity for schooling. However, the impact of these programmes varies because of their implementation designs. Keywords: Cash transfers, Children, Poverty, School
Comparative evaluation of maize (Zea mays L.) genotypes based on distinctness, uniformity and stability (DUS) testing using physiological and morphological characters

A major challenge facing those involved in the testing of new plant varieties for Distinctness, Uniformity and Stability (DUS) is the need to compare them against all those of â€˜common knowledgeâ€™. A set of maize inbred lines was used to compare how morphological and physio- logical characterization described variety relationships. An experiment was carried out to evaluate test of Distinctiveness, Uniformity and Stability using 26 physiological and 12 morphological characters. Minimum days for 50 % tasseling (50.66 and 50.66 days), minimum days for 50 % silking (53.66 and 53.66 days), minimum days for anthesis silking interval (3.0 and 2.6 days), maximum tassel branching (22.66 and 21.66), maximum cob height (89.70 and 89.16 cm) and maximum cob length (16.96 and 17.75 cm) were recorded in genotype AAIMS-1 in both experiments (2011 and 2012 respectively) and maximum cob width (12.51 and 13.11 cm) and maximum number of grain rows per cob (12.66 and 12.66) were recorded in genotype AAIMS-2 in both experiments (2011 and 2012 respectively). But maximum plant height (155.13 and 153.71cm), minimum days for maturity (86.00 and 88.00 days), maximum grain yield per plant (72.80 and 72.00 g) and maximum 100 seed weight (21.51 and 20.96 g) were recorded in genotype AAIMS-2 and AAIMS-1 respectively in both experiments conducted at experimental farm of Department of Genetics and Plant Breeding, Sam Higginbottom Institute of Agriculture, Technology & Sciences during the year 2011 and 2012 respectively.
Audiograms of howling monkeys: are extreme loud calls the result of runaway selection?

The eponymous vocalizations of howling monkeys (genus Alouatta) are associated with territorial defense and male-male competition, yet the extreme loudness of howls, which are among the loudest vocalizations of any terrestrial mammal, have yet to be fully explained. Loudness facilitates long-distance sound propagation but the effectiveness of any vocal signal depends in part on the auditory capabilities of the intended receiver, and the auditory sensitivities of howling monkeys are unknown. To better understand the evolution of loud calls, we used the auditory brainstem response (ABR) method to estimate the auditory sensitivities of Alouatta palliata. The mean estimated audiogram of four wild-caught adults displayed a w-shaped pattern with two regions of enhanced sensitivity centered at 0.7-1.0 and 11.3 kHz. The lower-frequency region of auditory sensitivity is pitched moderately higher than the fundamental frequencies of howling, whereas the higher-frequency region corresponds well with harmonics in an infant distress call, the wrah-ha. Fitness advantages from detecting infants amid low-frequency background noise, including howling, could explain the incongruity between our ABR thresholds and the fundamental frequencies of howling. Attending to infant calls is expected to enhance reproductive success within an infanticidal genus, and we suggest that the extraordinary loudness of male howling is an indirect (runaway) result of positive feedback between the selective pressures of hearing infant distress calls and deterring infanticide.
Liquid Fertility Management Bait Uptake by Urban Rats within New York City Subway Refuse Rooms

Author(s): Pyzyna, Brandy; Cunningham, Lindsey; Calloway, Elissa; Dyer, Cheryl; Mayer, Loretta; Cowan, Dave | Abstract: Traditional rodent management tools, such as traps and lethal rodenticides, are acute measures to reduce commensal rodent populations. Given the growing concerns regarding effectiveness, environmental safety, and animal welfare related to these tools, it has become imperative to find new methods. Fertility control is an emerging potential alternative to these tools as a safe, humane and effective method of long-term population management. SenesTech, Inc. has developed a liquid fertility management bait that causes follicle depletion in the ovaries of female Sprague Dawley rats and compromises sperm production in male Sprague Dawley rats in laboratory settings. These studies have shown significant decreases in litter sizes following bait consumption, but acceptance of this bait by wild rodents needed to be confirmed. Bait acceptance was tested within refuse rooms of the New York City subway system. Bait was provided ad libitum for 90 days. Uptake was evaluated by examining, via fluorescence microscopy, the presence of the bait marker rhodamine B, which manifests as fluorescent bands in whiskers. Presence of these bands indicated that 51% of the captured population had consumed the bait, and of these, 58% had taken the bait more than once. These results demonstrate that wild rats will consume a liquid fertility management bait, even in the presence of highly palatable and abundant food within the refuse rooms. This study establishes the successful acceptance of a bait by wild rats. Further investigation is needed to evaluate the effectiveness of this product for the management of urban Norway rat populations.