Miracle-dz/UniFAR-FTUs huggingface dataset:
The Use of Biodegradable Mulches in Pepper Production in the Southeastern United States

Plasticulture systems with polyethylene (PE) mulch and drip tape are common for production of peppers (Capsicum annuum L.) in the United States because of their soil warming, moisture conservation, and other advantageous effects. However, disadvantages include disposal costs and plastic pollution of the environment and temperature stress in warm climates with black mulch. Use of biodegradable plastic mulches (BDMs) is becoming more common, as they provide the same benefits of PE mulch without the disposal problems. In 2017 and 2018, we conducted experiments in Knoxville, TN, comparing production of pepper fruit with five different BDM [one white-on-black (WOB) and four black], one black PE mulch, one brown creped, paper mulch, and bare ground control treatments. We also measured the durability and effectiveness of weed suppression of the different mulches over the growing season compared with a hand-weeded bare ground control. Most mulches were degraded, with 40% to 60% of the soil exposed by the end of the season, with the exception of the paper mulch, which was completely degraded at the end of both seasons. Yields were similar among treatments in 2017, with the exception of Naturecycle, which had the lowest yield. Weed pressure was severe, especially in 2018, largely due to early penetration of all mulches except paper by nutsedge. Due to the early and season-long weed pressure and heat stress in black mulches, there were fewer healthy plants in all black-colored mulch treatments in 2018, leading to reduced yields in these treatments. Paper mulch was the only treatment that prevented nutsedge growth; therefore, this treatment and the hand-weeded bare ground treatment had the greatest yields in 2018. WOB also had yields comparable with paper and bare ground plots in 2018, likely due to the cooling effect of the white mulch. The results suggest that in hot climates and in fields infested with nutsedge, paper mulches perform best for midseason pepper cultivation due to the cooling effects and superior weed control.
Cell Specific eQTL Analysis without Sorting Cells

Expression quantitative trait locus (eQTL) mapping on tissue, organ or whole organism data can detect associations that are generic across cell types. We describe a new method to focus upon specific cell types without first needing to sort cells. We applied the method to whole blood data from 5,683 samples and demonstrate that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils.
Gross anatomical studies on the thyroid gland of chabro chicken reared in summer and winter seasons

Gross anatomical studies were conducted on the thyroid gland of eight weeks old 24 apparently healthy Chabro chickens procured from Poultry Farm, Mathura (India). The chickens were divided into two groups (12 chickens in each group) and reared in summer and winter season. The thyroid gland of chabro chicken was light pink, oval bodies i.e. right and left thyroid located on the ventral surface of the base of the neck just caudal to the junction of subclavian and common carotid arteries. There was 1.8 and three times increase in carcass weight of chicken and weight of thyroid gland, respectively from summer to winter season. The left thyroid gland was situated more cranially than the right thyroid. The average weight of thyroid and all biometrical parameters viz. length, width and thickness were more in winter season reared chickens.
Green grain of spelt (Triticum aestivum ssp. spelta) harvested at the stage of milk-dough as a rich source of valuable nutrients

The aim of this study was to compare the chemical composition of three spelt wheat cultivars harvested at the milk-dough stage (MDS) and at the fully ripe stage (FRS) in the organic farm in Poland. Green grain of cv. ‘Oberkulmer Rotkorn’ harvested at MDS showed a significantly higher content of P, K, Ca, Zn, Fe, Na and B, compared to grain harvested at FRS. In unripe grain of cv. ‘Rokosz’, the content of N, K, Zn, Mn and Na was significantly higher than in ripe grain at FRS. In the case of cv. ‘Wirtas’, the P, K, Mg, Ca, Zn, Mn and B content determined at MDS was higher than that found in ripe grain at FRS. The content of Lys, Met, Ala and Tyr in green grain of all the cultivars evaluated was higher than that determined at FRS. However, when the grain was harvested at the fully ripe stage, the increase of Arg, His, Leu, Phe, Val, Glu, Pro and Ser was found. The content of fat and α-linolenic fatty acid in green grain of spelt was higher than in ripe grain. The presence of cinnamic and dicarboxylic acids was only found in spelt harvested at MDS. Unripe grain was also characterized by a higher content of hydroxy and phenolic acids.
Multiple steps mediate ventricular layer attrition to form the adult mouse spinal cord central canal

The ventricular layer of the spinal cord is remodelled during embryonic development and ultimately forms the adult central canal, which retains neural stem cell potential. This anatomical transformation involves the process of dorsal collapse, however, accompanying changes in tissue organization and cell behaviour as well as the origin of cells contributing to the adult central canal are not well understood. Here we describe sequential localised cell rearrangements which contribute to the gradual attrition of the spinal cord ventricular layer during development. This includes local breakdown of the pseudostratified organisation of the dorsal ventricular layer prefiguring dorsal collapse and evidence for a new phenomenon, ventral dissociation, during which the ventral-most floor plate cells separate from a subset that are retained in the central canal. Using cell proliferation markers and cell-cycle reporter mice, we further show that following dorsal collapse, ventricular layer attrition involves an overall reduction in cell proliferation, characterised by an intriguing increase in the percentage of cells in G1/S. In contrast, programmed cell death does not contribute to ventricular layer remodelling. By analysing transcript and protein expression patterns associated with key signalling pathways, we provide evidence for a gradual decline in ventral sonic hedgehog activity and an accompanying ventral expansion of initial dorsal bone morphogenetic protein signalling, which comes to dominate the forming central canal. This study identifies multiple steps that contribute to spinal cord ventricular layer attrition and adds to increasing evidence for the heterogenous origin of the adult spinal cord central canal, which includes cells from the floor plate and the roof plate as well as ventral progenitor domain.
A 0.13 μm CMOS UWB RF Transmitter with an On‐Chip T/R Switch

This paper presents a fully integrated 0.13 μm CMOS MB‐OFDM UWB transmitter chain (mode 1). The proposed transmitter consists of a low‐pass filter, a variable gain amplifier, a voltage‐to‐current converter, an I/Q up‐mixer, a differential‐to‐single‐ended converter, a driver amplifier, and a transmit/receive (T/R) switch. The proposed T/R switch shows an insertion loss of less than 1.5 dB and a Tx/Rx port isolation of more than 27 dB over a 3 GHz to 5 GHz frequency range. All RF/analog circuits have been designed to achieve high linearity and wide bandwidth. The proposed transmitter is implemented using IBM 0.13 μm CMOS technology. The fabricated transmitter shows a −3 dB bandwidth of 550 MHz at each sub‐band center frequency with gain flatness less than 1.5 dB. It also shows a power gain of 0.5 dB, a maximum output power level of 0 dBm, and output IP3 of +9.3 dBm. It consumes a total of 54 mA from a 1.5 V supply.
Effect of Vitex agnus-castus plant extract on polycystic ovary syndrome complications in experimental rat model

Objective: To investigate ameliorative effects of Vitex agnus-castus (VAC) and VAC containing pharmaceutical supplement (VPS) against polycystic ovary syndrome (PCOS). Methods: PCOS in the rats was induced by daily administration of letrozole at 1 mg/kg body weight concentration for 21 d. PCOS rats were then treated daily either with metformin, VAC plant extract or VPS at 70, 8 or 8 mg/kg body weight concentration for 15 d. Rats that received none of these treatments were considered as control. Blood and ovaries were collected from all the rats. Serum glucose, cholesterol, triglyceride and high density lipoprotein-cholesterol were measured spectrophotometrically. Serum insulin, estrogen, progesterone, testosterone, luteinizing hormone, follicle-stimulation hormone, catalase, superoxide dismutase, malondialdehide and reduced glutathione were measured using enzyme-linked immunosorbent assay. Results: Rats treated with letrozole demonstrated a significant increase in serum testosterone, estrogen, cholesterol, luteinizing hormone, triglycerides, glucose, insulin, and malondialdehide levels, and a significant decline in progesterone, follicle-stimulating hormone, high density lipoprotein-cholesterol, catalase and reduced glutathione levels compared to control. Contrarily, no significant change in superoxide dismutase was noted in response to letrozole treatment. Rats treated with metformin, VAC or VPS showed a remarkable reversal in the levels of parameters affected by letrozole treatment. Conclusions: Data indicate that VAC and VPS exert potential ameliorative effects against PCOS through the modulation of hormonal and lipid profile as well as oxidative stress. Moreover, the favorable effects of these compounds are comparable to that of metformin.
Light-Dependent Regulation of Circadian Clocks in Vertebrates

Circadian clocks are intrinsic time-tracking systems that endow organisms with a survival advantage. The core of the circadian clock mechanism is a cell-autonomous and self-sustained oscillator called a cellular clock, which operates via a transcription-/translation-based negative feedback loop. Under natural conditions, circadian clocks are entrained to a 24-hour day by environmental time cues, most commonly light. In mammals, circadian clocks are regulated by cellular clocks located in the central nervous system, such as the suprachiasmatic nucleus (SCN), and in other peripheral tissues. Importantly, mammals have no photoreceptors in the peripheral tissues; therefore the effect of light on peripheral clocks is indirect. By striking contrast, zebrafish peripheral cellular clocks are directly light responsive. This characteristic of the zebrafish cellular clock has contributed to the identification of molecules and signaling pathways that are involved in the light-dependent regulation of the cellular clock. Here, selected light-dependent regulatory mechanisms of circadian clocks in mammals and zebrafish are described.
Comparison of nutritional, antioxidant vitamins and capsaicin contents in Capsicum annuum and C. frutescens

ABSTRACT Peppers (Capsicum spp.) contain several bioactive compounds with nutritional and pharmaceutical importance, and these differ between pepper types. The assessment of variation and relatedness among genotypes, varieties or accessions of plant species is important in breeding, conservation and management of genetic resources. Four varieties belonging to the Capsicum species: C. annuum L. and C. frutescens L. were characterized by their nutritional constituents, antioxidant vitamins and capsaicin contents. There was variability in nutritional, vitamins and capsaicin contents among varieties. Higher levels of vitamins were found in fresh than in dry samples. Capsaicin content was in the order: C. frutescens var. baccatum L. ˃C. annuum var. abbreviatum Fingerh. ˃C. annuum var. acuminatum Fingerh. ˃C. annuum var. grossum L. Sendt. The varieties were separated into two clusters. The C. frutescens var. baccatum and C. annuum var. abbreviatum were grouped together on the first cluster while C. annuum var. grossum and C. annuum var. acuminatum occupied the second cluster. The varieties of Capsicum spp. contain important micro- and macro-elements and antioxidative vitamins, in varying amounts. The content of the different bioactive compounds can provide significant proportions of the recommended daily allowance and help improve overall health of humans. The diversity in the nutrient and bioactive substances within Capsicum species, and varieties, could be used in pepper breeding to generate improved commercial hybrids.
The variability and adaptive value of visual learning performance in wild and domesticated colonies of the common eastern bumblebee, Bombus impatiens

THE VARIABILITY AND ADAPTIVE VALUE OF VISUAL LEARNING PERFORMANCE IN WILD AND DOMESTICATED COLONIES OF THE COMMON EASTERN BUMBLEBEE, BOMBUS IMPATIENS Harry Rusnock Advisor: University of Guelph, 2018 Prof. Nigel Raine This thesis examined the adaptive value of visual associative learning in the bumblebee Bombus impatiens, first by quantifying variation in performance across four laboratory colour-learning tasks for wild and domesticated colonies, and then by assessing the field foraging performance of individuals relative to their learning ability. Domesticated colonies differed significantly in terms of Learning Performance Index (LPI) in learning tasks. There was no evidence that colony LPI values were distributed differently in wild and domesticated populations. All colonies displayed similar behavioural patterns across learning tasks: learning performance was greatest when blue was the rewarded floral colour, and performance was significantly reduced after two reversals of the colour-reward association, indicating interference. Bees did not learn to prefer a novel, highly rewarding colour (green). In the field, bees with superior LPI scores collected significantly more pollen and nectar per foraging bout, but had similar overall productivity to bees with worse scores.
Geometrical Constraints Greatly Hinder Formin mDia1 Activity

Formins are one of the central players in the assembly of most actin networks in cells. The sensitivity of these processive molecular machines to mechanical tension is now well established. However, how the activity of formins is affected by geometrical constraints related to network architecture, such as filament crosslinking and formin spatial confinement, remains largely unknown. Combining microfluidics and micropatterning, we reconstituted in vitro mDia1 formin-elongated filament bundles induced by fascin, with different geometrical constraints on the formins, and measured the impact of these constraints on formin elongation rates and processivity. When filaments are not bundled, formins can be anchored to static or fluid surfaces, by either end of the proteins, without affecting their activity. We show that filament bundling by fascin reduces both unanchored formin elongation rate and processivity. Strikingly, when filaments elongated by surface-anchored formins are cross-linked together, formin elongation rate immediately decreases and processivity is reduced, up to 24-fold, depending on the cumulative impact of formin rotational and translational freedoms. Our results reveal an unexpected crosstalk between the constraints at the filament and the formin levels. We anticipate that in cells, the molecular details of formin anchoring to the plasma membrane, strongly modulate formin activity at actin filament barbed ends.
Longirostrine Crocodylians from the Bartonian of Morocco and Paleogene Climatic and Sea Level Oscillations in the Peri-Tethys Area

ABSTRACT The Eocene–Oligocene transition was a period of high faunal and floral turnover, often correlated with climatic deterioration. Crocodyliforms are climate sensitive, and they have been often used for reconstruction of paleoclimates. The description of crocodylian material from the Bartonian of Aaiun-Tarfaya Basin (Morocco) allows the recognition of at least two longirostrine crocodylians, including a gavialoid. This identification is important, because the migration of gavialoids to South America probably occurred during the late Eocene. Close relationships between late Eocene–early Oligocene Eogavialis africanum from Egypt, Argochampsa krebsi from the Paleocene of Morocco, and the South American gavialoid clade suggests that Morocco could have had a particular place in the gavialoid dispersal route to South America. The resemblance between Moroccan material described herein and E. africanum is thus important in this context. Analysis of the distribution of longirostrine crocodylians in the Peri-Tethys area through the Eocene–Oligocene shows a strong difference in the evolution of the distribution between longirostrine crocodylians and Diplocynodon. Whereas the freshwater Diplocynodon has a continuous distribution in western Europe, the mainly marine longirostrine crocodylians have a northern maximal expansion that moves southward during the middle Eocene, being restricted to North Africa during late Eocene–early Oligocene. European freshwater Asiatosuchus-like taxa also disappear during the late Eocene. Climatic deterioration, helped by sea level oscillations, may have strongly impacted the diversity and latitudinal distribution of the crocodylians, but we highlight a possible differential tolerance in range of climatic conditions between crocodylians. This could help to refine the use of crocodylians as paleoclimatic proxies.
Validation of COI metabarcoding primers for terrestrial arthropods

Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40–60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
Reliability-estimation and stopping-rules for software testing, based on repeated appearances of bugs

Software-testing (debugging) is one of the most important components in software development. An important question in the debugging process is, when to stop. The choice is usually based on one of two decision criteria: (1) when the reliability has reached a given threshold, and (2) when the gain in reliability cannot justify the testing cost. Various stopping rules and software reliability models are compared by their ability to deal with these two criteria. Two new stopping rules, initiated by theoretical study of the optimal stopping rule based on cost, are more stable than other rules for a large variety of bug structures. The 1-step-ahead stopping rules based on the Musa et. al. basic execution and logarithmic Poisson models, as well as the stopping rule by Dalal and Mallows (1990), work well for software with many relatively small bugs (bugs with very low occurrence rates). The comparison was done by simulation. >
Circulating levels of free 25(OH)D increase at the onset of rheumatoid arthritis

Objective Epidemiological studies suggest vitamin D deficiency as a potential risk factor for rheumatoid arthritis (RA) development, a chronic autoimmune disorder highly prevalent in indigenous North American (INA) population. We therefore profiled the circulating levels of 25-hydroxyvitaminD [25(OH)D], an active metabolite of vitamin D, in a cohort of at-risk first-degree relatives (FDR) of INA RA patients, a subset of whom subsequently developed RA (progressors). Methods 2007 onward, serum samples from INA RA patients and FDR were collected at the time of a structured baseline visit and stored at −20°C. Anti-citrullinated protein antibodies (ACPA), 25(OH)D, hs-CRP, vitamin-D binding protein (VDBP) levels were determined using ELISA and rheumatoid factor (RF) seropositivity was determined by nephelometry. Results We demonstrate that 25 (OH) D concentrations were lower in winter than summer (P=0.0538), and that serum 25(OH)D levels were higher in samples collected and stored after 2013 (P<0.0001). Analysis of samples obtained after 2013 demonstrated that 37.6% of study participants were 25(OH)D insufficient (<75nmol/L). Also, seropositive RA patients and FDR had lower 25(OH)D levels compared to ACPA-/FDR (P<0.05, P<0.01 respectively). Linear regression analysis showed 25(OH)D insufficiency was inversely associated with presence of RA autoantibodies. Longitudinal samples from 14 progressors demonstrated a consistent increase in 25(OH)D levels at the time they exhibited clinically detectable joint inflammation, without any significant change in VDBP levels. Conclusion We demonstrate that 25(OH)D levels in serum increased at RA onset in progressors. The potential role that vitamin D metabolites and their downstream effects play in RA transition requires further investigation.
A near perfect stable random access protocol for a broadcast channel

A near perfect stable random access protocol for a broadcast channel, the distributed queuing random access protocol (DQRAP), is presented and evaluated. The DQRAP protocol utilizes minislots to provide ternary channel feedback and two distributed queues to resolve contention and to schedule the transmission of messages. Modeling and simulation indicate that the DQRAP protocol, using as few as three minislots, achieves a performance level which approaches that of a hypothetical perfect scheduling protocol, i.e., the M/D/1 system, with respect to throughput and delay. The DQRAP protocol is stable and not sensitive to propagation delay and thus offers the potential of improved performance over current protocols in satellite, metropolitan and packet radio networks. <<ETX>>