Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetically Disparate Fayoumi Chicken Lines Show Different Response to Avian Necrotic Enteritis

Necrotic enteritis (NE) has reemerged as a significant problem as a result of growing restrictions of antibiotics in agricultural animal production and increasing concerns over antibiotic resistance in human pathogens. To enhance our understanding of host-pathogen immunobiology in NE, transcriptional analysis was conducted to compare changes in NE-induced intestinal transcripts and to identify immune-related genes whose expression are associated with NE disease resistance using two genetically disparate Fayoumi chicken lines, M5.1 and M15.2. NE was induced by co-infection of Eimeria maxima and Clostridium perfringens using an established disease model and two major NE-induced clinical signs, body weight loss and intestinal lesions, were measured in two inbred Fayoumi chicken lines, M5.1 and M15.2. In the clinical criteria, line M5.1 chickens were more resistant to NE compared to line 15.2 birds. Although they have the same genetic background, these two chicken lines are genetically disparate at their major histocompatibility complex (MHC) and this difference was reflected in the differential expression patterns of several inflammatory genes such as suppressor of cytokine signaling 3 (SOCS3), interleukin 8 (IL8), nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta (NFKBIZ), serpin peptidase inhibitor, clade F (alpha- 2 antiplasmin, pigment epithelium derived factor), member 1 (SERPINF1), and gap junction protein, alpha 1, 43kDa (GJA1) between NE-afflicted and uninfected chickens. These results will lead to increased insights on the NE disease resistance mechanisms and the role of host genes controlling host immune response to C. perfringens.
Hybrid Assembly of Whole Genome Shotgun Sequences of Two Sugar Beet (Beta vulgaris L.) Translocation Lines Carrying the Beet Cyst Nematode Resistance Gene Hs1-2 and Functional Analysis of Candidate Genes

Sugar beet (Beta vulgaris L. ssp. vulgaris) is a host of the beet cyst nematode (BCN) Heterodera schachtii Schmidt, which causes high yield losses. Resistance had been identified in the wild relative Patellifolia procumbens and was integrated into the sugar beet genome by a translocation to the end of chromosome 9. Two nematode resistant (TR520 and TR363) and two susceptible (TR659 and TR320), sugar beet translocation lines which share partly homologous sequences from P. procumbens chromosome 1, were the focus of my research. I hypothesized that a second gene for nematode resistance (Hs1-2) is located on a region shared by both resistance carrying translocations. The aim of this work was the identification of the Hs1-2 gene. The work includes a functional analysis of a candidate sequence for the Hs1-2 gene (ORF 702) which encodes a galactosyltransferase family protein and which had been identified in a previous work. Moreover, new gene candidates have been identified and characterized after whole genome shotgun (WGS) sequencing using the Illumina HiSeq platform of the translocation lines TR520 and TR363.
Gain Enhancement of Microstrip Antenna Using 3D Water-Based Metamaterial

In this paper, the totally transparent microstrip antenna consists of all dielectric materials is proposed for wireless communications. A water-based microstrip antenna is fed by an L-shaped probe. All dielectric water-based meta material (MM) unit-cell element consists of dielectric cubic boxes filled with water. It is designed and optimized for MM characteristics in the frequency band from 4 GHz to 4.4 GHz. A reconfigurable MM electric properties is achieved by changing the water height in the MM unit-cell element. A water-based MM lens consists of three layers is designed to collimate the radiation from the microstrip antenna. The phase compensation in the MM lens is achieved by changing the water heights in the MM unit-cell elements of the lens. A reconfigurable beam in different directions from −30° to +30° is steered by changing the water level distribution over the MM lens unit-cell elements. A fullwave analysis using the finite integration technique is used for the design and analysis of the water-based MM lens arrangements.
Accurate Extraction of Large Electromechanical Coupling in Piezoelectric MEMS Resonators

Recent advancements in the field of piezoelectric micro-resonators have produced devices, such as lithium niobate laterally vibrating resonators, with very high electromechanical coupling factors (<inline-formula> <tex-math notation="LaTeX">$k_{t}^{2}$ </tex-math></inline-formula>) and respectable quality factors (<inline-formula> <tex-math notation="LaTeX">${Q}$ </tex-math></inline-formula>). As a result, the records of the figure of merit (FoM) for radio-frequency MEMS resonators have been broken several times in the past five years. As exciting as these high FoMs are, they impose unique caveats in accurately extracting the electromechanical coupling often due to the presence of spurious modes. It is a less noted issue for micro-resonators with moderate <inline-formula> <tex-math notation="LaTeX">${k} _{t}^{2}$ </tex-math></inline-formula>, as spurious modes either are absent or do not significantly affect the common extraction technique based on identifying resonances and anti-resonances. This paper will first theoretically analyze how disregarding spurious modes can potentially lead to inaccurate extraction of <inline-formula> <tex-math notation="LaTeX">${k} _{t}^{2}$ </tex-math></inline-formula> of the intended mode and then offer a framework that accounts for spurious modes and accurately extracts electromechanical coupling using a multi-resonance recursive fitting. [2018-0209]
Efficient X-Band Transmitter With Integrated GaN Power Amplifier and Supply Modulator

In this paper, we present a high-efficiency transmitter based on an integrated circuit (IC) supply modulator implemented in the same 0.15-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> gallium nitride (GaN)-on-SiC RF process as the power amplifier (PA) monolithic microwave IC. The X-band 10-W two-stage PA is designed for stable operation with minimal drain capacitance, which enables fast supply modulation. The multilevel supply modulator provides eight voltage levels with 3-bit digital control [(power digital-to-analog converter (pDAC)], achieving a state-of-the-art slew rate of 5 kV/<inline-formula> <tex-math notation="LaTeX">$\mu \text{s}$ </tex-math></inline-formula>. Characterization of the dynamic <inline-formula> <tex-math notation="LaTeX">$R_{\mathrm{\scriptscriptstyle ON}}$ </tex-math></inline-formula> of the GaN switches allows the development of an efficiency model for the pDAC and an investigation of the effects of the pDAC internal resistance on the PA performance, resulting in a comprehensive efficiency model for the supply-modulated PA. The flexible compact transmitter consisting of the PA and pDAC ICs shows high efficiency in backoff for a variety of signals, both for radar and communications. Measured results for amplitude- and frequency-modulated radar pulses show a composite power-added efficiency (CPAE) of 44% with a peak power of 10 W at 9.57 GHz, with simultaneous spectral confinement and 52-dB improvement of the first time sidelobe. For a 20-MHz high peak-to-average ratio LTE signal, the CPAE increases from 11% to 32% compared to a fixed supply voltage transmitter, while linearity under dynamic supply operation is maintained through digital predistortion.
THE EVALUATION OF NITRIC OXIDE SCAVENGING ACTIVITY OF ACALYPHA INDICA LINN ROOT

Acalypha indica (Euphorbiaceae) is commonly known as Indian Copperleaf and Indian Nettle. It is a common annual herb, which grows in the hotter parts of India like Bihar, Assam and southwards of Kerala. The ethanol and aqueous extracts of root were screened for antioxidant activity using Nitric Oxide Scavenging activity method, which showed significant percentage of inhibition in dose dependent manner. As antioxidant therapy is found to be useful in complicated disease status related with free radical activity, the present study might be extended for the formulation and evaluation of different antioxidant herbal dosage forms.
Using Genome-Wide Approaches to Dissect Seed Development

Author(s): Le, Brandon | Advisor(s): Goldberg, Robert B | Abstract: Seeds are a major source of food for human and animal consumption and can account for a large majority of the caloric intake by human. A detailed understanding of seed development should provide strategies for improving seed yield or enhance seed nutrients. Seed development consists of three major structure — the embryo, endosperm, and seed coat — all developing in parallel. Each of these structures undergo major developmental and physiological changes during seed development; however, it is not known how the different developmental programs in these structure are coordinated to form a seed.How are genes regulated during seed development? What are the transcription factors playing a major role in controlling seed development? Are there genome-wide methylation changes during seed development, and if so, how do these changes affect seed activity? These were the driving questions that formed the basis of my Ph.D. research. To begin to address these questions, I used a variety of genomics tools [e.g., Sanger sequencing, next generation sequencing (NGS), GeneChip microarrays, laser capture microdissection (LCM)], with several plant species [e.g., Arabidopsis, soybean, scarlet runner bean (SRB)], to characterize seed transcriptomes and methylomes on a genome-wide basis. In addition, I used reverse genetics to knockout seed-specific transcription factors and determine what role they may play in seed development. Collectively, data generated from my Ph.D. research can contribute to understanding gene activity during seed development.
Haplotypes of parasitoid Tamarixia radiata (Waterston) (Hymenoptera: Eulophidae) in citrus in the state of Tamaulipas, Mexico

Tamarixia radiata (Waterston) (Hymenoptera: Eulophidae) is a specific ectoparasite of Diaphorina citri Kuwayama (Hemiptera: Liviidae) vector of Candidatus Liberibacter spp. , the causative agent of Huanglongbing, a devastating disease of citrus worldwide. The parasitoid was accidentally introduced to various regions of the Americas, including Mexico, where currently it is massively reproduced and released. Contributing to the knowledge of parasitoid wild populations use to benefit the Mexican citrus industry, this study aimed to genetically characterize T. radiate populations in the state of Tamaulipas, Mexico, by sequencing mitochondrial DNA (cytochrome oxidase subunit 1 gene), analyzing parasitoid samples collected during the years 2006-2013. From the specimens two haplotypes (H1 and H2) were found, from which H1 is present in most citrus areas infested by D. citri in Mexico, while H2 has only been detected so far in the states of Tamaulipas and Yucatan. The limited distribution of H2 suggests the possible entries of the parasitoid to Mexico, which is supported by the clustering of H2 in the statistical parsimony analysis with haplotypes only found in Florida so far.
Urofacial Syndrome: A genetic model to understand human urinary tract abnormalities.

Urofacial syndrome (UFS; MIM# 236730) is a rare autosomal recessive condition characterised by urinary bladder and bowel voiding dysfunction with a pathognomonic abnormality of facial movement with expression. UFS can be caused by biallelic putative loss-of-function mutations in HPSE2, which encodes heparanase 2. Failure to discover HPSE2 mutations in all cases of UFS suggests genetic heterogeneity. The urinary tract features of UFS overlap those seen in the spectrum of non-syndromic non-neurogenic voiding dysfunction and vesicoureteric reflux (VUR). This overlap suggests there may be some aspects of pathogenesis in common. The project aimed to define the genotypic and phenotypic spectrum associated with mutations in HPSE2 by Sanger sequencing and multiplex ligation-dependent probe amplification (MPLA) in newly referred cases of UFS and making comparison to a review of mutations and phenotypes seen in the literature. This work discovered five further families with HPSE2 associated UFS increasing known mutations whilst, reinforced that this is an under-recognised condition and emphasised the previously under-reported feature of facial weakness. The failure to discover HPSE2 mutations in all cases referred provided further evidence of genetic heterogeneity.The project also aimed to discover further genes associated with UFS. Autozygosity mapping and whole exome sequencing was carried out in cases of UFS without mutations in HPSE2. This led to the recognition that UFS is also caused by biallelic putative loss-of-function mutations in LRIG2 encoding the leucine-rich repeats and immunoglobulin-like domains 2 (LRIG2) protein in three families. Failure to identify LRIG2 mutations in all HPSE2 negative families suggests further genetic heterogeneity. To address the question of whether the pathogenesis of UFS overlaps more common conditions with a similar spectrum of urinary tract abnormalities I aimed to examine whether pathogenic variants in HPSE2 and LRIG2 were seen in these phenotypes. Unexpectedly this led to the discovering of further families affected by UFS but failed to show an association of variants in UFS genes with non-syndromic urinary tract abnormalities. However, variants of potential interest were discovered. As part of work toward understanding the pathogenesis of UFS and designing a model to test the pathogenesis of sequence variants expression studies in a Xenopus tropicalis hpse2 knock-down model of UFS were carried out. The knock-down model provided valuable insight in to the likely pathogenesis of UFS with evidence pointing towards a congenital peripheral neuropathy with failure of correct nerve path finding. Understanding the pathogenesis of UFS has the potential to direct further research in to therapeutic intervention.
Caracterización bioquímica de AmiJ33, una amilasa de Bacillus amyloliquefaciens aislada de suelos cultivados con caña de azúcar en la región del Papaloapan

Amylase (EC 3.2.1.1) from Bacillus amyloliquefaciens JJC33M (AmiJ33) was produced by submerged fermentation. Peptone, yeast extract, Ca+2 and the glycine effect over AmiJ33 production was analyzed shown that yeast extract and Ca+2 concentration increased in 2.5 times the AmiJ33 production. By mean precipitation using (NH4)2SO4, the enzyme was recovered and the protein was identified by SDS-PAGE demonstrating that AmiJ33 has a molecular weight of 50 kDa. Temperature and pH optimus were determined, the highest values of activity were observed at pH 6.0 and 80° C, however, using slightly acid conditions (pH 4.0 and 5.0) AmiJ33 kept 72% of activity. AmiJ33 was stable for 3 h at 40°C, and 30 min at 45-50° C, retaining 88 and 82% of residual activity respectively. At 60°C, the enzyme activity decreased 40%. The divalent ions increased slightly AmiJ33 activity, however EDTA did not inhibit its activity, while SDS inhibited it completely.
Using rainout shelters to evaluate climate change effects on the demography of Cryptantha flava

1 Precipitation in arid regions is temporally variable with much of it arriving in discrete, unpredictable pulses. Climate change models predict an increase in the variation of precipitation, with longer droughts and larger rainfall events, in addition to increased temperatures. 2 A life table response experiment (LTRE) was conducted with the herbaceous arid‐land perennial Cryptantha flava (Boraginaceae) from 1997 to 2000, in order to determine how variation in precipitation affects asymptotic population growth (l) and vital rates. Variation in precipitation took two forms, through rainout shelters erected just before and during the 1999 spring growing season, and through naturally occurring variation over the 4 years. 3 An unexpected effect of rainout shelters on l was observed that could not be attributed to drought. The l value decreased greatly in control census plots in the 1998–99 transition but did not decrease in sheltered of plots. The 1999 spring, when shelters were in place, was unusually cold, resulting in frost damage to unsheltered plants. Plants under shelters experienced elevated nighttime temperatures and escaped frost damage. The greater value of l in the sheltered plots is attributable almost entirely to greater contributions of survival, growth and stasis. 4 There were residual effects of the 1999 drought treatment in the 1999–2000 transition as l decreased in the sheltered populations while l increased in control populations. Compared to controls, there were large negative effects of survival, growth, and stasis and a large positive effect of retrogression in the droughted plots. 5 Natural variation in fecundity contributed considerably to inter‐annual variation in l in control plots. Annual variation in fecundity strongly paralleled annual variation in seedling establishment. The relative contributions of other vital rates varied greatly among the annual transitions. 6 Synthesis. The study illustrates the sensitivity of this arid‐land species to early season frost events and to variation in precipitation. It suggests the importance of considering the seasonal timing of precipitation events when projecting the population‐level consequences of global climate change, with particular attention given to precipitation that triggers germination and seedling establishment. Researchers using shelters to create drought treatments should consider their nighttime warming effects.
Medicinal plants for suppressing soil-borne plant diseases

Most plants exhibit inhibitory and stimulatory biochemical interactions with other plants and microorganisms, referred to as “allelopathy. ” Especially, through root exudates, higher plants are able to affect the microfiora in the rhizosphere. Production of biological active substances by higher plants that prevent phytopathogens (bacteria, fungi, and nema-todes) from infecting crops has been reported (Yoshihara et al. 1988; Schenk et al. 1991). In addition, many species of plants which have been widely used for medicinal purpose also exert an allelopathic effect (Fujii et al. 1991).
Three new species of the genus Adelophryne (Amphibia: Anura: Leptodactylidae) from northeastern Brazil, with remarks on the other species of the genus

In the present paper three new species of the genus Adelophryne from the coastal Atlantic forest in Brazil are described. The species are separated from the two species formerly known from the Amazon forest by caatinga vegetation and a distance of at least 1600 km. A. pachydactylus from Bahia has a reduced number of phalanges in the fourth finger, and large subdigital pads under fingers and toes. A. baturitensis has distinct subarticular tubercles under the toes and a relatively large size. A. maranguapensis has large discs on fingers and toes and is boldly patterned. During fieldwork in Amapa two specimens of A. gutturosa were collected and based on them additional data are provided and some concepts from the original description are revised. Literature data on this genus are incorporated and a key to the known species is provided.
Fat chance: genetic syndromes with obesity

Although obesity shows high heritability, we are aware of only a small number of genes that affect adipose mass in humans. Genetic syndromes with obesity represent unique opportunities to gain insight into the control of energy balance. The majority of obesity syndromes can be distinguished by the presence of mental retardation. We performed a systematic search of such syndromes and reviewed the literature with a focus on distinguishing clinical features, the characteristics of their obesity, and the underlying pathogenetic mechanisms. We predict that the study of these conditions will shed light on common forms of obesity.
The genetic structure of Aphis gossypii populations in Japanese fruit orchards

The genetic structure of Aphis gossypii Glover (Hemiptera: Aphididae) populations was characterized using microsatellite analysis of insects sampled from pear and citrus orchards at three locations in the summer seasons of 2001 and 2003. These data will enable more precise forecasting of infestation and will be of value to the development of better control methods. In total, 89 genotypes were found in 500 aphid samples. The diversity indices in aphid populations on pear trees fluctuated but showed a decrease with time in citrus orchards. Japanese aphid populations have greater variation in their microsatellite loci than African, European, or Southeast Asian populations. Approximately half of the genotypes were found in only one colony, whereas the remainder were identified in two or more colonies. Fifteen genotypes appeared in different years, in samples from different areas, or on different host plants. Our data suggest the existence of aphid populations with pear‐adapted genotypes and with a permanent parthenogenetic life cycle. Some of the genotypes included genes conferring resistance to pirimicarb and pyrethroid insecticides. Japanese A. gossypii populations may maintain their large genetic variation through differences in their life cycles.
Orodispersible Tablets: Novel Strategies and future challenges in Drug Delivery

Oral route is presented as the gold standard of drug delivery systems within the pharmaceutical industry being the most safe, non-invasive and the most economic route of administration. This in return elevates the patient compliance and adherence to the treatment as being approved as the most convenient drug delivery system. However, a special section of patients such as geriatrics, pediatrics, disabled and mentally-ill patients find some difficulties in handling conventional oral dosage forms like tablets and capsules. For example, elderly patients usually suffer from weak shaking hands, difficulty in swallowing and inability to drink water properly which make dealing with conventional oral dosage forms a hard mission. Also, another major section of patients can hardly use the oral conventional dosage forms as a result of sudden allergic attacks, motion sickness, nauseous, uncooperative patients and also travellers who might not have an easy water access. Moreover, oral drug delivery is usually incomplete if the drug is exposed to hepatic first pass effect, which in turn lowers the bioavailability of many drugs. Consequently, advancement in oral drug delivery systems provided a vast number of technologies including the production of orodispersible tablets (ODTs). Over many decades, these systems offered a successful alternative to conventional oral drug delivery systems. Since their production to the pharmaceutical market in the 1980s, they became one of the rapidly growing industrial channels. Many technologies including conventional and patented ones adopted the production of ODTs. In this article, several core aspects are discussed including the history of ODTs development, their advantages, disadvantages, techniques and patented technologies used in their preparation, also, Methods of evaluation and future challenges of ODTs.