Miracle-dz/UniFAR-FTUs huggingface dataset:
The Molecular Analysis of Hawaiian Bird Diets

The aim of this project is to utilize high-throughput molecular methods to investigate the diets of three nonnative and one native Hawaiian bird species. Next-generation sequencing (NGS) has made it possible to produce thousands of sequencing reads of DNA in a relatively short amount of time. This metabarcoding technology has been used to identify a range of different taxa, from bacteria in the human gut to fungi in the soil. More recently, this approach has been used to identify insects in the diets of birds and other species, including bees and bats. Samples underwent genomic sequencing using a targeted approach of the cytochrome oxidase I (COI) gene, a region that is present in all insects. DNA was extracted from bird feces and stomach contents using protocols designed for fecal material and a genomic region was amplified by polymerase chain reaction (PCR) using universal COI primers. The resulting amplified sequences were compared to an online reference database of millions of insect sequences for taxonomic identification. Data were analyzed for diet variation within and between each species of bird, as well as were compared to arthropods sampled from areas where these birds were observed foraging. The results showed there were a large variety of insects and spiders consumed by birds. There was overlap of insect order between the species of birds, but when diets were examined at a species level, bird species were preying on different insects.
Prenatal Metal Mixtures and Birth Weight for Gestational Age in a Predominately Lower-Income Hispanic Pregnancy Cohort in Los Angeles

Background: Reduced fetal growth increases the risk for adverse health outcomes. Growing evidence suggests that metal exposures contribute to reduced fetal growth, but little is known about the effects of complex metal mixtures. Objectives: We investigated the impact of a complex mixture of metals on birth weight for gestational age (BW for GA) in the Maternal and Developmental Risks from Environmental and Social Stressors study, a predominately lower-income Hispanic pregnancy cohort in Los Angeles, California. Methods: Cadmium (Cd), cobalt (Co), mercury (Hg), nickel (Ni), molybdenum (Mo), lead (Pb), antimony (Sb), tin (Sn), and thallium (Tl) were measured by inductively coupled plasma mass spectrometry (ICP-MS) in maternal urine samples collected in early pregnancy (median GA: 13.1 wk). Speciated urinary arsenic (As) (inorganic+monomethyl+dimethyl As) was measured by high-performance liquid chromatography coupled to ICP-MS. Primary analyses focused on a mixture of seven metals that have previously been associated individually with fetal growth (i.e., As, Cd, Co, Hg, Ni, Pb, Tl) (n=262). In exploratory analyses, we additionally examined three metals that have been less studied in relation to fetal growth (i.e., Mo, Sb, Sn). Covariate-adjusted Bayesian kernel machine regression was used to investigate metal mixture associations with BW for GA z-scores. Results: In primary analyses, Hg and Ni ranked highest as predictors of BW for GA. An inverse linear association was estimated for Hg, whereas a positive association was estimated for Ni at low-to-moderate concentrations. A potential interaction between Hg and Ni was also identified. In our exploratory analysis, Sb ranked highest as a predictor of BW for GA, followed by Hg and Ni. Conclusions: Our findings suggest that in this understudied population, Hg may reduce fetal growth, whereas Ni may promote fetal growth. We also identified Sb as a potential metal of concern for this population, which merits additional investigation. https://doi.org/10.1289/EHP7201
Investigation of Different Time-Frequency Representations for Intelligibility Assessment of Dysarthric Speech

Speech disorders linked to neurological problems affect person’s ability to communicate through speech. Dysarthria is one of the speech disorders caused due to muscle weakness producing slow, slurred and less intelligible speech. Automatic intelligibility assessment of dysarthria from speech can be used as a promising clinical tool in treatment. This paper explores the use of perceptually enhanced Fourier transform spectrograms and Constant-Q transform spectrograms with CNN to assess word level and sentence level intelligibility of dysarthric speech from UA and TORGO databases. Constant-Q transform and perceptually enhanced mel warped STFT spectrograms performed better in the classification task.
Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches

Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.
Revealing Alteration in the Hepatic Glucose Metabolism of Genetically Improved Carp, Jayanti Rohu Labeo rohita Fed a High Carbohydrate Diet Using Transcriptome Sequencing

Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved ‘Jayanti rohu’ Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPARγ. The insulin signaling pathways with enriched PPAR and mTOR were identified by Kyoto Encyclopedia of Genes and Genome (KEGG) as a result of high carbohydrates. This work revealed for the first time the atypical regulation transcripts associated with glucose metabolism and lipogenesis in the livers of Jayanti rohu due to the inclusion of high carbohydrate levels in the diet. This study also encourages the exploration of early nutritional programming for enhancing glucose efficiency in carp species, for sustainable and cost-effective aquaculture production.
Anti-Proliferative Activity of A Hydrophilic Extract of Manna from Fraxinus angustifolia Vahl through Mitochondrial Pathway-Mediated Apoptosis and Cell Cycle Arrest in Human Colon Cancer Cells

Manna is produced from the spontaneous solidification of the sap of some Fraxinus species, and, owing its content in mannitol, is used in medicine as a mild laxative. Manna is also a rich source of characteristic bio-phenols with reducing, antioxidant and anti-inflammatory properties. This study assesses the activity of a hydrophilic extract of manna (HME) on cellular and molecular events in human colon-rectal cancer cells. HME showed a time- and concentration-dependent anti-proliferative activity, measured by MTT assay, in all the cell lines examined, namely Caco-2, HCT-116 and HT-29. The amounts of HME that caused 50% of cell death after a 24 h treatment were 8.51 ± 0.77, 10.73 ± 1.22 and 28.92 ± 1.99 mg manna equivalents/mL, respectively; no toxicity was observed in normally differentiated Caco-2 intestinal cells. Hydroxytyrosol, a component of HME known for its cytotoxic effects on colon cancer cells, was ineffective, at least at the concentration occurring in the extract. Through flow-cytometric techniques and Western blot analysis, we show that HME treatment causes apoptosis, assessed by phosphatidylserine exposure, as well as a loss of mitochondrial membrane potential, an intracellular formation of reactive oxygen species (ROS), increases in the levels of cleaved PARP-1, caspase 3 and Bax, and a decrease in Bcl-2 expression. Moreover, HME interferes with cell cycle progression, with a block at the G1/S transition. In conclusion, the phytocomplex extracted from manna exerts an anti-proliferative activity on human colon cancer cells through the activation of mitochondrial pathway-mediated apoptosis and cell cycle arrest. Our data may suggest that manna could have the potential to exert chemo-preventive effects for the intestine.
Soft Template Electropolymerization of Polypyrrole for Improved pH-Induced Drug Delivery

Chronic wounds are characterized by a localized pH change from acidic (healthy) to alkaline (unhealthy), which can be harnessed to act as a switch for drug release from a polymer medium covering the wound for improved healing. To realize this, a new polymer dressing material is needed to help heal chronic wounds. Polypyrrole (PPy) is a biocompatible electroactive polymer that has been proven as a successful drug delivery mechanism, but currently lacks the capacity for scalable clinical applications due to its poor processability. In this study, PPy films with and without microstructures were produced using electrochemical oxidation and subsequently doped with fluorescein, a model drug molecule. To increase the drug loading capacity, microstructures were created through soft template polymerization of pyrrole around hydrogen gas bubbles. Fluorescein release was measured using UV spectroscopy over a pH range of 2 to 11, showing increased release at higher pH values. Microstructured films showed an increased doping capacity compared to flat PPy films, attributed to the increase in drug incorporation sites. The pH-activated release mechanism was shown to be successful and can be applied as a pH-sensitive biosensor and drug delivery system in vitro.
Candidate Gene Polymorphism vis-a-vis Immune Response to Important Infectious Diseases in Bovines

Livestock sector play an important role in socio economic development and the national economy of the country. With an overall contribution of ~4% to GDP, livestock sector play an important role in national economy whilst contributing to the nutrition security, household income along with generating gainful employment in the rural areas, particularly among the landless, small and marginal farmers. India’s livestock sector is one of the largest in the world and boasts of a huge array of animal genetic resource. As per the 19 th Livestock Census-2012, India is home to a total of 512.05 million livestock population comprising cattle, buffalo, sheep, goat, pig, horse and ponies, mules, donkeys, camels, mithun and yak. India ranks first in milk production, accounting for 18.81 % of world production, achieving an annual output of 165.4 million tonnes during 2016-17 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 08 (2018) Journal homepage: http://www.ijcmas. com
Emerging insights into the structure and function of ionotropic glutamate delta receptors

Glutamate delta‐1 (GluD1) and delta‐2 (GluD2) receptors belong to the orphan GluD subfamily of ionotropic glutamate receptors (iGluRs). GluDs were classified as ionotropic glutamate receptors based on their sequence similarity. Two decades after these GluDs were first cloned they are still considered “orphan” due to a lack of knowledge of the endogenous ligands that can activate them. Nevertheless, they are crucial for synapse formation, maturation and maintenance of CNS functions, and are implicated in multiple neuronal disorders, including schizophrenia, autism spectrum disorder and depressive disorders. Over the last decade significant discoveries have been made, include role of GluD receptors in mediating trans‐synaptic interactions and their unique non‐swapped architecture, which is distinct from other ionotropic glutamate receptors. Also, the prospect of GluD ionotropic activity being regulated by direct interaction with metabotropic glutamate receptors is exciting. These discoveries will likely drive the field in the future, providing direction to GluD research.
Effects of starvation and refeeding on growth performance, appetite, growth hormone–insulin-like growth factor axis levels and digestive function of Acipenser dabryanus

Abstract The aim of this study was to explore the effects and mechanisms of different starvation treatments on the compensatory growth of Acipenser dabryanus. A total of 120 fish (60·532 (sem 0·284) g) were randomly assigned to four groups (fasting 0, 3, 7 or 14 d and then refed for 14 d). During fasting, middle body weight decreased significantly with prolonged starvation. The whole-body and muscle composition, serum biochemical indexes, visceral indexes and digestive enzyme activities had been effected with varying degrees of changes. The growth hormone (GH) level in serum was significantly increased in 14D; however, insulin-like growth factor-1 (IGF-1) showed the opposite trend. The neuropeptide Y (npy) mRNA level in brain was significantly improved in 7D; peptide YY (pyy) mRNA level in intestine was significantly decreased during fasting. After refeeding, the final body weight, percentage weight gain, specific growth rate, feed intake, feed efficiency and protein efficiency ratio showed no difference between 0D and 3D. The changes of whole-body and muscle composition, serum biochemical indexes, visceral indexes and digestive enzyme activities had taken place in varying degrees. GH levels in 3D and 7D were significantly higher than those in the 0D; the IGF-1 content decreased significantly during refeeding. There was no significant difference in npy and pyy mRNA levels. These results indicated that short-term fasting followed by refeeding resulted in full compensation and the physiological and biochemical effects on A. dabryanus were the lowest after 3 d of starvation and 14 d of refeeding. Additionally, compensation in A. dabryanus may be mediated by appetite genes and GH, and the degree of compensation is also affected by the duration of starvation.
Effects of Morphologies of Thermo-sensitive Electrospun Nanofibers on Controllable Drug Release.

Electrospun nanofibers is a promising and versatile avenue for building controlled drug release system because of the facile fabrication and the broad range of polymer materials. This research systematically studied the morphological effect of thermo-sensitive electrospun nanofibers, including porous and coaxial structures, on controllable drug release. Three types of drugs, Nicotinamide, Paracetamol and Ibuprofen, with different hydrophilicity were applied in this study. The data of drug release were all fitted to the first-order kinetic model regardless of the drug properties, and the release rates paralleled with their hydrophilicity. Sol-gel phase transition of the thermo-sensitive PNIPAAm hydrogel led to slower drug release at 37 ℃ compared with those at 25 ℃. Regarding morphology, coaxial nanofibers could provide higher loading efficiency and slower drug release rather than porous nanofibers. Our research highlighted the overall effects of compound property, temperature and the morphological structures of thermo-sensitive electrospun nanofibers on the controlled drug release. Our results concluded that hydrophobic drug encapsulated in the core-shell PNIPAAm nanofibers could perform excellent sustained release and also controllable release under temperature stumuli.
A Local-Exchange Model of Folding Chain Surface of Polymer Crystal Based on Worm-Like Chain Model within Single-Chain in Mean-Field Theory

The structure of amorphous layer of folding surface controls the properties of the polymer lamellar crystal, which consists of chains with a loop conformation. The surface tension depends on the length and the distance between two injection points of the loop which involving the reptation motion and lateral exchange motion of the stems. In the present work, a local-exchange motion model based on the worm-like chain model is developed to investigate the effects of lateral motion of stems on the release the surface tension. The optimal distance between two injection points is determined by the balance of chain bending energy and conformational entropy. The numerical results provide evidences to the adjacent re-entry model for various loop lengths. A possible explanation involving density of injection points is proposed to interpret the mechanism.
Opportunistic Infection in Hospitalised Patients with Inflammatory Bowel Disease.

OBJECTIVE To investigate the incidence, clinical features, and risk factors of opportunistic infections in elderly patients with inflammatory bowel disease (IBD). STUDY DESIGN Observational study. PLACE AND DURATION OF STUDY Department of Digestive and Geriatrics Center, Sichuan University West China Hospital, China between January 2012 and January 2019. METHODOLOGY Patients (≥18 years) with IBD were enrolled in this study. Clinical data from the infected elderly group (age ≥60 years), non-infected elderly group (age ≥60 years) and infected adult group (age: 18-59 years) were compared. Logistic regression analysis was used for risk factors associated with opportunistic infection. RESULTS A total of 8.9% (307/3,456) of patients with IBD had opportunistic infection. The opportunistic infection rate of elderly group was 16.5% (80/485), which was significantly higher than that of adult group (7.6%, 227/2,971, p <0.05). Compared with infected adult group or non-infected elderly group, infected elderly group had less fever and leukocytosis, but more hypoproteinemia and several activities (p <0.05). Cytomegalovirus and Epstein-Barr virus were the most common agents in elderly group and adult group, respectively. Multiple episodes (three or more) were more common in infected elderly group; the time of opportunistic infections was associated with systemic inflammatory reaction syndrome (SIRS, p <0.05). Logistic regression analysis showed that age ≥60 years, corticosteroids, immunosuppressive and biological agents were risk factors for opportunistic infections in patients with IBD. CONCLUSION Hospitalised elderly IBD patients, receiving corticosteroids, immunosuppressive, and biological agents, are at higher risk for infection. The symptoms of opportunistic infections in elderly patients are atypical, but they are prone to multiple infections with poor prognosis. Key Words: Elderly patients, Inflammatory bowel disease, Opportunistic infection, Systemic inflammation reaction syndrome.
Temperature Correction to Enhance Blood Glucose Monitoring Accuracy Using Electrical Impedance Spectroscopy

Electrical methods are among the primarily studied non-invasive glucose measurement techniques; however, various factors affect the accuracy of the sensors used. Of these, the temperature is a critical factor; hence, the effects of temperature on the electrical properties of blood components are investigated in this study. Furthermore, the changes in the electrical properties of blood according to the glucose level are corrected by considering the effects of temperature on the electrical properties. An impedance sensor is developed and used to measure whole blood impedance in 10 healthy participants at various temperatures and glucose levels. Subsequently, the conductivities of the plasma and cytoplasm were extracted. Changes in the electrical properties of the blood components are then analyzed using linear regression and repeated measures ANOVA. The electrical conductivities of plasma and cytoplasm increased with increasing temperatures (plasma: 0.0397 (slope), 0.7814 (R2), cytoplasm: 0.014 (slope), 0.694 (R2)). At three values of increasing glucose levels (85.4, 158.1, and 271.8 mg/dL), the electrical conductivities of the plasma and cytoplasm decreased. These tendencies are more significant upon temperature corrections (p-values; plasma: 0.001, 0.001, cytoplasm: 0.003, 0.002). The relationships between temperature and electrical conductivity changes can thus be used for temperature corrections in blood glucose measurement.
A CRISPR/Cas9 Cleavage System for Capturing Fungal Secondary Metabolite Gene Clusters

More and more available fungal genome sequence data reveal a large amount of secondary metabolite (SM) biosynthetic ‘dark matter’ to be discovered. Heterogeneous expression is one of the most effective approaches to exploit these novel natural products, but it is limited by having to clone entire biosynthetic gene clusters (BGCs) without errors. So far, few effective technologies have been developed to manipulate the specific large DNA fragments in filamentous fungi. Here, we developed a fungal BGC-capturing system based on CRISPR/Cas9 cleavage in vitro. In our system, Cas9 protein was purified and CRISPR guide sequences in combination with in vivo yeast assembly were rationally designed. Using targeted cleavages of plasmid DNAs with linear (8.5 kb) or circular (8.5 kb and 28 kb) states, we were able to cleave the plasmids precisely, demonstrating the high efficiency of this system. Furthermore, we successfully captured the entire Nrc gene cluster from the genomic DNA of Neosartorya fischeri. Our results provide an easy and efficient approach to manipulate fungal genomic DNA based on the in vitro application of Cas9 endonuclease. Our methodology will lay a foundation for capturing entire groups of BGCs in filamentous fungi and accelerate fungal SMs mining.
Viruses in Cancers of the Digestive System: Active Contributors or Idle Bystanders?

The human virome, which is a collection of all the viruses that are present in the human body, is increasingly being recognized as an essential part of the human microbiota. The human gastrointestinal tract and related organs (e.g., liver, pancreas, and gallbladder)—composing the gastrointestinal (or digestive) system—contain a huge number of viral particles which contribute to maintaining tissue homeostasis and keeping our body healthy. However, perturbations of the virome steady-state may, both directly and indirectly, ignite/sustain oncogenic mechanisms contributing to the initiation of a dysplastic process and/or cancer progression. In this review, we summarize and discuss the available evidence on the association and role of viruses in the development of cancers of the digestive system.