Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting Development and Homeostasis of Thymic Regulatory T Cells in Type 1 Diabetes

Regulatory T cells (Tregs) seem to play a protective role in the pathogenesis of type 1 diabetes (T1D), a serious autoimmune disease. Studies using T1D murine models such as the non-obese diabetic (NOD) mouse have suggested that T1D is initiated partly due to either paucity and/or defectiveness of Tregs in the periphery, although other reports contradict this. In contrast Treg development in the thymus is thought to be normal in T1D-prone mice. However, these latter studies neglect to investigate different thymic Treg subpopulations such as precursor Tregs, newly developed Tregs and thymic resident Tregs. It is therefore important to establish a pattern of Treg populations for a better understanding of the relationship between regulatory cells and T1D. Using for the first time RAG-GFP reporter mice, this project re-investigated the Treg frequency and number in primary and secondary lymphoid organs in NOD mice in comparison to non-diabetes prone control mice. Time course flow cytometry studies revealed that there was a developmental fault in Treg generation in NOD mice; both precursor and mature Treg frequencies and numbers were increased with respect to control mice. However, further analysis of the mature Treg thymocytes demonstrated there was a paucity in newly developed Tregs compared to control mice, and concomitantly an increase in thymic resident Tregs in the NOD mice. These events were not related to intra-thymic IL-2 levels. Interestingly, B cells may have a role in Treg development and/or peripheral homeostasis in an age-dependent manner. The data presented in this project provides new evidence on the inticacies of the relationship between Tregs and T1D, and emphasize the importance of succinct analyses of distinct thymic Treg subpopulations to validate this relationship.
Variations Among Coffee (Coffea arabica L.) Genotypes for Sensitivity to Drought Induced by Soil Drying at Early stages of Growth in Ethiopia

In an attempt to screen Arabica coffee (Coffea arabica L.) genotypes for drought tolerance, an experiment was carried out at Jima Agricultural Research Center. The experiment was conducted in a rain shelter using 21 released varieties, two lowland materials and a promising genotype. Twelve months old seedlings of each of the 24 varieties were subjected to two watering regimes (water-stress by withholding irrigation and well-watered control) in a randomized complete block design with three replications. It was observed that there were significant differences among the cultivars for sensitivity to water deficit stress. Based on mean values of visual scoring and rate of stress development, cultivar F-59, 7395xF-59, J-19, 7454, 754, 75227 and Geisha were identified as more sensitive than 7487, 74110xF-59, 741, J-21, 744, 741xF-59, 74158, 77/85, 7395, F-35, 74148 and 74165, while 7440, 74140, 74110, 74112 and 8/85 were found to be relatively tolerant to the imposed soil drying treatment. Therefore, it was concluded that coffee genotypes could be grouped in to three categories (sensitive, moderately sensitive and relatively tolerant) based on preliminary observations and visual assessments. However, this results should further be verified with some morphological, physiological and biochemical studies both under field and nursery conditions.
A record of new lungfishes (Osteichthyes: Dipnoi) from the Carnian (Upper Triassic) of India

ABSTRACT Numerous tooth plates of different types were recovered from the Upper Triassic Tiki Formation of India. Sharp crested tooth plates with five acute ridges, tubercles on the crests, robust and deep furrows, wide spaces between successive ridges and reticulate ornamentation on the occlusal surfaces are assigned to a new species of the dipnoan genus Ptychoceratodus. Another tooth plate, characterized by four ridges with conical and cusplet-like denticles is identified as a Gnathorhiza. This is the first record of gnathorhizid fishes from the Upper Triassic sediments around the world. The Tiki aquatic realm was inhabited by different types of fishes including freshwater sharks, omnivorous/carnivorous dipnoans and other bony fishes. Palaeobiogeographic distribution of the dipnoans suggests that these were restricted to a high palaeolatitude in the southern hemisphere, where co-occurrences of several genera are seen in India.
Self-reported health without clinically measurable benefits among adult users of multivitamin and multimineral supplements: a cross-sectional study

Objective Multiple clinical trials fail to identify clinically measurable health benefits of daily multivitamin and multimineral (MVM) consumption in the general adult population. Understanding the determinants of widespread use of MVMs may guide efforts to better educate the public about effective nutritional practices. The objective of this study was to compare self-reported and clinically measurable health outcomes among MVM users and non-users in a large, nationally representative adult civilian non-institutionalised population in the USA surveyed on the use of complementary health practices. Design Cross-sectional analysis of the effect of MVM consumption on self-reported overall health and clinically measurable health outcomes. Participants Adult MVM users and non-users from the 2012 National Health Interview Survey (n=21 603). Primary and secondary outcome measures Five psychological, physical, and functional health outcomes: (1) self-rated health status, (2) needing help with routine needs, (3) history of 10 chronic diseases, (4) presence of 19 health conditions in the past 12 months, and (5) Kessler 6-Item (K6) Psychological Distress Scale to measure non-specific psychological distress in the past month. Results Among 4933 adult MVM users and 16 670 adult non-users, MVM users self-reported 30% better overall health than non-users (adjusted OR 1.31; 95% CI 1.17 to 1.46; false discovery rate adjusted p<0.001). There were no differences between MVM users and non-users in history of 10 chronic diseases, number of present health conditions, severity of current psychological distress on the K6 Scale and rates of needing help with daily activities. No effect modification was observed after stratification by sex, education, and race. Conclusions MVM users self-reported better overall health despite no apparent differences in clinically measurable health outcomes. These results suggest that widespread use of multivitamins in adults may be a result of individuals’ positive expectation that multivitamin use leads to better health outcomes or a self-selection bias in which MVM users intrinsically harbour more positive views regarding their health.
Climatic drivers of (changes in) bat migration phenology at Bracken Cave (USA)

Climate change is drastically changing the timing of biological events across the globe. Changes in the phenology of seasonal migrations between the breeding and wintering grounds have been observed across biological taxa, including birds, mammals, and insects. For birds, strong links have been shown between changes in migration phenology and changes in weather conditions at the wintering, stopover, and breeding areas. For other animal taxa, the current understanding of, and evidence for, climate (change) influences on migration still remains rather limited, mainly due to the lack of long‐term phenology datasets. Bracken Cave in Texas (USA) holds one of the largest bat colonies of the world. Using weather radar data, a unique 23‐year (1995–2017) long time series was recently produced of the spring and autumn migration phenology of Brazilian free‐tailed bats (Tadarida brasiliensis) at Bracken Cave. Here, we analyse these migration phenology time series in combination with gridded temperature, precipitation, and wind data across Mexico and southern USA, to identify the climatic drivers of (changes in) bat migration phenology. Perhaps surprisingly, our extensive spatiotemporal search did not find temperature to influence either spring or autumn migration. Instead, spring migration phenology seems to be predominantly driven by wind conditions at likely wintering or spring stopover areas during the migration period. Autumn migration phenology, on the other hand, seems to be dominated by precipitation to the east and north‐east of Bracken Cave. Long‐term changes towards more frequent migration and favourable wind conditions have, furthermore, allowed spring migration to occur 16 days earlier. Our results illustrate how some of the remaining knowledge gaps on the influence of climate (change) on bat migration and abundance can be addressed using weather radar analyses.
The Domestic Environment and the Lung Mycobiome

This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from the houses (ENV) of 20 of them (44.4%). Additionally, five bronchoscopes (BS) were also analyzed and negative controls were included for every procedure. All samples were processed for DNA extraction and cultures, which were performed in Sabouraud Dextrose and Potato Dextrose Agar. The fungal Internal Transcribed Spacer (ITS2) was sequenced by the Solexa/Illumina system and sequences were analyzed by QIIME 1.8. 0 and compared with the UNITE Database for identification. The similarity between the two fungal communities (BAL and ENV) for a specific patient was assessed via the percentage of coincidence in the detection of specific operational taxonomic units (OTUs), and about 75% of co-occurrence was detected between the mycobiome of the LRT and the houses. Cultures confirmed the presence of the core mycobiome species. However, the low rate of isolation from BAL suggests that most of its mycobiome corresponds to non-culturable cells. This likely depends on the patient’s immune system activity and inflammatory status.
Pharmaceutical evaluation of atorvastatin-loaded nanostructured lipid carriers incorporated into the gelatin/hyaluronic acid/polycaprolactone scaffold for the skin tissue engineering

In this study, gelatin/hyaluronic acid (HA) scaffolds containing different amounts of atorvastatin-loaded nanostructured lipid carriers (NLCs) coated entirely with polycaprolactone (PCL) film were fabricated for skin regeneration. 12 atorvastatin-loaded NLCs formulations were synthesized, and particle size, zeta potential, drug entrapment efficiency (EE), and drug release of the formulations were determined. The optimum freeze-dried atorvastatin-loaded NLCs were added in 3 different weight percentages to the gelatin and HA membranous scaffolds. Thereafter, the membranes were coated entirely by a thin layer of the PCL. They were characterized, and then mechanical properties, in vitro degradation and in vitro drug release were assessed. Moreover, human dermal fibroblasts (HDF) were cultured on the prepared nanocomposite scaffolds in order to investigate the cytotoxicity by the MTT assay after the first day, third day, and fifth day. Results revealed that the most favorable atorvastatin-loaded NLCs had 99.54 nm average particle size, −24.30 mV zeta potential, 97.98% EE, and 75.24% drug release within 237 hrs. Mechanical tests indicated that all the three scaffolds had approximately a 90 MPa elastic modulus which was more than two-fold of tensile modulus of normal human skin. The in vitro degradation test demonstrated that the membranes were degraded up to 98% after 5 days, and the scaffolds drug release efficiency (DRE) was in a range of 75–79% during those 5 days. The MTT assay results confirmed the cytocompatibility of the scaffolds. The scaffold containing 54.1 wt% NCLs was the optimum sample (S3). Scanning Electron Microscopy (SEM) images of the latter one showed the uniform distribution of the NLCs with an average size of 150 nm, and the images of cultured HDF illustrated the good cell attachment. In conclusion, suitable physicochemical and biological properties of the novel gelatin/HA/PCL nanocomposite scaffold containing 54.1 wt% atorvastatin-loaded NLCs (S3) can be a good candidate for skin regeneration.
Auditory processing in children: Role of working memory and lexical ability in auditory closure

We examined the relationship between cognitive-linguistic mechanisms and auditory closure ability in children. Sixty-seven school-age children recognized isolated words and keywords in sentences that were interrupted at a rate of 2.5 Hz and 5 Hz. In essence, children were given only 50% of speech information and asked to repeat the complete word or sentence. Children’s working memory capacity (WMC), attention, lexical knowledge, and retrieval from long-term memory (LTM) abilities were also measured to model their role in auditory closure ability. Overall, recognition of monosyllabic words and lexically easy multisyllabic words was significantly better at 2.5 Hz interruption rate than 5 Hz. Recognition of lexically hard multisyllabic words and keywords in sentences was better at 5 Hz relative to 2.5 Hz. Based on the best fit generalized “logistic” linear mixed effects models, there was a significant interaction between WMC and lexical difficulty of words. WMC was positively related only to recognition of lexically easy words. Lexical knowledge was found to be crucial for recognition of words and sentences, regardless of interruption rate. In addition, LTM retrieval ability was significantly associated with sentence recognition. These results suggest that lexical knowledge and the ability to retrieve information from LTM is crucial for children’s speech recognition in adverse listening situations. Study findings make a compelling case for the assessment and intervention of lexical knowledge and retrieval abilities in children with listening difficulties.
Advancements in the understanding of staphylococcal mastitis through the use of molecular tools

The objectives of this work were: 1) to complete a whole genome sequence of a Staphylococcus chromogenes isolate that is known to persist in the mammary gland of a cow, 2) to define a genetic target that could easily and reliably be used to differentiate Staphylococcus agnetis and Staphylococcus hyicus and to use this new assay along with pulsed-field gel electrophoresis (PFGE) strain typing to characterize a collection of non-Staphylococcus aureus coagulase positive staphylococci, 3) to determine if the recently described S. aureus Genotype B was present among previously characterized isolates from cases of bovine intramammary infection in the USA and to compare PFGE to the combination of ribosomal spacer PCR (RS-PCR) and virulence gene identification for strain typing of S. aureus, 4) to further the understanding of the association between body site colonization and intramammary infection before and after calving in heifers using molecular methods of speciation and strain typing, and 5) to describe the prevalence and distribution of Staphylococcus species on the teat and inguinal skin of dairy heifers throughout the heifer lifecycle using molecular speciation methods. A draft genome sequence of S. chromogenes MU 970, a strain that was isolated from the right rear quarter of a Holstein cow for 16 consecutive months, was completed. Whole genome sequences for S. chromogenes, S. hyicus, and S. agnetis were then used to construct a multiplex PCR used to differentiate S. hyicus, S. agnetis, and S. aureus. The multiplex PCR was then used to characterize a collection of isolates and found that S. agnetis was much more prevalent than S. hyicus. Furthermore, S. agnetis can cause persistent infections and can potentially be contagious. Next, RS-PCR plus toxin gene identification was explored as a possible strain typing method, however it was found to be less discriminatory than PFGE. Hence, PFGE was used as the strain typing method for the remainder of the dissertation research. The final two studies were conducted to characterize body site colonization with staphylococcal species and to explore the relationship of prepartum body site colonization to intramammary infections, both pre- and post-calving. MALDI-TOF was explored as a speciation method in these studies and was found to be accurate, rapid, and inexpensive. Overall, S. chromogenes was the most common species identified in prepartum mammary secretions and post-calving milk samples. Through PFGE strain typing, it was determined that many different strains of each species can be found on one heifer. Finally, it was determined that colonization of the inguinal region and teat skin was associated with age for S. agnetis, S. chromogenes, Staphylococcus devriesei, Staphylococcus equorum, Staphylococus haemolyticus, Staphylococcus lentus, Staphylococcus sciuri, Staphylococcus vitulinus, and Staphylococcus xylosus. Overall, these studies demonstrate that the staphylococcal species and subspecies associated with IMI are extremely abundant and diverse on dairy farms.
Nusinersen in type 0 spinal muscular atrophy: should we treat?

A male infant affected by type 0 SMA with one copy of SMN2 received early treatment with Nusinersen at the age of 13 days. He showed mild motor improvement 2 months after treatment started but despite also showing some minimal respiratory improvement, required tracheostomy at the age of 4 months and had increasing cardiac and autonomic dysfunction leading to exitus at 5 months. Our findings, expanding the results available on Nusinersen, confirm its relative efficacy in the most severely affected infants and provide clinical evidence to be used at the time requests for treating severe infants are discussed.
ADVENTITIOUS ROOTING COMPETENCE AND RESCUE OF ADULT MATE PLANTS BY CUTTINGS

ABSTRACT The competence of adult plants of mate (Ilex paraguariensis St. Hil.) to undergo adventitious rooting is essential to their vegetative rescue by cuttings. This study aimed to evaluate the adventitious rooting competence of adult mate plants, and then rescue these plants by making cuttings from epicormic shoots induced in different trunk positions. The percent survival and rooting of cuttings from epicormic shoots induced by girdling in seven adult plants were evaluated. The two stock plants whose cuttings had the highest rooting competence were further pruned and girdled to evaluate the effect of the position of epicormic shoots on their adventitious rooting competence. The potential success of rescuing of the same adult plants was also studied with cuttings of epicormic shoots induced by coppicing. The shoots were sectioned in single-bud cuttings, either treated with 3,000 mg L-1 indolebutyric acid or untreated, and then cultivated in a humid chamber for 60 days, and then the percent survival and rooting of cuttings was evaluated. In conclusion, we found that it is possible to rescue adult mate plants by cuttings from epicormic shoots induced by pruning, girdling, or coppicing. The adventitious rooting competence of cuttings differs among adult mate plants, and depends on the position of the epicormic shoots on the trunk from which epicormic shoots are collected.
Soil nematode functional diversity, successional patterns, and indicator taxa associated with vertebrate decomposition hotspots

Decomposition of vertebrate remains is a dynamic process that creates localized soil enrichment zones. A growing body of literature has documented effects of vertebrate decomposition on soil pH, electrical conductivity, oxygen levels, nitrogen and carbon speciation, microbial biomass, and microbial successional patterns. However, relatively few studies have examined the microfaunal members of the soil food web that function as secondary consumers, specifically nematodes. Nematodes are often used as indicators of enrichment in other systems, and initial observations from vertebrate decomposition zones have indicated there is an effect on nematode communities. Our goal was to catalog decomposition-induced nematode succession and changes to alpha, beta, and functional diversity, and identify potential indicator taxa associated with decomposition progression. Six adult beaver (Castor canadensis) carcasses were allowed to decompose in a forest ecosystem for one year. During this period soil temperature, moisture, and electrical conductivity were monitored. Soils samples were taken at two depths in order to assess nematode community dynamics: 30-cm cores and 1-cm interface samples. Nematode abundance, alpha, beta, and functional diversity all responded to soil enrichment at the onset of active decay, and impacts persisted through skeletonization. After one year, nematode abundances and alpha diversity had recovered to original levels, however both community membership and functional diversity remained significantly altered. We identified seven indicator taxa that marked major transitions in decomposition progression. Enrichment of Rhabditidae (B1) and Diplogasteridae (B1) coupled with depletion in Filenchus (F2) characterized active and advanced decay prior to skeletonization in both cores and interface soils. Enrichment of Acrobeloides (B2), Aphelenchoides (F2), Tylencholaimidae (F4) and Seinura (P2) occurred during a narrow period in mid-skeletonization (day 153). Our study has revealed soil nematode successional patterns during vertebrate decomposition and has identified organisms that may function as indicator taxa for certain periods during decomposition.
Dexmedetomidine inhibits inflammatory response and autophagy through the circLrp1b/miR-27a-3p/Dram2 pathway in a rat model of traumatic brain injury

Circular RNAs (circRNAs) have a regulatory function on inflammation and autophagy, of which rno-circRNA_010705 (circLrp1b) appears to be significantly up-regulated following traumatic brain injury (TBI). Dexmedetomidine (DEX) shows improvement effects in TBI by inhibiting NLRP3/caspase-1. However, whether circLrp1b plays critical roles in DEX-mediated TBI attenuation and the underlying mechanisms remain unclear. After TBI was established in rats by controlled cortical impact (CCI) to cause brain trauma, they received an intracerebroventricular injection of lentiviral vector, followed by intraperitoneal injection of DEX. Administration of DEX ameliorated autophagy in rats following TBI, accompanied by up-regulated circLrp1b and Dram2 and down-regulated miR-27a-3p. DEX promoted the effects of circLrp1b in attenuating TBI-induced neurologic impairment, autophagy, and inflammation, which was significantly reversed by inhibition of miR-27a-3p or Dram2 overexpression. Mechanistically, northern blot and luciferase reporter assays indicated that circLrp1b up-regulated Dram2 expression by functioning as a sponge for miR-27a-3p to promote autophagy involved in TBI, which was reversed by DEX treatment. Collectively, this study demonstrated that DEX inhibits inflammatory response and autophagy involved in TBI in vivo through inactivation of the circLrp1b/miR-27a-3p/Dram2 signaling pathway.