Miracle-dz/UniFAR-FTUs huggingface dataset:
New Insights Into Immunological Therapy for Retinal Disorders

In the twentieth century, a conspicuous lack of effective treatment strategies existed for managing several retinal disorders, including age-related macular degeneration; diabetic retinopathy (DR); retinopathy of prematurity (ROP); retinitis pigmentosa (RP); uveitis, including Behçet's disease; and vitreoretinal lymphoma (VRL). However, in the first decade of this century, advances in biomedicine have provided new treatment strategies in the field of ophthalmology, particularly biologics that target vascular endothelial growth factor or tumor necrosis factor (TNF)-α. Furthermore, clinical trials on gene therapy specifically for patients with autosomal recessive or X-linked RP have commenced. The overall survival rates of patients with VRL have improved, owing to earlier diagnoses and better treatment strategies. However, some unresolved problems remain such as primary or secondary non-response to biologics or chemotherapy, and the lack of adequate strategies for treating most RP patients. In this review, we provide an overview of the immunological mechanisms of the eye under normal conditions and in several retinal disorders, including uveitis, DR, ROP, RP, and VRL. In addition, we discuss recent studies that describe the inflammatory responses that occur during the course of these retinal disorders to provide new insights into their diagnosis and treatment.
Amplitude of high frequency oscillations as a biomarker of the seizure onset zone

Objective Studies of high frequency oscillations (HFOs) in epilepsy have primarily tested the HFO rate as a biomarker of the seizure onset zone (SOZ), but the rate varies over time and is not robust for all individual subjects. As an alternative, we tested the performance of HFO amplitude as a potential SOZ biomarker using two automated detection algorithms. Method HFOs were detected in intracranial electroencephalogram (iEEG) from 11 patients using a machine learning algorithm and a standard amplitude-based algorithm. For each detector, SOZ and non-SOZ channels were classified using the rate and amplitude of high frequency events, and performance was compared using receiver operating characteristic curves. Results The amplitude of detected events was significantly higher in SOZ. Across subjects, amplitude more accurately classified SOZ/non-SOZ than rate (higher values of area under the ROC curve and sensitivity, and lower false positive rates). Moreover, amplitude was more consistent across segments of data, indicated by lower coefficient of variation. Conclusion As an SOZ biomarker, HFO amplitude offers advantages over HFO rate: it exhibits higher classification accuracy, more consistency over time, and robustness to parameter changes. Significance This biomarker has the potential to increase the generalizability of HFOs and facilitate clinical implementation as a tool for SOZ localization.
Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (Hordeum Vulgare L.) in the Qinghai-Tibet Plateau

Barley (Hordeum vulgare L.) is one of the most important cereal crops worldwide. In the Qinghai-Tibet Plateau, six-rowed hulless (or naked) barley, called “qingke” in Chinese or “nas” in Tibetan, is produced mainly in Tibet. The complexity of the environment in the Qinghai-Tibet Plateau has provided unique opportunities for research on the breeding and adaptability of qingke barley. However, the genetic architecture of many important agronomic traits for qingke barley remains elusive. Heading date (HD), plant height (PH), and spike length (SL) are three prominent agronomic traits in barley. Here, we used genome-wide association (GWAS) mapping and GWAS with eigenvector decomposition (EigenGWAS) to detect quantitative trait loci (QTL) and selective signatures for HD, PH, and SL in a collection of 308 qingke barley accessions. The accessions were genotyped using a newly-developed, proprietary genotyping-by-sequencing (tGBS) technology, that yielded 14,970 high quality single nucleotide polymorphisms (SNPs). We found that the number of SNPs was higher in the varieties than in the landraces, which suggested that Tibetan varieties and varieties in the Tibetan area may have originated from different landraces in different areas. We have identified 62 QTLs associated with three important traits, and the observed phenotypic variation is well-explained by the identified QTLs. We mapped 114 known genes that include, but are not limited to, vernalization, and photoperiod genes. We found that 83.87% of the identified QTLs are located in the non-coding regulatory regions of annotated barley genes. Forty-eight of the QTLs are first reported here, 28 QTLs have pleotropic effects, and three QTL are located in the regions of the well-characterized genes HvVRN1, HvVRN3, and PpD-H2. EigenGWAS analysis revealed that multiple heading-date-related loci bear signatures of selection. Our results confirm that the barley panel used in this study is highly diverse, and showed a great promise for identifying the genetic basis of adaptive traits. This study should increase our understanding of complex traits in qingke barley, and should facilitate genome-assisted breeding for qingke barley improvement.
Onion Variety Response to Iris Yellow Spot Virus

S . Onion ( Allium cepa ) varieties for commercial production in eastern Oregon and southwestern Idaho are evaluated annually in replicated trials conducted at the near Ontario, Oregon. Characteristics evaluated include bulb yield, market grade, and the frequency of single centers. After the emergence of iris yellow spot virus (IYSV) as a threat to commercial onion production in the early 2000s, onion varieties at the Malheur Experiment Station have been evaluated for virus symptoms since 2004. Varieties showed differences in the severity of IYSV symptoms each year. Symptom severity increased over the years from 2004 to 2006, and variety virus ratings showed a strong negative correlation of severity with yield in 2005 and 2006. Marketable yield after 3 months of storage averaged 781, 534, and 551 cwt/acre in 2004, 2005, and 2006, respectively. Averaging over varieties, yield of bulbs larger than 4 inches in diameter was 438 cwt/acre, 56 cwt/acre, and 76 cwt/acre, and the average virus severity ratings were 1.1, 1.3, and 2.7 in 2004, 2005, and 2006, respectively. A few varieties showed a combination of high yield, large bulb size, low incidence of virus symptoms, and a predominance of single-centered bulbs. With the prevalence of IYSV, variety tolerance to IYSV has become an important production factor in the Treasure Valley.
Yield potentials of narbonne vetch (Vicia narbonensis L.) genotypes in different environmental conditions

The purpose of the research was to determine the yield potentials of narbonne vetch (Vicia narbonnesis L.) genotypes in different environmental conditions. Narbonne vetch genotypes were grown in three different locations of Trakya region during 2002-2004. Eight Narbonne vetch genotypes (genotype numbered 236, 512, 524, 570, 908, 14, Ege and one population) were used as material in the research. The results showed that seed yield, herbage yield and hay yield were significantly affected (P≤0.05) by genotypes, while branch number and pod number per plant were not significantly affected by genotypes. Therefore, plant height and thousand seed weight were significantly affected (P≤0.01) by genotypes. Plant height, seed yield, herbage yield and hay yield were significantly affected (P≤0.01) by locations and location x genotype interaction. Branch number per plant, pod number per plant and thousand seed weight were not affected significantly by locations. While the highest seed and forage yields were obtained in Hayrabolu location, seed and forage yields in Kirklareli were less than in the other locations. In the study; plant height, branch number, pod number, thousand seed weight, seed yield, herbage yield and hay yield were 43.02 - 78.85 cm, 1.40 - 3.17, 6.63 - 19.23, 173.83 - 239.09 g, 143.48 - 351.24 kg da -1 , 821.31 - 2710.79 kg da -1 and 134.63 - 482.16 kg da -1 , respectively. It was concluded that genotype numbered 908 in Hayrabolu, genotype numbered 512 in Tekirdag and genotype numbered 524 in Kirklareli were suitable for forage production whereas genotype numbered 908 in Hayrabolu, genotype numbered 908 and 570 in Tekirdag and genotype numbered 512 in Kirklareli for seed production. Narbonne vetch genotypes had different yield potentials in three environmental conditions of Trakya region which is in the Marmara region of Turkey.
THE PREVALENCE OF LERNAEID ECTOPARASITES IN GRASS CARP (CTENOPHARYNGODON IDELLA)

The present study was conducted to investigate the prevalence of lernaeid ectoparasites in grass carp (Ctenopharyngodon idella). For this purpose, 597 fishes (Ctenopharyngodon idella) were examined for lernaeid ectoparasites at a private fish farm located in Multan, Pakistan. Four species of the genus Lernaea i.e. L. cyprinacea, L. polymorpha, L. oryzophila, and L. lophiara were recorded. It was observed that L. polymorpha had the highest (P 20 cm.
Replication stress and FOXM1 drive radiation induced genomic instability and cell transformation

In contrast to the vast majority of research that has focused on the immediate effects of ionizing radiation, this work concentrates on the molecular mechanism driving delayed effects that emerge in the progeny of the exposed cells. We employed functional protein arrays to identify molecular changes induced in a human bronchial epithelial cell line (HBEC3-KT) and osteosarcoma cell line (U2OS) and evaluated their impact on outcomes associated with radiation induced genomic instability (RIGI) at day 5 and 7 post-exposure to a 2Gy X-ray dose, which revealed replication stress in the context of increased FOXM1 expression. Irradiated cells had reduced DNA replication rate detected by the DNA fiber assay and increased DNA resection detected by RPA foci and phosphorylation. Irradiated cells increased utilization of homologous recombination-dependent repair detected by a gene conversion assay and DNA damage at mitosis reflected by RPA positive chromosomal bridges, micronuclei formation and 53BP1 positive bodies in G1, all known outcomes of replication stress. Interference with the function of FOXM1, a transcription factor widely expressed in cancer, employing an aptamer, decreased radiation-induced micronuclei formation and cell transformation while plasmid-driven overexpression of FOXM1b was sufficient to induce replication stress, micronuclei formation and cell transformation.
Harbour seal movements and haul-out patterns: implications for monitoring and management

1.Compliance with conservation legislation requires knowledge on the behaviour, abundance and distribution of protected species. Seal life history is characterized by a combination of marine foraging and a requirement to haul out on a solid substrate for reproduction and moulting. Thus understanding the use of haul out sites, where seals are counted, as well as their at-sea movements is crucial for designing effective monitoring and management plans. 2.This study used satellite transmitters deployed on 24 harbour seals in western Scotland to examine movements and haul-out patterns. 3.The proportion of time harbour seals spent hauled out (daily means of between 11 and 27%) varied spatially, temporally and according to sex. The mean haul-out duration was 5 h, with a maximum of over 24 h. 4.Patterns of movement were observed at two geographical scales; while some seals travelled over 100 km, 50% of trips were within 25 km of a haul-out site. These patterns are important for the identification of a marine component to designated protected areas for the species. 5.On average seals returned to the haul-out sites they last used during 40% of trips, indicating a degree of site fidelity, though there was wide variation between different haul-out sites (range 0% to >75%). 6.Low fidelity haul-out sites could form a network of land-based protected areas, while high fidelity sites might form appropriate management units. Copyright © 2008 John Wiley & Sons, Ltd.
Dynamic community detection reveals transient reorganization of functional brain networks across a female menstrual cycle

Sex steroid hormones have been shown to alter regional brain activity, but the extent to which they modulate connectivity within and between large-scale functional brain networks over time has yet to be characterized. Here, we applied dynamic community detection techniques to data from a highly sampled female with 30 consecutive days of brain imaging and venipuncture measurements to characterize changes in resting-state community structure across the menstrual cycle. Four stable functional communities were identified consisting of nodes from visual, default mode, frontal control, and somatomotor networks. Limbic, subcortical, and attention networks exhibited higher than expected levels of nodal flexibility, a hallmark of between-network integration and transient functional reorganization. The most striking reorganization occurred in a default mode subnetwork localized to regions of the prefrontal cortex, coincident with peaks in serum levels of estradiol, luteinizing hormone, and follicle stimulating hormone. Nodes from these regions exhibited strong intra-network increases in functional connectivity, leading to a split in the stable default mode core community and the transient formation of a new functional community. Probing the spatiotemporal basis of human brain–hormone interactions with dynamic community detection suggests that ovulation results in a temporary, localized patterns of brain network reorganization. Author Summary Sex steroid hormones influence the central nervous system across multiple spatiotemporal scales. Estrogen and progesterone concentrations rise and fall throughout the menstrual cycle, but it remains poorly understood how day-to-day fluctuations in hormones shape human brain dynamics. Here, we assessed the structure and stability of resting-state brain network activity in concordance with serum hormone levels from a female who underwent fMRI and venipuncture for 30 consecutive days. Our results reveal that while network structure is largely stable over the menstrual cycle, there is temporary reorganization of several largescale functional brain networks during the ovulatory window. In particular, a default mode subnetwork exhibits increased connectivity with itself and with regions from temporoparietal and limbic networks, providing novel perspective into brain-hormone interactions.
Use of Wildlife Water Developments by Birds in Southwest Arizona During Migration

Abstract Anecdotal evidence suggests that desert water developments attract birds; however, few studies have focused on the role of surface water in habitat selection by migratory birds. Therefore, we studied bird use of wildlife water developments in the Sonoran Desert of southwestern Arizona, USA, using 2 observational approaches (bird surveys in washes with and without water developments and direct observations at water developments) and 1 experimental approach (direct observations at water sources with and without vegetation cover). In spring 2004, we conducted weekly bird surveys at 3 pairs (with and without water developments) of washes. In spring 2005, we designed an experiment to test whether migratory birds more frequently used water developments with than without vegetation cover. During spring, in both 2004 and 2005, we documented use of water by directly observing birds at 13 existing water developments. We found little evidence to support that water developments were important water sources for migratory birds. Migratory bird communities in desert washes near wildlife water developments did not differ in species richness, relative abundance, or density when compared with washes without water developments. This observation suggests that the wildlife water developments that we studied were not an attractant to migratory birds at the landscape scale. At a finer scale, migratory birds rarely (0.1% of all observations) used water developments and experimental water sources. However, resident bird species frequently were recorded (>69,000 observations) drinking and bathing at wildlife water developments. Based on our observations, we conclude that water developments are an important resource for local bird populations in the Sonoran Desert, USA, particularly during periods of drought.
Protein Kinase G Regulates Potassium Chloride Cotransporter-3 Expression in Primary Cultures of Rat Vascular Smooth Muscle Cells*

K-Cl cotransport (KCC) is activated by nitric oxide donors and appears to be regulated by the cGMP signaling pathway. Expression of KCC mRNAs (KCC1–KCC4) in rat vascular smooth muscle cells (VSMCs) is unknown. We have reported the presence of KCC1 and KCC3 mRNAs in primary cultures of VSMCs by specific reverse transcription-polymerase chain reaction. KCC2 mRNA appeared at extremely low levels. KCC4 mRNA was undetectable. Semiquantitative reverse transcription-polymerase chain reaction revealed a 2:1 KCC1/KCC3 mRNA ratio in VSMCs. Depletion of protein kinase G (PKG)-1 from VSMCs did not change KCC3 mRNA expression. Analogous results were obtained with PKG-1-catalytic domain- and vector only-transfected VSMCs lacking endogenous PKG, suggesting no involvement of PKG-1 in the maintenance of basal KCC3 mRNA expression. However, 8-bromo-cGMP, a PKG stimulator, acutely increased KCC3 mRNA expression in a concentration- and time-dependent fashion; this effect was blocked by the PKG inhibitor KT5823 but not by actinomycin D. These findings show that VSMCs express mainly two mRNA isoforms, KCC1 and KCC3, and suggest that PKG participates post-transcriptionally in the acute KCC3 mRNA regulation. The role of KCC3 on cell volume and electrolyte homeostasis in response to PKG modulators remains to be determined.
Associations between social support and verbal memory: 14-year follow-up of the English Longitudinal Study of Ageing cohort

Objective: Examine the longitudinal associations between social support and verbal memory among community-dwelling adults. Participants: In the English Longitudinal Study of Ageing, 10,837 participants aged 50-89 years were assessed at wave 1 (baseline: 2002-03) and followed-up over 14-years to wave 8 (2016-17). Methods: Verbal memory was assessed at each wave by tests of immediate and delayed word-recall. Positive and negative social support were measured across four types of relationship (spouse/partner, children, friends, extended family). Linear mixed effects modelling examined the between-person (PM) and within-person (PM) associations between social support and verbal memory. Interaction terms were fitted to estimate differences in the rate of change in verbal memory by social support. Results: When we summed scores across all relationships (global social support), higher-than-average (PM) positive social support was associated with higher baseline verbal memory ({beta}PM = 0.015; 95% Confidence Interval (CI): 0.008, 0.025; p < 0.001) and with slower decline ({beta}PM-by-time = 0.003; 95% CI: 0.001, 0.005; p = 0.003). Longitudinal associations were gender- and source-specific. Among men, slower decline in verbal memory was associated with higher positive social support from children ({beta}PM-by-time = 0.009; 95% CI: 0.002, 0.016; p = 0.011) and with lower negative social support from spouse/partner ({beta}PM-by-time = -0.016; 95% CI: -0.031, 0.000; p = 0.045) and from friends ({beta}PM-by-time = -0.021; 95% CI: -0.039, -0.004; p = 0.018). Among women, higher positive social support from extended family was associated with slower decline in verbal memory ({beta}PM-by-time = 0.008; 95% CI: 0.000, 0.015; p = 0.049). Conclusions: Between-person differences in social support were modestly associated with differential decline in verbal memory. Our findings can inform future research studies and intervention strategies designed to maximise the potential role of supportive relationships in promoting healthy cognitive ageing.
Effects of habitat patch size and isolation on dispersal by Hesperia comma butterflies : implications for metapopulation structure

1. Metapopulation dynamics of the silver-spotted skipper butterfly Hesperia comma were studied between 1982 and 1991 along a 25-km stretch of chalk hills on the North Downs, Surrey, UK. Sixty-nine patches of suitable habitat were identified, of which 48 were occupied in 1982. Over the 9-year period, 12 patches were colonized, seven went extinct and nine patches remained vacant. Patches were more likely to be colonized if they were relatively large and close to other large, occupied patches. Local populations in small, isolated patches were more likely to go extinct. 2. Within a 70-ha section of a metapopulation, mark-release-recapture techniques were used in 1994 to investigate the effects of local patch area and isolation on movement of individuals among local patches. 988 butterflies were marked of which 133 moved between patches. 67% of between-patch movements were less than 50 m, although the longest recorded distance moved was 1070 m. Butterflies were most likely to move between large patches that were close together. 3. Metapopulation models have assumed that the distribution of distances moved by migrants follows a negative-exponential function. In our study, this distribution fitted an inverse-power function better than a negative-exponential. The under-estimation of long-distance migration by negative exponentials, compared with inverse power functions, may explain why theoretical models have under-estimated the number of occupied patches in metapopulations of H. comma following natural colonization. 4. Per capita emigration and immigration rates were significantly higher in small patches (area < 0.07 ha) compared with medium-sized (0.33-0.78 ha) or large patches (5.66 ha). However, in absolute numbers, more emigrants came from the largest patch where the source population was the largest. 5. The population system studied here shares attributes of several theoretical types of spatially structured population (patchy population, metapopulation, mainland-island system, non-equilibrium system) depending on the temporal and spatial scale examined. The distribution and dynamics of metapopulations should be regarded as being affected by a variety of behavioural and population processes, and real metapopulations can rarely be characterized as a single theoretical type.
EFFECTS OF TREE LEAF LITTER ON HERBACEOUS VEGETATION IN DECIDUOUS WOODLAND

SUMMARY (1) In two areas of deciduous woodland, measurements were made of the spatial variation in the shoot biomass and species-composition of the ground flora and of the amount of persistent tree litter. (2) At each site, forty random 0.0625-iM2 samples were collected from the woodland floor in late spring. A negative correlation was found between total shoot biomass of the ground flora and the amount of tree leaf litter. (3) The largest amount of tree litter occurred in hollows, some of which were virtually devoid of herbaceous vegetation. The weight of tree litter varied between 11 and 636 g m-2, and ground flora species showed marked differences with respect to their pattern of occurrence within this range. In terms of their tendency to occur in areas with large litter accumulation, the main ground flora constituents could be arranged in the series Galeobdolon luteum, Endymion non-scriptus, Anemone nemorosa > Milium effusum, Holcus mollis, Poa trivialis > Mnium hornum. It is suggested that this series is related to the relative abilities of the shoots of the species concerned to penetrate layers of persistent tree leaf litter.