Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective Histone Deacetylase 6 Inhibitors Restore Cone Photoreceptor Vision or Outer Segment Morphology in Zebrafish and Mouse Models of Retinal Blindness

Blindness arising from retinal or macular degeneration results in significant social, health and economic burden. While approved treatments exist for neovascular (‘wet’) age-related macular degeneration, new therapeutic targets/interventions are needed for the more prevalent atrophic (‘dry’) form of age-related macular degeneration. Similarly, in inherited retinal diseases, most patients have no access to an effective treatment. Although macular and retinal degenerations are genetically and clinically distinct, common pathological hallmarks can include photoreceptor degeneration, retinal pigment epithelium atrophy, oxidative stress, hypoxia and defective autophagy. Here, we evaluated the potential of selective histone deacetylase 6 inhibitors to preserve retinal morphology or restore vision in zebrafish atp6v0e1–/– and mouse rd10 models. Histone deacetylase 6 inhibitor, tubastatin A-treated atp6v0e1–/– zebrafish show marked improvement in photoreceptor outer segment area (44.7%, p = 0.027) and significant improvement in vision (8-fold, p ≤ 0.0001). Tubastatin A-treated rd10/rd10 retinal explants show a significantly (p = 0.016) increased number of outer-segment labeled cone photoreceptors. In vitro, ATP6V0E1 regulated HIF-1α activity, but significant regulation of HIF-1α by histone deacetylase 6 inhibition in the retina was not detected. Proteomic profiling identified ubiquitin-proteasome, phototransduction, metabolism and phagosome as pathways, whose altered expression correlated with histone deacetylase 6 inhibitor mediated restoration of vision.
Vehicle-Mounted Optical Sensing

Visual evaluation of turfgrass quality is a subjective process that requires experienced personnel. Optical sensing of plant reflectance provides objective, quantitative turf quality evaluation and requires no turf experience. This study was conducted to assess the accuracy of optical sensing for evaluating turf quality, to compare the rating consistency among human evaluators and optical sensing, and to develop a model that describes a relationship between optically sensed measurements and visual turf quality. Visual evaluations for turf color, texture, percent live cover (PLC), and optically sensed measurements were collected on the National Turfgrass Evaluation Program (NTEP) tall fescue (Festuca arundinacea Schreb) and creeping bentgrass (Agrostis palustris Huds.) trials at Stillwater, OK. Measurements were made monthly for 12 consecutive months from June 1999 through May 2000. Red (R) and near infrared (NIR) reflectance were collected with sensors and converted to normalized difference vegetative indices (NDVI). The NDVI were closely correlated with visual evaluations for turf color, moderately correlated with percent live cover (PLC), and independent of texture. Measurements of turf color and PLC were evaluated more consistently with optical sensors than by visual ratings. Normalized difference vegetation index (Y) could be reliably predicted by the following generalized model for turf color (X) and PLC (Z): Y = B 0 + B 1 log 10X + B 2Z3 Optical sensing provided fast, reliable turf assessment and deserves consideration as a supplemental or replacement technique for evaluating turf quality.
Bats and Barometric Pressure: Conserving Limited Energy and Tracking Insects from the Roost

Studies were conducted to assess the response of a seasonal cave-dwelling bat and its insect prey to natural and experimental changes in barometric pressure. The Eastern Pipistrelle, Pipistrellus subflavus, tracks barometric pressure metabolically. Eastern Pipistrelles potentially use pressure as a cue for predicting the relative abundance of aerial insect prey outside the roost. Barometric pressure tracking affords these bats an opportunity to conserve limited energy and make appropriate foraging decisions. Barometric pressure tracking is viewed as an alternative evolutionary strategy to torpor and may be a widespread phenomenon among insect-feeding bats that roost deep within caves.
Location and scale-based CUSUM test with application to autoregressive models

This study aims to refine the residual cumulative sum (CUSUM) test for location-scale time series and to develop the location and scale-based CUSUM (LSCUSUM) test. This test clarifies the role of residuals in the CUSUM test well. In addition, it provides a much more convenient method for analysing time series models with more complicated structure and copious parameters when compared with the conventional estimate- and score vector-based CUSUM tests. The test comprises the two CUSUM test statistics featuring the location and scale parts, which are asymptotically independent and converge to the supremum of a Brownian bridge. The LSCUSUM test is applied to the vector AR, scalar ARMA, and infinite order AR models to demonstrate the merit of the method. In particular, special attention is paid to the vector AR model owing to its importance in applications. We show its validity through Monte Carlo simulations and conduct real data analysis for illustration.
Sleep Quality, Sleep Structure, and PER3 Genotype Mediate Chronotype Effects on Depressive Symptoms in Young Adults

Depression and its related mood disorders are a major global health issue that disproportionately affects young adults. A number of factors that influence depressive symptoms are particularly relevant to the young adult developmental stage, including sleep loss, poor sleep quality, and the tendency toward eveningness in circadian preferences. However, relatively few studies have examined the relationship between sleep and circadian phenotypes, and their respective influences on mood, or considered potential molecular mechanisms driving these associations. Here, we use a multi-year, cross-sectional study of 806 primarily undergraduates to examine the relationships between sleep-wake chronotype, sleep disturbance, depression and genotypes associated with the PER3 variable number of tandom repeats (VNTR) polymorphism—circadian gene variants associated with both chronotype and sleep homeostatic drive. In addition, we use objective, Fitbit-generated sleep structure data on a subset of these participants (n = 67) to examine the relationships between chronotype, depression scores, actual measures of sleep duration, social jetlag, and the percent of deep and rapid eye movement (REM) sleep per night. In this population, chronotype is weakly associated with depressive symptoms and moderately correlated with self-reported sleep disturbance. Sleep disturbance is significantly associated with depression scores, but objective sleep parameters are not directly correlated with Beck Depression Inventory (BDI-II) scores, with the exceptions of a moderate correlation between social jetlag and depression scores in females and a marginal correlation between sleep duration and depression scores. Multiple regression and path analyses reveal that chronotype effects on depressive symptoms in this population are mediated largely by sleep disturbance. The PER3 VNTR genotype significantly predicts depressive symptoms in a model with objective sleep parameters, but it does not significantly predict depressive symptoms in a model with chronotype or subjective sleep disturbance. Interestingly, PER35,5 genotypes, in males only, are independently related to chronotype and depression scores. Our results support hypotheses linking subjective sleep quality and chronotype and provide a first step in understanding how objective sleep structure may be linked to chronotype and depressive symptoms. Our results also suggest that circadian gene variants may show sex-specific effects linking sleep duration and sleep structure to depression.
Physiological and Behavioral Factors in Musicians’ Performance Tempo

Musicians display individual differences in their spontaneous performance rates (tempo) for simple melodies, but the factors responsible are unknown. Previous research suggests that musical tempo modulates listeners’ cardiovascular activity. We report an investigation of musicians’ melody performances measured over a 12-h day and subsequent changes in the musicians’ physiological activity. Skilled pianists completed four testing sessions in a single day as cardiac activity was recorded during an initial 5 min of baseline rest and during performances of familiar and unfamiliar melodies. Results indicated slower tempi for familiar and unfamiliar melodies at early testing times. Performance rates at 09 h were predicted by differences in participants’ alertness and musical training; these differences were not explained by sleep patterns, chronotype, or cardiac activity. Individual differences in pianists’ performance tempo were consistent across testing sessions: participants with a faster tempo at 09 h maintained a faster tempo at later testing sessions. Cardiac measures at early testing times indicated increased heart rates and more predictable cardiac dynamics during music performance than baseline rest, and during performances of unfamiliar melodies than familiar melodies. These findings provide the first evidence of cardiac dynamics that are unique to music performance contexts.
Differential Requirement of Beclin 1 for Regulating the Balance of Naïve and Activated CD4+ T Cells

Autophagy is highly regulated and plays a multitude of roles during T cell-mediated immune responses. It has been shown that autophagy deficiency in T cells results in a decrease in total T cells, including naïve T cells in young mice, but the mechanism is still not understood. Here, similar to what happened in young mice, we showed that T cell-specific deletion of Beclin 1/Atg6 (Becn1 −/−) resulted in decreases in the percentages of CD4+, CD8+, and regulatory T cells in adult mice. In addition, we found that the effector to naïve T cell ratio was increased in older mice. Also, as mice grew older, Becn1 −/− mice progressively lost weight and developed severe colitis. Analysis of inflamed tissues demonstrated increases in the portion and cytokine production of effector T cells. In contrast, the TCR-transgenic Becn1 −/− mice had similar numbers of naïve T cells compared to WT controls. Similar to bulk T cells, the TCR-transgenic Becn1 −/− T cells generated much lower numbers of effector T cells compared to WT controls after activation in vitro. These data suggest that autophagy is not required for maintaining the naïve T cell but required for the generation of effector T cells in vivo.
Therapeutic and protective effects of water-ethanolic extract from Rhizoma Alismatis on streptozotocin-induced diabetic mice

Aim To observe the therapeutic and protective effects of water-ethanolic extract from Rhizoma Alismatis (REA) on streptozotocin(STZ)-induced diabetic mice.Methods Mice were troated with STZ 150mg·kg -1 ip to induce diabetic animal model.The diabetic mice were treated with RAE 1.5g·kg -1 and 3.0g·kg -1 ig.Blood glucose (Glu) was determined before treatment and after treatment at 1,2,5h.Serum triglyceride,cholesterol and Glu were determined after treatment for 15 days.Pretreatment with RAE 1.5,3.0g·kg -1 ig for 3d continuously,then mice were treated with STZ 105mg·kg -1 ip,for another 3d.Insulin was determined by radio-immunoassay,and pancreas and islets were examined under microscope.Acute toxicity experiments were performed.Results Treatment with RAE,Glu and triglyceride were reduced significantly in STZ diabetic mice.Pretreatment plus treatment,RAE could antagonize the STZ-induced hyperglycemia and islet-injury changes.RAE also increased insulin releasing in STZ diabetic mice.Conclution RAE possesses the therapeutic and preventive effects on STZ diabetic mice.
Dominance Between Plasmids Determines the Extent of Biofilm Formation

Bacterial biofilms have an impact in medical and industrial environments because they often confer protection to bacteria against harmful agents, and constitute a source from which microorganisms can disperse. Conjugative plasmids can enhance bacterial ability to form biofilms because conjugative pili act as adhesion factors. However, plasmids may interact with each other, either facilitating or inhibiting plasmid transfer. Accordingly, we asked whether effects on plasmid transfer also impacts biofilm formation. We measured biofilm formation of Escherichia coli cells harboring two plasmid types, or when the two plasmids were present in the same population but carried in different cells. Using eleven natural isolated conjugative plasmids, we confirmed that some indeed promote biofilm formation and, importantly, that this ability is correlated with conjugative efficiency. Further we studied the effect of plasmid pairs on biofilm formation. We observed increased biofilm formation in approximately half of the combinations when both plasmids inhabited the same cell or when the plasmids were carried in different cells. Moreover, in approximately half of the combinations, independent of the co-inhabitation conditions, one of the plasmids alone determined the extent of biofilm formation – thus having a dominant effect over the other plasmid. The molecular mechanisms responsible for these interactions were not evaluated here and future research is required to elucidate them.
Combined Metabolomic Analysis of Plasma and Tissue Reveals a Prognostic Risk Score System and Metabolic Dysregulation in Esophageal Squamous Cell Carcinoma

Background: Esophageal squamous cell carcinoma (ESCC) is a gastrointestinal malignancy with a poor prognosis. Although studies have shown metabolic reprogramming to be linked to ESCC development, no prognostic metabolic biomarkers or potential therapeutic metabolic targets have been identified. Method: The present study investigated some circulating metabolites associated with overall survival in 276 curatively resected ESCC patients using liquid chromatography/mass spectrometry metabolomics and Kaplan-Meier analysis. Tissue metabolomic analysis of 23-paired ESCC tissue samples was performed to discover metabolic dysregulation in ESCC cancerous tissue. A method consisting of support vector machine recursive feature elimination and LIMMA differential expression analysis was utilized to select promising feature genes within transcriptomic data from 179-paired ESCC tissue samples. Joint pathway analysis with genes and metabolites identified relevant metabolic pathways and targets for ESCC. Results: Four metabolites, kynurenine, 1-myristoyl-glycero-3-phosphocholine (LPC(14:0)sn-1), 2-piperidinone, and hippuric acid, were identified as prognostic factors in the preoperative plasma from ESCC patients. A risk score consisting of kynurenine and LPC(14:0)sn-1 significantly improved the prognostic performance of the tumor-node-metastasis staging system and was able to stratify risk for ESCC. Combined tissue metabolomic analysis and support vector machine recursive feature elimination gene selection revealed dysregulated kynurenine pathway as an important metabolic feature of ESCC, including accumulation of tryptophan, formylkynurenine, and kynurenine, as well as up-regulated indoleamine 2,3-dioxygenase 1 in ESCC cancerous tissue. Conclusions: This work identified for the first time four potential prognostic circulating metabolites. In addition, kynurenine pathway metabolism was shown to be up-regulated tryptophan-kynurenine metabolism in ESCC. Results not only provide a metabolite-based risk score system for prognosis, but also improve the understanding of the molecular basis of ESCC onset and progression, and as well as novel potential therapeutic targets for ESCC.
Effects of large mammalian browsers on architecture, biomass, and nutrients of woody plants

Large generalist browsers commonly feed on many species of woody plants, which are used at different intensities and frequencies. Some plant species are used during all seasons, while others are taken only during a short period of time. We have chosen to concentrate our review on a relatively well-studied system, the large generalist herbivore the moose ( Alces alces ) and its use of and impact on some species of woody plants. By this choice, we can examine a set of mammal-plant interactions within a single environment in different seasons. As a result of our review, we conclude that there is no single coherent response of woody plants to herbivory by moose. Winter browsing and summer leaf-stripping generally lead to the following responses: decreased food resources for moose in terms of plant biomass (in some situations the response may be neutral or even slightly positive); shoot size increases after medium and high levels of winter browsing, especially for deciduous species, but shoot size decreases after summer browsing; branching of annual shoots increases after winter browsing, but decreased by summer browsing; leaf size increases after winter browsing, but the response to summer browsing is variable (no response to increase); winter browsing has a neutral or negative impact on nutrient characteristics of shoots, and fiber concentration increases; winter browsing increases leaf concentrations of K, Ca, and N, while the concentration of protein-precipitating compounds decreases; early-summer browsing decreases nitrogen concentration in leaves of the next summer, while late-summer browsing has the opposite effect, at least for 1 year. Repeated leaf-stripping during late summer, however, tends to decrease nitrogen concentration. Some of these responses (e.g., changes in plant biomass and size of food item) have the potential of being important to the herbivores that feed on the plants. As the food production of a whole tree most often decreases after browsing and some of the chemical properties are affected negatively from the animal's point of view, the most logical response by the herbivores should be to avoid browsed plants. However, some studies have shown that there is a higher probability for a browsed tree than for an unbrowsed tree to be browsed 1 year later.
Canopy photosynthesis and water-use efficiency in a deciduous forest

(1) The short-term canopy photosynthesis and water-use efficiency of a deciduous forest were measured with the eddy correlation method. Canopy photosynthetic rates were strongly dependent on photosynthetically active radiation and were highly correlated with transpiration. These rates were not correlated with vapour pressure deficit, air temperature and stomatal resistance since limiting conditions were not encountered. Water-use efficiency was found to be dependent on vapour pressure deficit but was independent of net radiation. (2) Measurements of canopy photosynthetic rates and water-use efficiency were compared with theoretical estimates. Canopy photosynthesis was computed by coupling the leaf photosynthesis model of Marshall & Biscoe (1980) with the canopy radiative transfer model of Baldocchi & Hutchison (1986). Considering the simplicity of the canopy photosynthesis model, the overall agreement between measured and computed values was reasonable. Water-use efficiency measurements agreed well with values computed with the model of Sinclair, Tanner & Bennett (1984). (3) Canopy-atmosphere gas exchange rates were lower than values commonly observed over agricultural crops. This was partly because deciduous forest is aerodynamically rougher than agricultural crops and deciduous trees have a greater canopy stomatal resistance than crops. The ratio between atmospheric CO2 uptake and canopy photosynthesis was different from that commonly measured over agricultural crops. This is because the floor of a deciduous forest has more detritus than an agricultural crop, which allows greater CO2 efflux from the forest floor.
New records of the Sordariaceae from East Africa

Triangularia tanzaniensis is described and illustrated from cow dung. Asordaria v. Arx et al. is rejected. Sordaria islandica {=Asordaria islandica Guarro & van der Aa) and Sordaria tenerifae {= Asordaria tenerifae v. Arx & Guarro) comb. nov. are proposed. Numerous records for previously recognized taxa are reported. Sordaria alcina, S. brevicollis and S. lappae are new to Africa. Sordaria superba, S. tomento-alba, Triangularia karachiensis, Tripterospora erostrata and T. ultima are additions for East Africa. A number of new substrates are recorded. The earliest report dealing exclusively with coprophilous fungi of East Africa was that by Schmidt (1913), who referred to several isolated records published previously by Eichelbaum (1906) and Hennings (1901,1905,1907). Schmidt included a number of taxa which currently are placed in the Sordariaceae, while additions were reported by Minoura (1969), Khan and Cain (1972), and Lundqvist (1973,1981), but no cornprehensive study of the coprophilous fungi for the region is available. Consequently, when it was possible to undertake field work in East Af? rica, an extensive sampling was made of weathered dung. These collections, obtained during the summer of 1966 by R. F. Cain, H. D. Griffin and J. C. Krug, form the basis for a detailed study ofthe coprophilous fungi. The samples were airdried and numbered as outlined by Khan and
Restricted pollination on Oceanic islands: pollination of Ceiba pentandra by flying foxes in Samoa

The very low diversity of animal pollinators on remote oceanic islands can act as a potent biotic filter to potential plant immigrants. To assess the relative difficulties faced by colonizing plant species, we studied the pollination ecology of kapok, Ceiba pentandra (Bombacaceae), a widespread aboriginal introduction to Pacific islands. The Samoan form of this tree is self-fertile, but requires pollination for fruit set. In continental areas C. pentandra attracts a diverse assemblage of pollinators, but in Samoa it is pollinated only by Pteropus tonganus (Megachiroptera: Pteropodidae)an example of a plant exclusively dependent on one bat species for pollination. The pollination system is dystrophic, however, since foraging flying foxes may destroy up to 50 percent of C. pentandra flowers and developing fruits. Though resource defense is regarded as rare in nectarivorous bats, P. tonganus vigorously defends small feeding territories on the rich, but readily depleted, C. pentandra nectar resource. This intraspecies conflict probably shapes patterns of pollen transfer within and among trees, and enhances cross-pollination. Our study highlights the importance of conserving pollinators in remote oceanic islands with depauperate pollinator faunas.
Population Structure and Genetic Diversity of Carya cathayensis Revealed by AFLP Analysis

With the dominant AFLP marker,genetic diversity of a natural population of Carya cathayensis was studied in terms of linkage disequilibria (LD). It had been revealed that a total of 32 polymorphic markers were detected with 11 pairs of primers;of all possible 4692 three-locus combinations,779(or 15.7%) were detected to display significant linkage disequilibria;and there existed a modest overall heterozygosity of 0.36. It indicated a low polymorphic level and a small to moderate level of genetic diversity for Carya cathayensis.
Thermal time, chill days and prediction of budburst in Picea sitchensis

where thermal time was day degrees > 5 IC accumulated from 1 February, and chill days were the number of days <5 "C counted from 1 November, both based on mean daily air temperature ((max. + min.)/2). This model may be used to estimate the date of budburst on young P. sitchensis of most provenances growing in upland Britain. (3) The following features or assumptions of the model were examined with reference to the literature and/or by experimentation: the small effect of provenance; linearity in the relationship between bud growth rate and temperature; the large effect of chilling on thermal time to budhurst; the omission of daylength and soil temperature as variables; the choice of starting dates for effective chilling and thermal time; and the use of simple fixed base temperatures. (4) The model was applied to mean daily temperatures at Eskdalemuir for the period 1912-82. The predicted dates of budburst ranged from 23 April in 1961 to 30 May in 1923, with a mean date of 12 May.