Miracle-dz/UniFAR-FTUs huggingface dataset:
Biology and fisheries of the spotted flounder (Citharus linguatula) caught by multiple gears with partial spatiotemporal overlaps

Obtaining data to study fish biology can be a challenge if a stock is fished by a variety of gears with different effort units and different selectivity, particularly if these gears only partially overlap in space and time. In this work, we attempted to study the biology of the spotted flounder Citharus linguatula in the Patraikos Gulf and the adjacent central Ionian Sea (eastern Mediterranean) and to evaluate the current fisheries management. We characterized age composition and growth, length-at-maturity, and catch-per-unit-effort (CPUE) of spotted flounder from the catches of bottom trawls, gillnets and trammel nets for the period autumn 2013–2014. Variation of fish total length, gonadosomatic index, hepatosomatic index and condition factor was analyzed using generalized additive models (GAMs) with regard to sex, date, fishing gear and depth. We also modeled CPUE fluctuations of each gear by date, depth, longitude and latitude using GAMs. Fish age ranged from 1 to 5 years. A slightly allometric growth was documented with females attaining larger sizes than males. Length-at-maturity was 163 mm for females and 169 mm for males. The seasonal change of gonad maturity stages and the gonadosomatic index indicated spawning in late summer-autumn. Changes in length frequencies indicated that recruitment to the fisheries occurred in late spring-early winter in shallow depth (<40 m). The catch composition of trawls and the CPUE model results suggested that the selectivity of this gear should be regulated to reduce catching immature individuals of spotted flounder. The results further indicated that the seasonal trawl closure of the Patraikos Gulf contributes to reduce catching juveniles.
Mapping neuronal morphology to physiology in a rhythmic motor circuit

Mapping neuronal morphology to physiology in a rhythmic motor circuit A dissertation presented to the Faculty of the Graduate School of Arts and Sciences of Brandeis University Waltham, Massachusetts By Adriane G. Otopalik A neuron’s unique physiological waveform arises from its palette of ion channels and receptors, as superimposed on its geometrical structure. The crustacean stomatogastric ganglion (STG), a small rhythmic motor circuit, exhibits fourteen identified neuron types with highly-conserved physiological waveforms and complex morphologies. In this thesis, I examine how morphology shapes neuronal physiology in the STG. Using high-resolution neuronal reconstructions and a suite of computational tools, I quantify numerous morphological features of four STG neuron types. This work revealed remarkable animal-to-animal variability in neuronal morphology. I also demonstrate that STG neurons do not adhere to current hypotheses regarding wiring optimization principles. I then studied the physiological consequences of animal-to-animal morphological variability in one neuron type, the Gastric Mill (GM) neuron. Utilizing focal photo-uncaging of glutamate in tandem with electrophysiological techniques, I characterize passive voltage signal propagation. I find that GM neurons, despite their complex structures, operate much like single compartments. Taken together, these studies suggest that relatively compact electrotonic structures may effectively compensate for the observed morphological
High-risk, Expression-Based Prognostic Long Noncoding RNA Signature in Neuroblastoma

Abstract Background Current clinical risk factors stratify patients with neuroblastoma (NB) for appropriate treatments, yet patients with similar clinical behaviors evoke variable responses. MYCN amplification is one of the established drivers of NB and, when combined with high-risk displays, worsens outcomes. Growing high-throughput transcriptomics studies suggest long noncoding RNA (lncRNA) dysregulation in cancers, including NB. However, expression-based lncRNA signatures are altered by MYCN amplification, which is associated with high-risk, and patient prognosis remains limited. Methods We investigated RNA-seq-based expression profiles of lncRNAs in MYCN status and risk status in a discovery cohort (n = 493) and validated them in three independent cohorts. In the discovery cohort, a prognostic association of lncRNAs was determined by univariate Cox regression and integrated into a signature using the risk score method. A novel risk score threshold selection criterion was developed to stratify patients into risk groups. Outcomes by risk group and clinical subgroup were assessed using Kaplan-Meier survival curves and multivariable Cox regression. The performance of lncRNA signatures was evaluated by receiver operating characteristic curve. All statistical tests were two-sided. Results In the discovery cohort, 16 lncRNAs that were differentially expressed (fold change ≥ 2 and adjusted P ≤ 0.01) integrated into a prognostic signature. A high risk score group of lncRNA signature had poor event-free survival (EFS; P < 1E-16). Notably, lncRNA signature was independent of other clinical risk factors when predicting EFS (hazard ratio = 3.21, P = 5.95E–07). The findings were confirmed in independent cohorts (P = 2.86E-02, P = 6.18E-03, P = 9.39E-03, respectively). Finally, the lncRNA signature had higher accuracy for EFS prediction (area under the curve = 0.788, 95% confidence interval = 0.746 to 0.831). Conclusions Here, we report the first (to our knowledge) RNA-seq 16-lncRNA prognostic signature for NB that may contribute to precise clinical stratification and EFS prediction.
Therapeutic Management of Zoonotic Sarcoptic scabei var cameli –A Study of 6 Camels

Sarcoptic mange in one humped-camels (Camelus dromedaries) caused by Sarcoptes scabiei var cameli is considered to be one of the most obstinate and economically important zoonotic and epizootic disease that can be spread among animals via direct physical contact with infested animal and indirectly through fomites (e.g., ropes, blankets and saddlery) especially in tropical and subtropical areas (Singh, 2005; Parsani et al., 2008; Wilson, 2008). The present paper demonstrates the successful therapeutic management of sarcoptic mange in camels.
Successful Identification of Duck Genome Region Determining Desirable Uniformity of Meat Performance Traits

I Poznan University of Life Sciences, Department of Mathematical and Statistical Methods, Wojska Polskiego st. 28, 60-637 Poznań, Poland II Experimental Unit Station of National Institute of Animal Production Koluda Wielka, Waterfowl Genetic Resource Station Dworzyska, 62-035 Kórnik, Poland III Poznan University of Life Sciences, Department of Genetics and Animal Breeding, Wołyńska st. 33, 60-637 Poznan, Poland
Weiterführende biochemische und physiologische Analysen zum tonoplastidären Dicarboxylat Transporter TDT in Arabidopsis thaliana

Im Verlauf dieser Dissertation konnte gezeigt werden, dass eine erhohte Expression des tonoplastidaren Dicarboxylat Transporters zu einem erhohten Gehalt an Malat bei gleichzeitig vermindertem Citratgehalt in den Uberexpressions-Pflanzen fuhrt. Somit konnte, ahnlich wie in den k.o. -Pflanzen, ein reziprokes Verhalten von Citrat und Malat aufgezeigt werden. Elektrophysiologische Analysen an Oozyten von X. laevis in Zusammenhang mit Aufnahmeversuchen an Proteoliposomen zeigten weiterhin, dass der Transport von Citrat ebenfalls durch den TDT katalysiert wird. Anhand eines negativen Einwarts-Strom an Oozyten konnte gezeigt werden, dass dieser Citrat-Transport elektrogen ist. Weiterhin konnte gezeigt werden, dass Citrat2-H die transportierte Form von Citrat darstellt. Dieses wird vermutlich zusammen mit drei Protonen transportiert. Die Dianionen Malat und Succinat, sowie hochstwahrscheinlich auch Fumarat, werden ebenfalls uber den TDT transportiert. Unter Standardbedingungen werden diese in die Vakuole importiert. Im Gegenzug wird Citrat aus der Vakuole exportiert. Die trans-stimulierende Wechselwirkung von Malat, Succinat und Fumarat auf den Citrat Transport und vice versa bestarkt den in dieser Arbeit postulierten Antiport der jeweiligen Carboxylate uber den Tonoplasten. Dieser ist jedoch nicht obligat, was an dem verringerten Transport von Citrat ohne Gegensubstrat uber die Membran gezeigt werden konnte. Unter Trockenstress und osmotischen Stress konnte ebenfalls gezeigt werden, dass die erhohte Expression des TDT masgeblich an der Akkumulation von Malat und der Mobilisierung von Citrat unter den genannten Stressbedingungen beteiligt ist. Letztlich konnte mittels Saurestressexperimenten nachgewiesen werden, dass die Malatakkumulation, bei gleichzeitigem Citrat Abbau nicht zwingend miteinander gekoppelt sind, unter Saurestress mussen daher weitere regulatorische Effekte auf den Malat-Import bzw. den Citrat-Export vorherrschen.
Pain-related fear - From different fear constructs to dissociable neural sources of

The ability to infer emotional states through self-reports is often limited. Their measurement becomes even more challenging when considering emotional phenomena such as pain-related fear where different associated fear constructs have been proposed. Demonstrating significant predictive value regarding disability in patients with persistent musculoskeletal pain, pain-related fear is assessed by questionnaires focusing of movement/(re)injury/kinesiophobia, fear avoidance beliefs or pain anxiety. Furthermore, the relationship of general anxiety measures such as trait anxiety to pain-related fear remains ambiguous. Advances in neuroimaging might help to support potential commonalities or differences across psychological constructs using appropriate machine learning techniques with the ability to reveal predictive relationships between neural information and questionnaire scores. Here, we applied a pattern regression approach using functional magnetic resonance imaging data of 20 non-specific chronic low back pain (LBP) patients. More specifically, we applied a novel approach using Multiple Kernel Learning that allows investigating the contribution of experimental conditions and regional neural information to a prediction model. We hypothesized to find evidence for or against a common fear construct by computing and comparing the prediction model of each questionnaire according to the contribution of fear-related neural information and conditions. The current results underpin the diversity of fear constructs among self-report measures of pain-related fear by demonstrating evidence of non-overlapping and differentially contributing neural sources within fear processing regions. Thus, the current approach might ultimately help to further understand and dissect the fear constructs captured by the various pain-related fear questionnaires. Pain-related fear, often assessed through self-reports such as questionnaires, has shown prognostic value and clinical utility for a variety of musculoskeletal pain disorders. However, it remains difficult to determine a common underlying fear construct of pain-related fear due to several proposed constructs among questionnaires. The current study describes a novel neuroscientific approach using machine learning of neural patterns within the fear network of chronic LBP patients that might have the potential to identify neural commonalities or differences among the various fear constructs. Ultimately, this approach might afford a deeper understanding of the suggested fear constructs of pain-related fear and might be also applied to other domains where ambiguity exists between emotional phenomena and underlying psychological constructs.
ADVANCES IN DIAGNOSIS OF INVASIVE FUNGAL INFECTIONS ( S CHEN , SECTION EDITOR ) MALDI-TOF MS and Filamentous Fungal Identification : A Success Story ?

Purpose of Review The diagnosis of invasive fungal disease remains challenging in the clinical laboratory. In this paper, the use of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of filamentous fungi as well as its application for antifungal resistance testing and strain typing is evaluated. Recent Findings Most studies report very high accuracy for the identification of filamentous fungi by MALDI-TOF MS. Its cost effectiveness, short analysis time, and low error rate and the fact that it can also discriminate between closely related and cryptic species make it appropriate for implementation in the clinical routine. Two drawbacks remain in the availability of extended reference spectra databases and the fact that this technique can only be applied on isolates. Summary More work on (simultaneous) antifungal susceptibility testing and strain typing is needed. The application of MALDI-TOF MS directly on clinical specimens would further improve the diagnosis of invasive fungal disease and improve its successful management.
Successful reproduction and pheromone production by the spruce bark beetle in evolutionary naïve spruce hosts with familiar terpenoid defences

The European spruce bark beetle Ips typographus is a damaging pest on spruce in Europe. Beetle interactions with tree species originating outside the natural range of the beetle are largely unknown and may be unpredictable because trees without a co‐evolutionary history with the beetle may lack effective defences. The terpenoid composition and breeding suitability for I. typographus of the historic host Norway spruce Picea abies were compared with two evolutionary naïve spruces of North American origin that are extensively planted in North‐West Europe: Sitka spruce Picea sitchensis and Lutz spruce Picea glauca x lutzii. The bark of all three species had a similar chemical composition and similar levels of total constitutive terpenoids, although Norway spruce had higher total induced terpenoid levels. Beetles tunnelling in the three spruce species produced similar amounts of aggregation pheromone. Controlled breeding experiments showed that I. typographus could produce offspring in all three species, with a similar offspring length and weight across species. However, total offspring production was much lower in Sitka and Lutz spruce. Overall, the results of the present study suggest that I. typographus will be able to colonize Sitka and Lutz spruce in European plantations and in native spruce forests in North America if introduced there.
The Annual Cycle and Natural History of a Subtropical Atlantic Forest Avifauna in Paraguay

We studied the avifauna in a subtropical humid forest around Hotel El Tirol, Department of Itapua, Paraguay. The study site is part of the Atlantic Forest biome, a critically endangered biodiversity hot spot. We recorded 205 species of birds in 45 families and provide information on their annual cycles and natural history from collected specimens and field observations. Increased knowledge will contribute to efforts to maintain and manage the bird species of this endangered biome. The annual cycle of the avifauna at El Tirol closely resembled that of birds at north temperate and subtropical latitudes. Birds entering reproductive phases were likely responding to increasing photoperiod and rainfall. In general, breeding was initiated in mid-August and began to decline in late November. Molt rose sharply in early December and continued into April, overlapping with breeding in 16 species. In some species, males replaced juvenal plumage with an immature plumage easily distinguishable from the adult form, which they acquired after several years. Most males in immature plumage bred. For most species skull pneumatization in young of the year was completed during their first year. In several species, however, the pneumatization process extended into year 2, and in other taxa, complete pneumatization requires multiple years or never occurs. The birds at El Tirol were predominantly insectivorous. About a quarter of the specimens in 134 species had noticeable body fat. In general, fat deposition peaked in June, with lesser peaks from February to mid-March and in late August and September. Twenty-seven of the species that we recorded were migratory. We compared the species of birds recorded at El Tirol with those recorded from San Rafael National Park, a large tract of Atlantic Forest farther north in Paraguay with a much more extensive avifauna. Some of the species we failed to record were likely overlooked. However, El Tirol is at the southwestern limit of the Atlantic Forest habitat; absences may reflect faunal attenuation as species reach the limits of their ecological ranges. The lower numbers may also indicate that diversity in forest patches is reduced. Regardless, such patches will play an important role in maintaining the Atlantic Forest avifauna.
Childhood socioeconomic status moderates genetic predisposition for peak smoking

Smoking is the leading cause of preventable disease and death in the U.S., and it is strongly influenced both by genetic predisposition and childhood socioeconomic status (SES). Using genetic variants exhibiting credible and robust associations with smoking, we construct polygenic risk scores (PGS) and evaluate whether childhood SES mediates genetic risk in determining peak-cigarette consumption in adulthood. We find a substantial protective effect of childhood SES for those genetically at risk of smoking: adult smokers who grew up in high-SES households tend to smoke roughly the same amount of cigarettesper day at peak (∼ 23 for low and ∼ 25 for high genetic risk individuals, or about 8%more), while individuals from low-SES backgrounds tend to smoke substantially more ifgenetically at risk (∼ 25 for low and ∼ 32 for high genetic risk individuals, or about 28% more).
Women and Reproduction: An Exploration of Factors Affecting Folate Status and Other Select Micronutrients Involved in One Carbon Metabolism

Optimal function of one carbon (1-C) metabolism is necessary during reproduction as it supplies 1-C units for purposes of synthesis or methylation of nucleic or amino acids. Maintaining nutrient status of the methyl vitamins folate, choline, vitamins B6 and B12 is crucial to prevent the nutrient imbalances linked to increased risk of neural tube (NTD) and other birth defects. There is little understanding of whether or not pregnancy and folic acid (FA) supplementation influence 1-C metabolism—for example shunting toward DNA synthesis in pregnancy. Using red blood cell forms as a mechanism to evaluate partitioning of folate early in erythropoiesis we examined the RBC folate forms in pregnant women consuming 1 mg of FA and non-pregnant women consuming 0, 1 and 5 mg supplemental FA (n=26). We found that neither pregnancy nor level of FA altered the relative distributions of the folate in RBC indicating no preferment for DNA synthesis. We then investigated if a comprehensive list of socio-demographic and lifestyle factors would improve our ability to predict if a woman was more likely to have RBC folate concentrations associated with NTD protection in women of childbearing years (WCBY), thereby removing the necessity for a blood sample (n=101). We found that a FA supplement of 200 μg/d or a multivitamin consumed
Environmental drivers of plant community assembly in Isla de los Estados at Southern Atlantic Ocean

The comprehensive assessment of environmental gradients influencing species assemblages is important for implementing new conservation strategies under climate change. This study aims to determine the multi-scale effect of altitudinal and longitudinal gradients as drivers of richness and plant community assembly in mountain landscapes of Isla de los Estados (Argentina) to identify areas with greater conservation value in Southern Patagonia. We chose three fjords across the island that extends from West to East and we categorized landscapes into four ecosystem types according to their vegetation type (forests and open-lands) and elevation (lower lands, 0–100 m.a.s.l. and upper lands, 300–400 m.a.s.l.). Forest structure, soil cover (woody debris, rocky outcrop and bare soil) and vegetation cover (vascular and non-vascular), including richness and growthforms (trees, shrubs, prostrate and erect herbs, tussock and rhizomatous grasses, ferns and inferior plants) were measured in 60 sampling areas (3 fjords × 2 vegetation types × 2 elevations × 5 replicates). ANOVAs and multivariate methods were used to analyse heterogeneity in forest structure, plant richness, and life-form. In addition, species richness and the Simpson’s diversity index were calculated to understand plant assembly at multiple-scales (α, β and γ). Our results showed that environmental gradients (altitudinal and longitudinal) are more important drivers of change of ecosystem type than forest spatial structure. Furthermore, forest structure significantly varied with altitudinal and longitudinal gradients affecting most of the studied variables. A greater similarity (in richness and cover) between open-lands of lower and higher elevations was detected, as well as between forests. Fjords showed a West-East gradient, where the western and center fjords were more closely related to each other than to the eastern fjord. A multi-scale diversity approach may play central role in improving our understanding the main environmental drivers of richness and plant community assembly in these forests, both theoretical and empirical, and may be used to identify the spatial scale at which ecosystem types have greater conservation value. This study indicates that for southern forest conservation at regional level, efforts must cover all environmental gradients, including the different vegetation types to assure ful conservation of all the species assemblages.
Characterization of biochemical and functional properties of water-soluble tempe flour

Tempe is popular fermented food in Ondonesia. The health benefits of tempe have been reported (Astuti et al., 2000). Zhan & Ho (2005) reported that tempe could significantly reduce total cholesterol, LDL, and triglycerides content in blood. Tempe was also reported to have a hepatoprotective effect (Mohd Yusof et al., 2013), ACE-inhibitory and antioxidant activity (Gibbs et al., 2004), and immunological impact on intestinal mucosa (Soka et al., 2014).
MYC transcription factors : masters in the regulation of jasmonate biosynthesis in Arabidopsis thaliana

Jasmonates (JAs) are crucial plant signaling molecules that regulate defense responses against wounding, insects and necrotrophic pathogens. The biosynthesis of JAs is regulated by a positive feedback loop. This thesis reveals the transcriptional regulatory mechanism behind this positive feedback loop in Arabidopsis. The studies show that the bHLH-domain transcription factors MYC2, MYC3 and MYC4 positively regulate most JAs biosynthesis genes directly and by controlling the expression of ORA47 gene, encoding a regulator of JAs biosynthesis.
Inoculation of Malus genotypes with a set of Erwinia amylovora strains indicates a gene‐for‐gene relationship between the effector gene eop1 and both Malus floribunda 821 and Malus ‘Evereste’

The Gram-negative bacterium Erwinia amylovora (Burrill) Winslow. et al., causal agent of fire blight disease in pome fruit trees, encodes a type three secretion system (T3SS) that functions to translocate effector proteins into plant cells that collectively function to suppress host defenses and enable pathogenesis. Until now, there is only a limited knowledge about the interaction of effector proteins and host resistance presented in several wild Malus species. In this study, we tested disease responses in several Malus wild species with a set of effector deletion mutant strains and several highly virulent Erwinia amylovora strains, which are assumed to influence the host resistance response of fire blight-resistant Malus species. Our findings confirm earlier studies that deletion of the T3SS abolished virulence of the pathogen. Furthermore, a new gene-for-gene relationship was established between the effector protein Eop1 and the fire blight resistant ornamental apple ‘Evereste’ and the wild species M. floribunda 821. Our results provide new insights into the host-pathogen-interactions between Malus sp. – Erwinia amylovora. This article is protected by copyright. All rights reserved.