Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservation and Management of Trachemys venusta venusta in Southern Mexico: A Genetic Approach

The Meso-American slider turtle (Trachemys venusta) is a freshwater turtle that is widely distributed from Mexico to Colombia. Due to the overexploitation of populations of this species in Mexico, it has been placed within the “subject to special protection” category formulated by the Official Mexican Standard NOM-059-ECOL-2010. In the state of Tabasco, Mexico, Management Units for the Conservation of Wildlife (UMA) were created to reduce the impact of overexploitation of freshwater turtles bred in captivity. However, no genetic management plan was considered. The present study was carried out in an UMA in the state of Tabasco. We obtained the level of genetic diversity of the founder individuals of the UMA in order to develop a management plan which will optimize reproduction in the UMA. Genetic diversity was compared between captive (n = 86) and wild (n = 45) individuals using 14 microsatellite molecular markers. The genetic diversity parameter determined in this study was slightly higher for captive than for wild population (He = 0.606 and He = 0.594 respectively), reflecting the mix of genetic sources in captive group (founding individuals from different localities) and demonstrating that the captive population contains a diverse subset of alleles from representative populations. The analysis of genetic structure revealed a relationship between captive and wild populations, indicating the influence of the two principal river basins in this region on the populations structure of freshwater turtles. Finally, according to the results obtained from the relationship analysis, we recommend the use of 19 females and 13 males to constitute the appropriate breeding group, generating a potential of 247 dyads with no relationship. However, in order to improve breeding program and the genetic diversity of captive population, we suggest to introduce wild-caught individuals. These results are the first regarding genetic management in a Mexican UMA and demonstrate the importance of molecular approaches in the management and conservation of captive species.
Identification of Terrestrial Predators at Two Little Penguin Colonies in South Australia

Identifying predators and determining their influence on bird population declines can be crucial in the implementation of appropriate conservation measures. In this study, we focus on the Little Penguin Eudyptula minor , a flightless seabird whose numbers have seriously declined in some populations across Australia and New Zealand, for a variety of reasons, some not fully understood. Using a combination of motion-camera monitoring at active burrows and postmortem examinations of carcasses, we present data on the identity, occurrence and impact of terrestrial predators at two colonies in South Australia: Granite Island and Emu Bay (Kangaroo Island). Terrestrial predation varied from 20% for carcasses found on Granite Island to 44% at Emu Bay. There was no evidence for predation at burrows on Granite Island but, at Emu Bay, we identified goannas (Heath Monitor Varanus rosenbergi) as predators of chicks (by using cameras), and Cats Felis catus as predators of chicks and juveniles (from postmortem examination of carcasses). In addition, 45% of the carcasses found at Emu Bay were categorised as chicks. We discuss potential biases in identifying causes of death from carcasses only and the importance of combining both direct and indirect evidence.
Wild strawberry shows genetic variation in tolerance but not resistance to a generalist herbivore

Abstract Plants’ defenses against herbivores usually include both resistance and tolerance mechanisms. Their deployment has predominantly been studied in either single‐plant genotypes or multiple genotypes exposed to single herbivores. In natural situations, however, most plants are attacked by multiple herbivores. Therefore, aims of this study were to assess and compare the effects of single and multiple herbivores on plant resistance and tolerance traits, and the consequences for overall plant performance. For this, we exposed multiple genotypes of wild woodland strawberry (Fragaria vesca) to jasmonic acid (JA), to mimic chewing herbivory and induce the plants’ defense responses, and then introduced the generalist herbivore Spodoptera littoralis to feed on them. We found that woodland strawberry consistently showed resistance to S. littoralis herbivory, with no significant genetic variation between the genotypes. By contrast, the studied genotypes showed high variation in tolerance, suggesting evolutionary potential in this trait. Prior JA application did not alter these patterns, although it induced an even higher level of resistance in all tested genotypes. The study provides novel information that may be useful for breeders seeking to exploit tolerance and resistance mechanisms to improve strawberry crops’ viability and yields, particularly when multiple herbivores pose significant threats.
Alteration of initial and residual healing potential of asphalt binders due to aging, rejuvenation, and polymer modification

Asphalt binders are known to exhibit an inherent ability to repair damage. Such self-healing potentially affects the fatigue damage performance of bituminous materials. There are contradicting findings about the effects of aging and polymer modification on healing. The effectiveness of rejuvenating agents also has not been sufficiently addressed. In the present study, three healing indices have been defined to provide a more complete representation with which to quantify the healing potential of binders. These indices have been defined using damage characteristic curves derived from interrupted linear amplitude sweep tests. Initial healing (IH) describes the immediate reduction in the damage accumulated after the rest period. Residual healing (RH) shows the lasting effect of healing and total healing (TH) is a combination of IH and RH. The results demonstrate that IH does not present a complete picture of healing, particularly at low and intermediate levels of damage. While, RH better exhibits the detrimental effect of aging, the healing ability of SBS (styrene–butadiene–styrene) binder at higher damage levels, and the positive effect of the use of the rejuvenating agent. The healing model shows that, irrespective of the healing index and binder, the effect of loading interruptions at higher levels of damage, along with increased stiffness because of aging, prevail over the positive effects of an increase in the duration of the rest period.
The DeepScoresV2 Dataset and Benchmark for Music Object Detection

In this paper, we present DeepScoresV2, an extended version of the DeepScores dataset for optical music recognition (OMR). We improve upon the original DeepScores dataset by providing much more detailed annotations, namely (a) annotations for 135 classes including fundamental symbols of non-fixed size and shape, increasing the number of annotated symbols by 23%; (b) oriented bounding boxes; (c) higher-level rhythm and pitch information (onset beat for all symbols and line position for noteheads); and (d) a compatibility mode for easy use in conjunction with the MUSCIMA++ dataset for OMR on handwritten documents. These additions open up the potential for future advancement in OMR research. Additionally, we release two state-of-the-art baselines for DeepScoresV2 based on Faster R-CNN and the Deep Watershed Detector. An analysis of the baselines shows that regular orthogonal bounding boxes are unsuitable for objects which are long, small, and potentially rotated, such as ties and beams, which demonstrates the need for detection algorithms that naturally incorporate object angles. The dataset, code and pre-trained models, as well as user instructions, are publicly available at https://zenodo.org/record/4012193.
Muokkausmenetelmien vaikutus maaperän mikrobistoon ja niiden tarjoamiin ekosysteemipalveluihin

Tiivistelmä Maatalous kohtaa ilmastonmuutoksen myötä entistä suurempia ympäristöhaasteita. Eroosioja ravinnekuorma vesistöihin kasvaa, mikäli talvet muuttuvat ennustetulla tavalla lauhemmiksi ja sateisemmiksi. Kasvipeitteisyys suojaa maan pintaa vähentäen eroosioja ravinnehuuhtoumariskiä, mutta kasvinjäte voi vaikeuttaa viljelyä ja luoda suotuisat olosuhteet maaja kasvinjätelevinteisille kasvitaudeille. SUCCESS-projekti toteutettiin osana MTT:n Muuttuva ilmasto ja maatalous tutkimusohjelmaa (2009–2012) ja Helsingin yliopiston Globaalin ympäristömuutoksen tutkimusohjelmaa (2008–2011). Tutkimuksen tavoitteena oli selvittää muokkausmenetelmien vaikutusta maaperämikrobistoon ja sen tuottamiin ekosysteemipalveluihin, kuten tautimikrobien tukahduttamiskykyyn. Maanäytteenotto tehtiin kuudelta erilliseltä peltoalalta, joissa pitkäaikaisina (8–12 vuotta) muokkauskäsittelyinä olivat suorakylvö ja kyntö. Kokoomanäytteet (vähintään 20 kairallista/ruutu) otettiin muokkauskerroksesta ennen syyskyntöä kolmelta eri syvyydeltä 0–5, 5–10 ja 10–20 cm (2009). Näytteistä analysoitiin sienija bakteerimikrobiyhteisöjen koostumus kolmella eri menetelmällä; PLFA rasvahapposormenjälki, PCR T-RFLP DNA-sormenjälki ja 454 FLX Titanium DNA-pyrosekvensoinnilla (Roche Applied science). Samanaikaisesti mitattiin laboratoriobiotestien avulla mallikasvitautisienen (punahome, Fusarium culmorum) kykyä kasvaa peltomaan päällä ja näin saatiin arvio maiden kasvitautien tukahduttamiskyvystä. Peltoalojen maaperän vaihtelusta riippumatta ja kaikilla käytettyillä mikrobiyhteisöjen kuvausmenetelmillä huomattiin, että suorakylvössä muodostuu selkeä syvyysgradientti mikrobioyhteisöihin. Vastaavaa gradienttia ei havaittu kyntökäsittelyssä. Suorakylvöruutujen syvyysgradientissa korostuivat etenkin suurimpien maaperän bakteeripääjaksojen suhteelliset osuudet (acidobakteerit, proteobakteerit ja aktinobakteerit) sekä nitriittiä nitraatiksi happettava Nitrospira pääjakso (Parittainen t-testi, Suorakylvö 0–5 vs. 10–20 cm, P<0,05). Käsittelyvaikutuksia havaittiin bakteeripääjaksojen suhteellisissa osuuksissa kyntöja suorakylvöruutujen välillä etenkin 0–5 ja 10–20 cm syvyyksissä. Suuren mikrobi(r = -0,7 P<0,02) ja sienibiomassan (r = -0,89 P<0,001) havaittiin hidastavan punahomeen kykyä kasvaa biotestissä maan pinnalla. Projektissa tuotettiin arvokasta tietoa viljelymaan mikrobiologiasta käyttäen uusimpia molekyylibiologian menenetelmiä, mikä on uutta Suomessa ja jopa Euroopan mittakaavassa. Muokkausmenetelmien vaikutus mikrobiyhteisöihin osoitettiin peltojen välisellä analyysillä, mikä osoittaa että muokkausmenetelmien valinnalla pystytään mahdollisesti vaikuttamaan maaperän mikrobiologisiin prosesseihin. Nämä ovat avainasemassa kun pyritään hyödyntämään maaperän ekosysteemipalveluita kasvipatogeenien torjunnassa ja ilmastonmuutoksen ehkäisyssä.
Leveraging spatial information to forecast nonlinear ecological dynamics

There has been a recent demand for forecasting in ecology, particularly in the field of ecosystem management. Empirical dynamic modelling (EDM), an equation‐free nonlinear forecasting method, is receiving growing attention, but it requires long time series to produce accurate predictions. Though most ecological time series are short, spatial replicates are often available. Here we explore how utilizing available spatial data can improve our ability to forecast ecological dynamics. There are several ways to incorporate spatial information into EDM and not all have been applied in ecology. We compare spatial EDM approaches used in ecology and physics and introduce a flexible Bayesian model that makes use of prior movement information. We test these methods on simulated data generated with three population dynamics models with varying levels of complexity, time series length, spatial symmetry and heterogeneity. Adding spatial data generally improves accuracy, though the best method depends on the spatial process. We applied the methods to empirical fisheries data, highlighting the complexity of real population dynamics. Leveraging spatial data is an effective way to overcome the problem of short ecological time series. Since the best forecasting method depends on the underlying dynamics, we suggest that users apply several in concert and that this may be useful in identifying spatial heterogeneity in dynamics.
Molecular cloning and characterization of porcine interferon-induced protein with tetratricopeptide repeats (IFIT) 5

Zhang, J., Shao, S. -y. , Li, L. -z. , Liu, D. and Yang, X. -q. 2015. Molecular cloning and characterization of porcine interferon-induced protein with tetratricopeptide repeats (IFIT) 5. Can. J. Anim. Sci. 95: 551-556. Interferon-induced protein with tetratricopeptide repeats (IFIT) family members play important roles in host defense against viral infection. In the present study, the complete coding sequence (CDS) of porcine IFIT5 gene was cloned using molecular biology techniques, and the genomic structure was determined using the bioinformatic method. The porcine IFIT5 is located on chromosome 14 containing 2 exons. Quantitative real-time PCR revealed that the transcripts of IFIT5 gene were unevenly distributed in all tissues studied, including heart, bladder, liver, large intestine, spleen, small intestine, lung, kidney, stomach, muscle, and lymph. Only one synonymous single nucleotide polymorphism was found in the complete CDS except for the first five nucleotides. IFIT5 is induced by poly(I:C) in a dose- and time-dependent manner, as revealed by using dual-luciferase analysis and reverse transcription-quantitative PCR methods. Furthermore, ectopic expression of porcine IFIT5 had no effect on the activation of interferon regulatory factor 3 (IRF3) significantly (P>0.05), suggesting it might not be a regulator of IRF3 signaling pathway.
Astrocyte control of neurotransmitter signalling

Astrocytes interact with, and regulate the activity of, neurons by various mechanisms. They can release molecules known as gliotransmitters which act on neuronal receptors, or they can regulate the concentration of neurotransmitters in the extracellular space through the expression of transporters. In this thesis I describe experiments on hippocampal astrocytes and neurons that examine both of these mechanisms. By recording glutamate transporter currents in astrocytes and NMDA-evoked currents in pyramidal neurons, I demonstrate that a relatively understudied G protein coupled receptor present in astrocytes, GPCR37L1, decreases the activity of astrocyte glutamate transporters and decreases neuronal NMDA receptor activity, presumably by regulating the release of modulatory molecules from astrocytes. In ischaemia, expression of GPCR37L1 and addition of an analogue of its agonist, prosaposin, are neuroprotective. This presumably reflects the smaller NMDA receptor-evoked Ca2+ entry occurring when GPR37L1 is active, and may also reflect decreased release of glutamate by reversal of glutamate transporters. A similar approach is used to show that the modulatory neurotransmitter noradrenaline reduces glutamate uptake currents in astrocytes. This action of noradrenaline is blocked by buffering intracellular calcium concentration in astrocytes and by blocking adrenergic receptors that lower the concentration of cyclic AMP. Furthermore, I demonstrate that the intracellular protein nischarin, shown previously by the Attwell and Kittler groups to interact with astrocyte GLT-1 glutamate transporters, decreases astrocyte glutamate transport. Lastly, I provide evidence for a role of astrocyte calcium signalling in maintaining the firing frequency of inhibitory interneurons in hippocampus. I also assessed the involvement of calcium concentration rises in astrocytes in regulating excitatory neurotransmission and the effect of noradrenaline on synaptic transmission to pyramidal cells. Overall, I demonstrate signalling mechanisms that regulate glutamate uptake by astrocytes (via GPCR37L1, nischarin, and adrenergic receptors), and how astrocytes modulate excitatory neurotransmission (presumably through the release of gliotransmitters) or maintain inhibitory transmission (through Ca2+ signalling).
Behavioral Patterns of Common Bottlenose Dolphins (Tursiops truncatus truncatus) Within the Galveston—Port Bolivar Ferry Lane

Abstract The objective of this study is to assess Tursiops truncatus truncatus (Common Bottlenose Dolphin) group behavior as a function of spatial, temporal, and vessel proximity variables within the Galveston—Port Bolivar ferry lane, in lower Galveston Bay, TX. This area is subjected to vessel traffic entering the Houston, Texas City, and Galveston ship channels and at risk for environmental accidents. We used the Galveston—Port Bolivar ferries as a platform of opportunity to observe group behavior within the ferry lane. We conducted 1412 hours of observation between 1 June and 30 November 2013 and then utilized canonical correspondence analysis to evaluate behavioral state as a function of spatial, temporal, and vessel-proximity variables. Principal response curve (PRC) analysis showed significant variation in behavioral states over time in the Bolivar and Galveston zones as compared to the passage zone. Chi-square goodness-of-fit tests showed significant deviations from expected behavior observation across zone and time block. These findings demonstrate finescale behavioral variability in an area of high anthropogenic activity.
Single-Level Posterolateral Fusion (PLF) Alone and Posterior Interbody Fusion (PLIF/TLIF) Alone Lead to a Decreased Risk of Short-Term Complications Compared to Combined PLF with PLIF/TLIF Procedures: A Matched Analysis.

STUDY DESIGN Retrospective review of a database cohort. OBJECTIVE To compare short-term outcome measures and complications between single-level posterolateral fusion (PLF), single-level posterior interbody fusion (PLIF/TLIF), and combined single-level PLF+PLIF/TLIF. SUMMARY OF BACKGROUND DATA Both PLF and interbody fusion are well-established procedures for degenerative spinal disease. However, there is lack of consensus as to the ideal surgical approach for specific applications. Additionally, the difference in risk of complications with traditional PLF, interbody fusion with posterior approach, and circumferential fusion is still contested. METHODS The ACS NSQIP database was used to identify 24,228 patients who underwent either a single-level PLF, single-level PLIF/TLIF, or combined single-level PLF+PLIF/TLIF between 2014 and 2017. To control for potential confounding variables, exact matching was used to pair individuals from each treatment group based on several factors, including sex, age, body mass index, various comorbidities, and American Society of Anesthesiologists classification. After appropriate matching, the rate of various short-term outcome measures and complications were compared between the three treatment groups. RESULTS After exact matching, 13,251 patients were included in the final analysis. The rates of non-home discharge, overall surgical complications, and bleeding requiring transfusion were significantly lower in the PLF group and PLIF/TLIF group relative to the PLF+PLIF/TLIF group (p < 0.001 for all comparisons). The rate of deep venous thrombosis was lower in the PLIF/TLIF group relative to the PLF group (p = 0.006). There were no significant differences in other medical complications, unplanned readmission, reoperation, or return to the OR between any of the treatment groups. CONCLUSIONS The combination of single-level PLF+PLIF/TLIF is associated with higher rates of short-term complications relative to either single-level PLF or PLIF/TLIF alone. The associated risks of this therapy should be considered when considering surgical management for lumbar disease. LEVEL OF EVIDENCE 3.
Estudos sobre o aumento da permeabilidade capilar na pele de rato por acao do piridoxal 5'-fosfato

tin» wmk-ftew.nhi»* the . ictk/try of UVMX;II h' i>husph. )ie (PLP) on the vascular permeability responsa, measo»ed in the Hbdominiil WHII nt I;IIS from the mimurit of extnivared Evans blue labelled with radioactive iodine 125 or 131. The PLP effect is relntod to hisinmirw release as it has heen showed by the use of antihistaminics. An attempt has been made in order to correlate structure and biologicnl activity by using PLP analogs, The intact molecule of PLP seems to he the proper active substance. The critical role of calcium in histamine release átt discussed in relation to our . observations. In the presence nf high concentrations of calcium and lantanium, PLP fatter»» to increase the vascular /'-'I' permeability; magnesium does no! show any influence. The calcium mobilization produced bv theophylline results in ' inhibition of the response. The course of the reaction between PLP and histamine in vitro w»r» followed; the synthetic cyc! ic product is deprived of activity and does not interfprp'^ith the intrinsic effects of PLP and histamine. REFERÊNCIAS BIBLIOGRÁFICAS 1. ALTOUNYAN, R. E. C; ORR, T. S. C , COX, J. S. G. Biological and pharmacological basis of disodium cromoglycate therapy. Folia allergol. , XT. 442-7, 1970. 2. ANDERSON, B. B. Plasma binding of vitamin B6 compounds. Nature, (London), 250(54661:502-4, 1974. 3. BECKER, E. L ; MOTA, I.; WONG, D. Inhibition by antihistamines of the vascular permeability increase induced by bradykinin. Br. J. Pharmac., 34330-6,1968. 4. BERALDO, W. T. Formation of bradykinin in anaphylactic and peptone shock. Am. J. Physiol., JJS3:283-9,1950. 5. BIANCHI, C. P. Cell calcium. London, Butterworths, 1968. 6. BUTCHER. R. W. & SUTHERLAND, E. E. Adenosine 3'. 5'-phosphate in biological materials. J. biol. Chem., 237:1244-50, 1962. 7. CABANTCHIK, I.; BALSHIN, M.; BREUbR, W.; ROTHSTEIN, A. Pyridoxal phosphate: an an ionic probe for protein ami no groups exposed on the outer and inner surfaces of intact human red blood cells. J. biol. Chem., 250(13)5130-6, 1975. 8. CHAMBAUT, A. Calcium binding properties and ATPase activity of rat liver plasma membranes. J. gen. Physiol. , 64(11:104-26, 1974. 9. CHANGEUX, J. P.; THIERY, J.; TUNG, I.; KITTEL, C. The cooperativity of biological membranes. Proc. natn, Acad. Sci. US, 57335-41, 1967. 10. COX, J. S. G. Disodium cromoglycate (FPL 670) ("Intal"): a specific inhibitor of reaginic antibodyantigen mechanisms. Nature (London), 216:1328-6, 1967. 11. COX, J. S. G. Disodium cromoglycate: mode of action and its possible relevance to the clinical use of the drug. Br. J. D is. Chest, §5:189 96, 1971. 12. DE GUBAREFF, T. &SLEATOR, W. Effects of caffeine on mammalian atrial muscle and its interaction with adenosine and calcium. J. Pharmac. nxp. Ther. , 148202-14. 1965. 13. DE SA, G. F. ; GIESBRECHT, E. & THOMPSON, L. C. Schiff base complexes with the lanthanide ions. An. Acad. bras. Cienc, 47(11:77-82, 1975.
The role of tumor necrosis factor (TNF) in angiogenesis

receptors for proangiogenic factors (IL8-R, flt-1, flk-1, flg) and activation of angiogenesis inhibitors such as angiopoetin-2. Moreover, TNF can influence angiogenesis indirectly by stimulation of other cells, especially macrophages and modulation of adhesion molecules expressed on endothelial cells. Since the high expression of particular integrins on these cells and higher amount of fibronectin in tumor vasculature substratum was found, adhesion is believed to be a very important event in angiogenesis. The results of in vitro and in vivo research suggest two critical variables responsible for TNF effect on angiogenesis: concentration of cytokine and time of exposure of target cells to the cytokine. Low doses of TNF and short time of exposure result in proangiogenic effect, while high doses and longer exposure can act as antiangiogenic conditions.