Miracle-dz/UniFAR-FTUs huggingface dataset:
Patch dynamics and species shifts in seagrass communities under moderate and high grazing pressure by green sea turtles

We studied 2 seagrass beds in the Mexican Caribbean that were grazed by green turtles. Grazing impact was moderate at Puerto Morelos (<20% of the area was grazed), whereas at Akumal, 45 to 55% of the bed was grazed. The turtles practiced rotational (cultivation) grazing and thereby increased the nitrogen leaf content in the dominant seagrass Thalassia testudinum by 30 to 33%. Average seagrass leaf productivity decreased under grazing at Puerto Morelos from 3.09 to 0.93 g dry wt m−2 d−1, whereas it did not change significantly at Akumal (0.88 to 1.17 g dry wt m−2 d−1). At Puerto Morelos, the turtles maintained grazing plots for 13 mo to >2 yr, creating a mosaic of patches that were grazed, ungrazed or recovering from grazing. Cover of the fastergrowing Halodule wrightii and rhizophytic algae increased in the grazing plots, whereas that of the dominant but slow-growing T. testudinum decreased. After the turtles stopped grazing the plots, the cover of T. testudinum gradually increased again, but recovery to pre-grazing conditions lasted >1 yr and was not observed in this study. Cover of Syringodium filiforme decreased when the turtles opened up new grazing areas but remained stable afterwards because the turtles usually avoided consumption of this seagrass. At Akumal, the system approached carrying capacity for grazing, and the turtles returned to grazing plots that had not fully recovered from past grazing. Here, the dominant climax seagrass T. testudinum became less abundant from 2008 until 2012, resulting in a less patchy landscape with low seagrass biomass and higher prevalence of the early seral species H. wrightii.
A 3D Surface Reconstruction Method for Large-Scale Point Cloud Data

Due to the memory limitation and lack of computing power of consumer level computers, there is a need for suitable methods to achieve 3D surface reconstruction of large-scale point cloud data. A method based on the idea of divide and conquer approaches is proposed. Firstly, the kd-tree index was created for the point cloud data. Then, the Delaunay triangulation algorithm of multicore parallel computing was used to construct the point cloud data in the leaf nodes. Finally, the complete 3D mesh model was realized by constrained Delaunay tetrahedralization based on piecewise linear system and graph cut. The proposed method performed surface reconstruction on the point cloud in the multicore parallel computing architecture, in which memory release and reallocation were implemented to reduce the memory occupation and improve the running efficiency while ensuring the quality of the triangular mesh. The proposed algorithm was compared with two classical surface reconstruction algorithms using multigroup point cloud data, and the applicability experiment of the algorithm was carried out; the results verify the effectiveness and practicability of the proposed approach.
Biochar amendment boosts photosynthesis and biomass in C3 but not C4 plants: A global synthesis

Biochar is a carbon (C)‐rich solid produced from the thermochemical pyrolysis of biomass. Its amendment to soils has been proposed as a promising mean to mitigate greenhouse gas emissions and simultaneously benefit agricultural crops. However, how biochar amendment affects plant photosynthesis and growth remains unclear, especially on a global scale. In this study, we conducted a global synthesis of 74 publications with 347 paired comparisons to acquire an overall tendency of plant photosynthesis and growth following biochar amendment. Overall, we found that biochar amendment significantly increased photosynthetic rate by 27.1%, and improved stomatal conductance, transpiration rate, water use efficiency, and chlorophyll concentration by 19.6%, 26.9%, 26.8%, and 16.1%, respectively. Meanwhile, plant total biomass, shoot biomass, and root biomass increased by 25.4%, 22.1%, and 34.4%, respectively. Interestingly, plant types (C3 and C4 plants) showed greater control over plant photosynthesis and biomass than a broad suite of soil and biochar factors. Biochar amendment largely boosted photosynthesis and biomass on C3 plants, but had a limited effect on C4 plants. Our results highlight the importance of the differential response of plant types to biochar amendment with respect to plant growth and photosynthesis, providing a scientific foundation for making reasonable strategies towards an extensive application of biochar for agricultural production management.
Susceptibility of Larvae of the Black Cutworm to Species of Entomopathogenic Bacteria, Fungi, Protozoa, and Viruses

About 25% of 63 microorganisms known to be pathogenic to insects (7 of 38 viruses, 5 of 8 bacteria, 2 of 6 fungi, 1 of 11 protozoans) were sufficiently active (induced greater than 30% mortality) against larvae of Agrotis ipsilon (Hufnagel) to warrant additional testing to obtain an estimated LC50. The LC50 for the protozoan, Vairimorpha necatrix (Kramer) was 68 spores/mm2 Nomuraea rileyi (Farlow) Samson and Metarrhizium anisopliae (Metchnikoff) Sorokin, both fungi, had LC50,s of 219 and 807 conidia/mm2, respectively. The LC50 for viruses ranged from 260 inclusion bodies/mm2 for the nucleopolyhedrosis virus (NPV) of Mamestra brassicae (L.) to 7263 inclusion bodies/mm2 for the NPV of Pseudopluisa includens (Walker). The LC50 for 5 preparations of the bacterium Bacillus thuringiensis Berliner ranged from 7.3 to 55.9 ng/mm2
Integral roles of a guanine nucleotide exchange factor, FARP2, in osteoclast podosome rearrangements

Podosomes are recently rediscovered highly dynamic actin‐rich structural and functional modules that form close contact with the surrounding substrate. They play a role in the control of migration’ tissue invasion’ and matrix remodeling of highly motile cells’ including lymphocytes’ macrophages’ dendritic cells’ and osteoclasts. In osteoclasts’ the compaction of podosomes induces the formation of a tight adhesive contact’ the sealing zone’ which defines a subosteoclastic environment specialized for bone resorption. Integrins and the Rho family small GTPases are key regulators of podosome rearrangements. However’ it remains to be determined how the activation of integrins and Rho family GTPases is regulated during osteoclast podosome rearrangements. Here’ we demonstrate a crucial role for the FERM domain‐containing guanine nucleotide exchange factor (GEF)’ FARP2’ in osteoclast podosome rearrangements and resorbing activity. We determine by live cell imaging and biochemical assays that FARP2 is required for localized activation of GTP‐bound Rac1 into podosome‐ring like structures. In addition’ FARP2 is relevant to integrin β3 activity during osteoclastogenesis. Furthermore’ FARP2 deficiency results in reduced formation of multinucle‐ated osteoclasts and resorption pits compared to wild‐type osteoclasts (controls). Collectively’ our findings reveal an integral role of FARP2 for regulation of Racl and integrin β3 throughout podosome rearrangement in osteoclastogenesis. —Takegahara’ N. ’ Kang’ S. ’ Nojima’ S. ’ Takamatsu’ H. ’ Okuno’ T. ’ Kikutani’ H. ’ Toyofuku’ T. ’ Kumanogoh’ A. Integral roles of a guanine nucleotide exchange factor’ FARP2’ in osteoclast podosome rearrangements. FASEB J. 24’ 4782–4792 (2010). www.fasebj. org
The 12th–14th type III repeats of fibronectin function as a highly promiscuous growth factor‐binding domain

It has recently been shown that some growth factors (GFs) have strong interactions with nonproteoglycan extracellular matrix proteins. Relevant here, the 12th‐14th type three repeats of fibronectin (FN III12–14) have been shown to bind insulin‐like growth factor binding‐protein‐3, fibroblast growth factor (FGF)‐2, and vascular endothelial growth factor (VEGF)‐A with high affinity. Since FN III12–14 is known to bind GFs from different families, we hypothesized that this domain could be highly promiscuous in its GF‐binding capacity. We used biochemical approaches and surface plasmon resonance to investigate such interactions with recombinant FN III12–14. We found that FN III12–14 binds most of the GFs from the platelet‐derived growth factor (PDGF)/VEGF and FGF families and some GFs from the transforming growth factor‐β and neurotrophin families, with KD values in the nanomolar range, without inhibiting GF activity. Overall, 25 new binding interactions were identified. In a clinically relevant fibrin matrix, a fibrin‐binding variant of FN III12–14 was highly effective as a GF delivery system. For instance, in matrices functional‐ized with FN III12–14, PDGF‐BB‐induced sprouting of human smooth muscle cell spheroids was greatly enhanced. We show that FN III12–14 is a highly promiscuous ligand for GFs and also holds great potential in clinical healing applications. —Martino, M. M. , Hubbell, J. A. The 12th‐14th type III repeats of fibronectin function as a highly promiscuous growth factor binding domain. FASEB J. 24, 4711–4721 (2010). www.fasebj. org
Protein expression of UCP3 differs between human type 1, type 2a, and type 2b fibers

Uncoupling protein 3 (UCP3) dissipates energy as heat in human skeletal muscle, thus enhancing energy expenditure and affecting body mass. UCP3 has been associated with insulin resistance, obesity, sleeping metabolic rate, and transmitochondrial membrane transport of fatty acid anions. Factors affecting UCP3 gene‐expression include fatty acids and GLUT4 content (up‐regulation) and endurance exercise (equivocal reports). Fatty acid‐induced up‐regulation of UCP3 is most prominent in glycolytic fibers, whereas endurance training down‐regulates UCP3 in slow fibers. A direct comparison between muscle fiber type and UCP3 protein expression in human muscle is essential to explore the physiological role of UCP3 further. We combined immunofluorescence with conventional fiber typing to study concurrently fiber type and UCP3 expression in human vastus lateralis muscle of healthy controls and type 2 diabetics. Here, we report for the first time that, in controls, as in diabetics, UCP3 protein expression is most abundant in type 2b fibers, less in type 2a fibers, and only moderately expressed in type 1 fibers. Of the potential roles of UCP3 or factors regulating UCP3 expression, only a role of UCP3 in preventing oxidative stress completely matches the reported fiber‐type specific UCP3 expression. UCP3‐induced dissipation of energy may therefore serve multiple fiber‐type specific goals.
Effect of fruit maturity on the incidence of bitter pit, senescent breakdown, and other post-harvest disorders in ‘Honeycrisp’tm apple

Summary This study examined the effect of harvest date (fruit maturity) on the occurrence of post-harvest disorders in ‘Honeycrisp’tm apple (Malus × domestica Borkh.). Fruit were sampled from six commercial orchards in the Annapolis Valley, Nova Scotia, Canada over two growing seasons and seven (in 2008) or nine harvest dates (in 2009). After 3 months storage in refrigerated air at 3. 5ºC without delayed-cooling, soft scald, low temperature breakdown (LTB; also called soggy breakdown), bitter pit, and senescent breakdown developed in the fruit and the incidence of each varied with harvest date. Bitter pit developed in immature fruit and declined with harvest date, whereas senescent breakdown was non-existent in immature fruit and increased with harvest date. Minimum bitter pit plus senescent breakdown (combined) occurred at the mid-point of the harvest period (at approx. week-5), when internal ethylene was just beginning to appear in the fruit. An increase in fruit size (to ≥ 250 g) appeared to increase the occurrence of these two disorders. This study has shown that there is an optimum maturity (harvest date) in ‘Honeycrisp’tm apples, when the fruit are of sufficient size and colour to meet market requirements, with minimum risk of manifesting the two calcium-related disorders, bitter pit and senescent breakdown. The incidence of these two disorders may increase if fruit are picked earlier (bitter pit) or later (senescent breakdown), especially in larger fruit (≥ 250 g).
Reproductive Patterns of Pollicipes Pollicipes (Cirripedia: Scalpellomorpha) on the Southwestern Coast of Portugal

The brooding period of Pollicipes pollicipes on the southwestern coast of Portugal in 1991 began in March and extended to October, and was more intense from April-September. Brooding activity in small animals (12.5-15 mm, rostrocarinal distance, RC) was significantly less than in large animals (RC > 15 mm). Brooding activity patterns of this species were considered to be similar at different tidal levels and subtidally. Crowded animals brooded less than uncrowded animals, but results could have been confounded by the fact that only one site was considered. Individuals apparently produce asynchronous broods. Estimates of the annual number of broods varied between 1 (crowded animals), 1 or 2 (small, uncrowded animals), and 4 (large, uncrowded animals). Small animals (mean RC = 15.4 mm; 16,229 eggs) produced about half the number of eggs of large animals (mean RC = 19.6 mm; 34,172 eggs). Fecundity was considered to be a function of size (RC) (after logarithmic transformation; r2 = 0.62). A variable number of eggs was produced by animals of the same size; animals with an RC from 23-25 mm ranging from 30,000-130,000 eggs per brood. Fecundity patterns were considered similar in relation to tidal level, crowding, and time in the reproductive season.
Cell penetration by transportan

Transportan is a 27 amino acid‐long peptide containing 12 functional amino acids from the amino terminus of the neuropeptide galanin and mastoparan in the carboxyl terminus, connected via a lysine. Transportan is a cell‐penetrating peptide as judged by indirect immunofluorescence using Nε13‐biotinyl‐transportan. The internalization of biotinyl‐transportan is energy independent and takes place efficiently at 37°,4°, and 0°C. Cellular uptake of transportan is probably not mediated by endocytosis, since it cannot be blocked by treating the cells with phenylarsine oxide or hyperosmolar sucrose solution and is nonsaturable. The kinetics of internalization was studied with the aid of the 125I‐labeled peptide. At 37°C, the maximal intracellular concentration is reached in about 20 min. The internalized transportan is protected from trypsin. The cell‐penetrating ability of transportan is not restricted by cell type, but seems to be a general feature of this peptide. In Bowes' melanoma cells, transportan first localizes in the outer membrane and cytoplasmatic membrane structures. This is followed by a redistribution into the nuclear membrane and uptake into the nuclei where transportan concentrates in distinct substructures, probably the nucleoli. —Pooga, M. , Hällbrink, M. , Zorko, M. , Langel, Ü. Cell penetration of transportan FASEB J. 12, 67–77 (1998)
Biological and biochemical consequences of global deletion of exon 3 from the ERα gene

To address issues resulting from α estrogen receptor‐knockout (αERKO) residual N‐terminal truncated estrogen receptor α, and to allow tissue‐selective deletion of ERα, we generated loxP‐flanked exon 3 mice. Initial characterization of global sox2 cre‐derived exon 3‐deleted Ex3αERKO mice indicated no ERα protein in uterine tissue and recapitulation of previously described female phenotypes, confirming successful ablation of ERα. Body weights of Ex3αERKO female mice were 1.4‐fold higher than wild‐tupe (WT) females and comparable to WT males. Microarray indicated the Ex3αERKO uterus is free of residual estrogen responses. RT‐PCR showed Nr4a1 is increased 41‐fold by estrogen in WT and 7.4‐fold in αERKO, and not increased in Ex3αERKO. Nr4a1, Cdknlα, and c‐fos transcripts were evaluated in WT and Ex3αERKO mice following estrogen, IGF1, or EGF injections. All 3 were increased by all treatments in WT. None were increased by estrogen in Ex3αERKO. Nr4α1 increased 24.5‐ and 14.7‐fold, Cddknlα increased 14.2‐ and 12.3‐fold, and c‐fos increased 20.9‐fold and 16.2‐fold after IGF1 and EGF treatments, respectively, in the Ex3αERKO mice, confirming that growth factor regulation is independent of ERα. Our Ex3α ERα model will be useful in studies of complete or selective ablation of ERα in target tissues. —Hewitt, S. C. , Kissling, G. E. , Fieselman, K. E. , Jayes, F. L. , Gerrish, K. E. , Korach, K. S. Biological and biochemical consequences of global deletion of exon 3 from the ERα gene. FASEBJ. 24, 4660–4667 (2010). www.fasebj. org
Tetrazolium violet staining of naturally and artificially moulded sorghum (Sorghum bicolor (L.) Moench) caryopses.

Sorghum grain mould (GM) is a yield-limiting disease characterized by damage to caryopsis embryo tissues. Caryopses were obtained from naturally weathered (n.w.) panicles and panicles inoculated with Fusarium thapsinum (FT) and Curvularia lunata (CL) at anthesis. Caryopses were assayed for tetrazolium violet (TZ) viability, embryo damage, germination, and pathogen isolation. In n.w. and artificially inoculated (a.i.) caryopses, Tx430 (GM-susceptible) showed low whole embryo TZ viability, whereas Sureno and Tx2911 (GMresistant) showed higher values. Tx430 had the greatest levels of non-staining scutellum, coleoptile, plumule, radicle tissues, non-staining tissues and damaged embryos under both inoculation regimes. In n.w. grain, TZ staining overestimated germination for some genotypes (especially Tx430), whereas TZ staining underestimated germination in most a.i. material. Correlations between TZ viability and germination were positive and significant for n.w. and a.i. caryopses. FT and F. proliferatum (FP) were the most commonly isolated fungi from n.w. grain. Correlations between yellow-pigmented-FT, FP, and CL incidence from sorghum caryopses and TZ viability were negative and significant. This study showed that TZ viability differs in a genotype- and pathogendependent manner. Therefore, this approach will have utility in screening sorghum germplasm for grain mould resistance at the whole embryo and tissue level.
Introduction

This issue of Hemodialysis International exemplifies the growth of the International Society for Hemodialysis and the enthusiasm and interest of scholars in hemodialysis to participate in this exciting educational effort. We are now including four regular features in each issue of Hemodialysis International: a scholarly review written by a leading authority and covering topics of current interest in hemodialysis; a trainee’s forum written by and for nephrology trainees that will provide important information for readers on the specific topic as well as a description of the training program itself; a core curriculum article that will, over time, fill the gaps in current training programs in the area of dialysis; and a clinical care section (starting in the April issue), described on the next page, that will offer opportunities for nonphysicians to publish articles for the entire dialysis care delivery team. The articles in each of these sections undergo peer review, as do original research articles, and are of the high quality typifying Hemodialysis International. This issue of Hemodialysis International also contains abstracts from the upcoming annual dialysis conference. This conference continues to be an outstanding opportunity for learning new concepts and approaches to patient care in dialysis and one that continues to work closely with Hemodialysis International and the International Society for Hemodialysis. I welcome your comments and suggestions for Hemodialysis International and we hope you enjoy the journal and find it of value in 2005.
Plasminogen stimulates propagation of protease‐resistant prion protein in vitro

To clarify the role of plasminogen as a cofactor for prion propagation, we conducted functional assays using a cell‐free prion protein (PrP) conversion assay termed protein misfolding cyclic amplification (PMCA) and prion‐infected cell lines. Here, we report that plasminogen stimulates propagation of the protease‐resistant scrapie PrP (PrPSc). Compared to control PMCA conducted without plasminogen, addition of plasminogen in PMCA using wild‐type brain material significantly increased PrP conversion, with an EC50 = ~56 nM. PrP conversion in PMCA was substantially less efficient with plasminogen‐deficient brain material than with wild‐type material. The activity stimulating PrP conversion was specific for plasminogen and conserved in its kringle domains. Such activity was abrogated by modification of plasminogen structure and interference of PrP‐plasminogen interaction. Kinetic analysis of PrPSc generation demonstrated that the presence of plasminogen in PMCA enhanced the PrPSc production rate to −0.97 U/µl/h and reduced turnover time to ~1 h compared to those (~0.4 U/µl/h and ~2.5 h) obtained without supplementation. Furthermore, as observed in PMCA, plasminogen and kringles promoted PrPSc propagation in ScN2a and Elk 21+ cells. Our results demonstrate that plasmino‐gen functions in stimulating conversion processes and represents the first cellular protein cofactor that enhances the hypothetical mechanism of prion propagation. —Mays, C. E. , Ryou, C. Plasminogen stimulates propagation of protease‐resistant prion protein in vitro. FASEB J. 24, 5102–5112 (2010). www.fasebj. org
Infection by human varicella‐zoster virus confers norepinephrine sensitivity to sensory neurons from rat dorsal root ganglia

Varicella‐zoster virus (VZV) is a widespread human herpes virus causing chicken pox on primary infection and persisting in sensory neurons. Reactivation causes shingles, which are characterized by severe pain and often lead to postherpetic neuralgia. To elucidate the mechanisms of VZV‐associated hyperalgesia, we elaborated an in vitro model for the VZV infection of sensory neurons from rat dorsal root ganglia. Between 35 and 50% of the neurons showed strong expression of the immediate‐early virus antigens IE62 and IE63 and the late glycoprotein gE. When the intracellular calcium concentration was monitored microfluorometrically for individual cells after infection, the sensitivity to GABA or capsaicin was similar in controls and in VZV‐infected neurons. However, the baseline calcium concentration was increased. Neurons became de novo sensitive to adrenergic stimulation after VZV infection. Norepinephrine‐responsive neurons were more frequent and calcium responses to norepinephrine were significantly higher after infection with wild‐type isolates than with the attenuated vaccine strain OKA. The adrenergic agonists phenylephrine and isoproterenol had similar efficacy. We suggest that the infection with wild‐type VZV isolates confers norepinephrine sensitivity to sensory neurons by using α1‐and/or β1‐adrenergic receptors providing a model for the pathophysiology of the severe pain associated with the acute reactivation of VZV. —Kress, M. , Fickenscher, H. Infection by human varicella‐zoster virus confers norepinephrine sensitivity to sensory neurons from rat dorsal root ganglia. FASEB J. 15, 1037–1043 (2001)