Miracle-dz/UniFAR-FTUs huggingface dataset:
Home range and survival of breeding painted buntings on Sapelo Island, Georgia

Abstract The southeastern United States population of the painted bunting (Passerina ciris) has decreased approximately 75% from 1966–1996 based on Breeding Bird Survey trends. Partners in Flight guidelines recommend painted bunting conservation as a high priority with a need for management by state and federal agencies. Basic information on home range and survival of breeding painted buntings will provide managers with required habitat types and estimates of land areas necessary to maintain minimum population sizes for this species. We radiotracked after-second-year male and after-hatching-year female buntings on Sapelo Island, Georgia, during the breeding seasons (late April–early August) of 1997 and 1998. We used the animal movement extension in ArcView to determine fixed-kernel home range in an unmanaged maritime shrub and managed 60–80-year-old pine (Pinus spp.)–oak (Quercus spp.) forest. Using the Kaplan-Meier method, we estimated an adult breeding season survival of 1.00 for males (n = 36) and 0.94 (SE = 0.18) for females (n = 27). Painted bunting home ranges were smaller in unmanaged maritime shrub (female: kernel x̄ = 3.5 ha [95% CI: 2.5–4.5]; male: kernel x̄ = 3.1 ha [95% CI: 2.3–3.9]) compared to those in managed pine–oak forests (female: kernel x̄ = 4.7 ha [95% CI: 2.8–6.6]; male: kernel x̄ = 7.0 ha [95% CI: 4.9–9.1]). Buntings nesting in the managed pine–oak forest flew long distances (≥300 m) to forage in salt marshes, freshwater wetlands, and moist forest clearings. In maritime shrub buntings occupied a compact area and rarely moved long distances. The painted bunting population of Sapelo Island requires conservation of maritime shrub as potential optimum nesting habitat and management of nesting habitat in open-canopy pine–oak sawtimber forests by periodic prescribed fire (every 4–6 years) and timber thinning within a landscape that contains salt marsh or freshwater wetland openings within 700 m of those forests.
Forward genetics to identify Listeria monocytogenes components that activate mammalian cytosolic surveillance pathways

Author(s): Witte, Chelsea Elaine | Advisor(s): Portnoy, Daniel A | Abstract: Listeria monocytogenes is Gram-positive facultative intracellular pathogen that is ubiquitously present in the environment. During infection, L. monocytogenes is phagocytosed by host cells and then rapidly escapes from the phagosome into the host cytosol. In the cytosol the bacterium is able to replicate and spread to neighboring cells without leaving the intracellular compartment. Maintenance of the intracellular niche is critical for L. monocytogenes pathogenesis, but there have been several reports indicating cytosolic bacteria can induce inflammasome-mediated host cell death. Additionally, our laboratory previously identified a host transcriptional profile induced by L. monocytogenes upon entry into the cytosol termed the cytosolic surveillance pathway, characterized by the robust upregulation of IFN-beta; and co-regulated genes. Although the host components of the signaling pathways leading to cell death and IFN-beta; production are becoming better defined, the bacterial ligands were largely unknown. To gain insight into the bacterial components and ligands required for stimulation of these two pathways, we performed a forward genetic screen and isolated mutants that affected induction of host cell death and/or IFN-beta. We identified a transposon insertion in lmo2473 that caused hyperstimulation of inflammasome-mediated cell death, pyroptosis. Further characterization revealed these mutants, and to a lesser extent wild-type L. monocytogenes, lysed in the macrophage cytosol. Intracellular bacteriolysis released bacterial DNA that was detected by the cytosolic DNA sensor AIM2 to trigger pyroptosis. Tight regulation of other bacterial factors capable of stimulating inflammasomes, such as flagellin, likely contribute to the low levels of pyroptosis induced by L. monocytogenes. We also isolated a mutant that harbored a transposon insertion in the gene lmo0052, renamed pdeA. Biochemical characterization of the gene product determined PdeA was a cyclic di-AMP phosphodiesterase. Inactivation of this protein resulted in accumulation of the nucleotide and increased stimulation of IFN-beta;. As cyclic di-AMP was only recently identified as a bacterial second messenger, we used mutants that modulate enzymatic processing of c-di-AMP to interrogate the role of its signaling in L. monocytogenes physiology and pathogenesis. This work implicates c-di-AMP, not only as the IFN-beta;-stimulatory ligand, but also as a critical molecule involved in bacterial growth, response to stress, and cell wall stability. In summary, using a forward genetic approach, we have identified mechanisms by which host cells recognize and respond to L. monocytogenes invasion of the cytosol. Other mutants isolated in this screen merit further characterization to potentially unveil additional bacterial components involved in these responses.
Shiga Toxin Selectively Upregulates Expression of Syndecan-4 and Adhesion Molecule ICAM-1 in Human Glomerular Microvascular Endothelium

Hemolytic uremic syndrome (HUS) is a severe renal disease that is often preceded by infection with Shiga toxin (Stx)-producing Escherichia coli (STEC). The exact mechanism of Stx-mediated inflammation on human glomerular microvascular endothelial cells (HGMVECs) during HUS is still not well understood. In this study, we investigated the effect of Stx1 on the gene expression of proteins involved in leucocyte-mediated and complement-mediated inflammation. Our results showed that Stx1 enhances the mRNA and protein expression of heparan sulfate proteoglycan (HSPG) syndecan-4 in HGMVECs pre-stimulated with tumor necrosis factor α (TNFα). CD44 was upregulated on mRNA but not on protein level; no effect on the mRNA expression of other tested HSPGs glypican-1 and betaglycan was observed. Furthermore, Stx1 upregulated the mRNA, cell surface expression, and supernatant levels of the intercellular adhesion molecule-1 (ICAM-1) in HGMVECs. Interestingly, no effect on the protein levels of alternative pathway (AP) components was observed, although C3 mRNA was upregulated. All observed effects were much stronger in HGMVECs than in human umbilical endothelial cells (HUVECs), a common model cell type used in endothelial studies. Our results provide new insights into the role of Stx1 in the pathogenesis of HUS. Possibilities to target the overexpression of syndecan-4 and ICAM-1 for STEC-HUS therapy should be investigated in future studies.
Nanostructured Chitosan/Maghemite Composites Thin Film for Potential Optical Detection of Mercury Ion by Surface Plasmon Resonance Investigation

In this study, synthesis and characterization of chitosan/maghemite (Cs/Fe2O3) composites thin film has been described. Its properties were characterized using Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM) and ultraviolet-visible spectroscopy (UV-Vis). FTIR confirmed the existence of Fe–O bond, C–N bond, C–C bond, C–O bond, O=C=O bond and O–H bond in Cs/Fe2O3 thin film. The surface morphology of the thin film indicated the relatively smooth and homogenous thin film, and also confirmed the interaction of Fe2O3 with the chitosan. Next, the UV-Vis result showed high absorbance value with an optical band gap of 4.013 eV. The incorporation of this Cs/Fe2O3 thin film with an optical-based method, i.e., surface plasmon resonance spectroscopy showed positive response where mercury ion (Hg2+) can be detected down to 0.01 ppm (49.9 nM). These results validate the potential of Cs/Fe2O3 thin film for optical sensing applications in Hg2+ detection.
A Mixed-Surface Polyamidoamine Dendrimer for In Vitro and In Vivo Delivery of Large Plasmids

Drug delivery to the brain is highly hindered by the presence of the blood–brain barrier (BBB), which prevents the entry of many potential drugs/biomolecules into the brain. One of the current strategies to achieve gene therapy for neurodegenerative diseases involves direct injection of a viral vector into the brain. There are various disadvantages of viral vectors, including limitations of cargo size and safety concerns. Nanomolecules, such as dendrimers, serve as an excellent alternative to viral delivery. In this study, as proof-of-concept, we used a surface-modified dendrimer complex and delivered large plasmids to cells in vitro and in vivo in healthy rats via intracranial injection. The dendrimers were biodegradable by chemicals found within cells and toxicity assays revealed that the modified dendrimers were much less toxic than unmodified amine-surface dendrimers. As mentioned in our previous publication, these dendrimers with appropriately modified surfaces are safe, can deliver large plasmids to the brain, and can overcome the cargo size limitations associated with viral vectors. The biocompatibility of this dendritic nanomolecule and the ability to finely tune its surface chemistry provides a gene delivery system that could facilitate future in vivo cellular reprograming and other gene therapies.
Neopapillarine, an Unusual Coumarino-Alkaloid from the Root Extract of Neocryptodiscus papillaris with Cytotoxic Activity on Renal Cancer Cells

Several simple and prenylated coumarin derivatives were isolated from the dichloromethane extract of the root of Neocryptodiscus papillaris based on moderate cytotoxic activity of the extract in COLO205, KM12 and MCF7 cancer cells. While the major prenylated furanocoumarin derivatives and osthol isolated from the dichloromethane extract were responsible for the activity in the colon and breast cancer cell lines, the 4′-acylated osthol derivatives including a novel coumarino-alkaloid; neopapillarine) demonstrated selective cytotoxic activity in A498 and UO31 renal cancer cell lines.
Phytochemical Evolution: The Redox Theory

Abstract Evolution of secondary metabolites in angiosperms is postulated to imply superposition of 1. stepwise abandonment of the intermediates of the shikimate pathway and their replacement by the intermediates of the acetate routes as biosynthetic precursors, and 2. gradual replacement of polyphenols by intermediate metabolites within binary antioxidant systems for the regulation of the oxidation level.
Effects of biofloc under different carbon sources and protein levels on water quality, growth performance and immune responses in black tiger shrimp Penaeus monodon (Fabricius, 1978)

A 75-day 2 × 3 factorial experiment was conducted to evaluate the effect of two levels of dietary protein (32 and 40%) and two different carbon sources (rice flour–R and molasses-M), and without carbohydrate (control–C) in black tiger shrimp Penaeus monodon juveniles (3.37 ± 0.04 g) at 100 nos. m−3 in 100 L fibre reinforced plastic tanks. Biofloc volume and total suspended solid were higher in molasses added groups (32 + M and 40 + M) followed by rice flour (32 + R and 40 + R) and controls (32C and 40C). Molasses and rice flour addition significantly reduced (P < 0.01) the total ammonia–N compared to controls. The highest Vibrio, Bacillus and Lactobacillus counts were recorded in 40 + M, 32 + M and 32 + R respectively. Among the treatments, significantly higher (P < 0.01) final body weight was recorded in 40 + R (8.5 ± 0.3 g), 40 + M (7.8 ± 0.3 g) and 32 + R (7.5 ± 0.4 g) compared to control groups, 32C (6.1 ± 0.3 g), 40C (6.4 ± 0.3 g) and molasses added group, 32 + M (5.7 ± 0.4 g). Rice flour supplementation significantly increased (P < 0.01) the total haemocyte count (×106 cells mL−1) in 32 + R (45.7 ± 3.7) and 40 + R (44.3 ± 3.1) compared to controls, 32C (27.3 ± 3.4) and 40C (25.8 ± 0.9). Similarly, higher superoxide dismutase, catalase, serum protein and glucose were recorded in the rice flour added groups, 40 + R followed by 32 + R. Among the treatments, the highest level of prophenoloxidase (OD 490 nm, 0.3 ± 0.0) and survival after challenge with Vibrio harveyi (55.6%) was observed in 32 + R. The study elucidates that rice flour addition produces optimum level of biofloc with better growth and immune responses compared to molasses and control. Furthermore, rice flour addition at 32% protein level could replace 40% protein feed.
A METHOD TO LOCATE BAD DATA IN LARGE POWER SYSTEM USING DISTRIBUTED APPROACH

: It is essential to determine the presence of bad data in power system networks and to identify the reasonable meters which cause bad data error. In this paper, a distributed approach is adopted which enables distribution of complex system network into different area and apply meter identification procedures separately in each area. The reasonable meters identified using individual error determination technique after grouping into distributed areas. It improves sensitivity as well as reliable detection of bad data along with locating the affected meters. The system works with MATLAB platform to verify meter identification.
Genetic analyses of non-native species Oithona davisae Ferrari F.D. & Orsi, 1984 in the Black Sea

A non-native species of the cyclopoid copepod in the genus Oithona was first recorded in the Black Sea in 2001 and was initially identified as Oithona brevicornis Giesbrecht, 1891. During the following years, this species became widely distributed first in the coastal then in the open areas of the Black Sea and later spread into the adjacent Sea of Azov through the Kerch Strait. Recent detailed re-examination of morphological features of this Oithona species indicated it is not O. brevicornis, but may be O. davisae Ferrari F.D. & Orsi, 1984 or perhaps one of the other species similar to O. brevicornis. This study examined the morphological features of this Oithona species collected from sites in the western and northeastern Black Sea, and genetic analyses were performed on specimens collected in the western Black Sea to clarify its identification. While we concluded the non-native species was not O. brevicornis or any of the native Oithona species, the lack of information on Oithona davisae in GenBank precludes definitive identification of taxonomic status. Additional genetic data are needed on O. davisae collected from its native and non-native range to allow definitive identification of specimens of this non-native species.
Convolutional Neural Network and Motor Current Signature Analysis during the Transient State for Detection of Broken Rotor Bars in Induction Motors

Although induction motors (IMs) are robust and reliable electrical machines, they can suffer different faults due to usual operating conditions such as abrupt changes in the mechanical load, voltage, and current power quality problems, as well as due to extended operating conditions. In the literature, different faults have been investigated; however, the broken rotor bar has become one of the most studied faults since the IM can operate with apparent normality but the consequences can be catastrophic if the fault is not detected in low-severity stages. In this work, a methodology based on convolutional neural networks (CNNs) for automatic detection of broken rotor bars by considering different severity levels is proposed. To exploit the capabilities of CNNs to carry out automatic image classification, the short-time Fourier transform-based time–frequency plane and the motor current signature analysis (MCSA) approach for current signals in the transient state are first used. In the experimentation, four IM conditions were considered: half-broken rotor bar, one broken rotor bar, two broken rotor bars, and a healthy rotor. The results demonstrate the effectiveness of the proposal, achieving 100% of accuracy in the diagnosis task for all the study cases.
Reproducible Large-Scale Isolation of Exosomes from Adipose Tissue-Derived Mesenchymal Stem/Stromal Cells and Their Application in Acute Kidney Injury

Acute kidney injury (AKI) is a fatal medical episode caused by sudden kidney damage or failure, leading to the death of patients within a few hours or days. Previous studies demonstrated that exosomes derived from various mesenchymal stem/stromal cells (MSC-exosomes) have positive effects on renal injuries in multiple experimental animal models of kidney diseases including AKI. However, the mass production of exosomes is a challenge not only in preclinical studies with large animals but also for successful clinical applications. In this respect, tangential flow filtration (TFF) is suitable for good manufacturing practice (GMP)-compliant large-scale production of high-quality exosomes. Until now, no studies have been reported on the use of TFF, but rather ultracentrifugation has been almost exclusively used, to isolate exosomes for AKI therapeutic application in preclinical studies. Here, we demonstrated the reproducible large-scale production of exosomes derived from adipose tissue-derived MSC (ASC-exosomes) using TFF and the lifesaving effect of the ASC-exosomes in a lethal model of cisplatin-induced rat AKI. Our results suggest the possibility of large-scale stable production of ASC-exosomes without loss of function and their successful application in life-threatening diseases.
Three-Dimensional Radiographic Outcome of Free-Handed Flaplessly Placed Mini Dental Implants in Edentulous Maxillae after 2-Years Function

Background: Free-handed, flaplessly placed mini dental implants (MDIs) are a valuable, more affordable and minimally invasive treatment to support overdentures in fully edentulous jaws, especially for medically compromised patients. However, critical 3D radiographic evaluation is lacking. This multicenter prospective case series assessed clinical outcome and carried out 3D- cone-beam computerized tomography (CBCT) analysis of free-handed flaplessly placed one-piece maxillary MDIs by an experienced maxillofacial surgeon. Methods: Thirty-one patients suffering from an ill-fitting maxillary denture relating to compromised bone volume (as confirmed on CBCT), with a dentate mandible, were selected. They received 5–6 MDIs free-hand flaplessly placed and mentally guided with preoperative CBCT. Final connection and attachment activation took place six months later. After two years each implant was individually assessed with CBCT for perforations on eight sites. Implant survival, prosthetic failure, clinical stability and sinus/nasal complaints were registered after three years. Results: 32/185 (17.3%) MDIs failed during the provisional loading with non-activated attachments; 17 replacements in 10 patients were performed. Of the 170 actively loaded 170 MDIs, 82.3% survived and 27/31 prostheses (87%) were fully functional. In total 98/170 MDIs showed no perforation. Based on 1360 CBCT observations, 231 perforations (16.9%) were registered. Of most perforations 37 (25%) were observed at the apical tip and 37 were positioned (21%) into the sinus/nasal cavity, although without clinical complaints. Conclusions: Given the compromised population, the minimally invasive procedure and the low treatment cost involved, a failure rate of 17% is substantial, however clinically acceptable given the critical bone condition. However, even in experienced surgical hands, freehanded and flapless placement yield a high risk for implant perforation, although this did not necessarily lead to complications.
Selling the role of salvage: Cell salvage past and present

The use of transfused blood, be it from an allogenic (donor) or autologous (same patient) source, is not a new treatment and in fact has been experimented with since the mid 1800s. The role of cell salvage and re-infusion of a patient’s own blood, however, has only begun to gain real popularity in the last 20 years, after the undertaking of several large scale meta-analyses which have shown that not only is autologous transfusion no less efficacious when compared to allogenic transfusion, but also potentially safer for a number of reasons. Autologous transfusion is also more cost effective overall and potentially quicker to initiate in an emergency situation. Despite the body of evidence to support the use of salvaged blood for transfusion, hesitation around its use still persists, with staff apprehension around set up of cell salvage equipment and general underestimation of intraoperative blood loss being key factors in its underuse.
Favorable Outcomes of Liver Transplantation from Controlled Circulatory Death Donors Using Normothermic Regional Perfusion Compared to Brain Death Donors

Background. Liver transplantation (LT) from controlled donation after circulatory death (cDCD) was initiated in France in 2015 under a protocol based on the use of normothermic regional perfusion (NRP) before organ procurement. The aim was to compare outcomes following cDCD LT with NRP and donation after brain death (DBD) LT. Methods. This is a multicenter retrospective study comparing cDCD LT with NRP and DBD LT. A case-matched study (1:2) was performed using the variables such as recipient and donor age, indication of LT. Results. A total of 50 patients from the cDCD group were matched to 100 patients from the DBD group. From postoperative days 1–4, serum transaminase release was significantly lower in the cDCD group compared to the DBD group (P < 0.05). Early allograft dysfunction (cDCD: 18% versus DBD: 32%; P = 0.11), acute kidney injury (26% versus 33%; P = 0.49), 90-d graft loss (2% versus 5%; P = 0.66), and arterial (4% versus 12%; P = 0.19) and biliary (16% versus 17%; P = 0.94) complications were similar between the 2 groups. The 2-y graft survival was 88% for cDCD group and 85% for DBD group (P = 0.91). The 2-y patient survival was 90% for cDCD group and 88% for DBD group (P = 0.68). Conclusions. This study provides evidence that cDCD LT following postmortem NRP can be safely and effectively performed in selected recipients with similar graft and patient survival outcomes, without increased rates of biliary complications and early graft dysfunction compared to DBD LT.
Natural variations in SlSOS1 contribute to the loss of salt tolerance during tomato domestication

Soil salinity is a major constraint on crop cultivability and productivity worldwide (Shabala 2013). The ion toxicity caused by high salinity is alleviated by the adjustment of cellular Na+ and K+ homeostasis through the functions of ion transporters such as SOS1 (Salt Overly Sensitive 1) and HKT1 (High-Affinity Potassium Transporter 1). SOS1 is a plasma membrane Na+ /H+ antiporter mediating Na+ extrusion in root epidermal cells to reduce Na+ accumulation in plants and in the parenchyma cells of root and shoot xylems to promote Na+ translocation from root to shoot, whereas the Na+ transporter HKT1 mediates retrieval of Na+ from the xylem and may contribute to Na+ recirculation from shoot to root (Zhu 2016). Natural variations in HKT1 have been implicated in salt tolerance in several plant species (An et al. 2017). However, the role of natural variations in SOS1 in adaptation to salt stress have not been reported.