Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Herring Bait to Farm Lobsters in the Gulf of Maine

Background Ecologists, fisheries scientists, and coastal managers have all called for an ecosystem approach to fisheries management, yet many species such as the American lobster (Homarus americanus) are still largely managed individually. One hypothesis that has yet to be tested suggests that human augmentation of lobster diets via the use of Atlantic herring (Clupea harengus) as bait may contribute to recent increases in lobster landings. Currently 70% of Atlantic herring landings in the Gulf of Maine are used as bait to catch lobsters in traps throughout coastal New England. Methodology/Principal Findings We examined the effects of this herring bait on the diet composition and growth rate of lobsters at heavily baited vs. seasonally closed (i.e., bait free) sites in coastal Maine. Our results suggest that human use of herring bait may be subsidizing juvenile lobster diets, thereby enhancing lobster growth and the overall economic value and yield of one of the most valuable fisheries in the U.S. Conclusions/Significance Our study illustrates that shifting to an ecosystem approach to fisheries management should require consideration of cross-fishery interactions.
Streptolysin-induced endoplasmic reticulum stress promotes group A streptococcal in vivo biofilm formation and necrotizing fasciitis

Group A Streptococcus (GAS) is a human pathogen that causes infections ranging from mild to fulminant and life-threatening. Biofilms have been implicated in acute GAS soft-tissue infections such as necrotizing fasciitis (NF). However, most in vitro models used to study GAS biofilms have been designed to mimic chronic infections and insufficiently recapitulate in vivo conditions and the host-pathogen interactions that might influence biofilm formation. Here we establish and characterize an in vitro model of GAS biofilm development on mammalian cells that simulates microcolony formation observed in a murine model of human NF. We show that on mammalian cells, GAS forms dense aggregates that display hallmark biofilm characteristics including a three-dimensional architecture and enhanced tolerance to antibiotics. In contrast to abiotic-grown biofilms, host-associated biofilms require the expression of secreted GAS streptolysins O and S (SLO, SLS) resulting in the release of a host-associated biofilm promoting-factor(s). Supernatants from GAS-infected mammalian cells or from cells treated with endoplasmic reticulum (ER) stressors restore biofilm formation to an SLO and SLS null mutant that is otherwise attenuated in biofilm formation on cells, together suggesting a role for streptolysin-induced ER stress in this process. In an in vivo mouse model, the streptolysin-null mutant is attenuated in both microcolony formation and bacterial spread, but pre-treatment of softtissue with an ER-stressor restores the ability of the mutant to form wild type like microcolonies that disseminate throughout the soft tissue. Taken together, we have identified a new role of streptolysin-driven ER stress in GAS biofilm formation and NF disease progression. Significance Statement Although it is well-accepted that bacterial biofilms are associated with many chronic infections, little is known about the mechanisms by which group A Streptococcus (GAS) biofilms contribute to acute soft tissue-invasive diseases like necrotizing fasciitis (NF). In this study, we establish a physiologically relevant in vitro model to study GAS biofilm formation on mammalian cells and validate our findings in a mouse model that mimics human NF. This study demonstrates a novel role of GAS streptolysin-mediated ER stress in the development and spread of GAS biofilms in acute softtissue infections. We also show that biofilm formation depends on the release of a host-associated factor that promotes microcolony formation and GAS dissemination in vivo.
Non-clinical adolescent girls at risk of eating disorder: under-reporters or restrained eaters?

BACKGROUND To evaluate the plausibility of self-reported energy intake, Goldberg et al proposed a technique to identify the miss-reporters. SUBJECTS After screening 2,967 adolescents by EAT-40 test, 132 at risk of ED and 151 as a control group were studied. AIM To determine whether subjects at risk of eating disorders that are identified as under reporters can be considered as UR or in turn as restrained eaters. METHODS We determined dietary energy intake, body mass index, body satisfaction, physical activity, psychopathology, dietary restraint factor, weight loss and diagnoses of eating disorders. We applied Goldberg's equations to identify under reporters. RESULTS 40.9% of girls at risk of eating disorders were identified as under reporters and only 7.3% were in the control group. A total of 64.4% of the Eating Disorders Not Otherwise Specified were under reporters. The body mass index of under reporters was significantly higher than in the other of subjects regardless of whether they were at risk of eating disorders. Girls at risk of eating disorders and under reporter had significantly lower body satisfaction than other groups. Multiple logistic regressions in all subjects showed that the risk of being UR was associated with an increase in the body mass index, increase in dietary restraint scores and weight loss; whereas, that only the body mass index was associated with the control group. CONCLUSION The prevalence of under reporter increases with the severity of the eating disorders several adolescent girls at risk of eating disorder and identified by Goldberg cut-off technique as under reporter may to be restricting their intake and therefore they would not be under reporter.
Comparative Analysis of RNAi-Based Methods to Down-Regulate Expression of Two Genes Expressed at Different Levels in Myzus persicae

With the increasing availability of aphid genomic data, it is necessary to develop robust functional validation methods to evaluate the role of specific aphid genes. This work represents the first study in which five different techniques, all based on RNA interference and on oral acquisition of double-stranded RNA (dsRNA), were developed to silence two genes, ALY and Eph, potentially involved in polerovirus transmission by aphids. Efficient silencing of only Eph transcripts, which are less abundant than those of ALY, could be achieved by feeding aphids on transgenic Arabidopsis thaliana expressing an RNA hairpin targeting Eph, on Nicotiana benthamiana infected with a Tobacco rattle virus (TRV)-Eph recombinant virus, or on in vitro-synthesized Eph-targeting dsRNA. These experiments showed that the silencing efficiency may differ greatly between genes and that aphid gut cells seem to be preferentially affected by the silencing mechanism after oral acquisition of dsRNA. In addition, the use of plants infected with recombinant TRV proved to be a promising technique to silence aphid genes as it does not require plant transformation. This work highlights the need to pursue development of innovative strategies to reproducibly achieve reduction of expression of aphid genes.
Bipolar disorder and neurophysiologic mechanisms

Recent studies have suggested that some variants of bipolar disorder (BD) may be due to hyperconnectivity between orbitofrontal (OFC) and temporal pole (TP) structures in the dominant hemisphere. Some initial MRI studies noticed that there were corpus callosum abnormalities within specific regional areas and it was hypothesized that developmentally this could result in functional or effective connectivity changes within the orbitofrontal-basal ganglia-thalamocortical circuits. Recent diffusion tensor imaging (DTI) white matter fiber tractography studies may well be superior to region of interest (ROI) DTI in understanding BD. A “ventral semantic stream” has been discovered connecting the TP and OFC through the uncinate and inferior longitudinal fasciculi and the elusive TP is known to be involved in theory of mind and complex narrative understanding tasks. The OFC is involved in abstract valuation in goal and sub-goal structures and the TP may be critical in binding semantic memory with person–emotion linkages associated with narrative. BD patients have relative attenuation of performance on visuoconstructional praxis consistent with an atypical localization of cognitive functions. Multiple lines of evidence suggest that some BD alleles are being selected for which could explain the enhanced creativity in higher-ability probands. Associations between ROI’s that are not normally connected could explain the higher incidence of artistic aptitude, writing ability, and scientific achievements among some mood disorder subjects.
Improved Dynamic Regret for Non-degenerate Functions

Recently, there has been a growing research interest in the analysis of dynamic regret, which measures the performance of an online learner against a sequence of local minimizers. By exploiting the strong convexity, previous studies have shown that the dynamic regret can be upper bounded by the path-length of the comparator sequence. In this paper, we illustrate that the dynamic regret can be further improved by allowing the learner to query the gradient of the function multiple times, and meanwhile the strong convexity can be weakened to other non-degenerate conditions. Specifically, we introduce the squared path-length, which could be much smaller than the path-length, as a new regularity of the comparator sequence. When multiple gradients are accessible to the learner, we first demonstrate that the dynamic regret of strongly convex functions can be upper bounded by the minimum of the path-length and the squared path-length. We then extend our theoretical guarantee to functions that are semi-strongly convex or self-concordant. To the best of our knowledge, this is the first time that semi-strong convexity and self-concordance are utilized to tighten the dynamic regret.
A Layered Analysis of Consensus

This paper introduces a simple notion of layering as a tool for analyzing well-behaved runs of a given model of distributed computation. Using layering, a model-independent analysis of the consensus problem is performed and then applied to proving lower bounds and impossibility results for consensus in a number of familiar and less familiar models. The proofs are simpler and more direct than existing ones, and they expose a unified structure to the difficulty of reaching consensus. In particular, the proofs for the classical synchronous and asynchronous models now follow the same outline. A new notion of connectivity among states in runs of a consensus protocol, called potence connectivity, is introduced. This notion is more general than previous notions of connectivity used for this purpose and plays a key role in the uniform analysis of consensus.
Effect of Music Therapy Intervention in Acute Postoperative Pain among Obese Patients

Background: Postoperative pain is an uncomfortable situation in the critical period of surgical recovery. Often, pain maybe increase stress response, abnormal vital sings and sleep disorders or maybe act as an appetite suppressant. Music therapy is described as non pharmaceutical intervention to accomplish individualized patients’ goals for hospital treatment. Aims: To determine the effect of music therapy in postoperative pain among obese patients who underwent a major abdomen surgery. Methodology: A prospective randomized clinical trial was conducted in a tertiary hospital, with a before and after intervention measurement. Data were collected from overweight or obese postoperative patients (n=87), who were randomly separated in two groups, the “music therapy” group (n1=45), and the “non music therapy” group (n2=42 subjects). Visual Analogue Scale (VAS) was used for pain perception. The period of the study was 3 months (from Jan 2012 to March 2012). Results: The patients in two groups had normal mean values in heart rate, respiration rate and SpO2, before and after the intervention, without any special abnormalities. Those patients who received music therapy, twice postoperatively, referred more decreased Δ-VAS score = -1.78 units (VAS after – VAS before: 2.64 4.42), in compare to the non-music patients group, which their Δ-VAS score was less decreased, only for -0.22 units (VAS after VAS before: 3.76 3.98). From all study variables, only “Mean Arterial Pressure” and “VAS” were found to be affected by the music therapy intervention. Conclusions: It seems that implementing music therapy in the acute postoperative period may be a useful intervention tool, in order to promote patients’ comfort and more tolerable perception against pain. Nurses are able to use this method, in daily clinical practice as a supplementary tool with the standard combination of analgesics.
Effects of Lateral Bracing and Stiffeners on the CFRP Failure of Strengthened Steel Beams

In this paper, the effects of lateral bracing and web stiffeners on the Carbon Fibre Reinforced Polymer (CFRP) failure modes and buckling strength of the CFRP strengthened wide-flange steel I-beams are investigated experimentally. The study consisted of eight beams tested under static gradual load until failure. The main test variables were steel plate stiffeners, lateral bracings, and bonding of CFRP plates to beam soffits. The results showed that the use of steel plate stiffeners did not only prevent stress concentration below the point load, but it could also help to delay debonding of the externally bonded CFRP plate. The use of lateral bracing indicated a significant effect in preventing the CFRP splitting failure mode. In addition, the use of stiffeners with lateral bracing simultaneously, showed improvement in the in-plane flexural strength, stiffness and ductility of the CFRP strengthened I-beams.
Synthesis, Characterization, and Antimicrobial Activity of a Novel Trisazo Dye from 3-Amino-4H-thieno[3,4-c][1]benzopyran-4-one

A new trisazo dye has been synthesized by coupling the diazonium ion of 3-amino-4H thieno[3,4-c][1]benzopyran-4-one with 2-tert-butyl-4-methoxyphenol. The newly prepared trisazo dye was characterized by its physical, elemental, and spectroscopic data. 2D-NMR (COSY, HSQC, and HMBC) techniques were used to secure the structural assignments. The new trisazo dye (compound 7) along with precursors 3, 4, and 6 was screened by microdilution susceptibility assay for antibacterial and antifungal activities towards eight bacterial strains and three yeasts selected on the basis of their relevance as human pathogens. The results showed that compound 7 (MIC = 2–128 μg/mL) was the most active as compared with its precursors. The most resistant microorganisms were V. cholerae NB2 and V. cholerae SG24, whereas the most sensitive microorganism was C. neoformans. The overall results of this study indicated that compound 7 had the greatest potential value against both yeasts and multidrug-resistant bacteria, so further investigation is warranted.
Enhancement of Non-photochemical Quenching as an Adaptive Strategy under Phosphorus Deprivation in the Dinoflagellate Karlodinium veneficum

Intensified water column stratification due to global warming has the potential to decrease nutrient availability while increasing excess light for the photosynthesis of phytoplankton in the euphotic zone, which together will increase the need for photoprotective strategies such as non-photochemical quenching (NPQ). We investigated whether NPQ is enhanced and how it is regulated molecularly under phosphorus (P) deprivation in the dinoflagellate Karlodinium veneficum. We grew K. veneficum under P-replete and P-depleted conditions, monitored their growth rates and chlorophyll fluorescence, and conducted gene expression and comparative proteomic analyses. The results were used to characterize NPQ modulation and associated gene expression dynamics under P deprivation. We found that NPQ in K. veneficum was elevated significantly under P deprivation. Accordingly, the abundances of three light-harvesting complex stress-related proteins increased under P-depleted condition. Besides, many proteins related to genetic information flow were down-regulated while many proteins related to energy production and conversion were up-regulated under P deprivation. Taken together, our results indicate that K. veneficum cells respond to P deprivation by reconfiguring the metabolic landscape and up-tuning NPQ to increase the capacity to dissipate excess light energy and maintain the fluency of energy flow, which provides a new perspective about what adaptive strategy dinoflagellates have evolved to cope with P deprivation.
Aspects of Robust Computational Modeling for Plain and Reinforced Concrete

The problems commonly encountered in the numerical analysis of reinforced structures are often related to biaxial stress states in the structure. In this study this problem is solved with the formulation of a composite plasticity model which describes both cracking and crushing of concrete within the framework of plasticity theory. The other issue which is treated in this study is the rational modeling of the interaction between concrete and reinforcement.
NG2 Colocalizes With Axons and Is Expressed by a Mixed Cell Population in Spinal Cord Lesions

The NG2 proteoglycan is of general interest after spinal cord injury because it is expressed by oligodendrocyte progenitors (OPCs), which contribute to central nervous system remyelination; however, NG2 may inhibit axon regeneration. We and others have examined the spatiotemporal expression of NG2 after spinal cord injury (SCI). Here, we extend those observations and provide a comprehensive analysis of the distribution, phenotype, and colocalization of NG2 cells with axons in a clinically relevant model of spinal contusion. Because contusion models mimic the majority of human SCI, this information is important for understanding endogenous processes that promote and/or prevent repair. The data demonstrate that NG2 levels rise significantly between 3 and 7 days postinjury (dpi) and remain elevated chronically throughout the lesions. NG2 within the lesions could be derived from an array of infiltrating cells; thus, a panel of antibodies was used to investigate NG2 cell phenotypes. First, platelet-derived growth factor-&agr; receptor (PDGF&agr;R) colocalization was examined because OPCs normally express both markers. PDGF&agr;R cells were present in lesions at all times examined. However, only 37% of NG2 cells coexpressed PDGF&agr;R at 14 dpi, which dropped to <1% by 70 dpi. This contrasts with the nearly complete overlap in spared tissue surrounding the lesion. In contrast, 40% to 60% of NG2 cells expressed p75 and approximately 84% expressed Sox10, suggesting that many NG2 cells were nonmyelinating Schwann cells. Despite rising levels of NG2, we noted robust and sustained axon growth into the lesions, many of which were located along NG2 profiles. Thus, spinal contusion produces an NG2-rich environment into which axons grow and in which the source of NG2 appears considerably different from that in surrounding spared tissue.
Interface-Resolving Simulations of Gas-Liquid Two-Phase Flows in Solid Structures of Different Wettability

This PhD study is devoted to numerical investigations of two-phase flows on and through elementary and complex solid structures of varying wettability. The phase-field method is developed and implemented in OpenFOAM®. The numerical method/code is verified by a series of test cases of two-phase flows, and then applied to investigate: (1) droplet wetting on solid surfaces; (2) air bubble rising and interacting with cellular structures and (3) gas-liquid interfacial flows in foam structures.
A Continuous Model For Ratings

We study rating systems, such as the famous Elo system, applied to a large number of players. We assume that each player is characterized by an intrinsic inner strength and follow the evolution of their rating evaluations by deriving a new continuous model, a kinetic-like equation. We then investigate the validity of the rating systems by looking at their large time behavior as one would ideally expect the rating of each player to converge to their actual strength. The simplistic case when all players interact indeed yields an exponential convergence of the ratings. However, the behavior in the more realistic cases with only local interactions is more complex with several possible equilibria depending on the exact initial distribution of initial ratings and possibly very slow convergence.
Customer-developer links in software development

Many of the best ideas for new products and product improvements come from the customer or end user of the product [15]. In the software arena, tapping into this source of information requires the establishment of one or more customer-developer links. These links are defined as the techniques and/or channels that allow customers and developers to exchange information.
Pharmacology and pharmacodynamics of bevacizumab as monotherapy or in combination with cytotoxic therapy in preclinical studies.

Preclinical models have examined the pharmacologic and pharmacodynamic activities of an anti-vascular endothelial growth factor (VEGF) humanized, monoclonal antibody, bevacizumab, and/or its murine equivalent A4.6. 1. These studies found that single-agent therapy with bevacizumab/A4.6. 1 resulted in tumor growth inhibition of 20 different human tumor cell lines (13 tumor types) implanted into nude mice irrespective of the route of administration or tumor location. Several of these studies also observed significant inhibition of tumor metastases. Various studies have examined the feasibility of combining anti-VEGF therapy with cytotoxic or biological agents. Combining bevacizumab/A4.6. 1 with doxorubicin, topotecan, paclitaxel, docetaxel, or radiotherapy resulted in additive or synergistic tumor growth inhibition. Changes in vascular functions were frequently reported, including decreased vessel diameter, density, and permeability in response to treatment. A reduction in interstitial fluid pressure was also observed. In some studies, these improvements resulted in an increase in intratumoral uptake of chemotherapy, implying that the most effective use of anti-VEGF therapy is in combination with chemotherapy. Alternatively, combination treatment with radiation increased tumor oxygenation and tumor growth inhibition. Interestingly, anti-VEGF therapy has also been reported to reduce the development of ascites in ovarian mouse models. Finally, safety pharmacology studies with bevacizumab in cynomolgus monkeys showed that this agent is generally well tolerated with no unexpected adverse events.
In vitro evaluation of immunological properties of extracellular polysaccharides produced by Lactobacillus delbrueckii strains

We investigated the variation in immunological properties of the extracellular polysaccharides (EPSs) produced by different Lactobacillus delbrueckii strains as well as that of their monosaccharide composition. The monosaccharide composition of each EPS produced by L. delbrueckii strains, as determined by thin layer chromatography (TLC), showed an appreciable variation in a strain-dependent manner, which could be broadly assigned to 4 TLC groups. Meanwhile, the immunological properties of the EPSs produced by 10 L. delbrueckii strains were evaluated in a semi-intestinal model using a Transwell co-culture system, which employed human intestinal epithelial Caco-2 cells on the apical side and murine macrophage RAW264.7 cells on the basolateral side. Each EPS was added to the apical side to allow direct contact with Caco-2 cells and incubated for 6 hr. After incubation, the amounts of TNF-α and several cytokines that had been released by either RAW264.7 or Caco-2 cells were then quantified by cytotoxic activity on L929 cells or the RT-PCR method. It was found that the EPS-stimulated RAW264.7 cells express different profiles of cytokine production via Caco-2 cells but that the profile difference could not be related to the above TLC grouping. The evidence suggests that the EPSs of L. delbrueckii strains are diverse not only in their biochemical structure but also in their immunological properties.