Miracle-dz/UniFAR-FTUs huggingface dataset:
Quorum Sensing and Density-Dependent Dispersal in an Aquatic Model System

Many organisms use cues to decide whether to disperse or not, especially those related to the composition of their environment. Dispersal hence sometimes depends on population density, which can be important for the dynamics and evolution of sub-divided populations. But very little is known about the factors that organisms use to inform their dispersal decision. We investigated the cues underlying density-dependent dispersal in inter-connected microcosms of the freshwater protozoan Paramecium caudatum. In two experiments, we manipulated (i) the number of cells per microcosm and (ii) the origin of their culture medium (supernatant from high- or low-density populations). We found a negative relationship between population density and rates of dispersal, suggesting the use of physical cues. There was no significant effect of culture medium origin on dispersal and thus no support for chemical cues usage. These results suggest that the perception of density – and as a result, the decision to disperse – in this organism can be based on physical factors. This type of quorum sensing may be an adaptation optimizing small scale monitoring of the environment and swarm formation in open water.
The ‘dark side’ of knowledge brokering

Deploying knowledge brokers to bridge the ‘gap’ between researchers and practitioners continues to be seen as an unquestionable enabler of evidence-based practice and is often endorsed uncritically. We explore the ‘dark side’ of knowledge brokering, reflecting on its inherent challenges which we categorize as: (1) tensions between different aspects of brokering; (2) tensions between different types and sources of knowledge; and (3) tensions resulting from the ‘in-between’ position of brokers. As a result of these tensions, individual brokers may struggle to maintain their fragile and ambiguous intermediary position, and some of the knowledge may be lost in the ‘in-between world’, whereby research evidence is transferred to research users without being mobilized in their day-to-day practice. To be effective, brokering requires an amalgamation of several types of knowledge and a multidimensional skill set that needs to be sustained over time. If we want to maximize the impact of research on policy and practice, we should move from deploying individual ‘brokers’ to embracing the collective process of ‘brokering’ supported at the organizational and policy levels.
The Effect of Wind on the Rate of Heat Loss from Avian Cup-Shaped Nests

Forced convection can significantly influence the heat loss from birds and their offspring but effects may be reduced by using sheltered micro-sites such as cavities or constructing nests. The structural and thermal properties of the nests of two species, the spiny-cheeked honeyeater (Acanthagenys rufogularis) and yellow-throated miner (Manorina flavigula), were measured in relation to three wind speeds. Nest dimensions differ between the two species, despite the similar body mass of the incubating adults, however nest conductance is comparable. As wind speed increases, so does the rate of heat loss from the nests of both species, and further still during incubation recesses. The significance of forced convection through the nest is a near-doubling in heat production required by the parent, even when incubating at relatively low wind speeds. This provides confirmation that selecting a sheltered nest site is important for avian reproductive success.
Symptom Interpretation in Women With Diabetes and Myocardial Infarction

Purpose The purpose of this study was to describe the role of diabetes in acute myocardial infarction (MI) symptom interpretation. Methods This is a secondary data analysis of a study of treatment-seeking delay in women with acute MI (N = 52). This study included a subsample of those with diabetes (n = 16). Women were interviewed while hospitalized with MI about their actions, thoughts, and feelings from symptom onset to entry into the health care system. Qualitative description was the method of analysis. Results Three major themes were identified in the qualitative data: diabetes and decision making, presenting symptoms, and symptom attribution. Not all women included information about diabetes in their story, but those who checked blood sugars generally found it to be elevated. Diabetes was a factor in decision making for more than half of the sample. Presenting symptoms were variable but raised hypotheses about shortness of breath as a common presenting symptom for women with diabetes and MI. The third theme, symptom attribution, revealed confusion as to the cause of symptoms. Conclusions These results provide insight into symptom interpretation in women with diabetes and MI. Women with diabetes should consider atypical symptoms such as shortness of breath, gastrointestinal symptoms, and fluctuating blood sugars as reasons to seek care. Education for women with diabetes should include action plans for how to recognize and respond to symptoms. More research on the influence of diabetes on MI symptom attribution and decision making is needed.
Risk factors for early and late intrahepatic recurrence in patients with single hepatocellular carcinoma without macrovascular invasion after curative resection.

BACKGROUND Prognostic factors of postoperative early and late recurrence in patients with hepatocellular carcinoma (HCC) undergoing curative resection remain to be clarified. The aim of this study was to identify risk factors for postoperative early (≤ 2 year) and late (> 2 year) intrahepatic recurrences in patients with single HCCs without macrovascular invasion. METHODS A total of 280 patients from December 2004 to December 2007 were retrospectively included in this study. Intrahepatic recurrence was classified into early (≤ 2 year) and late (> 2 year) and the Chi-Square test or Fisher's exact test and multivariate logistic regression analysis were performed to determine significant risk factors. RESULTS During the follow-up, 124 patients had intrahepatic recurrence, early and late in 82 and 42 patients, respectively. Multivariate logistic regression analysis showed that microvascular invasion (p=0.006, HR: 2.397, 95% CI: 1.290-4.451) was the only independent risk factor for early recurrence, while being female (p = 0.031, HR: 0.326, 95% CI: 0.118-0.901), and having a high degree of cirrhosis (P=0.001, HR: 2.483, 95% CI: 1.417-4.349) were independent risk factors for late recurrence. CONCLUSIONS Early and late recurrence of HCC is linked to different risk factors in patients with single HCC without macrovascular invasion. This results suggested different emphases of strategies for prevent of recurrence after curative resection, more active intervention including adjuvant therapy, anti-cirrhosis drugs and careful follow-up being necessary for patients with relevant risk factors.
Structural Insights into HIV-1 Vif-APOBEC3F Interaction

ABSTRACT The HIV-1 Vif protein inactivates the cellular antiviral cytidine deaminase APOBEC3F (A3F) in virus-infected cells by specifically targeting it for proteasomal degradation. Several studies identified Vif sequence motifs involved in A3F interaction, whereas a Vif-binding A3F interface was proposed based on our analysis of highly similar APOBEC3C (A3C). However, the structural mechanism of specific Vif-A3F recognition is still poorly understood. Here we report structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Alanine-scanning analysis of Vif revealed that six residues located within the conserved Vif F1-, F2-, and F3-box motifs are essential for both A3C and A3F degradation, and an additional four residues are uniquely required for A3F degradation. Modeling of the Vif structure on an HIV-1 Vif crystal structure revealed that three discontinuous flexible loops of Vif F1-, F2-, and F3-box motifs sterically cluster to form a flexible A3F interaction interface, which represents hydrophobic and positively charged surfaces. We found that the basic Vif interface patch (R17, E171, and R173) involved in the interactions with A3C and A3F differs. Furthermore, our crystal structure determination and extensive mutational analysis of the A3F C-terminal domain demonstrated that the A3F interface includes a unique acidic stretch (L291, A292, R293, and E324) crucial for Vif interaction, suggesting additional electrostatic complementarity to the Vif interface compared with the A3C interface. Taken together, these findings provide structural insights into the A3F-Vif interaction mechanism, which will provide an important basis for development of novel anti-HIV-1 drugs using cellular cytidine deaminases. IMPORTANCE HIV-1 Vif targets cellular antiviral APOBEC3F (A3F) enzyme for degradation. However, the details on the structural mechanism for specific A3F recognition remain unclear. This study reports structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Three discontinuous sequence motifs of Vif, F1, F2, and F3 boxes, assemble to form an A3F interaction interface. In addition, we determined a crystal structure of the wild-type A3F C-terminal domain responsible for the Vif interaction. These results demonstrated that both electrostatic and hydrophobic interactions are the key force driving Vif-A3F binding and that the Vif-A3F interfaces are larger than the Vif-A3C interfaces. These findings will allow us to determine the configurations of the Vif-A3F complex and to construct a structural model of the complex, which will provide an important basis for inhibitor development.
Disease Mention Recognition with Specific Features

Despite an increasing amount of research on biomedical named entity recognition, there has been not enough work done on disease mention recognition. Difficulty of obtaining adequate corpora is one of the key reasons which hindered this particular research. Previous studies argue that correct identification of disease mentions is the key issue for further improvement of the disease-centric knowledge extraction tasks. In this paper, we present a machine learning based approach that uses a feature set tailored for disease mention recognition and outperforms the state-of-the-art results. The paper also discusses why a feature set for the well studied gene/protein mention recognition task is not necessarily equally effective for other biomedical semantic types such as diseases.
Long‐term clinical and prosthetic outcomes of soft liner and clip attachments for bar/implant overdentures: a randomised controlled clinical trial

Long-term clinical and prosthetic outcomes of soft liner attachments for bar/implant overdentures were not sufficiently investigated. The aim of this trial was to evaluate clinical and prosthetic outcomes of resilient liner and clip attachments for bar/implant-retained mandibular overdenture after 7 years. Thirty edentulous male participants received two implants in the canine areas of the mandible. Three months later, implants were splinted with a resilient bar. Mandibular overdentures were connected to the bars with either clip (CR group, n = 15) or resilient liner (RR group, n = 15) attachments. Plaque index (PI), gingival index (GI), probing depth (PD), vertical bone loss (VBL), horizontal bone loss (HBLO) and prosthetic complications (PCs) were evaluated at denture delivery (T0), 6 (T6m ), 12 (T1), 24 (T2), 36 (T3), 48 (T4), 60 (T5), 72 (T6) and 84 (T7) months after insertion. PI and GI increased significantly with time for CR and decreased significantly for RR (P < 0·001). PD increased at T1 (CR) and T6 m (RR) and then decreased thereafter (P < 0·05). VBL increased significantly with time in both groups (P < 0·005). HBLO increased at T2 (CR) and T1 (RR) and then decreased thereafter. CR recorded significant higher PI, GI, PD, VBLO and HBLO compared to RR at all observation times (P < 0·042). The survival rates were 96·6% and 100% for CR and RR after 7 years. The most common PCs for CR and RR were clip wears and separation of the resilient liner from the denture base, respectively. Within the limitations of this study, resilient liner attachments are recommended for bar/implant-retained mandibular overdentures than clip attachments in terms of peri-implant tissue health and prosthetic complications after 7 years.
Effect of a porous collagen-glycosaminoglycan copolymer on early tendon healing in a novel animal model

The effects of a collagen-glycosaminoglycan (CG) copolymer on the early healing of transected Achilles tendon were studied. A novel rabbit model that isolates the tendon defect site from surrounding tissue during healing was developed in order to evaluate the effects of implanting the defect site with analogs of extracellular matrix. The objective of this study was to investigate the effect of resorbable (CG) matrices with different pores diameters on the early healing response of Achilles tendon in this animal model. The animal model consisted of creating a lesion gap of 11±1 mm and isolating it from the surrounding tissue by a silicone tube into which the tendon stumps were inserted. In one group of animals, the tube was empty and, in the other three, it contained a CG matrix with average pore diameter of 25, 60, or 120 pm. The lesion site was protected from mechanical loading in the early stages of healing. Animals were sacrificed at intervals of 1.5, 3, 6 and 12 weeks. Tissue sections were evaluated histomorphometrically, immunohistochemically and ultrastructurally. The results showed that the tendon stumps induced synthesis of a tissue cable inside the silicone tube in both the presence and absence of CG matrix. Histologically and ultrastructurally, the tissue cable did not appear similar to normal tendon. At 12 weeks, the new tissue in the empty tubes consisted of a dense aggregate of crimped fibers with a wavelength that was significantly shorter that in normal tendon. The average collagen fibril diameter was significantly smaller for the healing tissue compared to normal. Tubes filled with CG matrix contained a significantly greater volume of tissue at all time periods. The presence of the CG matrix appeared to modify the kinetics of tendon healing. Unlike tissue in the empty tube, by 12 weeks, tissue in the CG-filled tubes did not have a crimp pattern. CG matrices with the 120 pm pore size appeared to have a greater percentage of fibrous tissue than CG matrices with 25 and 60 pm pore sizes. CG matrices were resorbed by 12 weeks. Thesis Supervisor: loannis V. Yannas Title: Professor of Polymer Science and Engineering
Quid-Pro-Quo-tocols: Strengthening Semi-honest Protocols with Dual Execution

Known protocols for secure two-party computation that are designed to provide full security against malicious behavior are significantly less efficient than protocols intended only to thwart semi-honest adversaries. We present a concrete design and implementation of protocols achieving security guarantees that are much stronger than are possible with semi-honest protocols, at minimal extra cost. Specifically, we consider protocols in which a malicious adversary may learn a single (arbitrary) bit of additional information about the honest party's input. Correctness of the honest party's output is still guaranteed. Adapting prior work of Mohassel and Franklin, the basic idea in our protocols is to conduct two separate runs of a (specific) semi-honest, garbled-circuit protocol, with the parties swapping roles, followed by an inexpensive secure equality test. We provide a rigorous definition and prove that this protocol leaks no more than one additional bit against a malicious adversary. In addition, we propose some heuristic enhancements to reduce the overall information a cheating adversary learns. Our experiments show that protocols meeting this security level can be implemented at cost very close to that of protocols that only achieve semi-honest security. Our results indicate that this model enables the large-scale, practical applications possible within the semi-honest security model, while providing dramatically stronger security guarantees.
Nationwide Study of Turner Syndrome in Ukrainian Children: Prevalence, Genetic Variants and Phenotypic Features

Objective: We aimed to investigate the prevalence of Turner syndrome (TS) in the Ukrainian population, the frequency of karyotype variants, the age of children at diagnosis, the degree of short stature and phenotypic features in TS girls. Methods: A retrospective analysis was made in 538 TS girls aged 0.11-18.2 years within the time period of 2005-2015 with detailed examination of 150 patients. Results: The prevalence of TS in Ukraine is 77.5 in 100.000 live female births. The average age at diagnosis is 9.33±4.93 years. The relative proportions of karyotypic abnormalities found were: 45,X (59.3%); mosaicism 45,X/46,XX (22.9%); and structural abnormalities in chromosome X (17.8%). The most frequently encountered findings were growth delay (98.8%), shortening of the 4th and 5th metacarpal bones (74.6%), abnormal nails (73.3%), broad chest (60.7%), short neck (58.6%), hypertelorism of nipples (51.4%), malformations of the cardiovascular (19.6%) and urinary systems (13.8%) and pathology related to vision (20.1%) and hearing (22.0%). Conclusion: In the Ukrainian population, the highest proportion of patients with TS had a karyotype 45,X. TS was accompanied by a lower frequency of malformations of internal organs compared to other countries.
Using Plant Functional Traits to Explain Diversity–Productivity Relationships

Background The different hypotheses proposed to explain positive species richness–productivity relationships, i.e. selection effect and complementarity effect, imply that plant functional characteristics are at the core of a mechanistic understanding of biodiversity effects. Methodology/Principal Findings We used two community-wide measures of plant functional composition, (1) community-weighted means of trait values (CWM) and (2) functional trait diversity based on Rao’s quadratic diversity (FDQ) to predict biomass production and measures of biodiversity effects in experimental grasslands (Jena Experiment) with different species richness (2, 4, 8, 16 and 60) and different functional group number and composition (1 to 4; legumes, grasses, small herbs, tall herbs) four years after establishment. Functional trait composition had a larger predictive power for community biomass and measures of biodiversitity effects (40–82% of explained variation) than species richness per se (<1–13% of explained variation). CWM explained a larger amount of variation in community biomass (80%) and net biodiversity effects (70%) than FDQ (36 and 38% of explained variation respectively). FDQ explained similar proportions of variation in complementarity effects (24%, positive relationship) and selection effects (28%, negative relationship) as CWM (27% of explained variation for both complementarity and selection effects), but for all response variables the combination of CWM and FDQ led to significant model improvement compared to a separate consideration of different components of functional trait composition. Effects of FDQ were mainly attributable to diversity in nutrient acquisition and life-history strategies. The large spectrum of traits contributing to positive effects of CWM on biomass production and net biodiversity effects indicated that effects of dominant species were associated with different trait combinations. Conclusions/Significance Our results suggest that the identification of relevant traits and the relative impacts of functional identity of dominant species and functional diversity are essential for a mechanistic understanding of the role of plant diversity for ecosystem processes such as aboveground biomass production.
Intracellular Redox State Alters NMDA Receptor Response during Aging through Ca2+/Calmodulin-Dependent Protein Kinase II

The contribution of the NMDA receptors (NMDARs) to synaptic plasticity declines during aging, and the decline is thought to contribute to memory deficits. Here, we demonstrate that an age-related shift in intracellular redox state contributes to the decline in NMDAR responses through Ca2+/calmodulin-dependent protein kinase II (CaMKII). The oxidizing agent xanthine/xanthine oxidase (X/XO) decreased the NMDAR-mediated synaptic responses at hippocampal CA3–CA1 synapses in slices from young (3–8 months) but not aged (20–25 months) rats. Conversely, the reducing agent dithiothreitol (DTT) selectively enhanced NMDAR response to a greater extent in aged hippocampal slices. The enhancement of NMDAR responses facilitated induction of long-term potentiation in aged but not young animals. The DTT-mediated growth in the NMDAR response was not observed for the AMPA receptor-mediated synaptic responses. A similar increase was observed by intracellular application of the membrane-impermeable reducing agent, l-glutathione (l-GSH), through the intracellular recording pipette, indicating that the increased NMDAR response was dependent on intracellular redox state. DTT enhancement of the NMDAR response was dependent on CaMKII activity and was blocked by the CaMKII inhibitor—myristoylated autocamtide-2-related inhibitory peptide (myr-AIP)—but not by inhibition of the activity of protein phosphatases—PP1 and calcineurin (CaN/PP2B) or protein kinase C. CaMKII activity assays established that DTT increased CaMKII activity in CA1 cytosolic extracts in aged but not in young animals. These findings indicate a link between oxidation of CaMKII during aging, a decline in NMDAR responses, and altered synaptic plasticity.
An update and guidance on narrowband ultraviolet B phototherapy: a British Photodermatology Group Workshop Report

Summary These guidelines for use of narrowband (TL‐01) ultraviolet B have been prepared for dermatologists by the British Photodermatology Group on behalf of the British Association of Dermatologists. They present evidence‐based guidance for treatment of patients with a variety of dermatoses and photodermatoses, with identification of the strength of evidence available at the time of preparation of the guidelines, and a brief overview of background photobiology.
Nitrogen‐Coordinated Single Cobalt Atom Catalysts for Oxygen Reduction in Proton Exchange Membrane Fuel Cells

Due to the Fenton reaction, the presence of Fe and peroxide in electrodes generates free radicals causing serious degradation of the organic ionomer and the membrane. Pt‐free and Fe‐free cathode catalysts therefore are urgently needed for durable and inexpensive proton exchange membrane fuel cells (PEMFCs). Herein, a high‐performance nitrogen‐coordinated single Co atom catalyst is derived from Co‐doped metal‐organic frameworks (MOFs) through a one‐step thermal activation. Aberration‐corrected electron microscopy combined with X‐ray absorption spectroscopy virtually verifies the CoN4 coordination at an atomic level in the catalysts. Through investigating effects of Co doping contents and thermal activation temperature, an atomically Co site dispersed catalyst with optimal chemical and structural properties has achieved respectable activity and stability for the oxygen reduction reaction (ORR) in challenging acidic media (e.g., half‐wave potential of 0.80 V vs reversible hydrogen electrode (RHE). The performance is comparable to Fe‐based catalysts and 60 mV lower than Pt/C ‐60 μg Pt cm−2). Fuel cell tests confirm that catalyst activity and stability can translate to high‐performance cathodes in PEMFCs. The remarkably enhanced ORR performance is attributed to the presence of well‐dispersed CoN4 active sites embedded in 3D porous MOF‐derived carbon particles, omitting any inactive Co aggregates.