Miracle-dz/UniFAR-FTUs huggingface dataset:
Positive and Negative Effects of Habitat-Forming Algae on Survival, Growth and Intra-Specific Competition of Limpets

Understanding the effects of environmental change on the distribution and abundance of strongly interacting organisms, such as intertidal macroalgae and their grazers, needs a thorough knowledge of their underpinning ecological relationships. Control of grazer-plant interactions is bi-directional on northwestern European coasts: grazing by limpets structures populations of macroalgae, while macroalgae provide habitat and food for limpets. Scottish shores dominated by the macroalga Fucus vesiculosus support lower densities and larger sizes of limpets Patella vulgata than shores with less Fucus. These patterns may be due to differences in inter-size-class competitive interactions of limpets among shores with different covers of Fucus. To examine this model, densities of small and large limpets were manipulated in plots with and without Fucus. Amounts of biofilm were measured in each plot. The presence of Fucus increased survival but hindered growth of small (15 mm TL) limpets, which were negatively affected by the presence of large limpets (31 mm TL). In contrast, large limpets were not affected by the presence of Fucus or of small limpets. This suggests the occurrence of asymmetric inter-size-class competition, which was influenced by the presence of macroalgae. Macroalgae and increased densities of limpets did not influence amounts of biofilm. Our findings highlight the role of interactions among organisms in generating ecological responses to environmental change.
Clinical and Genetic Risk Factors for Biofilm-Forming Staphylococcus aureus

ABSTRACT The molecular and clinical factors associated with biofilm-forming methicillin-resistant Staphylococcus aureus (MRSA) are incompletely understood. Biofilm production for 182 MRSA isolates obtained from clinical culture sites (2004 to 2013) was quantified. Microbiological toxins, pigmentation, and genotypes were evaluated, and patient demographics were collected. Logistic regression was used to quantify the effect of strong biofilm production (versus weak biofilm production) on clinical outcomes and independent predictors of a strong biofilm. Of the isolates evaluated, 25.8% (47/182) produced strong biofilms and 40.7% (74/182) produced weak biofilms. Strong biofilm-producing isolates were more likely to be from multilocus sequence typing (MLST) clonal complex 8 (CC8) (34.0% versus 14.9%; P = 0.01) but less likely to be from MLST CC5 (48.9% versus 73.0%; P = 0.007). Predictors for strong biofilms were spa type t008 (adjusted odds ratio [aOR], 4.54; 95% confidence interval [CI], 1.21 to 17.1) and receipt of chemotherapy or immunosuppressants in the previous 90 days (aOR, 33.6; 95% CI, 1.68 to 673). Conversely, patients with high serum creatinine concentrations (aOR, 0.33; 95% CI, 0.15 to 0.72) or who previously received vancomycin (aOR, 0.03; 95% CI, 0.002 to 0.39) were less likely to harbor strong biofilm-producing MRSA. Beta-toxin-producing isolates (aOR, 0.31; 95% CI, 0.11 to 0.89) and isolates with spa type t895 (aOR, 0.02 95% CI, <0.001 to 0.47) were less likely to produce strong biofilms. Patient outcomes also varied between the two groups. Specifically, patients with strong biofilm-forming MRSA were significantly more likely to be readmitted within 90 days (aOR, 5.43; 95% CI, 1.69 to 17.4) but tended to have decreased 90-day mortality (aOR, 0.36; 95% CI, 0.12 to 1.06). Patients that harbored t008 and received immunosuppressants were more likely to have strong biofilm-producing MRSA isolates. Clinically, patients with strong biofilm-forming MRSA were less likely to die at 90 days but five times more likely to be readmitted.
Haptic Search for Hard and Soft Spheres

In this study the saliency of hardness and softness were investigated in an active haptic search task. Two experiments were performed to explore these properties in different contexts. In Experiment 1, blindfolded participants had to grasp a bundle of spheres and determine the presence of a hard target among soft distractors or vice versa. If the difference in compliance between target and distractors was small, reaction times increased with the number of items for both features; a serial strategy was found to be used. When the difference in compliance was large, the reaction times were independent of the number of items, indicating a parallel strategy. In Experiment 2, blindfolded participants pressed their hand on a display filled with hard and soft items. In the search for a soft target, increasing reaction times with the number of items were found, but the location of target and distractors appeared to have a large influence on the search difficulty. In the search for a hard target, reaction times did not depend on the number of items. In sum, this showed that both hardness and softness are salient features.
Does Suicidal Ideation Influence Memory? A Study of the Role of Violent Daydreaming in the Relationship Between Suicidal Ideation and Everyday Memory

Individuals at risk for suicide experience periods of emotional, enduring, and vivid thoughts about their death by suicide and frequently report violent daydreams about death. Daydreaming is associated with forgetfulness and memory impairments. However, no studies have examined whether suicidal ideation is associated with deficits in everyday memory capabilities and whether violent daydreaming may influence these relationships. This study tested these hypotheses in a sample of 512 young adults. Self-report measures of subjective everyday memory capabilities, violent daydreaming, and suicidal ideation were administered. Results indicated that suicidal ideation and violent daydreaming were each significantly associated with greater impairments in everyday memory retrieval and everyday memory encoding (i.e., attentional tracking). Furthermore, violent daydreaming accounted for the relationship between suicidal ideation and impairments in everyday memory retrieval and memory encoding. Notably, findings remained after controlling for gender and depressive symptoms, a robust predictor of memory impairments. Implications and limitations are discussed.
On predictive models and user-drawn graphical passwords

In commonplace text-based password schemes, users typically choose passwords that are easy to recall, exhibit patterns, and are thus vulnerable to brute-force dictionary attacks. This leads us to ask whether other types of passwords (e.g., graphical) are also vulnerable to dictionary attack because of users tending to choose memorable passwords. We suggest a method to predict and model a number of such classes for systems where passwords are created solely from a user's memory. We hypothesize that these classes define weak password subspaces suitable for an attack dictionary. For user-drawn graphical passwords, we apply this method with cognitive studies on visual recall. These cognitive studies motivate us to define a set of password complexity factors (e.g., reflective symmetry and stroke count), which define a set of classes. To better understand the size of these classes and, thus, how weak the password subspaces they define might be, we use the “Draw-A-Secret” (DAS) graphical password scheme of Jermyn et al. [1999] as an example. We analyze the size of these classes for DAS under convenient parameter choices and show that they can be combined to define apparently popular subspaces that have bit sizes ranging from 31 to 41—a surprisingly small proportion of the full password space (58 bits). Our results quantitatively support suggestions that user-drawn graphical password systems employ measures, such as graphical password rules or guidelines and proactive password checking.
Chondrichthyan Diversity, Conservation Status, and Management Challenges in Costa Rica

Understanding key aspects of the biology and ecology of chondrichthyan fishes (sharks, rays, and chimaeras), as well as the range of threats affecting their populations is crucial given the rapid rate at which some species are declining. In the Eastern Tropical Pacific (ETP), the lack of knowledge, unreliable (or nonexistent) landing statistics and limited enforcement of existing fisheries regulations has hindered management and conservation efforts for chondrichthyan species. This review evaluated our current understanding of Costa Rican chondrichthyans and their conservation status. Specifically, we (1) provide an updated checklist on the species richness, habitat use and distribution patterns, (2) summarise the most relevant chondrichthyan studies (scientific publications, theses, and official technical reports), (3) identify knowledge gaps, (4) discuss fisheries-related threats, and (5) highlight the management challenges and research needs to effectively protect their populations. A total of 99 chondrichthyan species are formally recorded in Costa Rican waters, from which 15% are threatened with extinction and 41% are “Data Deficient” based on the IUCN (International Union for Conservation of Nature) Red List. A total of 121 studies were published between 1891 and 2017; 82% in the Pacific (24% from Isla del Coco) and only 18% from the Caribbean Sea. These results highlight the need to redirect research efforts on specific taxonomic groups and geographic regions (i.e., Caribbean). Based on our review, improving the quality and quantity of fisheries landing statistics, as well as determining the degree of overlap between chondrichthyans and small-scale coastal/pelagic fisheries remains a priority. We proposed an adaptive management framework for chondrichthyan fisheries in data-poor countries where management goals/targets are clearly defined. This framework could strengthen the conservation of chondrichthyan populations in Costa Rica and the region.
Estimating HIV Incidence among Adults in Kenya and Uganda: A Systematic Comparison of Multiple Methods

Background Several approaches have been used for measuring HIV incidence in large areas, yet each presents specific challenges in incidence estimation. Methodology/Principal Findings We present a comparison of incidence estimates for Kenya and Uganda using multiple methods: 1) Epidemic Projections Package (EPP) and Spectrum models fitted to HIV prevalence from antenatal clinics (ANC) and national population-based surveys (NPS) in Kenya (2003, 2007) and Uganda (2004/2005); 2) a survey-derived model to infer age-specific incidence between two sequential NPS; 3) an assay-derived measurement in NPS using the BED IgG capture enzyme immunoassay, adjusted for misclassification using a locally derived false-recent rate (FRR) for the assay; (4) community cohorts in Uganda; (5) prevalence trends in young ANC attendees. EPP/Spectrum-derived and survey-derived modeled estimates were similar: 0.67 [uncertainty range: 0.60, 0.74] and 0.6 [confidence interval: (CI) 0.4, 0.9], respectively, for Uganda (2005) and 0.72 [uncertainty range: 0.70, 0.74] and 0.7 [CI 0.3, 1.1], respectively, for Kenya (2007). Using a local FRR, assay-derived incidence estimates were 0.3 [CI 0.0, 0.9] for Uganda (2004/2005) and 0.6 [CI 0, 1.3] for Kenya (2007). Incidence trends were similar for all methods for both Uganda and Kenya. Conclusions/Significance Triangulation of methods is recommended to determine best-supported estimates of incidence to guide programs. Assay-derived incidence estimates are sensitive to the level of the assay's FRR, and uncertainty around high FRRs can significantly impact the validity of the estimate. Systematic evaluations of new and existing incidence assays are needed to the study the level, distribution, and determinants of the FRR to guide whether incidence assays can produce reliable estimates of national HIV incidence.
Response of a Specialist Bat to the Loss of a Critical Resource

Human activities have negatively impacted many species, particularly those with unique traits that restrict their use of resources and conditions to specific habitats. Unfortunately, few studies have been able to isolate the individual and combined effects of different threats on population persistence in a natural setting, since not all organisms can be associated with discrete habitat features occurring over limited spatial scales. We present the results of a field study that examines the short-term effects of roost loss in a specialist bat using a conspicuous, easily modified resource. We mimicked roost loss in the natural habitat and monitored individuals before and after the perturbation to determine patterns of resource use, spatial movements, and group stability. Our study focused on the disc-winged bat Thyroptera tricolor, a species highly morphologically specialized for roosting in the developing furled leaves of members of the order Zingiberales. We found that the number of species used for roosting increased, that home range size increased (before: mean 0.14±SD 0.08 ha; after: 0.73±0.68 ha), and that mean association indices decreased (before: 0.95±0.10; after: 0.77±0.18) once the roosting habitat was removed. These results demonstrate that the removal of roosting resources is associated with a decrease in roost-site preferences or selectivity, an increase in mobility of individuals, and a decrease in social cohesion. These responses may reduce fitness by potentially increasing energetic expenditure, predator exposure, and a decrease in cooperative interactions. Despite these potential risks, individuals never used roost-sites other than developing furled leaves, suggesting an extreme specialization that could ultimately jeopardize the long-term persistence of this species' local populations.
Assessment of Border Control Measures and Community Containment Measures Used in Japan during the Early Stages of Pandemic (H1N1) 2009

Background In the early stages of Pandemic (H1N1) 2009, border control measures were taken by quarantine stations to block the entry of infected individuals into Japan and community containment measures were implemented to prevent the spreading. The objectives of this study were to describe these measures and the characteristics of infected individuals, and to assess the measures' effectiveness. Methodology/Principal Findings Border control and community containment measures implemented from April to June (Period I: April 28–May 21, Period II: May 22–June 18) 2009 were described. Number of individuals identified and disease characteristics were analyzed. For entry screening, a health declaration form and an infrared thermoscanner were used to detect symptomatic passengers. Passengers indicated for the rapid influenza test underwent the test followed by RT-PCR. Patients positive for H1N1 were isolated, and close contacts were quarantined. Entry cards were handed out to all asymptomatic passengers informing them about how to contact a health center in case they developed symptoms. Nine individuals were identified by entry screening and 1 during quarantine to have Pandemic (H1N1) 2009. Health monitoring by health centers was performed in period I for passengers arriving from affected countries and in period II for those who had come into contact with the individuals identified by entry screening. Health monitoring identified 3 infected individuals among 129,546 in Period I and 5 among 746 in Period II. Enhanced surveillance, which included mandatory reporting of details of the infected individuals, identified 812 individuals, 141 (18%) of whom had a history of international travel. Twenty-four of these 141 passengers picked up by enhanced surveillance had been developing symptoms on entry and were missed at screening. Conclusion/Significance Symptomatic passengers were detected by the various entry screening measures put in place. Enhanced surveillance provided data for the improvement of public health measures in future pandemics.
A Lyapunov Analysis of Momentum Methods in Optimization

Momentum methods play a significant role in optimization. Examples include Nesterov's accelerated gradient method and the conditional gradient algorithm. Several momentum methods are provably optimal under standard oracle models, and all use a technique called estimate sequences to analyze their convergence properties. The technique of estimate sequences has long been considered difficult to understand, leading many researchers to generate alternative, "more intuitive" methods and analyses. We show there is an equivalence between the technique of estimate sequences and a family of Lyapunov functions in both continuous and discrete time. This connection allows us to develop a simple and unified analysis of many existing momentum algorithms, introduce several new algorithms, and strengthen the connection between algorithms and continuous-time dynamical systems.
Complex electrophysiological remodeling in postinfarction ischemic heart failure

Significance Cardiac arrhythmias often occur in heart failure (HF) patients, but drug therapies using selective ion channel blockers have failed clinical trials and effective drug therapies remain elusive. Here we systematically study the major ionic currents during the cardiac action potential (AP) and arrhythmogenic Ca2+ release in postinfarction HF. We found that changes in any individual current are relatively small, and alone could mislead as to consequences. However, differential changes in multiple currents integrate to shorten AP in the infarct border zone but prolong AP in the remote zone, increasing AP repolarization inhomogeneity. Our findings help explain why single channel-blocker therapy may fail, and highlight the need to understand the integrated changes of ionic currents in treating arrhythmias in HF. Heart failure (HF) following myocardial infarction (MI) is associated with high incidence of cardiac arrhythmias. Development of therapeutic strategy requires detailed understanding of electrophysiological remodeling. However, changes of ionic currents in ischemic HF remain incompletely understood, especially in translational large-animal models. Here, we systematically measure the major ionic currents in ventricular myocytes from the infarct border and remote zones in a porcine model of post-MI HF. We recorded eight ionic currents during the cell’s action potential (AP) under physiologically relevant conditions using selfAP-clamp sequential dissection. Compared with healthy controls, HF-remote zone myocytes exhibited increased late Na+ current, Ca2+-activated K+ current, Ca2+-activated Cl− current, decreased rapid delayed rectifier K+ current, and altered Na+/Ca2+ exchange current profile. In HF-border zone myocytes, the above changes also occurred but with additional decrease of L-type Ca2+ current, decrease of inward rectifier K+ current, and Ca2+ release-dependent delayed after-depolarizations. Our data reveal that the changes in any individual current are relatively small, but the integrated impacts shift the balance between the inward and outward currents to shorten AP in the border zone but prolong AP in the remote zone. This differential remodeling in post-MI HF increases the inhomogeneity of AP repolarization, which may enhance the arrhythmogenic substrate. Our comprehensive findings provide a mechanistic framework for understanding why single-channel blockers may fail to suppress arrhythmias, and highlight the need to consider the rich tableau and integration of many ionic currents in designing therapeutic strategies for treating arrhythmias in HF.
Quadrupedal bounding with an actuated spinal joint

Most legged vertebrates use flexible spines and supporting muscles to provide auxiliary power and dexterity for dynamic behaviors, resulting in higher speeds and additional maneuverability during locomotion. However, most existing legged robots capable of dynamic locomotion incorporate only a single rigid trunk with actuation limited to legs and associated joints. In this paper, we investigate how quadrupedal bounding can be achieved in the presence of an actuated spinal joint and characterize associated performance improvements compared to bounding with a rigid robot body. In the context of both a new controller structure for bounding with a body joint and existing bounding controllers for the rigid trunk, we use optimization methods to identify the highest performance gait parameters and establish that the spinal joint allows increased forward speeds and hopping heights.
Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

ABSTRACT Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance.
Increased Host Investment in Extrafloral Nectar (EFN) Improves the Efficiency of a Mutualistic Defensive Service

Extrafloral nectar (EFN) plays an important role as plant indirect defence through the attraction of defending ants. Like all rewards produced in the context of a mutualism, however, EFN is in danger of being exploited by non-ant consumers that do not defend the plant against herbivores. Here we asked whether plants, by investing more in EFN, can improve their indirect defence, or rather increase the risk of losing this investment to EFN thieves. We used the obligate plant-ant Acacia-Pseudomyrmex system and examined experimentally in the field during the dry and the rainy seasons how variations in EFN secretion are related to (i) ant activity, to (ii) the ant-mediated defence against herbivores and (iii) the exploitation of EFN by non-ant consumers. Extrafloral investment enhanced ant recruitment and was positively related to the ant mediated defence against herbivores. The ant-mediated protection from exploiters also increased in proportion to the nectar sugar concentration. Although the daily peak of EFN production coincided with the highest activity of EFN thieves, Pseudomyrmex ferrugineus ants protected this resource effectively from exploiters. Nevertheless, the defensive effects by ants differed among seasons. During the dry season, plants grew slower and secreted more EFN than in the rainy season, and thus, experienced a higher level of ant-mediated indirect defence. Our results show that an increased plant investment in an indirect defence trait can improve the resulting defensive service against both herbivores and exploiters. EFN secretion by obligate ant-plants represents a defensive trait for which the level of investment correlates positively with the beneficial effects obtained.