Miracle-dz/UniFAR-FTUs huggingface dataset:
Is there a direct neural correlate for memory-trace formation in audition?

Recently, Haenschel et al. (2005) suggested that a positive event-related potential wave called ‘repetition positivity’ (RP) is a direct neural correlate of the formation of sensory memory traces. We investigated whether RP is elicited by familiar vowels that have previously been suggested to form accurate memory representations faster than unfamiliar sounds. No evidence for RP elicitation was found, however, even though memory representations for the vowels were formed. Instead of finding an increasing positive response along with stimulus repetition predicted by the RP hypothesis, we found that N1 and sustained potential were enhanced in amplitude for the familiar vowels as compared with unfamiliar sounds, indicating stronger activation at the auditory cortex.
Hybrid governance tensions fuelling self-reflexivity in Alternative Food Networks: the case of the Brussels GASAP (solidarity purchasing groups for peasant agriculture)

ABSTRACT This paper applies the concept of Hybrid Governance to the analysis of the GASAP (Groupe d’Achats Solidaires de l’Agriculture Paysanne), a solidarity-based producers–consumers network established in Brussels in 2006. The Hybrid Governance concept allows to capture the role of key governance tensions in driving the self-organisation, scaling out and self-reflexive dynamics of Alternative Food Networks (AFNs). The approach provides a multifaceted and sound socio-political account of the ways AFNs arise, self-organise, associate and build networks in the pursuit of their food allocation objectives, often facing a contradictory socio-institutional environment. Three types of governance tensions, i.e. organisational, resource, and institutional, as well as the interactions among them, are analysed throughout the life-course of the GASAP network. The analysis identifies three phases in the GASAP’s life-course, showing how governance tensions and their interrelations arise and play a critical role in conditioning the overall development of the organisation through time. The paper concludes with highlighting prospective values of the hybrid governance approach for the analysis of AFNs in general. These values relate to: the role of the hybrid approach in illuminating on key drivers behind the scaling out of AFNs; the hybrid governance as a tool to conceptualise and sustain the self-reflexive capacity of local food initiatives and the ways by which this approach unravels challenges to build cooperative alliances and networks among a diversity of agents in the food arena.
Identification of Ciliate Grazers of Autotrophic Bacteria in Ammonia-Oxidizing Activated Sludge by RNA Stable Isotope Probing

ABSTRACT It is well understood that protozoa play a major role in controlling bacterial biomass and regulating nutrient cycling in the environment. Little is known, however, about the movement of carbon from specific reduced substrates, through functional groups of bacteria, to particular clades of protozoa. In this study we first identified the active protozoan phylotypes present in activated sludge, via the construction of an rRNA-derived eukaryote clone library. Most of the sequences identified belonged to ciliates of the subclass Peritrichia and amoebae, confirming the dominance of surface-associated protozoa in the activated sludge environment. We then demonstrated that 13C-labeled protozoan RNA can be retrieved from activated sludge amended with 13C-labeled protozoa or 13C-labeled Escherichia coli cells by using an RNA stable isotope probing (RNA-SIP) approach. Finally, we used RNA-SIP to track carbon from bicarbonate and acetate into protozoa under ammonia-oxidizing and denitrifying conditions, respectively. RNA-SIP analysis revealed that the peritrich ciliate Epistylis galea dominated the acquisition of carbon from bacteria with access to CO2 under ammonia-oxidizing conditions, while there was no evidence of specific grazing on acetate consumers under denitrifying conditions.
A Connectionist Approach to Mapping the Human Connectome Permits Simulations of Neural Activity Within an Artificial Brain

Data-driven models drawn from statistical correlations between brain activity and behavior are used to inform theory-driven models, such as those described by computational models, which provide a mechanistic account of these correlations. This article introduces a novel multivariate approach for bootstrapping neurologically-plausible computational models that accurately encodes cortical effective connectivity from resting state functional neuroimaging data (rs-fMRI). We show that a network modularity algorithm finds comparable resting state networks within connectivity matrices produced by our approach and by the benchmark method. Unlike existing methods, however, ours permits simulation of brain activation that is a direct reflection of this cortical connectivity. Cross-validation of our model suggests that neural activity in some regions may be more consistent between individuals, providing novel insight into brain function. We suggest this method to make an important contribution toward modeling macro-scale human brain activity, and it has the potential to advance our understanding of complex neurological disorders and the development of neural connectivity.
How does linguistic complexity influence intelligibility in a German audiometric sentence intelligibility test?

Abstract Objective: We investigated if linguistic complexity contributes to the variation of the speech reception threshold in noise (SRTN) and thus should be employed as an additional design criterion in sentence tests used for audiometry. Design: Three test lists were established with sentences from the Göttingen sentence test (25). One list contained linguistically simple sentences, the other two lists contained sentences with two types of linguistic complexity. For each listener the SRTN was determined for each list. Study Sample: Younger and older listeners with normal hearing and older listeners with hearing impairment were tested. Results: Younger listeners with normal hearing showed significantly worse SRTNs on the complex lists than on the simple list. This difference could not be found for either of the older groups. Conclusions: The effect of linguistic complexity on speech recognition seems to depend on age and/or hearing status. Hence, pending further research, linguistic complexity seems less relevant as a sentence test design criterion for clinical-audiological purposes, but we argue that a test with larger variation in linguistic complexity across sentences might show a relation between linguistic complexity and speech recognition even in a clinical population. Sumario Objetivo: Investigamos si la complejidad lingüística contribuye a la variaciones en el umbrales de recepción del lenguaje en ruido (SRTN) y por tanto, si deberían usarse como un criterio adicional de diseño en las pruebas con frases que se usan en audiometría. Diseño: Se establecieron tres listas de pruebas con frases de la Prueba de Frases de Göttingen (Kollmeirer & Wesselkamp, 1997). Una lista contenía frases lingüísticamente simples, las otras dos contenían frases con dos tipos distintos de complejidad lingüística. Se determino el SRTN para cada sujeto en cada lista. Muestra del Estudio: Se evaluaron sujetos jóvenes y viejos con audición normal y sujetos viejos con alteraciones auditivas. Resultados: Los sujetos más jóvenes con audición normal mostraron resultados de SRTN significativamente peores en las listas complejas que en la lista simple. Esta diferencia no fue encontrada en ninguno de los dos grupos de sujetos más viejos. Conclusiones: Por tanto, el efecto de la complejidad lingüística sobre el reconocimiento del lenguaje parece depender de la edad y/o de la condición auditiva. Portanto – pendiente de una investigación ulterior – la complejidad lingüística parece menos relevante como criterio de diseño de pruebas de frases para propósitos clínico-audiológicos. Pero argumentamos que una prueba con una mayor variación en la complejidad lingüística en sus frases podría mostrar una relación entre complejidad lingüística y el reconocimiento del lenguaje, aún en una población clínica.
General Framework for Network Throughput Maximization in Sink-Based Energy Harvesting Wireless Sensor Networks

Due to the advancement in energy harvesting wireless sensor networks (EH-WSNs), the data collection from one-hop stationary sensor nodes using a path-constrained mobile sink has become one of the challenging issues. Toward the throughput improvement, we propose a general framework for network throughput maximization (NTM) problem by optimizing practically feasible parameters. For each proposed scenario, a mixed integer linear programming (MILP) optimization model is introduced for the problem formulation. Due to the NP-Hardness of the MILP models, we design two efficient algorithms namely as ODSAA and ODAA for two practically implementable scenarios. Having a preknowledge about the deployed location of nodes, the proposed algorithms run centrally by sink and find the sub-optimal solutions within a reasonable computation time. Furthermore, under the uniform distribution of energy harvesting, we find out two threshold points on, respectively, energy harvesting mean and battery capacity of nodes after which the network throughput reaches a stable point. Finally, simulations are conducted on a different set of node deployments, which the results confirm that the proposed algorithms significantly improve the data throughput collected by sink and also the theoretical thresholds provide a confidence interval of 90 percent.
Arming the Peace: Foreign Security Assistance and Human Rights Conditions in Post-Conflict Countries

ABSTRACT What are the effects of foreign security assistance on the quality of the peace in post-conflict countries? Despite the stakes, and the tremendous amount of weaponry and other forms of foreign military aid flowing to governments of post-conflict countries, the academic literature provides little guidance as to what effects policymakers and practitioners should expect from this type of aid. Military assistance provided to the government of a country emerging from the turmoil of civil war could enable the state to establish a monopoly on the legitimate use of force, leading to a more durable peace and greater human security. However, we contend that significant flows of military aid and weapons from foreign governments may encourage regimes to adopt more repressive approaches to governance. We investigate the impact of security assistance on human rights conditions after 171 internal armed conflicts that ended between 1956 and 2012 using a novel measure of military aid and an instrumented measure of weapons transfers. We find strong evidence that both military aid and arms transfers to post-conflict governments increase state repression.
Addressing the issue of sequence‐to‐structure alignments in comparative modeling of CASP3 target proteins

During a blind protein structure prediction experiment (the third round of the Critical Assessment of Techniques for Protein Structure Prediction; URL http://PredictionCenter.llnl.gov/casp3/), four target proteins, T0047, T0048, T0055, and T0070, were modeled by comparison. These proteins display 62%, 29%, 24%, and 19% sequence identity, respectively, to the structurally homologous proteins most similar in sequence. The issue of sequence‐to‐structure alignment in cases of low sequence homology was the main emphasis. Selection of alignments was made by constructing and evaluating three‐dimensional models based on series of samples produced mainly by automatic multiple sequence alignments. Sequence‐to‐structure alignments were correct in all but two regions, in which significant changes in target structures compared with related proteins were the source of errors. Template choice is an important determinant of model quality, and a correct selection was made of a lower homology template for modeling of T0070; however, in the case of T0055, a template with 8% greater sequence homology proved deceptive. Loops and some ungapped template regions were assigned conformations taken from other proteins. Using fragments from homologous structures led to improvement over template backbone more often than cases in which nonhomologous structures were the source. The results also indicate that side‐chain prediction accuracy depends not only on sequence similarity but also on accuracy of the backbone. Proteins Suppl 1999;3:73–80. Published 1999 Wiley‐Liss, Inc.
Muscle Size Not Density Predicts Variance in Muscle Strength and Neuromuscular Performance in Healthy Adult Men and Women

Abstract Weeks, BK, Gerrits, TAJ, Horan, SA, and Beck, BR. Muscle size not density predicts variance in muscle strength and neuromuscular performance in healthy adult men and women. J Strength Cond Res 30(6): 1577–1584, 2016—The purpose of this study was to determine the relationships between peripheral quantitative computed tomography (pQCT)–derived measures of muscle area and density and markers of muscle strength and performance in men and women. Fifty-two apparently healthy adults (26 men, 26 women; age 33.8 ± 12.0 years) volunteered to participate. Dual-energy x-ray absorptiometry (XR-800; Norland Medical Systems, Inc., Trumbull, CT, USA) was used to determine whole body and regional lean and fat tissue mass, whereas pQCT (XCT-3000; Stratec, Pforzheim, Germany) was used to determine muscle cross-sectional area (MCSA) and muscle density of the leg, thigh, and forearm. Ankle plantar flexor and knee extensor strengths were examined using isokinetic dynamometry, and grip strength was examined with dynamometry. Impulse generated during a maximal vertical jump was used as an index of neuromuscular performance. Thigh, forearm, and leg MCSA strongly predicted variance in knee extensor (R 2 = 0.77, p < 0.001) and grip strength (R 2 = 0.77, p < 0.001) and weakly predicted variance in ankle plantar flexor strength (R 2 = 0.20, p < 0.001), respectively, whereas muscle density was only a weak predictor of variance in knee extensor strength (R 2 = 0.18, p < 0.001). Thigh and leg MCSA accounted for 79 and 69% of the variance in impulse generated from a maximal vertical jump (p < 0.001), whereas thigh muscle density predicted only 18% of the variance (p < 0.002). In conclusion, we found that pQCT-derived muscle area is more strongly related to strength and neuromuscular performance than muscle density in adult men and women.
Whose Ground Truth? Accounting for Individual and Collective Identities Underlying Dataset Annotation

Human annotations play a crucial role in machine learning (ML) research and development. However, the ethical considerations around the processes and decisions that go into building ML datasets has not received nearly enough attention. In this paper, we survey an array of literature that provides insights into ethical considerations around crowdsourced dataset annotation. We synthesize these insights, and lay out the challenges in this space along two layers: (1) who the annotator is, and how the annotators' lived experiences can impact their annotations, and (2) the relationship between the annotators and the crowdsourcing platforms and what that relationship affords them. Finally, we put forth a concrete set of recommendations and considerations for dataset developers at various stages of the ML data pipeline: task formulation, selection of annotators, platform and infrastructure choices, dataset analysis and evaluation, and dataset documentation and release.
Telemonitoring for chronic obstructive pulmonary disease: a cost and cost-utility analysis of a randomised controlled trial

We compared the costs and cost-effectiveness of telemonitoring vs usual care for patients with chronic obstructive pulmonary disease (COPD). A total of 256 patients were randomised to either telemonitoring or usual care. In the telemonitoring arm, the touch-screen telemonitoring equipment transmitted data to clinical teams monitoring the patients. Total healthcare costs were estimated over a 12-month period from a National Health Service perspective and quality adjusted life year (QALYs) were estimated by the EQ-5D tool. Telemonitoring was not significantly more costly than usual care (mean difference per patient £2065.90 (P < 0.18). The increased costs were predominantly due to telemonitoring service costs and non-significantly higher secondary care costs. Telemonitoring for COPD was not cost-effective at a base case of £137,277 per QALY with only 15% probability of being cost-effective at the usual threshold of £30,000 per QALY. Although there was some statistical and methodological uncertainty in the measures used, telemonitoring was not cost-effective in the sensitivity analyses performed. It seems unlikely that a telemonitoring service of the kind that was trialled would be cost-effective in providing care for people with COPD.
A non‐contact suspension culture approach to the culture of osteogenic cells derived from a CD49elow subpopulation of human bone marrow‐derived cells

We demonstrate that adult human bone marrow (BM) contains a population of mesenchymal stromal cells (MSCs) that can be expanded in non‐adherent, cytokine‐dependent, suspension culture conditions for at least 42 days. The cells generated during suspension culture lacked detectable levels of gene expression associated with differentiated mesenchymal cell types, including bone, muscle and fat, suggesting that suspension culture maintains MSCs in an uncommitted state. However, when these undifferentiated cells were taken out of suspension culture and placed in adherent osteogenic conditions, osteogenic genes were upregulated and morphologically identifiable bone matrix was elaborated. Flow cytometric analysis of uncultured, density gradient‐separated human BM revealed that colony forming unit‐fibroblast (CFU‐F) and CFU‐osteoblast (CFU‐O) activity was associated with a CD45− CD49elow phenotype. Importantly, suspension‐grown MSCs, capable of CFU‐F and CFU‐O development, maintained the CD45−CD49elow phenotype whereas MSCs directly cultured under adherent conditions rapidly upregulated CD49e expression and were associated with a CD45−CD49ehigh phenotype. Tracking the CD49elow expression under suspension culture conditions provides a mechanism to isolate an expanding suspension‐grown MSC population with osteogenic potential. This could provide a potential strategy to isolate populations of MSCs, with functional osteogenic capacity, in a scalable and controllable culture system for therapeutic applications. Biotechnol. Bioeng. 2007;98: 1195–1208. © 2007 Wiley Periodicals, Inc.
Roles for fibrinogen, immunoglobulin and complement in platelet activation promoted by Staphylococcus aureus clumping factor A

Staphylococcus aureus is an important cause of infective endocarditis (IE) in patients without a history of prior heart valve damage. The ability to stimulate the activation of resting platelets and their subsequent aggregation is regarded as an important virulence factor of bacteria that cause IE. Clumping factor A is the dominant surface protein responsible for platelet activation by S. aureus cells in the stationary phase of growth. This study used Lactococcus lactis as a surrogate host to study the mechanism of ClfA‐promoted platelet activation. Expression of ClfA from a nisin‐inducible promoter demonstrated that a minimum level of surface‐expressed ClfA was required. Using platelets that were purified from plasma, the requirement for both bound fibrinogen and immunoglobulin was demonstrated. The immunoglobulin G (IgG) requirement is consistent with the potent inhibition of platelet activation by a monoclonal antibody specific for the platelet FcγRIIa receptor. Furthermore the IgG must contain antibodies specific for the ClfA A domain. A model is proposed whereby bacterial cells armed with a sufficient number of surface‐bound fibrinogen molecules can engage resting platelet glycoprotein GPIIb/IIIa, aided by bound IgG molecules, which encourages the clustering of FcγRIIa receptors. This can trigger activation of signal transduction leading to activation of GPIIb/IIIa and aggregation of platelets. In addition, analysis of a mutant of ClfA totally lacking the ability to bind fibrinogen revealed a second, although less efficient, mechanism of platelet activation. The fibrinogen‐independent pathway required IgG and complement deposition to trigger platelet aggregation
Effects of Harvesting Flowers from Shrubs on the Persistence and Abundance of Wild Shrub Populations at Multiple Spatial Extents

Abstract: Wildflower harvesting is an economically important activity of which the ecological effects are poorly understood. We assessed how harvesting of flowers affects shrub persistence and abundance at multiple spatial extents. To this end, we built a process‐based model to examine the mean persistence and abundance of wild shrubs whose flowers are subject to harvest (serotinous Proteaceae in the South African Cape Floristic Region). First, we conducted a general sensitivity analysis of how harvesting affects persistence and abundance at nested spatial extents. For most spatial extents and combinations of demographic parameters, persistence and abundance of flowering shrubs decreased abruptly once harvesting rate exceeded a certain threshold. At larger extents, metapopulations supported higher harvesting rates before their persistence and abundance decreased, but persistence and abundance also decreased more abruptly due to harvesting than at smaller extents. This threshold rate of harvest varied with species’ dispersal ability, maximum reproductive rate, adult mortality, probability of extirpation or local extinction, strength of Allee effects, and carrying capacity. Moreover, spatial extent interacted with Allee effects and probability of extirpation because both these demographic properties affected the response of local populations to harvesting more strongly than they affected the response of metapopulations. Subsequently, we simulated the effects of harvesting on three Cape Floristic Region Proteaceae species and found that these species reacted differently to harvesting, but their persistence and abundance decreased at low rates of harvest. Our estimates of harvesting rates at maximum sustainable yield differed from those of previous investigations, perhaps because researchers used different estimates of demographic parameters, models of population dynamics, and spatial extent than we did. Good demographic knowledge and careful identification of the spatial extent of interest increases confidence in assessments and monitoring of the effects of harvesting. Our general sensitivity analysis improved understanding of harvesting effects on metapopulation dynamics and allowed qualitative assessment of the probability of extirpation of poorly studied species.