Miracle-dz/UniFAR-FTUs huggingface dataset:
Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity

Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and DNA sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches.
A Conserved Telomerase Motif within the Catalytic Domain of Telomerase Reverse Transcriptase Is Specifically Required for Repeat Addition Processivity

ABSTRACT Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of the telomere terminal repeats. The catalytic protein subunit of the telomerase complex, known as TERT, possesses a reverse transcriptase (RT) domain that mediates nucleotide addition. The RT domain of TERT is distinguishable from retroviral and retrotransposon RTs in having a sizable insertion between conserved motifs A and B′, within the so-called fingers domain. Sequence analysis revealed the existence of conserved residues in this region, named IFD (insertion in fingers domain). Mutations of some of the conserved residues in Saccharomyces cerevisiae TERT (Est2p) abolished telomerase function in vivo, testifying to their importance. Significant effects of the mutations on telomerase activity in vitro were observed, with most of the mutants exhibiting a uniform reduction in activity regardless of primer sequence. Remarkably, one mutant manifested a primer-specific defect, being selectively impaired in extending primers that form short hybrids with telomerase RNA. This mutant also accumulated products that correspond to one complete round of repeat synthesis, implying an inability to effect the repositioning of the DNA product relative to the RNA template that is necessary for multiple repeat addition. Our results suggest that the ability to stabilize short RNA-DNA hybrids is crucial for telomerase function in vivo and that this ability is mediated in part by a more elaborate fingers domain structure.
The Impact of Social Media on Dissemination and Implementation of Clinical Practice Guidelines: A Longitudinal Observational Study

Background Evidence-based clinical practice guidelines (CPGs) are statements that provide recommendations to optimize patient care for a specific clinical problem or question. Merely reading a guideline rarely leads to implementation of recommendations. The American Academy of Neurology (AAN) has a formal process of guideline development and dissemination. The last few years have seen a burgeoning of social media such as Facebook, Twitter, and LinkedIn, and newer methods of dissemination such as podcasts and webinars. The role of these media in guideline dissemination has not been studied. Systematic evaluation of dissemination methods and comparison of the effectiveness of newer methods with traditional methods is not available. It is also not known whether specific dissemination methods may be more effectively targeted to specific audiences. Objective Our aim was to (1) develop an innovative dissemination strategy by adding social media-based dissemination methods to traditional methods for the AAN clinical practice guidelines “Complementary and alternative medicine in multiple sclerosis” (“CAM in MS”) and (2) evaluate whether the addition of social media outreach improves awareness of the CPG and knowledge of CPG recommendations, and affects implementation of those recommendations. Methods Outcomes were measured by four surveys in each of the two target populations: patients and physicians/clinicians (“physicians”). The primary outcome was the difference in participants’ intent to discuss use of complementary and alternative medicine (CAM) with their physicians or patients, respectively, after novel dissemination, as compared with that after traditional dissemination. Secondary outcomes were changes in awareness of the CPG, knowledge of CPG content, and behavior regarding CAM use in multiple sclerosis (MS). Results Response rates were 25.08% (622/2480) for physicians and 43.5% (348/800) for patients. Awareness of the CPG increased after traditional dissemination (absolute difference, 95% confidence interval: physicians 36%, 95% CI 25-46, and patients 10%, 95% CI 1-11) but did not increase further after novel dissemination (physicians 0%, 95% CI -11 to 11, and patients -4%, 95% CI -6 to 14). Intent to discuss CAM also increased after traditional dissemination but did not change after novel dissemination (traditional: physicians 12%, 95% CI 2-22, and patients 19%, 95% CI 3-33; novel: physicians 11%, 95% CI -1 to -21, and patients -8%, 95% CI -22 to 8). Knowledge of CPG recommendations and behavior regarding CAM use in MS did not change after either traditional dissemination or novel dissemination. Conclusions Social media-based dissemination methods did not confer additional benefit over print-, email-, and Internet-based methods in increasing CPG awareness and changing intent in physicians or patients. Research on audience selection, message formatting, and message delivery is required to utilize Web 2.0 technologies optimally for dissemination.
MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs

We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs). The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD) and Multicluster, Mobile, Multimedia radio network (MMM), consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes) of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime.
Testing the Legend: Horace, Silius Italicus and the Case of Marcus Atilius Regulus

After Marcus Atilius Regulus made inroads into North Africa as consul in 256 B.C. during the first Punic War, the Carthaginians were apparently ready to negotiate a settlement, but Regulus offered terms so harsh that they were refused out of hand. At this point Xanthippus, the Spartan mercenary-general, arrived on the Carthaginian side and soon made an impact as a shrewd and uplifting leader, not least because, in a dramatic reversal of fortunes, he captured Regulus, by then proconsul, by ambush in 255. Regulus' subsequent fate, embellished in the later literary-historical tradition, was enshrined in die familiar version here represented by Valerius Maximus: Sed quae ad custodiam religionis attinent, nescio an omnes M. Atilius Regulus praecesserit, qui ex victore speciosissimo insidiis Hasdrubalis et Xanthippi Lacedaemonii ducis ad miserabilem captiui fortunam deductus ac missus ad senatum populumque Romanum legatus, ut se et uno et sene complures Poenorum iuuenes pensarentur, in contrarium dato consilio Carthaginem petiit, non quid ignarus ad quam crudeles quamque merito sibi infestos † deos † reuerteretur, uerum quia iis iurauerat, si captiui eorum redditi non forent, ad eos sese rediturum. potuerunt profecto di immortales efferatam mitigare saeuitiam. ceterum, quo clarior esset Atili gloria, Carthaginienses moribus suis uti passi sunt, tertio Punico bello religiosissimi spiritus tarn crudeliter uexati urbis eorum interitu iusta exacturi piacula.
Multi-Agent Simulations of the Evolution of Combinatorial Phonology

A fundamental characteristic of human speech is that it uses a limited set of basic building blocks (phonemes, syllables), that are put to use in many different combinations to mark differences in meaning. This article investigates the evolution of such combinatorial phonology with a simulated population of agents. We first argue that it is a challenge to explain the transition from holistic to combinatorial phonology, as the first agent that has a mutation for using combinatorial speech does not benefit from this in a population of agents that use a holistic signaling system. We then present a solution for this evolutionary deadlock. We present experiments that show that when a repertoire of holistic signals is optimized for distinctiveness in a population of agents, it converges to a situation in which the signals can be analyzed as combinatorial, even though the agents are not aware of this structure. We argue that in this situation adaptations for productive combinatorial phonology can spread.
An Integrated Self-Aware Cognitive Architecture

Abstract : The result of our BICA Phase I research effort is the specification of a computational cognitive architecture that is capable of human-like cognition, learning and social behavior in a wide range of real-world situations and paradigms set in virtual environments. Our architecture focuses on the higher-level cognitive processes involved in human cognition and is designed to be integrated into a larger end-to-end architecture that includes lower level sensing and action. The main feature of our architecture is the notion of self aware cognition that we believe is necessary for human-like cognitive growth. Our approach is inspired by studies of the human brain-mind: in particular, by theoretical models of representations of agency in the higher associative human brain areas. This feature (a theory of mind including representations of one's self) allows the system to maintain human-like attention, focus on the most relevant features and aspects of a situation, and come up with ideas and initiatives that may not follow from formal logic. The result is a robust cognitive system capable of significant cognitive growth.
Linear Classification and Selective Sampling Under Low Noise Conditions

We provide a new analysis of an efficient margin-based algorithm for selective sampling in classification problems. Using the so-called Tsybakov low noise condition to parametrize the instance distribution, we show bounds on the convergence rate to the Bayes risk of both the fully supervised and the selective sampling versions of the basic algorithm. Our analysis reveals that, excluding logarithmic factors, the average risk of the selective sampler converges to the Bayes risk at rate N-(1+α)(2+α)/2(3+α) where N denotes the number of queried labels, and α > 0 is the exponent in the low noise condition. For all α > √ - 1 ≈ 0.73 this convergence rate is asymptotically faster than the rate N-(1+α)/(2+α) achieved by the fully supervised version of the same classifier, which queries all labels, and for α → ∞ the two rates exhibit an exponential gap. Experiments on textual data reveal that simple variants of the proposed selective sampler perform much better than popular and similarly efficient competitors.
The use of mixed distribution models to determine bout criteria for analysis of animal behaviour.

Feeding behaviour consists of feeding events, separated by non-feeding intervals. Feeding events are often clustered into bouts, which may be called meals. Grouping feeding events into meals requires the determination of a bout or meal criterion, that is, the longest interval accepted as part of a meal. Tolkamp & Kyriazakis (1999a) proposed a three-Gaussian model to estimate meal criteria. The three Gaussians each described the frequency distribution of the log(e)-transformed lengths of a population of intervals. These populations were thought to be: (1) short intervals within meals; (2) intervals within meals during which animals drink; (3) intervals between meals. This model predicted that the probability of an animal starting a meal would first increase, and then decrease with time since the last meal. This contrasts with expectations based on the satiety concept, which predicts that the probability of an animal starting a meal will increase with time since the last meal. This discrepancy is related to the symmetrical nature of the Gaussian distribution. Alternatively, the two-parameter Weibull distribution can take a skewed form and perhaps is more suitable to describe the different populations of intervals. In this study, models consisting of combinations of Gaussian and Weibull distributions were examined for their suitability to describe the observed feeding behaviour of cows. Weibulls did not improve the description of the populations of within-meal intervals, compared to Gaussians. However, the Weibull distribution was found to describe the between-meal population of intervals statistically better than the Gaussian. Additionally, this inclusion of a Weibull, as opposed to a Gaussian, resulted in predictions that were in better agreement with the satiety concept over the entire range of interval lengths observed. A model based on Gaussians to describe the within-meal populations of intervals and a Weibull to describe the population of between-meal intervals is, therefore, proposed. This model leads to biologically more satisfactory estimates of bout criteria than previous models and is likely to be applicable both across species and behaviours.
Surveillance face hallucination via variable selection and manifold learning

In this paper, we propose a new two-step face hallucination method to induce a high-resolution (HR) face image from a low-resolution (LR) observation. Especially for low-quality surveillance face image, an RBF-PLS based variable selection method is presented for the reconstruction of global face image. Further more, in order to compensate for the reconstruction errors, which are lost high frequency detailed face features, the Neighbor Embedding (NE) based residue face hallucination algorithm is used. Compared with current methods, the proposed RBF-PLS based method can generate a global face more similar to the original face and less sensitive to noise, moreover, the NE algorithm can reduce the reconstruction errors caused by misalignment on the basis of a carefully designed search strategy. Experiments show the superiority of the proposed method compared with some state-of-the-art approaches and the efficacy both in simulation and real surveillance condition.
Differential Buck DC–DC Chopper Mode Inverters With High-Frequency Link

A circuit configuration and a circuit topological family of differential buck dc-dc chopper mode inverter with high-frequency link are proposed in this paper. The circuit configuration, the topology family, the instantaneous output voltage and the capacitance current feedback control strategy, the steady principle characteristic, and the design criteria for the key circuit parameters are fully investigated in this paper. The circuit configuration is differentially composed of two identical isolated bidirectional buck dc-dc choppers with the same input and output LC filters. These two choppers generate unipolarity sinusoidal pulse width modulation voltage waveforms with positive and negative half low-frequency cycle separately. Each dc-dc chopper consists of high frequency inverter, high frequency transformer, and high frequency rectifier. The circuit topological family includes six circuit topologies, namely, one-transistor forward mode, push-pull mode, push-pull forward mode, two-transistor forward mode, half-bridge mode, and full-bridge mode. Taking one-transistor mode circuit topology as example, the prototype is designed and implemented. The results from the theoretical analysis and principle test indicate that the inverters have advantages of high frequency galvanic isolation, simple topology, bidirectional power flow, single-stage power conversion, high conversion efficiency, high-quality output voltage waveform, and strong adaptability to various loads.
Bit loading with BER-constraint for multicarrier systems

We present discrete adaptive bit loading algorithms for multicarrier systems with uniform (nonadaptive) power allocation operating in a frequency selective fading environment. The algorithms try to maximize the overall throughput of the system while guaranteeing that the mean bit error rate (BER) remains below a prescribed threshold. We also study the impact of imperfect subcarrier signal-to-noise ratio information on throughput performance. Results show that the proposed algorithms have approximately the same throughput and mean BER as the optimal allocation while having a significantly lower computational complexity relative to other algorithms with near-optimal allocations. Moreover, when compared with algorithms that employ approximations to water filling, the computational complexity is comparable while the overall throughput is closer to the optimum.
Beringian Standstill and Spread of Native American Founders

Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the intial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.
Validation of publication of new names and new combinations previously effectively published outside the IJSEM.

Correspondence Jean Euzéby email address can be found at www.bacterio. net The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
Multi-Recipient Encryption Schemes: Security Notions and Randomness Re-Use

This paper begins by rening Kurosawa’s [Ku] denitions of security for multi-recipient encryption schemes (MRESs). It then considers a subclass of MRESs, that are formed by transforming standard encryption schemes via a natural technique called randomness re-use, and that oer important performance benets. The main result is a way to avoid ad-hoc analyses of such schemes: we provide a general test that can be applied to a standard encryption scheme to determine whether the associated randomness re-using MRES is secure. This is applied to identify numerous specic secure and ecient randomness re-using MRESs. The results and applications cover both asymmetric and symmetric encryption.
GLVR1, a receptor for gibbon ape leukemia virus, is homologous to a phosphate permease of Neurospora crassa and is expressed at high levels in the brain and thymus

The human gene GLVR1 has been shown to render mouse cells sensitive to infection by gibbon ape leukemia virus. This indication that the GLVR1 protein acts as a virus receptor does not reveal the protein's normal physiological role. We now report that GLVR1 is homologous to pho-4+, a phosphate permease of Neurospora crassa, at a level sufficiently high to predict that GLVR1 is also a transport protein, although the substrate transported remains unknown. To characterize the gene further, we have cloned cDNA for the mouse homolog of the gene, Glvr-1. The sequence of the murine protein differs from that of the human protein in 10% of residues, and it may be presumed that some of these differences are responsible for the inability of gibbon ape leukemia virus to infect mouse fibroblasts. Glvr-1 RNA is most abundant in mouse brain and thymus, although it is present in all tissues examined. The pattern of RNA expression found in mouse tissues was also found in rat tissues, in which the RNA was expressed at high levels in all compartments of the brain except the caudate nucleus and was expressed most abundantly early in embryogenesis. Thus, high-level expression of Glvr-1 appears to be restricted to specific tissues and may have developmental consequences.