Miracle-dz/UniFAR-FTUs huggingface dataset:
Author ' s personal copy A stochastic model for the development of Bateson – Dobzhansky – Muller incompatibilities that incorporates protein interaction networks

Speciation is characterized by the development of reproductive isolating barriers between diverging groups. Intrinsic post-zygotic barriers of the type envisioned by Bateson, Dobzhansky, and Muller are deleterious epistatic interactions among loci that reduce hybrid fitness, leading to reproductive isolation. The first formal population genetic model of the development of these barriers was published by Orr in 1995, and here we develop a more general model of this process by incorporating finite protein–protein interaction networks, which reduce the probability of deleterious interactions in vivo. Our model shows that the development of deleterious interactions is limited by the density of the protein–protein interaction network. We have confirmed our analytical predictions of the number of possible interactions given the number of allele substitutions by using simulations on the Saccharomyces cerevisiae protein– protein interaction network. These results allow us to define the rate at which deleterious interactions are expected to form, and hence the speciation rate, for any protein–protein interaction network. 2012 Elsevier Inc. All rights reserved.
An Iterative Method for Calculating Robust Rating Scores

Online rating systems are widely used to facilitate making decisions on the web. For fame or profit, people may try to manipulate such systems by posting unfair evaluations. Therefore, determining objective rating scores of products or services becomes a very important yet difficult problem. Existing solutions are mostly majority based, also employing temporal analysis and clustering techniques. However, they are still vulnerable to sophisticated collaborative attacks. In this paper we propose an iterative rating algorithm which is very robust against collusion attacks as well as random and biased raters. Unlike previous iterative methods, our method is not based on comparing submitted evaluations to an approximation of the final rating scores, and it entirely decouples credibility assessment of the cast evaluations from the ranking itself. This makes it more robust against sophisticated collusion attacks than the previous iterative filtering algorithms. We provide a rigorous proof of convergence of our algorithm based on the existence of a fixed point of a continuous mapping which also happens to be a stationary point of a constrained optimization objective. We have implemented and tested our rating method using both simulated data as well as real world movie rating data. Our tests demonstrate that our model calculates realistic rating scores even in the presence of massive collusion attacks and outperforms well-known algorithms in the area. The results of applying our algorithm on the real-world data obtained from MovieLens conforms highly with the rating scores given by Rotten Tomatoes movie critics as domain experts for movies.
A rmative Action in a Competitive Economy

We consider a model of endogenous human capital formation with competitively determined wages. In the presence of two distinguishable, but ex ante identical groups of workers, we show that discrimination is sustainable in equilibrium, even if the corresponding model with a single group of workers has a unique equilibrium. An a rmative action policy consisting of a quota may \fail" in the sense that there still may be equilibria where groups are treated di erently. However, the incentives to invest for agents in the discriminated group are improved by a rmative action if the initial equilibrium is the most discriminatory equilibrium in the model without the policy. The welfare e ects are ambiguous. We demonstrate that it is possible that the policy makes the intended bene ciaries worse o : even if the starting point is the most discriminatory equilibrium the expected payo may decrease for all agents in the target group.
C-reactive protein level and risk of aging macula disorder: The Rotterdam Study.

OBJECTIVE To examine whether C-reactive protein (CRP) level is a risk factor for aging macula disorder (AMD) in a general population. METHODS We examined serum high-sensitivity CRP (HsCRP) levels in 4914 participants of the population-based Rotterdam Study at risk for AMD. After a mean follow-up of 7.7 years, 561 cases of early and 97 cases of late incident AMD (iAMD) were identified. We used Cox proportional hazards regression models to estimate hazard ratios and corresponding 95% confidence intervals (CIs). RESULTS After adjustment for age and sex, hazard ratios were 1.11 (95% CI, 1.02-1.21) per standard deviation increase in HsCRP level for early iAMD and 1.28 (95% CI, 1.02-1.60) for late iAMD. Hazard ratios for early iAMD increased per quartile increase in HsCRP level as follows: second quartile, 1.19 (95% CI, 0.94-1.52); third quartile, 1.29 (95% CI, 1.01-1.64); and fourth quartile, 1.33 (95% CI, 1.05-1.70). The risk of late iAMD was higher in all upper quartiles of HsCRP. CONCLUSION Elevated baseline levels of HsCRP were associated with the development of early and late AMD in this large population-based cohort.
Geographic mosaic of symbiont selectivity in a genus of epiphytic cyanolichens

In symbiotic systems, patterns of symbiont diversity and selectivity are crucial for the understanding of fundamental ecological processes such as dispersal and establishment. The lichen genus Nephroma (Peltigerales, Ascomycota) has a nearly cosmopolitan distribution and is thus an attractive model for the study of symbiotic interactions over a wide range of spatial scales. In this study, we analyze the genetic diversity of Nephroma mycobionts and their associated Nostoc photobionts within a global framework. The study is based on Internal Transcribed Spacer (ITS) sequences of fungal symbionts and tRNALeu (UAA) intron sequences of cyanobacterial symbionts. The full data set includes 271 Nephroma and 358 Nostoc sequences, with over 150 sequence pairs known to originate from the same lichen thalli. Our results show that all bipartite Nephroma species associate with one group of Nostoc different from Nostoc typically found in tripartite Nephroma species. This conserved association appears to have been inherited from the common ancestor of all extant species. While specific associations between some symbiont genotypes can be observed over vast distances, both symbionts tend to show genetic differentiation over wide geographic scales. Most bipartite Nephroma species share their Nostoc symbionts with one or more other fungal taxa, and no fungal species associates solely with a single Nostoc genotype, supporting the concept of functional lichen guilds. Symbiont selectivity patterns within these lichens are best described as a geographic mosaic, with higher selectivity locally than globally. This may reflect specific habitat preferences of particular symbiont combinations, but also the influence of founder effects.
WINDMILL-THE USE OF A PARSING ALGORITHM TO PRODUCE PREDICTIONS FOR DISABLED PERSONS

Augmentative and Alternative Communication (AAC) systems are designed to enable people to communicate with those around them when they are unable to do so themselves. Such people include those su ering from congenital diseases, such as cerebral palsy; progressive diseases, such as motor-neuron disease and multiple sclerosis; or those who have been the victim of a trauma, such as a head injury. The devices employed to aid such subjects can be categorised into four groups:
Exact Bayesian structure learning from uncertain interventions

We show how to apply the dynamic programming algorithm of Koivisto and Sood [KS04, Koi06], which computes the exact posterior marginal edge probabilities p(Gij = 1|D) of a DAG G given data D, to the case where the data is obtained by interventions (experiments). In particular, we consider the case where the targets of the interventions are a priori unknown. We show that it is possible to learn the targets of intervention at the same time as learning the causal structure. We apply our exact technique to a biological data set that had previously been analyzed using MCMC [SPP05, EW06, WGH06].
Leveraging low-dimensional postures to resolve coiled shapes in the nematode C . elegans

Low-dimensionality appears as both an aid in the analysis of complex systems, as well as a framework for understanding the underlying processes. Here, we further exploit the previously observed low-dimensionality of C. elegans 2D body postures to develop a video tracking algorithm. The novel algorithm, based on a generative model for C. elegans body shapes, is able to accurately quantify the motor behavior of the worm — not just for simple body shapes, but also for complex, self-occluding body shapes that occur during reorientation manoeuvres. We apply our algorithm to fully quantify C. elegans behavior during two different scenarios: a thermally-induced escape response, and free crawling. Surprisingly, we find that the deep turns of C. elegans (‘omega turns’) are not a single class of behavior, but that they can be classified into two distinct types, based on their amplitude and overall orientation change. A manuscript based on Chapters 4 and 5 has been accepted for publication in eLife as: O.D. Broekmans, J.B. Rodgers, W.S. Ryu and G.J. Stephens, Resolving coiled shapes reveals new reorientation behaviors in C. elegans (2016). For this work, JBR performed the experiments. GJS conceived the research. I performed the data analysis, wrote data analysis software and tracking algorithms, and wrote the text of the chapter. WSR and GJS provided input on the data analysis and the manuscript.
Central Contributions to Acoustic Variation in Birdsong

Birdsong is a learned behavior remarkable for its high degree of stereotypy. Nevertheless, adult birds display substantial rendition-by-rendition variation in the structure of individual song elements or “syllables. ” Previous work suggests that some of this variation is actively generated by the avian basal ganglia circuitry for purposes of motor exploration. However, it is unknown whether and how natural variations in premotor activity drive variations in syllable structure. Here, we recorded from the premotor nucleus robust nucleus of the arcopallium (RA) in Bengalese finches and measured whether neural activity covaried with syllable structure across multiple renditions of individual syllables. We found that variations in premotor activity were significantly correlated with variations in the acoustic features (pitch, amplitude, and spectral entropy) of syllables in approximately a quarter of all cases. In these cases, individual neural recordings predicted 8.5 ± 0.3% (mean ± SE) of the behavioral variation, and in some cases accounted for 25% or more of trial-by-trial variations in acoustic output. The prevalence and strength of neuron–behavior correlations indicate that each acoustic feature is controlled by a large ensemble of neurons that vary their activity in a coordinated manner. Additionally, we found that correlations with pitch (but not other features) were predominantly positive in sign, supporting a model of pitch production based on the anatomy and physiology of the vocal motor apparatus. Collectively, our results indicate that trial-by-trial variations in spectral structure are indeed under central neural control at the level of RA, consistent with the idea that such variation reflects motor exploration.
Diagnosis of Whooping Cough in Switzerland: Differentiating Bordetella pertussis from Bordetella holmesii by Polymerase Chain Reaction

Bordetella holmesii, an emerging pathogen, can be misidentified as Bordetella pertussis by routine polymerase chain reaction (PCR). In some reports, up to 29% of the patients diagnosed with pertussis have in fact B. holmesii infection and invasive, non-respiratory B. holmesii infections have been reported worldwide. This misdiagnosis undermines the knowledge of pertussis' epidemiology, and may lead to misconceptions on pertussis vaccine's efficacy. Recently, the number of whooping cough cases has increased significantly in several countries. The aim of this retrospective study was to determine whether B. holmesii was contributing to the increase in laboratory-confirmed cases of B. pertussis in Switzerland. A multiplex species-specific quantitative PCR assay was performed on 196 nasopharyngeal samples from Swiss patients with PCR-confirmed Bordetella infection (median age: 6 years-old, minimum 21 days-old, maximum 86 years-old), formerly diagnosed as Bordetella pertussis (IS481+). No B. holmesii (IS481+, IS1001−, hIS1001+) was identified. We discuss whether laboratories should implement specific PCR to recognize different Bordetella species. We conclude that in Switzerland B. holmesii seems to be circulating less than in neighboring countries and that specific diagnostic procedures are not necessary routinely. However, as the epidemiological situation may change rapidly, periodic reevaluation is suggested.
Model transitions in descending FLVQ

Fuzzy learning vector quantization (FLVQ), also known as the fuzzy Kohonen clustering network, was developed to improve performance and usability of on-line hard-competitive Kohnen's vector quantization and soft-competitive self organizing map (SOM) algorithms. The FLVQ effectiveness seems to depend on the range of change of the weighting exponent m(t). In the first part of this work, extreme m(t) values (1 and 1, respectively) are employed to investigate FLVQ asymptotic behaviors. This analysis shows that when m(t) tends to either one of its extremes, FLVQ is affected by trivial vector quantization, which causes centroids collapse in the grand mean of the input data set. No analytical criterion has been found to improve the heuristic choice of the range of m(t) change. In the second part of this paper, two FLVQ and SOM classification experiments of remote sensed data are presented. In these experiments the two nets are connected in cascade to a supervised second stage, based on the delta rule. Experimental results confirm that FLVQ performance can be greatly affected by the user's definition of the range of change of the weighting exponent. Moreover, FLVQ shows instability when its traditional termination criterion is applied. Empirical recommendations are proposed for the enhancement of FLVQ robustness. Both the analytical and the experimental data reported seem to indicate that the choice of the range of m(t) change is still open to discussion and that alternative clustering neural-network approaches should be developed to pursue during training: 1) monotone reduction of the neurons' learning rate and 2) monotone reduction of the overlap among neuron receptive fields.
Arabic phonemes recognition system based on malay speakers using neural network

Arabic language can be used by native and nonnative speakers; due to Arabic is the language of the holy book of Muslims. In this paper, Arabic phoneme recognition system is proposed based on Malay speakers. This system consists of three main stages. The first stage is noise reduction and it aims to enhance the phoneme signals by excluding the unvoiced signals and keep only the voiced signal. Wiener filter is adapted to accomplish this task. The second stage is based on Mel-Frequency Cepstral Coefficients method to extract a vector of features to represent each phoneme signal. Eventually, pattern recognition neural network is designed as recognizer. The proposed system produces sufficient outcomes with 20 hidden neurons.
The severity of developmental hearing loss does not determine the magnitude of synapse dystfunction

The loss of auditory experience can disrupt synapse function, particularly when it occurs during development. However, the extent of hearing loss can vary from mild to profound, and the duration of hearing loss can vary from days to years. Here, we asked whether the dysfunction of central auditory synapses scales with the severity of hearing loss. The manipulations range from mild sound attenuation to complete deafferentation at the time of hearing onset. Synapse function is measured in central auditory structures from the cochlear nucleus to cortex. The core finding is that even a ~25 dB attenuation in sensation level produces a quantitatively similar change to synaptic currents and membrane properties, as compared to deafferentation. Therefore, profound changes to central processing may occur even when developmental hearing loss is mild, provided it occurs when sound is first transduced.
Perception of Affordances for Striking Regulates Interpersonal Distance Maneuvers of Intermediate and Expert Players in Kendo Matches

ABSTRACT In daily life and in many sports, people must adjust interpersonal distance between themselves and others based on task constraints and goals. For example, in martial arts such as boxing and kendo, players must adjust interpersonal distance before starting or defending strikes. However, it is not clear what players perceive and how players use this perceptual information to maneuver interpersonal distance and start strikes during real matches. We investigated players' perception of affordances and the criteria for perception and behaviors, and how these change with expertise, using real kendo matches as a one-on-one opponent task. Players perceived affordances for striking for themselves and for their opponent based on subtle interpersonal distance changes and clearly switched stepping forward and backward. In addition, players perceived affordances for strike success and entered closer interpersonal distance than the possible striking distance to increase their own striking ability and exited the closer distance to decrease their opponent's striking ability, respectively. Furthermore, expert players stayed in and moved into the critical interpersonal distance more frequently than intermediate players did. Our research indicates a relationship between action-scaled affordance perception of and maneuvers associated with interpersonal distance in one-on-one situations that occur in daily life and in many sports.
Differentiated Instruction: One School’s Survey Analysis

The purposes of this study are to investigate teachers’ perceptions of differentiated instruction and its implementation in day-to-day teaching within the classroom. A small sample of thirty-seven middle school teachers participated in this study. Thirty-three of them completed a fifty-item survey and four participated in a semi-structured individual interview. The findings support the premise that teachers know what differentiated instruction is theoretically or conceptually, but may not be implementing the corresponding strategies in their classrooms. One important implication of this study is that future staff development should continue to reinforce the necessity of differentiated instruction, correct the various misconceptions about differentiated instruction, and provide adequate training for the actual implementation of differentiated instruction.
Transient Global Amnesia as the First Clinical Symptom for Malignant B-Cell Lymphoma with Central Nervous System Involvement

We present the case of an elderly male who was diagnosed with transient global amnesia (TGA), only to be diagnosed with B-cell lymphoma with central nervous system involvement a few weeks later. This is the first ever case reported in literature with lymphoma presenting as TGA. Literature review and pertinent points regarding high-yield imaging protocol for presumed TGA patients are discussed.
University Students' Perceptions of Electronic Rubric-Based Assessment.

Integrating technology into assessment processes in university contexts can change educational practices, in some cases by fostering self-regulated learning and in others by enabling more interactivity and participation among users. In this paper, we examine the opportunity to use electronic rubrics (erubrics) to assess learning. We report a student perception analysis on the process of assessment with electronic rubric at the university level. In this study, erubrics are applied in a Preschool (3-6 year-olds) and Primary Education (6-12 year-olds) pre-service teacher context. 87 students from two Spanish universities enrolled in a quarterly course of Education Technologies in the Faculty of Education used erubrics (© Gtea) for self- and peer assessment. Through a design-based research, the study concluded that electronic rubric is an assessment facilitating resource for students as participants in the assessment process. Students tend to be satisfied with their use in both self- and peer assessment and acknowledge certain advantages regarding rubric features, implementation process and impact on learning process
Pharmacokinetics and pharmacodynamics of plasma clofarabine and cellular clofarabine triphosphate in patients with acute leukemias.

PURPOSE The purpose of our study was to investigate the pharmacology of clofarabine and its triphosphate and the pharmacodynamic actions in circulating blasts obtained from acute leukemia patients who entered a Phase I clinical trial of clofarabine. EXPERIMENTAL DESIGN Adults with refractory acute leukemias including lymphoblastic (ALL), myelogenous (AML) and chronic myelogenous leukemia in blastic phase (CML-BP) received clofarabine from 4 mg/m(2) to 55 mg/m2/day for 5 days as a 1-h i.v. infusion. A total of 26 of the 32 patients were studied for pharmacological investigations. RESULTS The maximum tolerated dose was 40 mg/m2/day for 5 days. Plasma pharmacology studies done in 25 patients indicate a linear increase in the plasma clofarabine concentration with increasing doses. At 40 mg/m2 the median plasma clofarabine level was 1.5 micro M (range, 0.42-3.2 micro M; n = 7). Cellular pharmacokinetic studies done at the end of the first clofarabine infusion in 26 patients appeared dose proportional but showed a wide variation in the concentrations of clofarabine triphosphate. At the maximum tolerated dose, the concentration was a median 19 micro M (range, 3-52 micro M). In the majority of cases, more than 50% of the analog triphosphate was present at 24 h after infusion. Compared with clofarabine triphosphate concentration, the endogenous level of dATP was low, resulting in a favorable ratio of analog triphosphate:normal deoxynucleoside triphosphate (dNTP) for incorporation into DNA. In association with the accumulation of triphosphate, there was a decrease in DNA synthesis. At 40- and 55-mg/m2 doses, the inhibition of DNA synthesis was maintained to 24 h. CONCLUSIONS Clofarabine at the maximum tolerated dose was effective with regard to inhibition of DNA synthesis and decline in circulating leukemia blasts. Given the clinical activity of clofarabine in adult acute leukemias, it is of interest to conduct a detailed characterization of the cellular pharmacology of clofarabine triphosphate and its relationship to clinical responses.