Miracle-dz/UniFAR-FTUs huggingface dataset:
Using observation-level random effects to model overdispersion in count data in ecology and evolution

Overdispersion is common in models of count data in ecology and evolutionary biology, and can occur due to missing covariates, non-independent (aggregated) data, or an excess frequency of zeroes (zero-inflation). Accounting for overdispersion in such models is vital, as failing to do so can lead to biased parameter estimates, and false conclusions regarding hypotheses of interest. Observation-level random effects (OLRE), where each data point receives a unique level of a random effect that models the extra-Poisson variation present in the data, are commonly employed to cope with overdispersion in count data. However studies investigating the efficacy of observation-level random effects as a means to deal with overdispersion are scarce. Here I use simulations to show that in cases where overdispersion is caused by random extra-Poisson noise, or aggregation in the count data, observation-level random effects yield more accurate parameter estimates compared to when overdispersion is simply ignored. Conversely, OLRE fail to reduce bias in zero-inflated data, and in some cases increase bias at high levels of overdispersion. There was a positive relationship between the magnitude of overdispersion and the degree of bias in parameter estimates. Critically, the simulations reveal that failing to account for overdispersion in mixed models can erroneously inflate measures of explained variance (r2), which may lead to researchers overestimating the predictive power of variables of interest. This work suggests use of observation-level random effects provides a simple and robust means to account for overdispersion in count data, but also that their ability to minimise bias is not uniform across all types of overdispersion and must be applied judiciously.
Hypnosis as neurophenomenology

Hypnosis research binds phenomenology and neuroscience. Here we show how recent evidence probing the impact of hypnosis and suggestion can inform and advance a neurophenomenological approach. In contrast to meditative practices that involve lengthy and intensive training, hypnosis induces profound alterations in subjective experience following just a few words of suggestion. Individuals highly responsive to hypnosis can quickly and effortlessly manifest atypical conscious experiences as well as override deeply entrenched processes. These capacities open new avenues for suspending habitual modes of attention and achieving refined states of meta-awareness. Furthermore, hypnosis research sheds light on the effects of suggestion, expectation, and interpersonal factors beyond the narrow context of hypnotic procedures. Such knowledge may help to further foster phenomenological interviewing methods, improve experiential reports, and elucidate the mechanisms of contemplative practices. Incorporating hypnosis and suggestion into the broader landscape of neurophenomenology, therefore, would likely help bridge subjective experience and third-person approaches to the mind.
Word sense discovery based on sense descriptor dissimilarity

In machine translation, information on word ambiguities is usually provided by the lexicographers who construct the lexicon. In this paper we propose an automatic method for word sense induction, i.e. for the discovery of a set of sense descriptors to a given ambiguous word. The approach is based on the statistics of the distributional similarity between the words in a corpus. Our algorithm works as follows: The 20 strongest first-order associations to the ambiguous word are considered as sense descriptor candidates. All pairs of these candidates are ranked according to the following two criteria: First, the two words in a pair should be as dissimilar as possible. Second, although being dissimilar their co-occurrence vectors should add up to the co-occurrence vector of the ambiguous word scaled by two. Both conditions together have the effect that preference is given to pairs whose co-occurring words are complementary. For best results, our implementation uses singular value decomposition, entropy-based weights, and second-order similarity metrics.
Lightweight Data Compression Algorithms: An Experimental Survey (Experiments and Analyses)

Lightweight data compression algorithms are frequently applied in in-memory database systems to tackle the growing gap between processor speed and main memory bandwidth. In recent years, the vectorization of basic techniques such as delta coding and null suppression has considerably enlarged the corpus of available algorithms. As a result, today there is a large number of algorithms to choose from, while different algorithms are tailored to different data characteristics. However, a comparative evaluation of these algorithms under different data characteristics has never been sufficiently conducted in the literature. To close this gap, we conducted an exhaustive experimental survey by evaluating several state-of-the-art compression algorithms as well as cascades of basic techniques. We systematically investigated the influence of the data properties on the performance and the compression rates. The evaluated algorithms are based on publicly available implementations as well as our own vectorized reimplementations. We summarize our experimental findings leading to several new insights and to the conclusion, that there is no single-best algorithm.
The challenge facing migration research: a case for greater awareness

The author critically examines an article by Keith Halfacree and Paul Boyle, in which the authors made a case for a biographical approach to migration research. "My point of contention--incredulous disbelief might be more accurate--stems from their conclusion that the biographical approach should be the ¿new' methodological base for an improved paradigm in migration studies. "
Incidence and Trends of Infection with Pathogens Transmitted Commonly Through Food — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 1996–2012

Foodborne diseases are an important public health problem in the United States. The Foodborne Diseases Active Surveillance Network* (FoodNet) conducts surveillance in 10 U.S. sites for all laboratory-confirmed infections caused by selected pathogens transmitted commonly through food to quantify them and monitor their incidence. This report summarizes 2012 preliminary surveillance data and describes trends since 1996. A total of 19,531 infections, 4,563 hospitalizations, and 68 deaths associated with foodborne diseases were reported in 2012. For most infections, incidence was highest among children aged <5 years; the percentage of persons hospitalized and the percentage who died were highest among persons aged ≥65 years. In 2012, compared with the 2006-2008 period, the overall incidence of infection† was unchanged, and the estimated incidence of infections caused by Campylobacter and Vibrio increased. These findings highlight the need for targeted action to address food safety gaps.
Earthquake clustering in modern seismicity and its relationship with strong historical earthquakes around Beijing, China

XI or more) than the reported epicentre. The present-day event rates are similar to those predicted by the modiﬁed Omori law but there is no evidence of ongoing decay in event rates. Accordingly, the index is more likely to be picking out the location of persistent weaknesses in the lithosphere. Our results imply zones of high seismic density index could be used in principle to indicate the location of unrecorded historical of palaeoseismic events, in China and elsewhere.
Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity

The claim that genetic properties of neurons significantly influence their synaptic network structure is a common notion in neuroscience. The nematode Caenorhabditis elegans provides an exciting opportunity to approach this question in a large-scale quantitative manner. Its synaptic connectivity network has been identified, and, combined with cellular studies, we currently have characteristic connectivity and gene expression signatures for most of its neurons. By using two complementary analysis assays we show that the expression signature of a neuron carries significant information about its synaptic connectivity signature, and identify a list of putative genes predicting neural connectivity. The current study rigorously quantifies the relation between gene expression and synaptic connectivity signatures in the C. elegans nervous system and identifies subsets of neurons where this relation is highly marked. The results presented and the genes identified provide a promising starting point for further, more detailed computational and experimental investigations.
Effect of L-carnitine on diabetes-induced changes of skeletal muscles in rats

Abstract Background: Patients with diabetes mellitus (DM) are at risk of experiencing chronic complications such as retinopathy, nephropathy and myopathy. We aimed to evaluate the effects of L-carnitine on type II DM (T2DM)-induced biochemical, contractile and pathological changes in skeletal muscles of rats. Methods: Thirty-two male Sprague Dawley rats were divided into the control, control+L-carnitine, T2DM and T2DM+L-carnitine groups. Plasma levels of glucose, insulin, malondialdehyde and antioxidants such as reduced glutathione, catalase and superoxide dismutase, haemoglobin A1c (HbA1c), insulin sensitivity index (ISI) as well as the contractile properties of the gastrocnemius muscle were measured. Also, histopathological studies and immunohistochemical examination of the gastrocnemius muscle using the MuRF1 (muscle RING-finger protein-1) marker were performed. Results: In diabetic rats, malondialdehyde, glucose, insulin, HbA1c and MuRF1 were increased, whereas ISI and antioxidants were decreased and the contractile properties deteriorated. L-carnitine decreased malondialdehyde, glucose, insulin, HbA1c and MuRF1 and increased ISI and antioxidants. Also, L-carnitine improves the contractile properties in diabetic rats. Histopathological studies confirm our data. Conclusions: We conclude that L-carnitine exhibits protective effects on skeletal muscles of T2DM rats through its hypoglycemic and antioxidant actions as well as its inhibitory effect on protein degradation.
Kindling-induced long-lasting changes in synaptic transmission in the basolateral amygdala.

1. Intracellular current-clamp recordings were obtained from neurons of the basolateral amygdala (BLA) in an in vitro slice preparation from control and kindled animals. Postsynaptic potentials, elicited by stimulation of the stria terminalis (ST) or lateral amygdaloid nucleus (LA), were used to investigate the role of excitatory and inhibitory amino acid transmission in kindling-induced epileptiform activity. The contributions of glutamatergic and GABAergic receptor subtypes were analyzed by use of the non-N-methyl-D-aspartate (non-NMDA) antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), the NMDA antagonist DL-2-amino-5-phosphonovaleric acid (APV), and the GABAA antagonist bicuculline methiodide (BMI). 2. The synaptic waveform evoked in control neurons consisted of an excitatory postsynaptic potential (EPSP), a fast inhibitory postsynaptic potential (f-IPSP), and a slow inhibitory postsynaptic potential (s-IPSP). Stimulation of the ST or LA pathways evoked a burst-firing response in BLA neurons contralateral from the site of stimulation of kindled animals. 3. APV (50 microM) reduced, but CNQX (10 microM) completely blocked, the burst-firing response in BLA neurons from kindled animals and bicuculline-induced bursting in control neurons. 4. Kindling significantly increased the amplitude of both the slow NMDA- and the fast non-NMDA-receptor-mediated components of synaptic transmission (s- and f-EPSPs, respectively). Furthermore, the stimulus intensities required to evoke EPSPs just subthreshold for action potential generation were significantly lower in slices from kindled animals. 5. In kindled neurons no significant change was observed in the membrane input resistance and resting membrane potential or in the number of action potentials elicited in response to depolarizating current injection. 6. Kindling resulted in a pathway-specific loss of ST- and LA-evoked feedforward GABAergic synaptic transmission and of spontaneous IPSPs. In the same BLA neurons, direct GABAergic inhibition via stimulation of the LA was not affected by kindling. 7. The enhanced glutamatergic transmission was not due to disinhibition, because, in the presence of BMI (and CNQX to prevent BMI-induced bursting), the s-EPSP amplitude was still greater in kindled than in control neurons. 8. These results provide evidence that the epileptiform activity observed in BLA neurons after kindling results from an increase in excitatory NMDA- and non-NMDA-receptor-mediated glutamatergic transmission and a decrease in inhibitory gamma-aminobutyric acid (GABA)-receptor-mediated transmission; the enhanced excitatory transmission cannot be accounted for by reduced inhibition. (ABSTRACT TRUNCATED AT 400 WORDS)
Targeting IL‐13Rα2 in human pancreatic ductal adenocarcinoma with combination therapy of IL‐13‐PE and gemcitabine

Pancreatic cancer is an aggressive disease with only limited therapeutic options available. We have identified that 71% pancreatic ductal adenocarcinoma (PDA) express high levels of IL‐13Rα2, a high‐affinity receptor for IL‐13. To target IL‐13Rα2, we have developed a recombinant immunotoxin, which is a fusion of IL‐13 and Pseudomonas exotoxin (IL‐13‐PE). Since IL‐13‐PE and a commonly used cytotoxic drug gemcitabine act by a different mechanism, we hypothesized that they synergize in mediating antitumor response. Both IL‐13‐PE and gemcitabine‐mediated cytotoxicity to two pancreatic cancer cell lines and when combined synergistic cytotoxicity was observed. This synergism was also demonstrated in vivo in an orthotopic mouse model of human PDA. IL‐13‐PE and gemcitabine showed complete eradiation of tumors as assessed by whole body imaging of GFP‐transfected tumors in 57% of mice in an early cancer model resulting into prolongation of survival. In contrast, monotherapy with either agent did not produce complete eradiation, but tumor volumes were significantly decreased. In advanced PDA model, combination therapy also produced dramatic reduction in tumor growth and enhanced survival compared to animals treated with either agent alone. When IL‐13Rα2 was knocked‐down by RNAi prior to tumor implantation, IL‐13‐PE and gemcitabine did not synergize indicating that IL‐13Rα2 is essential. Mechanistically, gemcitabine increased IL‐13Rα2 expression in vitro and in vivo, which resulted in a synergism of combination therapy. Interestingly, PDA cancer stem cells were resistant to gemcitabine, but not to IL‐13‐PE. These results suggest that combination therapy with IL‐13‐PE and gemcitabine may be a useful strategy for PDA therapy.
MT Quality Estimation: The CMU System for WMT‘13

In this paper we present our entry to the WMT’13 shared task: Quality Estimation (QE) for machine translation (MT). We participated in the 1.1, 1.2 and 1.3 sub-tasks with our QE system trained on features from diverse information sources like MT decoder features, n-best lists, mono- and bi-lingual corpora and giza training models. Our system shows competitive results in the workshop shared task.
Linguistic categorization and complexity

This paper presents a memoryless categorization learner that predicts differences in category complexity found in several psycholinguistic and psychological experiments. In particular, this learner predicts the order of difficulty of learning simple Boolean categories, including the advantage of conjunctive categories over the disjunctive ones (an advantage that is not typically modeled by the statistical approaches). It also models the effect of labeling (positive and negative labels vs. positive labels of two different kinds) on category complexity. This effect has implications for the differences between learning a single category (e.g., a phonological class of segments) vs. a set of non-overlapping categories (e.g., affixes in a morphological paradigm).
Análisis cinemático del pedaleo ciclista mediante sistemas de captura del movimiento en 2D y 3D = Kinematic analysis of the bicycle pedaling using 2D and 3D motion capture systems.

The aim of this study was to check the validity and sensibility of a low-cost 2D motion capture system for the bicycle pedaling kinematics, comparing it with a sophisticated 3D system. To achieve this purpose, the three joints involved in the pedaling movement (hip, knee and ankle) were studied, as well as the trunk angle with the horizontal line of the floor, due to its relationship with aerodynamics. Twelve cyclists of different levels with more than 3 years of experience in cycling were analyzed in three different saddle heights at a random order: their preferred one, 2% lower and 2% higher. High correlation was found between 2D and 3D systems, and their differences did not depend on the measured value. The 2D system has shown to be as sensitive as the 3D one to small changes in saddle height. In addition, the angular kinematic values recorded in both left and right sides of the body with 3D system did not show any significant difference. In conclusion, the 2D motion capture system is valid and sensitive for kinematic pedaling analysis. However, to compare its values with the 3D ones it is necessary to add 2o to hip extension and 2-3o to knee extension, as well as subtract 3-4o to hip flexion, 2o to knee flexion and 1o to ankle flexion.
Endovascular Repair of a Symptomatic Subclavian Artery Aneurysm in a Patient With Marfan Syndrome: A Case Report

Endovascular techniques are being employed with increasing frequency in the management of peripheral arterial aneurysms. A 57-year-old patient with Marfan syndrome presented with a symptomatic 5 cm left subclavian artery aneurysm. He underwent successful endovascular exclusion of the aneurysm with immediate improvement of his symptoms. Duplex ultrasound 3 months after the procedure confirmed a patent graft and complete exclusion of the aneurysm.
Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico

Introduction Mathematical models and field data suggest that human mobility is an important driver for Dengue virus transmission. Nonetheless little is known on this matter due the lack of instruments for precise mobility quantification and study design difficulties. Materials and methods We carried out a cohort-nested, case-control study with 126 individuals (42 cases, 42 intradomestic controls and 42 population controls) with the goal of describing human mobility patterns of recently Dengue virus-infected subjects, and comparing them with those of non-infected subjects living in an urban endemic locality. Mobility was quantified using a GPS-data logger registering waypoints at 60-second intervals for a minimum of 15 natural days. Results Although absolute displacement was highly biased towards the intradomestic and peridomestic areas, occasional displacements exceeding a 100-Km radius from the center of the studied locality were recorded for all three study groups and individual displacements were recorded traveling across six states from central Mexico. Additionally, cases had a larger number of visits out of the municipality´s administrative limits when compared to intradomestic controls (cases: 10.4 versus intradomestic controls: 2.9, p = 0.0282). We were able to identify extradomestic places within and out of the locality that were independently visited by apparently non-related infected subjects, consistent with houses, working and leisure places. Conclusions Results of this study show that human mobility in a small urban setting exceeded that considered by local health authority’s administrative limits, and was different between recently infected and non-infected subjects living in the same household. These observations provide important insights about the role that human mobility may have in Dengue virus transmission and persistence across endemic geographic areas that need to be taken into account when planning preventive and control measures. Finally, these results are a valuable reference when setting the parameters for future mathematical modeling studies.
HEXAGONAL ARRAY OF SUBUNITS IN TIGHT JUNCTIONS SEPARATED FROM ISOLATED RAT LIVER PLASMA MEMBRANES

Solubilization of isolated rat liver plasma membranes in 1% deoxycholate and centrifugation yielded a fraction (pellet) that consisted mainly of tight junctions (zonulae occludentes). An hexagonal array of subunits similar to that previously found in a number of the unfractionated plasma membranes was demonstrated in all the membrane sheets of these preparations by negative staining. It is concluded that the hexagonal subunit pattern is present in the tight junctions, and that this structural differentiation may be related to the intercellular diffusion afforded by the junctional membrane.
An uncorrelated state for the cortex?

The spike trains of nearby neurons in the sensory cortex are typically thought to be correlated due to mutual connections and common input. Multiple studies have measured these correlations and found them to be substantial (in the range of 10-40%). Two recent papers, however, reported that average correlations can be an order of magnitude smaller. Such low correlations could indicate an ‘uncorrelated state’ for the cortex, where cortical neurons act independently even in the face of strong common input.
Two-dimensional differential demodulation for OFDM

The possibility of combining differential demodulators in time direction and frequency direction for orthogonal frequency-division multiplexing (OFDM) frames is investigated. The proposed algorithm uses not only the direction in which the information is modulated, but also joins it with other symbols in time or frequency direction of the OFDM frame, resulting in an additional second direction that is differentially demodulated as well. In the special case that is investigated here, the second direction does not carry any modulated information. Nevertheless, it is shown that it can be used for the two-dimensional demodulation process without changing the transmitter. Therefore, the proposed algorithm is applicable for existing digital transmission systems, for example, digital audio broadcasting, as well as new systems.
An Efficient Multiple Cell Upsets Tolerant Content-Addressable Memory

Multiple cell upsets (MCUs) become more and more problematic as the size of technology reaches or goes below 65 nm. The percentage of MCUs is reported significantly larger than that of single cell upsets (SCUs) in 20 nm technology. In SRAM and DRAM, MCUs are tackled by incorporating single-error correcting double-error detecting (SEC-DED) code and interleaved data columns. However, in content-addressable memory (CAM), column interleaving is not practically possible. A novel error correction code (ECC) scheme is proposed in this paper that will cater for ever-increasing MCUs. This work demonstrated that m parity bits are sufficient to cater for up to m-bit MCUs, with an understanding of the physical grouping of MCUs. The results showed that the proposed scheme requires 85% fewer parity bits compared to traditional Hamming distance based schemes.
Suppression of cortical representation through backward conditioning

Temporal stimulus reinforcement sequences have been shown to determine the directions of synaptic plasticity and behavioral learning. Here, we examined whether they also control the direction of cortical reorganization. Pairing ventral tegmental area stimulation with a sound in a backward conditioning paradigm specifically reduced representations of the paired sound in the primary auditory cortex (AI). This temporal sequence-dependent bidirectional cortical plasticity modulated by dopamine release hypothetically serves to prevent the over-representation of frequently occurring stimuli resulting from their random pairing with unrelated rewards.