Miracle-dz/UniFAR-FTUs huggingface dataset:
Bmp4 and Morphological Variation of Beaks in Darwin's Finches

Darwin's finches are a classic example of species diversification by natural selection. Their impressive variation in beak morphology is associated with the exploitation of a variety of ecological niches, but its developmental basis is unknown. We performed a comparative analysis of expression patterns of various growth factors in species comprising the genus Geospiza. We found that expression of Bmp4 in the mesenchyme of the upper beaks strongly correlated with deep and broad beak morphology. When misexpressed in chicken embryos, Bmp4 caused morphological transformations paralleling the beak morphology of the large ground finch G. magnirostris.
The Role of Pitch and Timbre in Voice Gender Categorization

Voice gender perception can be thought of as a mixture of low-level perceptual feature extraction and higher-level cognitive processes. Although it seems apparent that voice gender perception would rely on low-level pitch analysis, many lines of research suggest that this is not the case. Indeed, voice gender perception has been shown to rely on timbre perception and to be categorical, i.e., to depend on accessing a gender model or representation. Here, we used a unique combination of acoustic stimulus manipulation and mathematical modeling of human categorization performances to determine the relative contribution of pitch and timbre to this process. Contrary to the idea that voice gender perception relies on timber only, we demonstrate that voice gender categorization can be performed using pitch only but more importantly that pitch is used only when timber information is ambiguous (i.e., for more androgynous voices).
Estimating the Local Radius of Convergence for Picard Iteration

In this paper, we propose an algorithm to estimate the radius of convergence for the Picard iteration in the setting of a real Hilbert space. Numerical experiments show that the proposed algorithm provides convergence balls close to or even identical to the best ones. As the algorithm does not require to evaluate the norm of derivatives, the computing effort is relatively low.
Vocal flexibility in nonhuman primates and the origins of human language

Nobuo Masataka (University of Kyoto, Japan), Alban Lemasson (University of Rennes 1, France) and their colleagues have been collaborating for over a decade on projects investigating nonhuman primates' vocal behaviour and tackling the issue of the evolutionary origins of human language. They have worked together on topics including vocal flexibility under social influences in adults, the development of communicative abilities during ontogeny, and auditory and visual perception of social and non-social stimuli. In this paper, we review this work within the theoretical framework of language evolution.
Single Molecule PCR Reveals Similar Patterns of Non-Homologous DSB Repair in Tobacco and Arabidopsis

DNA double strand breaks (DSBs) occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ). We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum) by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (1–20 bp) deletions occurred at a minority (25–45%) of repair junctions. Approximately ∼1.5% of the observed repair events contained larger deletions (>20 bp) and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ.
Conception and design of a RISC CPU for the use as embedded controller within a parallel multimedia architecture

In this paper, the problem of defining a high performance control structure for a parallel motion estimation architecture for MPEG2 coding is addressed. Various design and architecture choices are discussed and the final architecture is described. It represents a combined MIMD-SIMD approach which is based on a small but efficient ASIP with subword parallelism.
The relationship between male moth density and female mating success in invading populations of Lymantria dispar

The successful establishment of non‐native species in new areas can be affected by many factors including the initial size of the founder population. Populations comprised of fewer individuals tend to be subject to stochastic forces and Allee effects (positive‐density dependence), which can challenge the ability of small founder populations to establish in a new area. Although the conceptual relationship between initial colony size and establishment success has been previously documented, it is not trivial to estimate precisely the colony size needed to ensure colony persistence. Over the last 40 years, there have been many studies on the probability of mating success of female Lymantria dispar (L.) (Lepidoptera: Lymantriidae) in the USA related to background male moth densities. We were motivated by this wealth of data and sought to combine the results from these prior studies with the goal of estimating a robust measure of the male moth density required to achieve varying levels of female mating success. Although the data are specific to L. dispar, the pheromone communication system in L. dispar is not unique and thus the results of this analysis could be broadly applicable to our general understanding of Lepidoptera mating behavior.
On a Newton-Type Method for Differential-Algebraic Equations

This paper deals with the approximation of systems of differential-algebraic equations based on a certain error functional naturally associated with the system. In seeking to minimize the error, by using standard descent schemes, the procedure can never get stuck in local minima but will always and steadily decrease the error until getting to the solution sought. Starting with an initial approximation to the solution, we improve it by adding the solution of some associated linear problems, in such a way that the error is significantly decreased. Some numerical examples are presented to illustrate the main theoretical conclusions. We should mention that we have already explored, in some previous papers (Amat et al., in press, Amat and Pedregal, 2009, and Pedregal, 2010), this point of view for regular problems. However, the main hypotheses in these papers ask for some requirements that essentially rule out the application to singular problems. We are also preparing a much more ambitious perspective for the theoretical analysis of nonlinear DAEs based on this same approach.
Herpes Simplex Virus Infection in Pregnancy

Infection with herpes simplex is one of the most common sexually transmitted infections. Because the infection is common in women of reproductive age it can be contracted and transmitted to the fetus during pregnancy and the newborn. Herpes simplex virus is an important cause of neonatal infection, which can lead to death or long-term disabilities. Rarely in the uterus, it occurs frequently during the transmission delivery. The greatest risk of transmission to the fetus and the newborn occurs in case of an initial maternal infection contracted in the second half of pregnancy. The risk of transmission of maternal-fetal-neonatal herpes simplex can be decreased by performing a treatment with antiviral drugs or resorting to a caesarean section in some specific cases. The purpose of this paper is to provide recommendations on management of herpes simplex infections in pregnancy and strategies to prevent transmission from mother to fetus.
Prevalence of Permanent Congenital Hypothyroidism in Children in Yazd, Central Iran

Abstract Background Congenital hypothyroidism is a condition of thyroid hormone deficiency. Approximately 1 in 4000 newborn infants has a deficiency of thyroid function. The aim of this study is determination of the prevalence of permanent and transient congenital hypothyroidism (CH) in Yazd, Iran. Methods From May 2006 to June 2008, 35377 newborns were screened by measuring serum TSH obtained by heel prick. The neonates who had a TSH≥5mU/L were recalled for measurement of serum T4 and thyroid stimulating hormone (TSH) in venous samples. Based on the results of the secondary measurements (between days 7 and 28), neonates were considered hypothyroid if their T4 was <6.5 mg/dl and their TSH was ≥10mIU/L. In 22 primarily diagnosed as cases of CH, treatment was discontinued at age 3 years for 4 weeks and T4 and TSH were measured again. Permanent or transient CH was determined from the results of these tests; Patients with TSH levels ≥5 mIU/l were diagnosed with permanent CH. Results The incidence of congenital hypothyroidism was found to be 1:1608 with a female to male ratio of 0.69:1. In 22 patients with CH, 10 patients were diagnosed with permanent CH (45.5%) and 12 with transient hypothyroidism (54.5%). Permanent CH was associated with higher TSH levels at first measurement than transient hypothyroidism (P-value=0.041). Conclusion The rate of transient CH in our study was higher than the comparable worldwide rate, so more and larger studies are needed to find clear information about the etiologic factors of this disease.
Finger pad friction and its role in grip and touch

Many aspects of both grip function and tactile perception depend on complex frictional interactions occurring in the contact zone of the finger pad, which is the subject of the current review. While it is well established that friction plays a crucial role in grip function, its exact contribution for discriminatory touch involving the sliding of a finger pad is more elusive. For texture discrimination, it is clear that vibrotaction plays an important role in the discriminatory mechanisms. Among other factors, friction impacts the nature of the vibrations generated by the relative movement of the fingertip skin against a probed object. Friction also has a major influence on the perceived tactile pleasantness of a surface. The contact mechanics of a finger pad is governed by the fingerprint ridges and the sweat that is exuded from pores located on these ridges. Counterintuitively, the coefficient of friction can increase by an order of magnitude in a period of tens of seconds when in contact with an impermeably smooth surface, such as glass. In contrast, the value will decrease for a porous surface, such as paper. The increase in friction is attributed to an occlusion mechanism and can be described by first-order kinetics. Surprisingly, the sensitivity of the coefficient of friction to the normal load and sliding velocity is comparatively of second order, yet these dependencies provide the main basis of theoretical models which, to-date, largely ignore the time evolution of the frictional dynamics. One well-known effect on taction is the possibility of inducing stick–slip if the friction decreases with increasing sliding velocity. Moreover, the initial slip of a finger pad occurs by the propagation of an annulus of failure from the perimeter of the contact zone and this phenomenon could be important in tactile perception and grip function.
Epipolar Geometry from Two Correspondences

A novel algorithm for robust RANSAC-like estimation of epipolar geometry (of uncalibrated camera pair) from two correspondences of local affine frames (LAFs) is presented. Each LAF is constructed from three points independently detected on a maximally stable extremal region. The algorithm assumes that a sufficiently accurate approximation of the fundamental matrix is obtained from two LAF correspondences by the 6-point algorithm of Stewenius et al. The so-far-the-best hypotheses are further processed by so-called local optimization to estimate the epipolar geometry. Special attention is paid to planar sample degeneracy, since the probability of drawing two coplanar LAF correspondences is not negligible. Combining the 6-point solver, local optimization, and the degeneracy test enables RANSAC to draw samples of only two LAFs to generate hypotheses and thus to reduce the number of samples drawn. We experimentally show that using the 6-point algorithm (approximating the real camera by camera with unit aspect ratio, zero skew, principal point in the center of image, and a common unknown focal length) generates hypotheses that are sufficient for EG estimation in LO-RANSAC framework
Effectiveness of alteplase in the very elderly after acute ischemic stroke

Alteplase has traditionally been the only pharmacologic agent available for treating acute ischemic stroke worldwide, and is considered an effective and safe therapeutic drug for acute cerebral ischemia. However, the drug is usually indicated for use in patients aged <81 years due to insufficient literature regarding the drug’s safety in older individuals. Nevertheless, the elderly can benefit from alteplase after they experience an acute ischemic stroke. Age differences have been observed in the clinical presentation of acute ischemic stroke; however, the safety and efficacy of alteplase for patients with acute ischemic stroke do not depend on age or sex. Evidence of an increasing rate of intracerebral hemorrhage among the elderly with acute ischemic stroke, following alteplase treatment, has not been reported. Severe intracranial hemorrhage is a known side effect of alteplase but is not associated with age in patients with acute ischemic stroke. Alteplase can be used safely and effectively to treat elderly patients who suffer an acute ischemic stroke, including those over the age of 80 years.
Optimizing Machine Translation by Learning to Search

We present a novel approach to training discriminative tree-structured machine trans- lation systems by learning to search. We describe three primary innovations in this work: a new parsing coordinator architecture and algorithms to generate the required training examples for the learning algorithm; a new semiring that provides an unbiased way to compare translations; and a new training objective that measures whether a translation inference improves the quality of a translation. We also apply the reinforcement learning concept of exploration to SMT. Finally, we empirically evaluate our innovations.
von Willebrand Factor-Rich Platelet Thrombi in the Liver Cause Sinusoidal Obstruction Syndrome following Oxaliplatin-Based Chemotherapy

Oxaliplatin-based chemotherapy is widely used to treat advanced colorectal cancer (CRC). Sinusoidal obstruction syndrome (SOS) due to oxaliplatin is a serious type of chemotherapy-associated liver injury (CALI) in CRC patients. SOS is thought to be caused by the sinusoidal endothelial cell damage, which results in the release of unusually-large von Willebrand factor multimers (UL-VWFMs) from endothelial cells. To investigate the pathophysiology of CALI after oxaliplatin-based chemotherapy, we analyzed plasma concentration of von Willebrand factor (VWF) and the distribution of VWFMs in CRC patients. Twenty-three patients with advanced CRC who received oxaliplatin-based chemotherapy with (n = 6) and without (n = 17) bevacizumab were analyzed. CALI (n = 6) and splenomegaly (n = 9) were found only in patients who did not treated with bevacizumab. Plasma VWF antigen (VWF:Ag) and serum aspartate aminotransferase (AST) levels increased after chemotherapy only in patients without bevacizumab. VWFM analysis in patients who did not receive bevacizumab showed the presence of UL-VWFMs and absence of high molecular weight VWFMs during chemotherapy, especially in those with CALI. In addition, plasma VWF:Ag and AST levels increased after chemotherapy in patients with splenomegaly (n = 9), but not in patients without splenomegaly (n = 14). Histological findings in the liver tissue of patients who did not receive bevacizumab included sinusoidal dilatation and microthrombi in the sinusoids. Many microthrombi were positive for both anti-IIb/IIIa and anti-VWF antibodies. Plasma UL-VWFM levels might be increased by damage to endothelial cells as a result of oxaliplatin-based chemotherapy. Bevacizumab could prevent CALI and splenomegaly through inhibition of VWF-rich platelet thrombus formation.
An economical class of digital filters for decimation and interpolation

A class of digital linear phase finite impulse response (FIR) filters for decimation (sampling rate decrease) and interpolation (sampling rate increase) are presented. They require no multipliers and use limited storage making them an economical alternative to conventional implementations for certain applications. A digital filter in this class consists of cascaded ideal integrator stages operating at a high sampling rate and an equal number of comb stages operating at a low sampling rate. Together, a single integrator-comb pair produces a uniform FIR. The number of cascaded integrator-comb pairs is chosen to meet design requirements for aliasing or imaging error. Design procedures and examples are given for both decimation and interpolation filters with the emphasis on frequency response and register width.
Dietary supplementation and rapid catch-up growth after acute diarrhoea in childhood

Diarrhoea is a major cause of short-term growth faltering in children of the developing world. If catch-up weight gain is delayed by inadequate dietary intake, or by further bouts of diarrhoea, progressive growth failure occurs. To test the hypothesis that early refeeding is as effective as later feeding after acute diarrhoea with weight loss, we measured the effects of a timed dietary intervention on weight gain after acute diarrhoea in underweight Gambian children. Thirty-four children aged 4–22 months with weight loss following acute diarrhoea were given a high-energy-protein supplement for 14 d beginning either immediately after rehydration or a fortnight later. With a 50% increase in energy intake and a 100% increase in protein intake there was a rapid and highly significant (P < 0.001) gain in weight within a fortnight whether the supplement was given immediately or 2 weeks after presentation. Rates of weight increase were similar whether supplementation was provided early or late, but over the full 28 d (of intervention and non-intervention) children who received late supplementation had greater overall weight gain (P < 0.02) than those supplemented early. Vigorous and early feeding with a high-energy-protein supplement should be central to the management of malnourished children with acute diarrhoea in developing countries, and may be as important as control of diarrhoea in preventing malnutrition and growth failure. This may be achieved in the community using IocaUy available foods, in the face of continuing diarrhoea
Sensitive Limits on the Water Abundance in Cold Low-Mass Molecular Cores

We present Submillimeter Wave Astronomy Satellite observations of water vapor in two cold starless clouds, B68 and core D in ρ Ophiuchi. Sensitive nondetections of the 110-101 transition of o-H2O are reported for each source. Both molecular cores have been previously examined by detailed observations that have characterized the physical structure. Using these rather well-defined physical properties and a Monte Carlo radiation transfer model, we have removed one of the largest uncertainties from the abundance calculation and set the lowest water abundance limit to date in cold low-mass molecular cores. These limits are x(o-H2O) < 3 × 10-8 (relative to H2) and x(o-H2O) < 8 × 10-9 in B68 and ρ Oph D, respectively. Such low abundances confirm the general lack of ortho-water vapor in cold (T < 20 K) cores. Provided that the ortho/para ratio of water is not near zero, these limits are well below theoretical predictions and appear to support the suggestion that most of the water in dense low-mass cores is frozen onto the surfaces of cold dust grains.
TfR2 localizes in lipid raft domains and is released in exosomes to activate signal transduction along the MAPK pathway

Transferrin receptor 2 (TfR2) possesses a YQRV motif similar to the YTRF motif of transferrin receptor 1 (TfR1) responsible for the internalization and secretion through the endosomal pathway. Raft biochemical dissection showed that TfR2 is a component of the low-density Triton-insoluble (LDTI) plasma membrane domain, able to co-immunoprecipitate with caveolin-1 and CD81, two structural raft proteins. In addition, subcellular fractionation experiments showed that TfR1, which spontaneously undergoes endocytosis and recycling, largely distributed to intracellular organelles, whereas TfR2 was mainly associated with the plasma membrane. Given the TfR2 localization in lipid rafts, we tested its capability to activate cell signalling. Interaction with an anti-TfR2 antibody or with human or bovine holotransferrin showed that it activated ERK1/ERK2 and p38 MAP kinases. Integrity of lipid rafts was required for MAPK activation. Co-localization of TfR2 with CD81, a raft tetraspanin exported through exosomes, prompted us to investigate exosomes released by HepG2 and K562 cells into culture medium. TfR2, CD81 and to a lesser extent caveolin-1, were found to be part of the exosomal budding vesicles. In conclusion, the present study indicates that TfR2 localizes in LDTI microdomains, where it promotes cell signalling, and is exported out of the cells through the exosome pathway, where it acts as an intercellular messenger.
Self‐organized criticality in a landslide model

From landslide mapping it is known that the frequency of landslide occurence as a function of their magnitude can be described by a power law in many regions. In order to investigate the magnitude distribution of landslides from a theoretical point of view, we present a physically based landslide model combining aspects of slope stability and mass movement. If the long term driving processes (fluvial or tectonic) are integrated, the model shows self‐organized criticality (SOC). The results coincide with results obtained from landslide mapping, so that our model suggests that landsliding may be seen as a SOC process. In contrast to other models showing SOC that are mostly based on cellular automata, our model is based on partial differential equations. The results show that SOC is not a fashion of cellular automata, but can also occur in differential equation models.
A calibration method for odometry of mobile robots based on the least-squares technique: theory and experimental validation

For a mobile robot, odometry calibration consists of the identification of a set of kinematic parameters that allow reconstructing the vehicle's absolute position and orientation starting from the wheels' encoder measurements. This paper develops a systematic method for odometry calibration of differential-drive mobile robots. As a first step, the kinematic equations are written so as to underline linearity in a suitable set of unknown parameters; thus, the least-squares method can be applied to estimate them. A major advantage of the adopted formulation is that it provides a quantitative measure of the optimality of a test motion; this can be exploited to drive guidelines on the choice of the test trajectories and to evaluate accuracy of a solution. The proposed technique has been experimentally validated on two different mobile robots and, in one case, compared with other existing approaches; the obtained results confirm the effectiveness of the proposed calibration method.