Miracle-dz/UniFAR-FTUs huggingface dataset:
Hox genes control vertebrate body elongation by collinear Wnt repression

In vertebrates, the total number of vertebrae is precisely defined. Vertebrae derive from embryonic somites that are continuously produced posteriorly from the presomitic mesoderm (PSM) during body formation. We show that in the chicken embryo, activation of posterior Hox genes (paralogs 9–13) in the tail-bud correlates with the slowing down of axis elongation. Our data indicate that a subset of progressively more posterior Hox genes, which are collinearly activated in vertebral precursors, repress Wnt activity with increasing strength. This leads to a graded repression of the Brachyury/T transcription factor, reducing mesoderm ingression and slowing down the elongation process. Due to the continuation of somite formation, this mechanism leads to the progressive reduction of PSM size. This ultimately brings the retinoic acid (RA)-producing segmented region in close vicinity to the tail bud, potentially accounting for the termination of segmentation and axis elongation. DOI: http://dx.doi. org/10.7554/eLife.04379. 001
A probabilistic framework for floodplain mapping using hydrological modeling and unsteady hydraulic modeling

ABSTRACT Prediction of design hydrographs is key in floodplain mapping using hydraulic models, which are either steady state or unsteady. The former, which require only an input peak, substantially overestimate the volume of water entering the floodplain compared to the more realistic dynamic case simulated by the unsteady models that require the full hydrograph. Past efforts to account for the uncertainty of boundary conditions using unsteady hydraulic modeling have been based largely on a joint flood frequency–shape analysis, with only a very limited number of studies using hydrological modeling to produce the design hydrographs. This study therefore presents a generic probabilistic framework that couples a hydrological model with an unsteady hydraulic model to estimate the uncertainty of flood characteristics. The framework is demonstrated on the Swannanoa River watershed in North Carolina, USA. Given its flexibility, the framework can be applied to study other sources of uncertainty in other hydrological models and watersheds.
Using analogy to acquire commonsense knowledge from human Contributors

The goal of the work reported here is to capture the commonsense knowledge of non-expert human contributors. Achieving this goal will enable more intelligent human-computer interfaces and pave the way for computers to reason about our world. In the domain of natural language processing, it will provide the world knowledge much needed for semantic processing of natural language. To acquire knowledge from contributors not trained in knowledge engineering, I take the following four steps: (i) develop a knowledge representation (KR) model for simple assertions in natural language, (ii) introduce cumulative analogy, a class of nearest-neighbor based analogical reasoning algorithms over this representation, (iii) argue that cumulative analogy is well suited for knowledge acquisition (KA) based on a theoretical analysis of effectiveness of KA with this approach, and (iv) test the KR model and the effectiveness of the cumulative analogy algorithms empirically. To investigate effectiveness of cumulative analogy for KA empirically, Learner, an open source system for KA by cumulative analogy has been implemented, deployed, and evaluated. Learner acquires assertion-level knowledge by constructing shallow semantic analogies between a KA topic and its nearest neighbors and posing these analogies as natural language questions to human contributors. Suppose, for example, that based on the knowledge about “newspapers” already present in the knowledge base, Learner judges “newspaper” to be similar to “book” and “magazine. ” Further suppose that assertions “books contain information” and “magazines contain information” are also already in the knowledge base. Then Learner will use cumulative analogy from the similar topics to ask humans whether “newspapers contain information. ” 1The site, “1001 Questions,” is publicly available at http://teachcomputers.org/learner.html at the time of writing.
The far-infrared/radio correlation and radio spectral index of galaxies in the SFR–M∗ plane up to z~2

We study the evolution of the radio spectral index and far-infrared/radio correlation (FRC) across the star-formation rate – stellar masse (i.e. SFR–M∗) plane up to z ~ 2. We start from a stellar-mass-selected sample of galaxies with reliable SFR and redshift estimates. We then grid the SFR–M∗ plane in several redshift ranges and measure the infrared luminosity, radio luminosity, radio spectral index, and ultimately the FRC index (i.e. qFIR) of each SFR–M∗–z bin. The infrared luminosities of our SFR–M∗–z bins are estimated using their stacked far-infrared flux densities inferred from observations obtained with the Herschel Space Observatory. Their radio luminosities and radio spectral indices (i.e. α, where Sν ∝ ν−α) are estimated using their stacked 1.4 GHz and 610 MHz flux densities from the Very Large Array and Giant Metre-wave Radio Telescope, respectively. Our far-infrared and radio observations include the most widely studied blank extragalactic fields – GOODS-N, GOODS-S, ECDFS, and COSMOS – covering a total sky area of ~2.0 deg2. Using this methodology, we constrain the radio spectral index and FRC index of star-forming galaxies with M∗ > 1010 M⊙ and 0 <z< 2.3. We find that α1.4 GHz610 MHz does not evolve significantly with redshift or with the distance of a galaxy with respect to the main sequence (MS) of the SFR–M∗ plane (i.e. Δlog (SSFR)MS = log [ SSFR(galaxy) /SSFRMS(M∗,z) ]). Instead, star-forming galaxies have a radio spectral index consistent with a canonical value of 0.8, which suggests that their radio spectra are dominated by non-thermal optically thin synchrotron emission. We find that the FRC index, qFIR,displays a moderate but statistically significant redshift evolution as qFIR(z) = (2.35 ± 0.08) × (1 + z)−0.12 ± 0.04, consistent with some previous literature. Finally, we find no significant correlation between qFIR and Δlog (SSFR)MS, though a weak positive trend, as observed in one of our redshift bins (i.e. Δ [ qFIR ]/Δ [ Δlog (SSFR)MS ] = 0.22 ± 0.07 at 0.5 <z< 0.8), cannot be firmly ruled out using our dataset.
Enhancing Proprioceptive Input to Motoneurons Differentially Affects Expression of Neurotrophin 3 and Brain-Derived Neurotrophic Factor in Rat Hoffmann-Reflex Circuitry

The importance of neurotrophin 3 (NT-3) for motor control prompted us to ask the question whether direct electrical stimulation of low-threshold muscle afferents, strengthening the proprioceptive signaling, could effectively increase the endogenous pool of this neurotrophin and its receptor TrkC in the Hoffmann-reflex (H-reflex) circuitry. The effects were compared with those of brain-derived neurotrophic factor (BDNF) and its TrkB receptor. Continuous bursts of stimuli were delivered unilaterally for seven days, 80 min daily, by means of a cuff-electrode implanted over the tibial nerve in awake rats. The H-reflex was recorded in the soleus muscle to control the strength of stimulation. Stimulation aimed at activation of Ia fibers produced a strong increase of NT-3 protein, measured with ELISA, in the lumbar L3-6 segments of the spinal cord and in the soleus muscle. This stimulation exerted much weaker effect on BDNF protein level which slightly increased only in L3-6 segments of the spinal cord. Increased protein level of NT-3 and BDNF corresponded to the changes of NT-3 mRNA and BDNF mRNA expression in L3-6 segments but not in the soleus muscle. We disclosed tissue-specificity of TrkC mRNA and TrkB mRNA responses. In the spinal cord TrkC and TrkB transcripts tended to decrease, whereas in the soleus muscle TrkB mRNA decreased and TrkC mRNA expression strongly increased, suggesting that stimulation of Ia fibers leads to sensitization of the soleus muscle to NT-3 signaling. The possibility of increasing NT-3/TrkC signaling in the neuromuscular system, with minor effects on BDNF/TrkB signaling, by means of low-threshold electrical stimulation of peripheral nerves, which in humans might be applied in non-invasive way, offers an attractive therapeutic tool.
Coulomb Stress Transfer Influences Fault Reactivation in Areas of Wastewater Injection

We explore the role of Coulomb stress transfer in the fault reactivation in Woodward, Oklahoma—a wastewater injection area. We address this issue by first defining fault segments from earthquake spatiotemporal clustering then parameterizing the geometries of each segment by combining seismicity and focal mechanisms. Finally, we calculate Coulomb stress transfer along each fault segment. Our results reveal a fault system characterized by a flower structure with strike‐slip fault at deeper depth and distributed normal faults at shallower depth. Further, Coulomb stress analysis reveals that the fault reactivation initiates at the fault bend and sequentially migrates to northeast and southwest due to interevent stress interaction. The amplitude of Coulomb stress transfer is at least comparable to pore pressure and poroelastic stress changes estimated from fluid injection. Overall, our observations suggest that fault structure and Coulomb stress transfer constitute important factors in seismogenic fault reactivation within areas of wastewater injection.
Management of the failing Fontan circulation

The ‘Fontan circulation' has evolved to include a variety of surgical procedures designed to overcome the absence of two distinct ventricular chambers.1 w1–w3 Inherent to this circulation is chronic elevation of right atrial and vena caval pressure, and absence of a dedicated power source to serve the pulmonary circulation, making low pulmonary vascular resistance and optimal systemic ventricular function the essential ingredients of a successful Fontan circulation.2 Originally designed for the single left ventricle, modifications to the original atriopulmonary connections extended repairs to complex ventricular anatomy, and are now most commonly performed for single right ventricular anatomy associated with hypoplastic left heart syndrome. Together with improved perioperative management, creation of the Fontan circulation in two stages (superior cavopulmonary anastomosis followed by later Fontan completionw4), and performance of Fontan procedures at a younger age, have led to reduced operative mortality associated with the Fontan procedure of ≤5% (compared with 15–30% in earlier decades); survival at 20 years is presently 85%. 3 w5 Over the last two decades, the initial survivors of the atriopulmonary Fontan repairs have reached adulthood, bringing a multiplicity of haemodynamic complications and sequelae of their abnormal circulatory status. The atriopulmonary connection is now obsolete as a surgical option, and the current surviving adults with this circulation do not reflect contemporary Fontan outcomes. Nonetheless, their attendant compendium …
Extracting Individual Properties from Global Behaviour: First-order Reversal Curve Method Applied to Magnetic Nanowire Arrays

The behaviour of a group cannot be simply reduced to the sum of the behaviour of individuals (Le Bon, 1895). Examples abound in nature: school of fish or swarms of insect act like a single individual, but with emergent properties, i.e. properties which none of the individuals in the group possess, but which appear when these individuals are grouped into a system. A key element characterising a crowd is that the individuals should know that they are part of an ensemble (Le Bon, 1895). In other words, there must be interactions between them, on a short or long range. Otherwise they only constitute a system of several isolated individuals without emergent properties. Whatever the system, it is usually much easier to access its global behaviour, compared to the behaviour of individuals and their method of communication. However, the understanding of the global behaviour, in order to be able to control it subsequently, necessarily requires the knowledge of individual behaviour and of their interactions. According to these criteria, the magnetic behaviour of structures composed of magnetic entities embedded in a non-magnetic matrix must be considered as a crowd: entities "talking" to each other via exchange or dipo lar interactions depending upon the distance that separates them. Therefore, the behaviour of the global (or collective) structure may differ from that of the local (or individual) entities. This difference will be accentuated in the presence of non-uniformit y (geometric, structural, etc.) of the entities. To access the magnetostatic properties of a system (coercivity, remanence, interactions, etc.), one usually uses a magnetometer to measure the major hysteresis curve. It is possible to use the same experimental setup to obtain the local magnetostatic properties of the system, by measuring
Sequences required for coordinate induction of adeno-associated virus p19 and p40 promoters by Rep protein

A series of contiguous 30-bp deletions were introduced into the regions upstream of the p19 and p40 promoters of adeno-associated virus (AAV), and the effects of these deletions on induction of AAV transcription by the rep gene products was evaluated. A novel complementation system was devised for supplying wild-type Rep protein when mutations disrupted the trans activation activity of the Rep protein. Transcription from the p40 promoter was eliminated upon deletion of the TATA sequence located between -4 and -33 from the cap site. Deletions which removed sequences from -34 to -123 bp from the p40 mRNA start site substantially reduced Rep induction of p40 transcription. p19 transcription was also undetectable when the p19 TATA sequence between -4 and -33 was deleted. In contrast to the p40 region, two types of cis-active sequences were found associated with the p19 promoter. Sequences between -4 and -63 bp relative to the p19 cap site were essential for Rep induction only from the p19 promoter. Deletions between -94 and -153 bp relative to the p19 cap site reduced Rep induction of both the p19 and p40 promoters coordinately. These two noncontiguous regions were separated by a 30-bp sequence that was not essential for transcription control. Further deletion analysis delineated a second cis-active element, associated with the p5 promoter (AAV nucleotides 191 to 320), which was also necessary for coordinate Rep activation of both the p19 and p40 promoters. Finally, the dependence of p40 transcription on the Rep-responsive elements within the p5 and p19 regions could be overcome by the presence of the AAV terminal repeats, suggesting that the terminal repeats contained redundant Rep-responsive elements. These results implied an interdependence in cis between the three AAV promoters and suggested a novel mechanism for coordinate regulation of gene expression in response to the trans-activating Rep protein. Coordinate induction appeared to be the result of a simultaneous interaction between the Rep protein and sequence elements associated with two or all three of the AAV promoters.
Robotic Manipulation of a Rotating Chain

This paper considers the problem of manipulating a uniformly rotating chain: the chain is rotated at a constant angular speed around a fixed axis using a robotic manipulator. Manipulation is quasi-static in the sense that transitions are slow enough for the chain to be always in “rotational equilibrium. ” The curve traced by the chain in a rotating plane—its shape function—can be determined by a simple force analysis, yet it possesses a complex multisolutions behavior that is typical of nonlinear systems. We prove that the configuration space of the uniformly rotating chain is homeomorphic to a two-dimensional surface embedded in $\mathbb {R}^3$. Using that representation, we devise a manipulation strategy for transiting between different rotation modes in a stable and controlled manner. We demonstrate the strategy on a physical robotic arm manipulating a rotating chain. Finally, we discuss how the ideas developed here might find fruitful applications in the study of other flexible objects, such as in circular aerial manipulation with UAVs.
Growth history of a diffusely venting sulfide structure from the Juan de Fuca Ridge: A petrological and geochemical study

Centimeter‐scale mineralogical and chemical analyses of a diffusely venting, ∼280°C sulfide structure (called Roane) from the Mothra Hydrothermal Field on the Juan de Fuca Ridge reveal a complex growth history. These analyses document four well‐defined zones, which from the exterior to the interior of the structure include a barite‐silica zone (Fossil Worm Tube Zone), a silica‐sulfide zone (Silica Zone), a sulfide‐silica zone (Outer Sulfide Zone), and a sulfide ± gordaite ± silica zone (Inner Sulfide Zone). These features are a product of a myriad of processes that include extensive mineral replacement, ingress of seawater, fracturing and breakout of hot hydrothermal fluids, significant conductive cooling, and the sustained, broad‐scale outflow of warm fluids from the walls through a porous and permeable matrix. Roane lacks an open, throughgoing, chalcopyrite‐lined, central conduit. Instead, it hosts an anastomosing, discontinuous network of tortuous channels within the interior of a sponge‐like matrix of amorphous silica, sulfide, sulfate, and clay minerals. Megafaunal communities at the summit and sides of this mature, diffusely venting chimney provide a constructional framework for new growth. Isolation of hydrothermal fluid from seawater during progressive fossilization of megafauna and the early formation of barite‐silica assemblages promote flow of higher‐temperature fluids within the interior. Continued isolation of interior higher‐temperature fluids, through increased mineral precipitation and expansion of the structure, leads to a Zn sulfide + pyrite‐dominated permeable matrix and a network of tortuous channels that form a central porous conduit. This conduit is shielded by a weakly silicified, metal sulfide inner wall and a strongly silicified outer wall. The most outer portions of the walls are highly porous and sites of significant advection and mixing between hydrothermal fluids and seawater. The mineralogy and chemistry of Roane are strongly affected by ammonia‐ammonium buffering of the pH during cooling of the hydrothermal fluids. The two major results of the buffering are (1) precipitation of Zn sulfide at higher temperatures than are typical for bare‐rock systems, leading to the correlation of Cu, Zn, Cd, and Se and (2) increased deposition of amorphous silica and clay minerals.
Benefits and detriments of unilateral cochlear implant use on bilateral auditory development in children who are deaf

We have explored both the benefits and detriments of providing electrical input through a cochlear implant in one ear to the auditory system of young children. A cochlear implant delivers electrical pulses to stimulate the auditory nerve, providing children who are deaf with access to sound. The goals of implantation are to restrict reorganization of the deprived immature auditory brain and promote development of hearing and spoken language. It is clear that limiting the duration of deprivation is a key factor. Additional considerations are the onset, etiology, and use of residual hearing as each of these can have unique effects on auditory development in the pre-implant period. New findings show that many children receiving unilateral cochlear implants are developing mature-like brainstem and thalamo-cortical responses to sound with long term use despite these sources of variability; however, there remain considerable abnormalities in cortical function. The most apparent, determined by implanting the other ear and measuring responses to acute stimulation, is a loss of normal cortical response from the deprived ear. Recent data reveal that this can be avoided in children by early implantation of both ears simultaneously or with limited delay. We conclude that auditory development requires input early in development and from both ears.
Safety-Critical Geometric Control for Systems on Manifolds Subject to Time-Varying Constraints

We address the safety-critical control problem for systems whose dynamics evolve on manifolds using the concepts of control Lyapunov functions (CLFs) and control Barrier functions (CBFs). We first extend the concepts of CLFs and CBFs from Cartesian spaces to manifolds, resulting in geometric CLFs and CBFs. We then formulate a state-dependent online quadratic program (QP) that imposes the constraints of the geometric CLF and geometric CBF to compute the control input. The resulting geometric CBF-CLF-QP controller trades-off between tracking stability and critical safety. We test the controller’s performance, with both time invariant and time-varying safety constraints, on simple mechanical systems such as, a 3D moving point mass, a spherical pendulum, and a 3D pendulum. Keywords—Geometric Control Lyapunov Function, Geometric Control Barrier Function, Time-varying Safety Critical Control.
Clinical Characteristics of Proper Robot-Assisted Gait Training Group in Non-ambulatory Subacute Stroke Patients

Objective To identify the clinical characteristics of proper robot-assisted gait training group using exoskeletal locomotor devices in non-ambulatory subacute stroke patients. Methods A total of 38 stroke patients were enrolled in a 4-week robotic training protocol (2 sessions/day, 5 times/week). All subjects were evaluated for their general characteristics, Functional Ambulatory Classification (FAC), Fugl-Meyer Scale (FMS), Berg Balance Scale (BBS), Modified Rankin Scale (MRS), Modified Barthel Index (MBI), and Mini-Mental Status Examination (MMSE) at 0, 2, and 4 weeks. Statistical analysis were performed to determine significant clinical characteristics for improvement of gait function after robot-assisted gait training. Results Paired t-test showed that all functional parameters except MMSE were improved significantly (p<0.05). The duration of disease and baseline BBS score were significantly (p<0.05) correlated with FAC score in multiple regression models. Receiver operating characteristic (ROC) curve showed that a baseline BBS score of '9' was a cutoff value (AUC, 0.966; sensitivity, 91%–100%; specificity, 85%). By repeated-measures ANOVA, the differences in improved walking ability according to time were significant between group of patients who had baseline BBS score of '9' and those who did not have baseline BBS score of '9' Conclusion Our results showed that a baseline BBS score above '9' and a short duration of disease were highly correlated with improved walking ability after robot-assisted gait training. Therefore, baseline BBS and duration of disease should be considered clinically for gaining walking ability in robot-assisted training group.
Early retinal neurodegeneration and impaired Ran-mediated nuclear import of TDP-43 in progranulin-deficient FTLD

Ward et al. report retinal thinning in humans with progranulin mutations that precedes dementia onset, and an age-dependent retinal neurodegenerative phenotype in progranulin null mice. Nuclear depletion of TDP-43 precedes retinal neuronal loss and is accompanied by reduced GTPase Ran, with overexpression of Ran restoring nuclear TDP-43 and neuronal survival.