Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vivo Tractography of Fetal Association Fibers

Association fibers connect different cortical areas within the same hemisphere and constitute an essential anatomical substrate for a diverse range of higher cognitive functions. So far a comprehensive description of the prenatal in vivo morphology of these functionally important pathways is lacking. In the present study, diffusion tensor imaging (DTI) and tractography were used to visualize major association fiber tracts and the fornix in utero in preselected non-motion degraded DTI datasets of 24 living unsedated fetuses between 20 and 34 gestational weeks (GW). The uncinate fasciculus and inferior fronto-occipital fasciculus were depicted as early as 20 GW, while in vivo 3D visualization of the inferior longitudinal fasciculus, cingulum and fornix was successful in older fetuses during the third trimester. Provided optimal scanning conditions, in utero DTI and tractography have the potential to provide a more accurate anatomical definition of developing neuronal networks in the human fetal brain. Knowledge about the normal prenatal 3D association tract morphology may serve as reference for their assessment in common developmental diseases.
SAME BUT DIFFERENT: TWO NOVEL BICARINATE SPECIES OF EXTANT CALCAREOUS DINOPHYTES (THORACOSPHAERACEAE, PERIDINIALES) FROM THE MEDITERRANEAN SEA 1

The diversity of extant calcareous dinophytes (Thoracosphaeraceae, Dinophyceae) is currently not sufficiently recorded. The majority of their coccoid stages are cryptotabulate or entirely atabulate, whereas relatively few forms exhibit at least some degree of tabulation more than the archeopyle. A survey of coastal surface sediment samples from the Mediterranean Sea resulted in the isolation and cultivation of several strains of calcareous dinophytes showing a prominent tabulation. We investigated the morphologies of the thecate and the coccoid cells and conducted phylogenetic analyses using Maximum Likelihood and Bayesian approaches. The coccoid cells showed a distinct reflection of the cingulum (and were thus cingulotabulate), whereas thecal morphology corresponded to the widely distributed and species‐rich Scrippsiella. As inferred from molecular sequence data (including 81 new GenBank entries), the strains belonged to the Scrippsiella sensu lato clade of the Thoracosphaeraceae and represented two distinct species. Morphological details likewise indicated two distinct species with previously unknown coccoid cells that we describe here as new, namely S. bicarinata spec. nov. and S. kirschiae spec. nov. Cingulotabulation results from the fusion of processes representing the pre‐ and postcingular plate series in S. bicarinata, whereas the ridges represent sutures between the cingulum and the pre‐ and postcingular series in S. kirschiae, respectively. Bicarinate cingulotabulation appears homoplasious among calcareous dinophytes, which is further supported by a comparison to similar, but only distantly related fossil forms.
On the Elasticity of the Perron Root of a Nonnegative Matrix

Let A=(ai,j) be an n × n nonnegative irreducible matrix whose Perron root is $\lambda$. The quantity $e_{i,j}=\frac{a_{i,j}}{\lam}\frac{\partial \lambda}{\partial a_{i,j}}$ is known as the elasticity of $\lambda$ with respect to ai,j. In this paper, we give two proofs of the fact that $\frac{\partial e_{i,j}}{\partial a_{i,j}} \geq 0$ so that ei,j is increasing as a function of ai,j. One proof uses ideas from symbolic dynamics, while the other, which is matrix theoretic, also yields a characterization of the case when $\frac{\partial e_{i,j}}{\partial a_{i,j}}=0$. We discuss a resulting connection between the elements of A and the elements of the group inverse of $\lambda I -A. $
Building extraction from multiple data sources : a data fusion framework for reconstruction of generic models

Automated building extraction from multi-source data has attracted great attention in recent years. This paper presents an approach to automated building extraction by fusion of image data, height data and 2D ground plans. In this approach buildings are detected using ground plans and height data. A split-and-merge process is applied to fuse image and height data and derive the parametric forms of roof planes. Vegetation regions are identified and discarded using the image information in red and infrared channels. Walls are reconstructed as vertical planes upon the ground plan. The model planar faces are finally intersected and resulting plane patches are assembled together to form a generic polyhedral model. Results of the experimental testing indicate the promising performance of the proposed approach in automatic detection and reconstruction of buildings.
Biologically inspired climbing with a hexapedal robot

This paper presents an integrated, systems‐level view of several novel design and control features associated with the biologically inspired, hexapedal, RiSE (Robots in Scansorial Environments) robot. RiSE is the first legged machine capable of locomotion on both the ground and a variety of vertical building surfaces including brick, stucco, and crushed stone at speeds up to 4 cm/s, quietly and without the use of suction, magnets, or adhesives. It achieves these capabilities through a combination of bioinspired and traditional design methods. This paper describes the design process and specifically addresses body morphology, hierarchical compliance in the legs and feet, and sensing and control systems that enable robust and reliable climbing on difficult surfaces. Experimental results illustrate the effects of various behaviors on climbing performance and demonstrate the robot's ability to climb reliably for long distances. © 2008 Wiley Periodicals, Inc.
N-terminal splicing extensions of the human MYO1C gene fine-tune the kinetics of the three full-length myosin IC isoforms

The MYO1C gene produces three alternatively spliced isoforms, differing only in their N-terminal regions (NTRs). These isoforms, which exhibit both specific and overlapping nuclear and cytoplasmic functions, have different expression levels and nuclear–cytoplasmic partitioning. To investigate the effect of NTR extensions on the enzymatic behavior of individual isoforms, we overexpressed and purified the three full-length human isoforms from suspension-adapted HEK cells. MYO1CC favored the actomyosin closed state (AMC), MYO1C16 populated the actomyosin open state (AMO) and AMC equally, and MYO1C35 favored the AMO state. Moreover, the full-length constructs isomerized before ADP release, which has not been observed previously in truncated MYO1CC constructs. Furthermore, global numerical simulation analysis predicted that MYO1C35 populated the actomyosin·ADP closed state (AMDC) 5-fold more than the actomyosin·ADP open state (AMDO) and to a greater degree than MYO1CC and MYO1C16 (4- and 2-fold, respectively). On the basis of a homology model of the 35-amino acid NTR of MYO1C35 (NTR35) docked to the X-ray structure of MYO1CC, we predicted that MYO1C35 NTR residue Arg-21 would engage in a specific interaction with post-relay helix residue Glu-469, which affects the mechanics of the myosin power stroke. In addition, we found that adding the NTR35 peptide to MYO1CC yielded a protein that transiently mimics MYO1C35 kinetic behavior. By contrast, NTR35, which harbors the R21G mutation, was unable to confer MYO1C35-like kinetic behavior. Thus, the NTRs affect the specific nucleotide-binding properties of MYO1C isoforms, adding to their kinetic diversity. We propose that this level of fine-tuning within MYO1C broadens its adaptability within cells.
Effect of bite force on orthodontic mini-implants in the molar region: Finite element analysis

Objective To examine the effect of bite force on the displacement and stress distribution of orthodontic mini-implants (OMIs) in the molar region according to placement site, insertion angle, and loading direction. Methods Five finite element models were created using micro-computed tomography (microCT) images of the maxilla and mandible. OMIs were placed at one maxillary and two mandibular positions: between the maxillary second premolar and first molar, between the mandibular second premolar and first molar, and between the mandibular first and second molars. The OMIs were inserted at angles of 45° and 90° to the buccal surface of the cortical bone. A bite force of 25 kg was applied to the 10 occlusal contact points of the second premolar, first molar, and second molar. The loading directions were 0°, 5°, and 10° to the long axis of the tooth. Results With regard to placement site, the displacement and stress were greatest for the OMI placed between the mandibular first molar and second molar, and smallest for the OMI placed between the maxillary second premolar and first molar. In the mandibular molar region, the angled OMI showed slightly less displacement than the OMI placed at 90°. The maximum Von Mises stress increased with the inclination of the loading direction. Conclusions These results suggest that placement of OMIs between the second premolar and first molar at 45° to the cortical bone reduces the effect of bite force on OMIs.
Numerical simulations of tropical cyclone‐ocean interaction with a high‐resolution coupled model

The tropical cyclone-ocean interaction was investigated using a high-resolution tropical cyclone ocean coupled model. The model design consisted of the NOAA Geophysical Fluid Dynamics Laboratory tropical cyclone prediction model which was coupled with a multilayer primitive equation ocean model. Coupling between the hurricane and the ocean models was carried out by passing into the ocean model the wind stress, heat, and moisture fluxes computed in the hurricane model. The new sea surface temperature (SST) calculated by the ocean model was then used in the tropical cyclone model. A set of idealized numerical experiments were performed in which a tropical cyclone vortex was embedded in both easterly and westerly basic flows of 2.5, 5, and 7.5 m s−1 with a fourth experiment run with no basic flow specified initially. The profile of the tangential wind for Hurricane Gloria at 1200 UTC 22, September 1985 was used as the initial condition of the tropical cyclone for each of the experiments. The model ocean was initially horizontally homogenous and quiescent. To clarify the impact of the ocean response to the hurricane's behavior, analogous experiments were also carried out with the SST kept constant (control cases). The experiments indicated that the cooling of the sea surface induced by the tropical cyclone resulted in a significant impact on the ultimate storm intensity due to the reduction of total heat flux directed into the tropical cyclone above the regions of decreased SST. The sea surface cooling produced by the tropical cyclones was found to be larger when the storms moved slower. In the experiments run without an initial basic flow, the maximum SST anomaly was about −5.6°C with a resulting difference in the minimum sea level pressure and maximum surface winds of 16.4 hPa and −7 m s−1, respectively. In contrast, in the experiments run with the 7.5 m s −1 basic flow, the maximum SST anomalies ranged from about 2.6° to 3.0°C with a difference in the minimum sea level pressure and maximum surface winds of about 7.3 hPa and −2.7 m s−1. The tropical cyclone-ocean coupling significantly influenced the storm track only for the case with no basic flow and the 2.5 m s−1 easterly flow. In these cases the storm with the ocean interaction turned more to the north and east (no basic flow) or the north (2.5 m s−1 easterly flow) of the experiments with constant SST. In the first case, the storm by 72 hours was located over 70 km to the east-southeast of the control case. A possible explanation for this track deviation is related to a systematic weakening of the mean tangential flow at all radii of the storm due to the interaction with the ocean and resulting alteration of the beta drift.
Improving locals stack placement in Java with Soot

Efficient allocation of locals has traditionally been one of the most important parts of an optimizing compiler, typically giving gains in runtime of 25% compared to code compiled with simplistic allocators. However, finding the optimal allocation is an NP-complete problem, and it is therefore crucial to find approximation algorithms that give economic packings on average. It is often not practical to spend a lot of time compiling a program, such as during development where more time spent compiling means less time spent testing, or in a JIT where compilation time takes its toll on runtime. Therefore, it is important that the allocation strategy can complete in a reasonable timeframe. I look at how such allocation strategies can apply to the Java Virtual Machine. The Java Virtual Machine is a stack-based machine that lacks registers, keeping locals on a per-method locals stack. Bytecode instructions are used to store and load locals to and from the locals stack onto the operand stack. There are five load instructions and five corresponding store instructions for each basic type in the Java Virtual Machine. The first four are one-byte nullary instructions which address the top four positions on the locals stack, while the remaining load and store are unary instructions relying on an immediate operand to supply the position of the local. The nullary loads and stores are therefore smaller and should be faster to execute than the unary loads and stores. It would therefore be beneficial to store the most frequently accessed locals on top of the stack, hopefully leading to faster execution of the program. I show that for certain basic types, namely integers, addresses and doubles, there is a measurable decrease in execution time when using only the nullary bytecodes in comparison to using only unary bytecodes to load and store locals. I show how two existing weight-based heuristics for register allocation can be applied to placing locals on the JVM locals stack. The locals placement algorithms are then implemented in Soot, the Java Optimization Framework, where we show that although there are improvements in runtime, more work is needed to find a better heuristic for locals placement.
Role of cytochrome P-450 arachidonate metabolites in endothelin signaling in rat proximal tubule.

We examined the rat proximal tubule (PT) response to endothelin-1 (ET-1) in terms of 20-hydroxyeicosatetraenoic acid (HETE) dependency. Arachidonic acid (AA) (1 microM) decreased ouabain-sensitive (86)Rb uptake from 2.1 +/- 0.1 to 0.3 +/- 0.08 ng Rb. 10 microg protein(-1). 2 min(-1) (P < 0.05); 20-HETE (1 microM) had similar effects. Dibromododecenoic acid (DBDD) (2 microM), an inhibitor of omega-hydroxylase, abolished the inhibitory action of AA on (86)Rb uptake whereas the PT response to 20-HETE was unaffected. ET-1 at 0.1, 1, 10, and 100 nM reduced (86)Rb uptake from 2.8 +/- 0.3 in control PTs to 2.4 +/- 0.2, 1.7 +/- 0.1, 0.67 +/- 0.08, and 0.1 +/- 0.03 ng Rb. 10 microg protein(-1). 2 min(-1), respectively. DBDD (2 microM) abolished the inhibitory effect of ET-1 on (86)Rb uptake as did BMS182874 (1 microM), an ET(A)-selective receptor antagonist. ET-1 (100 nM) significantly increased PT 20-HETE release by approximately 50%, an effect prevented by DBDD. N(omega)-nitro-L-arginine-methyl ester (L-NAME), given for 4 days to inhibit nitric oxide synthase (NOS), increased arterial pressure from 92 +/- 12 to 140 +/- 8 mmHg and increased endogenous release of 20-HETE from isolated PTs (measured by gas chromatography/mass spectrometry). In L-NAME-treated PTs, but not in control PTs, 0.1 microM AA inhibited ouabain-sensitive (86)Rb uptake by > 40%; the response to AA was attenuated by DBDD. We conclude that, in the PTs, 1) 20-HETE is a second messenger for ET-1 and 2) conversion of AA to 20-HETE is augmented when NOS is inhibited.
Forebrain Arginine Vasotocin Correlates of Alternative Mating Strategies in Cricket Frogs

In cricket frogs, Acris crepitans, sexually active males can switch between calling and noncalling (satellite) mating strategies and injections of the neuropeptide arginine vasotocin (AVT) stimulate calling behavior. We report here that this behavioral variation of animals under field conditions is associated with variations in AVT-immunoreactive (AVT-ir) staining in distinct brain nuclei. In both calling and satellite males, one AVT-ir brain region was found in a continuous string of cells between the medial amygdala and the nucleus accumbens (ACC). Satellite males possessed significantly more AVT-ir staining in the brain (cells and fibers) than calling males at the level of the ACC, although not in the medial amygdala. This difference in AVT-ir staining in the ACC can, in part, be explained by differences in the density of staining within the cells and in cell size. In addition, satellite males had significantly higher AVT-ir staining in the fibers medial to the ACC than calling males. Because other studies have demonstrated that AVT stimulates calling behavior, a plausible hypothesis is that calling males are releasing more AVT from neurons in the ACC, depleting reserves within the cells, and that the released AVT elicits calling behavior. AVT immunoreactivity levels are also higher in the ACC in both calling and satellite males than in female cricket frogs, which do not call. Satellite males may therefore have AVT reserves that might allow them to call depending on the social conditions.
Same-day identification scheme for colonies of Listeria monocytogenes

A diagnostic scheme is described for the same-day identification of food-borne cells of Listeria monocytogenes that emerge in 40 h at 30 degrees C as large colonies, representatives of which are used to advantage as heavy inocula on agar plates for the rapid determination of hemolytic activity and acidification of rhamnose and xylose. Additional tests consisting of phase-contrast microscopy for cell morphology and motility, the catalase production test, and the KOH viscosity test in place of Gram staining complete the rapid identification scheme.
Associations between Nighttime Traffic Noise and Sleep: The Finnish Public Sector Study

Background: Associations between traffic noise and sleep problems have been detected in experimental studies, but population-level evidence is scarce. Objectives: We studied the relationship between the levels of nighttime traffic noise and sleep disturbances and identified vulnerable population groups. Methods: Noise levels of nighttime–outdoor traffic were modeled based on the traffic intensities in the cities of Helsinki and Vantaa, Finland. In these cities, 7,019 public sector employees (81% women) responded to postal surveys on sleep and health. We linked modeled outdoor noise levels to the residences of the employees who responded to the postal survey. We used logistic regression models to estimate associations of noise levels with subjectively assessed duration of sleep and symptoms of insomnia (i.e., difficulties falling asleep, waking up frequently during the night, waking up too early in the morning, nonrestorative sleep). We also used stratified models to investigate the possibility of vulnerable subgroups. Results: For the total study population, exposure to levels of nighttime–outside (Lnight, outside) traffic noise > 55 dB was associated with any insomnia symptom ≥ 2 nights per week [odds ratio (OR) = 1.32; 95% confidence interval (CI): 1.05, 1.65]. Among participants with higher trait anxiety scores, which we hypothesized were a proxy for noise sensitivity, the ORs for any insomnia symptom at exposures to Lnight, outside traffic noises 50.1–55 dB and > 55 dB versus ≤ 45 dB were 1.34 (95% CI: 1.00, 1.80) and 1.61 (95% CI: 1.07, 2.42), respectively. Conclusions: Nighttime traffic noise levels > 50 dB Lnight, outside was associated with insomnia symptoms among persons with higher scores for trait anxiety. For the total study population, Lnight, outside > 55 dB was positively associated with any symptoms.
High-affinity Activators of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Chloride Conductance Identified by High-throughput Screening*

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) protein that reduce cAMP-stimulated Cl− conductance in airway and other epithelia. The purpose of this investigation was to identify new classes of potent CFTR activators. A collection of 60,000 diverse drug-like compounds was screened at 10 μmtogether with a low concentration of forskolin (0.5 μm) in Fisher rat thyroid epithelial cells co-expressing human CFTR and a green fluorescent protein-based Cl− sensor. Primary screening yielded 57 strong activators (greater activity than reference compound apigenin), most of which were unrelated in chemical structure to known CFTR activators, and 284 weaker activators. Secondary analysis of the strong activators included analysis of CFTR specificity, forskolin requirement, transepithelial short-circuit current, activation kinetics, dose response, toxicity, and activation mechanism. Three compounds, the most potent being a dihydroisoquinoline, activated CFTR by elevating cellular cAMP, probably by phosphodiesterase inhibition. Fourteen compounds activated CFTR without cAMP elevation or phosphatase inhibition, suggesting direct CFTR interaction. The most potent compounds had tetrahydrocarbazol, hydroxycoumarin, and thiazolidine core structures. These compounds induced CFTR Cl− currents rapidly (<5 min) with Kd down to 200 nm and were CFTR-selective, reversible, and nontoxic. Several compounds, the most potent being a trifluoromethylphenylbenzamine, activated the CF-causing mutant G551D, but with much weaker affinity (Kd > 10 μm). When added for 10 min, none of the compounds activated ΔPhe508-CFTR in transfected cells grown at 37 °C (with ΔPhe508-CFTR trapped in the endoplasmic reticulum). However, after correction of trafficking by 48 h of growth at 27 °C, tetrahydrocarbazol andN-phenyltriazine derivatives strongly stimulated Cl− conductance with Kd < 1 μm. The new activators identified here may be useful in defining molecular mechanisms of CFTR activation and as lead compounds in CF drug development.
Three-Dimensional Diagnosis of Pavement Damage using CT Scanner

Pavement quality is currently evaluated by examining the surface deformation and deflection, either visually, or by an automated pavement surface measuring device. However, these methods evaluate only the pavement surface or estimate the quality of each layer. In this study, the authors developed a technique for three-dimensionally diagnosing the causes and degrees of pavement damage. A 3-D crack analysis of each sample was conducted using an X-ray CT scanner (CT) and a 3-D void analysis program. 3-D images of in-situ specimens showed that longitudinal cracking occurred not from the surface or bottom, but from within the pavement. The technique can thus be used to directly identify the 3-D pavement damage of each layer; and it can easily and precisely diagnosis the position and level of damage in asphalt concrete pavement.
The gap‐filling sequence on the left arm of chromosome 2 in fission yeast Schizosaccharomyces pombe

We report a gap‐filling sequence between SPBPB21E7.09 (in contig c1348) and SPBPB10D8.01 (in contig pB10D8) on the left arm of chromosome 2 in the fission yeast, Schizosaccharomyces pombe. The sequence was determined from a BAC clone overlapping SPBPB21E7.01c (eno102) (in contig c1348) and SPBC1683.07 (mal1) (in contig pB10D8). The gap‐filling sequence is 17 881 bp in length and contains five putative open reading frames, which were systematically named as SPBC460.01c, SPBC460.02c, SPBC460.03, SPBC460.04c and SPBC460.05. Their deduced amino acid sequences respectively include protein motifs corresponding to amino acid permease, glutathione S‐transferase C‐terminal domain, taurine catabolism dioxygenase TauD TfdA family and major facilitator superfamily, whereas their functions are unknown. The sequence has been submitted to the international DNA database (DDBJ/EMBL/GenBank) under Accession No. AB325691. Copyright © 2008 John Wiley & Sons, Ltd.