Miracle-dz/UniFAR-FTUs huggingface dataset:
Germline stem cell number in the Drosophila ovary is regulated by redundant mechanisms that control Dpp signaling

The available experimental data support the hypothesis that the cap cells (CpCs) at the anterior tip of the germarium form an environmental niche for germline stem cells (GSCs) of the Drosophila ovary. Each GSC undergoes an asymmetric self-renewal division that gives rise to both a GSC, which remains associated with the CpCs, and a more posterior located cystoblast (CB). The CB upregulates expression of the novel gene, bag of marbles (bam), which is necessary for germline differentiation. Decapentaplegic (Dpp), a BMP2/4 homologue, has been postulated to act as a highly localized niche signal that maintains a GSC fate solely by repressing bam transcription. Here, we further examine the role of Dpp in GSC maintenance. In contrast to the above model, we find that an enhancer trap inserted near the Dpp target gene, Daughters against Dpp (Dad), is expressed in additional somatic cells within the germarium, suggesting that Dpp protein may be distributed throughout the anterior germarium. However, Dad-lacZ expression within the germline is present only in GSCs and to a lower level in CBs, suggesting there are mechanisms that actively restrict Dpp signaling in germ cells. We demonstrate that one function of Bam is to block Dpp signaling downstream of Dpp receptor activation, thus establishing the existence of a negative feedback loop between the action of the two genes. Moreover, in females doubly mutant for bam and the ubiquitin protein ligase Smurf, the number of germ cells responsive to Dpp is greatly increased relative to the number observed in either single mutant. These data indicate that there are multiple, genetically redundant mechanisms that act within the germline to downregulate Dpp signaling in the Cb and its descendants, and raise the possibility that a Cb and its descendants must become refractory to Dpp signaling in order for germline differentiation to occur.
Observations of Aseismic Slip Driven by Fluid Pressure Following the 2016 Kaikōura, New Zealand, Earthquake

In this paper we examine a short‐lived aseismic slip episode which began immediately following the 2016 Kaikōura earthquake in the South Island of New Zealand. Using synthetic aperture radar data, we form an interferometric synthetic aperture radar time series over the epicentral region of the Kaikōura mainshock. Immediately following the earthquake, we observe 150 mm of localized uplift over an ∼25‐km2 region which is best explained by an increase in pore pressure within a shallow fluid trap as a result of a coseismic permeability change. After the initial uplift stops, deformation becomes focused along a NE‐SW trending discontinuity which cuts through the uplifted region. The fault lies within a large (∼−4 MPa) stress shadow induced by the coseismic stress change suggesting that failure should be inhibited. However, a reduction in the effective normal stress caused by the local pore pressure increase was sufficient to induce a short‐lived aseismic slip episode.
Classification using String Kernels

We propose a novel approach for categorizing text documents based on the use of a special kernel. The kernel is an inner product in the feature space generated by all subsequences of length k. A subsequence is any ordered sequence of k characters occurring in the text though not necessarily contiguously. The subsequences are weighted by an exponentially decaying factor of their full length in the text, hence emphasising those occurrences that are close to contiguous. A direct computation of this feature vector would involve a prohibitive amount of computation even for modest values of k, since the dimension of the feature space grows exponentially with k. The paper describes how despite this fact the inner product can be efficiently evaluated by a dynamic programming technique. Experimental comparisons of the performance of the kernel compared with a standard word feature space kernel (Joachims, 1998) show positive results on modestly sized datasets. The case of contiguous subsequences is also considered for comparison with the subsequences kernel with different decay factors. For larger documents and datasets the paper introduces an approximation technique that is shown to deliver good approximations efficiently for large datasets.
Minimal analytical characterization of engineered nanomaterials needed for hazard assessment in biological matrices

Abstract This paper presents the outcomes from a workshop of the European Network on the Health and Environmental Impact of Nanomaterials (NanoImpactNet). During the workshop, 45 experts in the field of safety assessment of engineered nanomaterials addressed the need to systematically study sets of engineered nanomaterials with specific metrics to generate a data set which would allow the establishment of dose-response relations. The group concluded that international cooperation and worldwide standardization of terminology, reference materials and protocols are needed to make progress in establishing lists of essential metrics. High quality data necessitates the development of harmonized study approaches and adequate reporting of data. Priority metrics can only be based on well-characterized dose-response relations derived from the systematic study of the bio-kinetics and bio-interactions of nanomaterials at both organism and (sub)-cellular levels. In addition, increased effort is needed to develop and validate analytical methods to determine these metrics in a complex matrix.
Neuroplastic changes in resting-state functional connectivity after stroke rehabilitation

Most neuroimaging research in stroke rehabilitation mainly focuses on the neural mechanisms underlying the natural history of post-stroke recovery. However, connectivity mapping from resting-state fMRI is well suited for different neurological conditions and provides a promising method to explore plastic changes for treatment-induced recovery from stroke. We examined the changes in resting-state functional connectivity (RS-FC) of the ipsilesional primary motor cortex (M1) in 10 post-acute stroke patients before and immediately after 4 weeks of robot-assisted bilateral arm therapy (RBAT). Motor performance, functional use of the affected arm, and daily function improved in all participants. Reduced interhemispheric RS-FC between the ipsilesional and contralesional M1 (M1-M1) and the contralesional-lateralized connections were noted before treatment. In contrast, greater M1-M1 functional connectivity and disturbed resting-state networks were observed after RBAT relative to pre-treatment. Increased changes in M1-M1 RS-FC after RBAT were coupled with better motor and functional improvements. Mediation analysis showed the pre-to-post difference in M1-M1 RS-FC was a significant mediator for the relationship between motor and functional recovery. These results show neuroplastic changes and functional recoveries induced by RBAT in post-acute stroke survivors and suggest that interhemispheric functional connectivity in the motor cortex may be a neurobiological marker for recovery after stroke rehabilitation.
An examination of mathematics preparation for and progress through three introductory computer science courses

The pipeline of three introductory computer science courses at our university have low pass rates. As part of our efforts to improve the pass rates in these courses, we examine the students' mathematics preparation and their progress from one course to the next. We find that the minority of students who enter the university with good mathematics preparation are likely to succeed in our introductory computer science courses. For the majority of students, we suggest a series of interventions throughout the pipeline. Prior to taking Computer Science 1, students could gain more experience with problem solving during the Introduction to Computer Science and Introduction to Computer Engineering courses. We suggest adding precalculus as a prerequisite for Computer Science 2. For students who do not earn an A in Computer Science 2, we plan to examine whether taking a class in a second programming language before taking Computer Science 3 will improve performance in Computer Science 3. Our goal is to improve student learning and retention through these efforts, combined with continual innovation in the classroom.
An Improved Genetic Algorithm with Recurrent Search for the Job-Shop Scheduling Problem

A genetic algorithm with some improvement is proposed to avoid the local optimum for job-shop scheduling problem (JSP). There is recurrent searching process of genetic operation in the improved genetic algorithm. The improved crossover operation can shake current population from local optimum in genetic algorithm. The recurrent crossover operation and mutation operation can inherit excellent characteristics from parent chromosomes and accelerate the diversity of offspring. Both benchmark FT(6times6) and LA1(10times5) job-shop scheduling problems are used to show the effectiveness of the proposed method. Experimental results demonstrate that the proposed genetic algorithm does not get stuck at a local optimum easily, and it is fast in convergence, simple to be implemented
Rheological and Quality Characteristics of Taftoon Bread as Affected by Salep and Persian Gums

Effects of salep gum at concentrations of 0.5%, 1%, 3%, and 5% (w/w flour basis) and the Persian gum at concentrations of 0.5%, 1%, and 3% (w/w flour basis) and combination of the two gums at concentrations of 0.5% + 0.5%, 0.75% + 0.25%, and 0.25% + 0.75% on rheological properties of the wheat flour dough and quality of Taftoon bread were studied with regard to retardation of staling. Rheological (farinograph and extensograph) characteristics, staling, and organoleptic evaluations were performed on the dough and the resulting Taftoon bread. Statistical results showed that the salep gum at 5% and Persian gum at 3% (w/w flour basis) had a significant effect on the dough properties. Salep and Persian gums when each separately added increased and decreased dough water absorption, respectively. Both hydrocolloids increased the dough resistance to extension and decreased its extensibility. Persian gum shows dual nature in water absorption and some other baking properties. Textural studies revealed that addition of 5% salep gum (w/w flour basis) reduced the bread crumb firmness and delayed the staling process of the Taftoon bread. X-ray diffraction study also confirmed this result.
Tilings, Quasicrystals, Discrete Planes, Generalized Substitutions, and Multidimensional Continued Fractions

The aim of this paper is to give an overview of recent results about tilings, discrete approximations of lines and planes, and Markov partitions for toral automorphisms.The main tool is a generalization of the notion of substitution. The simplest examples which correspond to algebraic parameters, are related to the iteration of one substitution, but we show that it is possible to treat arbitrary irrationalexamples by using multidimensional continued fractions.We give some non-trivial applications to Diophantine approximation, numeration systems and tilings, and we expose the main unsolved questions.
Power Allocation Schemes for Amplify-and-Forward MIMO-OFDM Relay Links

We consider a two-hop MIMO-OFDM communication scheme with a source, an amplify-and-forward relay, and a destination. We examine the possibilities of power allocation (PA) over the subchannels in frequency and space domains to maximize the instantaneous rate of this link if channel state information at the transmitter (CSIT) is available. We consider two approaches: (i) separate optimization of the source or the relay PA with individual per node transmit power constraints and (ii) joint optimization of the source and the relay PA with joint transmit power constraint. We provide the optimal PA at the source (or the relay) with a node transmit power constraint that maximizes the instantaneous rate for a given relay (or source) PA. Furthermore, we show that repeating this separate optimization of the source and the relay PA alternately converges and improves the achievable rate of the considered link. Since the joint optimization of the source and the relay PA is analytically not tractable we use a high SNR approximation of the SNR at the destination. This approximation leads to rates which are quite tight to the optimum.
Hierarchical Ontology-Based Robust Video Shots Indexation Using Global MPEG-7 Visual Descriptors

This paper proposes to improve our previous work on the concept-based video shot indexing, by considering an ontological concept construction in the TRECVid 2007 video retrieval, based on two steps. First, each single concept is modeled independently. Second, an ontology-based concept is introduced via the representation of the influence relations between concepts and the ontological readjustment of the confidence values. The main contribution of this paper is in the exploitation manner of the inter-concepts similarity in our indexing system, where three measures are represented: co-occurrence, visual similarity and LSCOM-lite ontology path length contribution. The experimental results report the efficiency and the significant improvement provided by the proposed scheme.
The Influence of Symmetry on Children's Judgments of Facial Attractiveness

In experiment 1, we examined developmental changes in the influence of symmetry on judgments of attractiveness by showing adults and children pairs of individual faces in which one face was transformed 75% toward perfect symmetry, while the other face was transformed by exaggerating its asymmetries by 75%. Adults and 9-year-olds, but not 5-year-olds, rated the more symmetric faces as more attractive than the less symmetric faces, although the effect was stronger in adults than 9-year-olds. The preference for symmetry was stronger for male than female faces, and stronger for adults' than children's faces. In experiment 2, comparisons of the symmetry of the original male and female faces revealed no measured differences but lower ratings by adults of symmetry in the male faces. Overall, the results suggest that the influence of symmetry on attractiveness judgments emerges after the age of 5 years, and matures after the age of 9 years. The stronger effects for adult viewers may reflect an increase in sensitivity to symmetry as experience with faces increases and/or as the visual system matures. As well, attractiveness may become more salient after puberty, so that honest signals of mate quality, such as symmetry, have a stronger effect for adult viewers, especially when judging adult faces.
Iterative design process for robots with personality

P revious research has shown that autonomous robots tend to induce the perception of a personality through their behavior and appearance. It has therefore been suggested that the personality of a robot can be used as a design guideline. A well- defined and clearly communicated personality can serve as a mental model of the robot and facilitate the interaction. From design perspective, this raises the question what kind of personality to design for a robot and how to express this personality? In this paper, we describe a process to design and evaluate personality and expressions for products. We applied this to design the personality and expressions in the behavior of a domestic robot.
The Significance of Giant Phaeodarians (Rhizaria) to Biogenic Silica Export in the California Current Ecosystem

In marine ecosystems, many planktonic organisms precipitate biogenic silica (bSiO2) to build silicified skeletons. Among them, giant siliceous rhizarians (>500 μm), including Radiolaria and Phaeodaria, are important contributors to oceanic carbon pools but little is known about their contribution to the marine silica cycle. We report the first analyses of giant phaeodarians to bSiO2 export in the California Current Ecosystem. We measured the silica content of single rhizarian cells ranging in size from 470 to 3,920 μm and developed allometric equations to predict silica content (0.37–43.42 μg Si/cell) from morphometric measurements. Using sediment traps to measure phaeodarian fluxes from the euphotic zone on four cruises, we calculated bSiO2 export produced by two families, the Aulosphaeridae and Castanellidae. Biogenic silica export ranged from <0.01 to 0.63 mmol Si · m−2 · day−1. These two families alone contributed on average 10% (range 0–80%) of total bSiO2 export from the euphotic zone. Their proportional contributions increased substantially in more oligotrophic regions with lower bSiO2 fluxes. Using the in situ Underwater Vision Profiler 5, we characterized vertical distributions of the giant phaeodarian family Aulosphaeridae to a depth of 500 m and inferred their contribution to bSiO2 export in deeper waters. We found a significant increase of Aulosphaeridae export (<0.01 to 2.82 mmol Si · m−2 · day−1) when extended to mesopelagic depths. Using a global data set of in situ profiles, we estimated the significance of Aulosphaeridae to bSiO2 export and revealed that they can act as major exporters of bSiO2 to the mesopelagic zone in various regions.
Bone morphogenetic protein 4 inhibits TGF‐β2 stimulation of extracellular matrix proteins in optic nerve head cells: Role of gremlin in ECM modulation

The characteristic cupping of the optic nerve head (ONH) in glaucoma is associated with elevated TGF‐β2 and increased synthesis and deposition of extracellular matrix (ECM) proteins. In addition to TGF‐β2, the human ONH also expresses bone morphogenetic proteins (BMPs) and BMP receptors, which are members of the TGF‐β superfamily. We examined the potential effects of BMP4 and the BMP antagonist gremlin on TGF‐β2 induction of ECM proteins in ONH cells. BMP‐4 dose dependently inhibited TGF‐β2‐induced fibronectin (FN) and PAI‐1 expression in ONH astrocytes and lamina cribrosa (LC) cells and also reduced TGF‐β2 stimulation of collagen I, collagen VI, and elastin. Addition of gremlin blocked this BMP‐4 response, increasing cellular and secreted FN as well as PAI‐1 levels in both cell types. Gremlin was expressed in ONH tissues and ONH cells, and gremlin protein levels were significantly increased in the LC region of human glaucomatous ONH tissues. Interestingly, recombinant gremlin dose dependently increased ECM protein expression in cultured ONH astrocytes and LC cells. Gremlin stimulation of ECM required activation of TGF‐β receptor and R‐Smad3. TGF‐β2 increased gremlin mRNA expression and protein levels in ONH cells. Inhibition of either the type I TGF‐β receptor or Smad3 phosphorylation blocked TGF‐β2‐induced gremlin expression. In conclusion, BMP4 blocked the TGF‐β2 induction of ECM proteins in ONH cells. The BMP antagonist gremlin reversed this inhibition, allowing TGF‐β2 stimulation of ECM synthesis. Increased expression of gremlin in the glaucomatous ONH may further exacerbate TGF‐β2 effects on ONH ECM metabolism by inhibiting BMP‐4 antagonism of TGF‐β2 signaling. Modulation of the ECM via gremlin provides a novel therapeutic target for glaucoma. © 2008 Wiley‐Liss, Inc.
Outcomes of Non‐Tunneled Non‐Cuffed Hemodialysis Catheters in Patients on Chronic Hemodialysis in a Resource Limited Sub‐Saharan Africa Setting

The aim of the present study was to investigate the adverse outcomes of non‐tunneled hemodialysis catheters and determinants in chronic hemodialysis patients receiving care at the Yaoundé General Hospital hemodialysis center, Cameroon. This was a prospective study of 11 months duration (February–December 2008) involving 81 non‐tunneled non‐cuffed catheters (63 femoral, 18 internal jugular) placed in 72 adults (47 men, 65.3%) on chronic hemodialysis. Baseline clinical and laboratory parameters associated with catheter‐related complications during follow‐up were investigated. The difference between variables was assessed using the χ2 test and equivalents. Sixty‐five (80.2%) catheters were inserted for emergency dialysis, 11 (13.6%) for a failed native arteriovenous fistula and five (6.2%) for a failed prior catheter. The mean time‐to‐catheter removal was 35 ± 28 days. Catheter‐related complications accounted for a third of catheter removals. The main catheter‐related complications were infections (17/27, 62.9%) and bleeding (6/27, 22.2%), which were associated with unemployment (P = 0.0002) and longer duration of catheter (P = 0.004). The catheter‐related infections were sepsis (11.8%), exit‐site (29.4%) and both (58.8%); leading to death in 11/17 (64.7%) cases. Fever (94.1%), pain (88.2%) and pus (70.6%) were the main infectious signs with Staphylococcus aureus involved in 70.6%. Unemployment was significantly frequent in patients with infectious complications (76.5% vs. 26.6%, P = 0.0004). Non‐tunneled hemodialysis catheters are mainly used for emergency dialysis through the femoral vein in this setting. Catheter‐related infections due to Staphylococci are the leading complications associated with unemployment and longer utilization. Efforts are needed to improve early transfer of patients to nephrologists for better preparation for renal replacement therapy.
DTM generation from the point cloud using a progressive geodesic morphology and a modified Particle Swarm Optimization

ABSTRACT The digital terrain model (DTM) is an important geospatial product used in many applications of geo-information systems. Advances in light detection and ranging technology leads to generate a dense and accurate point cloud from the Earth’s surface. Because of the existence of various types of non-ground object in the complex terrain, filtering of the point cloud data and DTM interpolation is still a challenging topic. In this article, a progressive geodesic morphology has been proposed to filter the non-ground points from the point cloud. In this regard, the noises were eliminated and the point cloud was gridded and rasterized. Then, an iterative procedure was carried out based on an elevation vector constructed by considering the terrain topography. The geodesic dilation and opening operators were applied in each iteration and some pixels were detected as the non-ground points. These pixels were labelled by the connected component analysis and the generated parcels were investigated using some geometric and structural features such as the object height, the slope of the terrain, the slope of the object boundary, as well as the boundary factor in order to decide about the considered parcel entity. Afterwards, the non-ground points were removed and the DTM was interpolated using the bare Earth points. A modified Particle Swarm Optimization (PSO) has been proposed to optimize the coefficients of the polynomial interpolation for generating a DTM with high accuracy. Results showed that the error of the proposed progressive geodesic morphology was on average 3.42% using an optimized set of parameters and 4.00% using a single set of parameters, respectively. These results represented the stability of the proposed filtering method against the predefined thresholds and this is an important factor to make it a practical method. In comparing the proposed modified PSO with the other interpolation algorithms, the evaluation results indicated that the proposed modified PSO interpolated data only with 0.0884 cm error, averagely. This means the proposed modified PSO has a significant performance in generating DTM.