Miracle-dz/UniFAR-FTUs huggingface dataset:
PII: S0925-4773(01)00331-8

The ®rst haematopoietic stem cells in mammalian and non-mammalian vertebrates are derived from mesoderm, therefore genes that are important in mesoderm patterning and formation might also play an essential role in haematopoietic stem cell commitment and differentiation. Several members of the Wnt gene family are expressed in very speci®c patterns in embryonic mesoderm and have previously been shown to act as haematopoietic growth factors. In order to investigate in detail the role that such secreted proteins play in the biology of early haematopoietic commitment we have used in vitro differentiation of murine embryonal stem (ES) as a model system. Using reversetranscriptase polymerase chain reaction analysis we identi®ed several candidate Wnt genes whose expression pattern was consistent with a role in generation, maintenance and/or differentiation of early haematopoietic progenitor cells including three genes previously shown to have a role in haematopoiesis (Wnt5a, Wnt2b and Wnt10b). The most interesting candidate was Wnt3, because of its strong and regulated expression during in vitro differentiation of murine ES cells as well as its early embryonic expression in mesoderm. Overexpression of Wnt3 was suf®cient to cause a consistent increase in the number of embryoid bodies committing to haematopoiesis further strengthening the evidence that this protein can enhance haematopoietic commitment during in vitro differentiation of ES cells. In addition, overexpression of Wnt3 caused a marked upregulation of Brachyury expression, thus providing some evidence that Brachyury may be one of the target genes for the Wnt3 signalling pathway. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00156-2

Pattern formation along the anterior-posterior (A/P) axis of the developing Drosophila wing depends on Decapentaplegic (Dpp), a member of the conserved transforming growth factor b (TGFb ) family of secreted proteins. Dpp is expressed in a stripe along the A/P compartment boundary of the wing imaginal disc and forms a long-range concentration gradient with morphogen-like properties which generates distinct cell fates along the A/P axis. We have monitored Dpp expression and Dpp signalling in endocytosis-mutant wing imaginal discs which develop severe pattern defects speci®cally along the A/P wing axis. The results show that the size of the Dpp expression domain is expanded in endocytosis-mutant wing discs. However, this expansion did not result in a concommittant expansion of the functional range of Dpp activity but rather its reduction as indicated by the reduced expression domain of the Dpp target gene spalt. The data suggest that clathrinmediated endocytosis, a cellular process necessary for membrane recycling and vesicular traf®cking, participates in Dpp action during wing development. Genetic interaction studies suggest a link between the Dpp receptors and clathrin. Impaired endocytosis does not interfere with the reception of the Dpp signal or the intracellular processing of the mediation of the signal in the responder cells, but rather affects the secretion and/or the distribution of Dpp in the developing wing cells. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00432-4

Drosophila Spitz is a homolog of transforming growth factor a (TGF-a) and is an activating ligand for the EGF receptor (Egfr). It has been shown that Star is required for Spitz activity. Here we show that Star is quantitatively limiting for Spitz production during eye development. We also show that Star and Spitz proteins colocalize in Spitz sending cells and that this association is not coincident with the site of translation ± consistent with a function for Star in Spitz processing or transmission. Finally, we have de®ned minimal sequences within both Spitz and Star that mediate a direct interaction and show that this binding can occur in vivo. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(00)00187-5

We studied the changes and invariances of foveal motion detection upon dark adaptation. It is well-documented that dark adaptation affects both spatial and temporal aspects of visual processing. The question we were interested in is how this alters motion coherence detection for moving random texture. To compare motion sensitivity at different adaptation levels, we adjusted the viewing distance for equal detectability of a stationary pattern. At these viewing distances we then measured velocity tuning curves for moving random pixel arrays (RPAs). Mean luminance levels ranged from 50 down to 0.005 cd m. Our main conclusion is that foveal velocity tuning is amazingly close to luminance-invariant, down to a level of 0.05 cd m. Because different viewing distances, and hence, retinal image sizes were used, we performed two control experiments to assess variations of these two parameters separately. We examined the effects of retinal inhomogeneities using discs of different size and annuli filled with RPAs. Our conclusion is that the central visual field, including the near periphery is still rather homogeneous for motion detection at 0.05 cd m, but the fovea becomes unresponsive at the lowest luminance level. Variations in viewing distance had marked effects on velocity tuning, both at the light adapted level and the 0.05 cd m level. The size and type of these changes indicated the effectiveness of distance scaling, and show that deviations from perfect invariance of motion coherence detection were not due to inaccurate distance scaling. © 2000 Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(01)00338-0

In vertebrates, each vertebra along the anteroposterior axis has a characteristic structure. It has recently been shown that several transcription factors and cell signaling molecules expressed in the primitive streak ectoderm and/or the tailbud play essential roles in establishing the correct anteroposterior speci®cation of vertebrae during mouse development. Here, we report that Wnt-3a mutants exhibit homeotic transformations in the vertebrae along their entire body axis. In addition, reduced expression of cdx-1, the mutation of which results in an anterior transformation, as occurs in Wnt-3a mutants, was observed in the primitive streak and tail bud region of Wnt-3a mutant embryos. These results indicate that Wnt-3a is necessary for correct anteroposterior patterning of vertebra, and that cdx-1 may be one of the mediator genes of Wnt-3a signaling in this process. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00220-8

Skeletal abnormalities are described that appeared in Zic1-de®cient mice. These mice show multiple abnormalities in the axial skeleton. The deformities are severe in the dorsal parts of the vertebrae, vertebral arches, but less so in the vertebral bodies (spina bi®da occulta). The proximal ribs are deformed having ectopic processes. The abnormalities found in the vertebral arches can be traced back to disturbed segmental patterns of dorsal sclerotome. The Zic1/Gli3 double mutants showed severe abnormalities of vertebral arches not found in single mutants. The abnormalities in the vertebral arches were less severe in Zic1/Pax1 mutants than Zic1/Gli3 mutants, but signi®cantly more pronounced than in Zic1 single mutants. The three genes may act synergistically in the development of the vertebral arches. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
EFSTRATIADIS A new whiff of monoallelic expression Odorant receptor genes reveal a new case of monoallelic

Until recently, only three cases of 'functional hemizygosity' or 'monoallelic expression' in which transcription of a gene is epigenetically restricted to just one of the two available alleles were known in mammals, namely, X-chromosome inactivation, parental imprinting and allelic exclusion of immunoglobulin and T-cell receptor loci (for reviews, see [1-6]). A recent paper by Chess, Axel and colleagues [7] has brought to light a fourth case, involving odorant receptor genes. Although I have heard persisting rumours about the tremendous importance of the olfactory sense for human sexuality, until now my personal interest in smell did not go beyond my attempts at gourmet cooking. Now that monoallelic expression one of my current obsessions has come into play, however, I thought it was time I learnt something about olfaction; hence this article.
Zebrafish contains twoPax6genes involved in eye development

ThePax6genes of both vertebrates and invertebrates are expressed in the developing eye and in the central nervous system. These genes encode transcription factors with two DNA-binding domains, an N-terminal paired domain and a homeodomain separated by a flexible linker region. Ectopic eye structures are obtained upon targeted expression of Dros phila, squid, ascidian or mouse Pax6genes in various imaginal disc primordia of Drosophila. We have previously cloned a Pax6cDNA from zebrafish. Here we report the cloning of a novel Pax6homolog from zebrafish denoted Pax6.2. The coding sequences of the two genes show 82% identity whereas the deduced amino acid sequences are 95% identical with complete conservation of the pairedand homeodomains. The embryonic expression patterns of P x6.1 andPax6.2reveal both overlapping and discrete expression domains suggesting a division of labor between these two very similar gene products during development of brain and eye structures. Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. Both Pax6.1andPax6.2are able to induce ectopic eyes in Drosophila, while Pax2 is not, suggesting that eye induction is not a general feature of Pax family genes but a distinct characteristic of Pax6and its direct homologs. Attempts to detect Pax6. 2 homologs in chick, mice or humans proved unsuccessful suggesting that this gene either was lost during evolution of higher vertebrates or, more likely, arose as part of a larger scale duplication of chromosome segments occurring in the zebrafish lineage.  1998 Elsevier Science Ireland Ltd. All rights reserved
PII: S0042-6989(97)00033-3

Achromatic losses in glaucoma would be expected to be greater than, or equal to, red-green chromatic losses if the following assumptions are made: (1) the function of the remaining axons is either unchanged or non-selectively reduced; (2) red-green chromatic information is signaled by the midget ganglion cell system; and (3) the function of the magnocellular system is reduced at least as much as that of the midget ganglion cells. This prediction was tested by measuring red-green (along with blue-yellow) mixture thresholds for I deg, 0.2 sec test spots presented on a color monitor on a white background of 50 cd/m 2. Ellipses were fitted to plots of green contrast as a function of red contrast (or yellow as a function of blue), and major and minor axes of these ellipses were taken as measures of chromatic and achromatic thresholds, respectively. The study population consisted of 29 eyes in 29 patients with early glaucoma; control data were derived from a data bank of 83 normal eyes. Red-green losses were significantly (P < 0.05) greater than achromatic losses in 6 out of the 11 eyes which showed significant losses of either chromatic or achromatic sensitivity (or both). It is concluded that, for these eyes, at least one of the above three assumptions is incorrect. © 1997 Elsevier Science Ltd.
PII: S0925-4773(00)00515-3

We are interested in the early mechanisms that initiate regional patterning in the dorsal telencephalon, which gives rise to cerebral cortex. Members of the LIM-homeodomain (LIM-HD) family of transcription factors are implicated in patterning and cell fate speci®cation in several systems including the mammalian forebrain. Mice in which Lhx2 is disrupted were reported to have reduced telencephalic development, and the hippocampal primordium appeared to be missing, by morphological observation. We hypothesized that this may be due to a defect in the cortical hem, a Wntand Bmp-rich putative signaling center in the medial telencephalon, a source of regulatory signals for hippocampal development. We asked if the expression of any known hem-speci®c signaling molecule is de®cient in Lhx22/2 mice. Our results reveal, unexpectedly, that at embryonic day (E)12.5, what appears to be some spared `lateral' cortex is instead an expanded cortical hem. Normally restricted to the extreme medial edge of the telencephalon, the hem covers almost the entire dorsal telencephalon in the Lhx22/2 mice. This indicates a role for Lhx2 in the regulation of the extent of the cortical hem. In spite of an expanded, mislocated hem in the Lhx22/2 telencephalon, a potential source of ectopic dorsalizing cues, no hippocampal differentiation is detected in tissue adjacent to the mutant hem, nor does the overall dorsoventral patterning appear perturbed. We propose that Lhx2 is involved at a crucial early step in patterning the telencephalon, where the neuroepithelium is ®rst divided into presumptive cortical tissue, and the cortical hem. The defect in the Lhx22/2 telencephalon appears to be at this step. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00026-6

The homeobox gene superfamily is highly conserved during evolution. These genes act as transcription factors during several important developmental processes through their 60 amino acid homeodomains that recognize and bind to the regulatory region of their target genes. We isolated a novel homeobox gene designated Tex1 from a mouse testis cDNA library by degenerate oligonucleotide polymerase chain reaction (PCR) screening. Three extra amino acid residues, AYP, are inserted between the first and second helices of the homeodomain, which makes Tex1 a TGIF subclass homeobox gene. Tex1 was expressed specifically in the testis as seen by both Northern blot and RT-PCR analysis. Tex1 expression is initiated at around day 20 of testes. Furthermore, the results of in situ hybridization analysis reveal that the expression of Tex1 in testis is restricted in the germ cells at spermatid stage. Based on these data, it is suggested that Tex1, a novel testis homeobox gene, may play a crucial role during spermatogenesis. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00183-1

Each sensory organ of the Drosophila peripheral nervous system is derived from a single sensory organ precursor cell (SOP). These originate in territories defined by expression of the proneural genes of the Achaete–Scute complex (AS–C). Formation of ectopic sensilla outside these regions is prevented by transcriptional repression of proneural genes. We demonstrate that the BTB/POZ-domain transcriptional repressor Tramtrack (Ttk) co-operates in this repression. Ttk is expressed ubiquitously, except in proneural clusters and SOPs. Ttk over-expression represses proneural genes and sensilla formation. Loss of Ttk enhances bristle-promoting mutants. Using neural repression as an assay, we dissected functional domains of Ttk, confirming the importance of the bric-à-brac–tramtrack–broad complex (BTB) motif. We show that the Ttk BTB domain is a protein–protein interaction motif mediating tetramer formation. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
Machine learning models for DOTA 2 outcomes prediction

Prediction of the real-time multiplayer online battle arena (MOBA) games' match outcome is one of the most important and exciting tasks in Esports analytical research. This research paper predominantly focuses on building predictive machine and deep learning models to identify the outcome of the Dota 2 MOBA game using the new method of multi-forward steps predictions. Three models were investigated and compared: Linear Regression (LR), Neural Networks (NN), and a type of recurrent neural network Long Short-Term Memory (LSTM). In order to achieve the goals, we developed a data collecting python server using Game State Integration (GSI) to track the real-time data of the players. Once the exploratory feature analysis and tuning hyper-parameters were done, our models' experiments took place on different players with dissimilar backgrounds of playing experiences. The achieved accuracy scores depend on the multi-forward prediction parameters, which for the worse case in linear regression 69\% but on average 82\%, while in the deep learning models hit the utmost accuracy of prediction on average 88\% for NN, and 93\% for LSTM models.
Universality in Decaying Turbulence at High Reynolds Numbers

In the limit of very large Reynolds numbers for homogeneous isotropic turbulence of an incompressible fluid, the statistics of the velocity differences between two points in space are expected to approach universal power laws at scales smaller than those at which energy is injected. Even at the highest Reynolds numbers available in laboratory and natural flows such universal power laws have remained elusive. On the other hand, power laws have been observed empirically in derived quantities, namely in the relative scaling in statistics of different orders according to the Extended Self Similarity hypothesis. Here we present experimental results from the Max Planck Variable Density Turbulence Tunnel over an unprecedented range of Reynolds numbers. We find that the velocity difference statistics take a universal functional form that is distinct from a power law. By applying a self-similar model derived for decaying turbulence to our data, an effective scaling exponent for the second moment can be derived that agrees well with that obtained from Extended Self Similarity.
Normalizing Flows for Knockoff-free Controlled Feature Selection

Controlled feature selection aims to discover the features a response depends on while limiting the false discovery rate (FDR) to a predefined level. Recently, multiple deep-learning-based methods have been proposed to perform controlled feature selection through the Model-X knockoff framework. We demonstrate, however, that these methods often fail to control the FDR for two reasons. First, these methods often learn inaccurate models of features. Second, the"swap"property, which is required for knockoffs to be valid, is often not well enforced. We propose a new procedure called FlowSelect to perform controlled feature selection that does not suffer from either of these two problems. To more accurately model the features, FlowSelect uses normalizing flows, the state-of-the-art method for density estimation. Instead of enforcing the"swap"property, FlowSelect uses a novel MCMC-based procedure to calculate p-values for each feature directly. Asymptotically, FlowSelect computes valid p-values. Empirically, FlowSelect consistently controls the FDR on both synthetic and semi-synthetic benchmarks, whereas competing knockoff-based approaches do not. FlowSelect also demonstrates greater power on these benchmarks. Additionally, FlowSelect correctly infers the genetic variants associated with specific soybean traits from GWAS data.
Robust Reference-based Super-Resolution via C2-Matching

Reference-based Super-Resolution (Ref-SR) has recently emerged as a promising paradigm to enhance a low-resolution (LR) input image by introducing an additional high-resolution (HR) reference image. Existing Ref-SR methods mostly rely on implicit correspondence matching to borrow HR textures from reference images to compensate for the information loss in input images. However, performing local transfer is difficult because of two gaps between input and reference images: the transformation gap (e.g. scale and rotation) and the resolution gap (e.g. HR and LR). To tackle these challenges, we propose C2-Matching in this work, which produces explicit robust matching crossing transformation and resolution. 1) For the transformation gap, we propose a contrastive correspondence network, which learns transformation-robust correspondences using augmented views of the input image. 2) For the resolution gap, we adopt a teacher-student correlation distillation, which distills knowledge from the easier HR-HR matching to guide the more ambiguous LR-HR matching. 3) Finally, we design a dynamic aggregation module to address the potential misalignment issue. In addition, to faithfully evaluate the performance of Ref-SR under a realistic setting, we contribute the Webly-Referenced SR (WR-SR) dataset, mimicking the practical usage scenario. Extensive experiments demonstrate that our proposed C2-Matching significantly outperforms state of the arts by over 1dB on the standard CUFED5 benchmark. Notably, it also shows great generalizability on WR-SR dataset as well as robustness across large scale and rotation transformations 1.
Heart Sound Classification Considering Additive Noise and Convolutional Distortion

Cardiac auscultation is an essential point-of-care method used for the early diagnosis of heart diseases. Automatic analysis of heart sounds for abnormality detection is faced with the challenges of additive noise and sensor-dependent degradation. This paper aims to develop methods to address the cardiac abnormality detection problem when both types of distortions are present in the cardiac auscultation sound. We first mathematically analyze the effect of additive and convolutional noise on short-term filterbank-based features and a Convolutional Neural Network (CNN) layer. Based on the analysis, we propose a combination of linear and logarithmic spectrogram-image features. These 2D features are provided as input to a residual CNN network (ResNet) for heart sound abnormality detection. Experimental validation is performed on an open-access heart sound abnormality detection dataset involving noisy recordings obtained from multiple stethoscope sensors. The proposed method achieves significantly improved results compared to the conventional approaches, with an area under the ROC (receiver operating characteristics) curve (AUC) of 91.36%, F-1 score of 84.09%, and Macc (mean of sensitivity and specificity) of 85.08%. We also show that the proposed method shows the best mean accuracy across different source domains including stethoscope and noise variability, demonstrating its effectiveness in different recording conditions. The proposed combination of linear and logarithmic features along with the ResNet classifier effectively minimizes the impact of background noise and sensor variability for classifying phonocardiogram (PCG) signals. The proposed method paves the way towards developing computer-aided cardiac auscultation systems in noisy environments using low-cost stethoscopes.
Towards Cost-Optimal Policies for DAGs to Utilize IaaS Clouds with Online Learning

Premier cloud service providers (CSPs) offer two types of purchase options, namely on-demand and spot instances, with time-varying features in availability and price. Users like startups have to operate on a limited budget and similarly others hope to reduce their costs. While interacting with a CSP, central to their concerns is the process of cost-effectively utilizing different purchase options possibly in addition to self-owned instances. A job in data-intensive applications is typically represented by a directed acyclic graph which can further be transformed into a chain of tasks. The key to achieving cost efficiency is determining the allocation of a specific deadline to each task, as well as the allocation of different types of instances to the task. In this paper, we propose a framework that determines the optimal allocation of deadlines to tasks. The framework also features an optimal policy to determine the allocation of spot and on-demand instances in a predefined time window, and a near-optimal policy for allocating self-owned instances. The policies are designed to be parametric to support the usage of online learning to infer the optimal values against the dynamics of cloud markets. Finally, several intuitive heuristics are used as baselines to validate the cost improvement brought by the proposed solutions. We show that the cost improvement over the state-of-the-art is up to 24.87% when spot and on-demand instances are considered and up to 59.05% when self-owned instances are considered.