Miracle-dz/UniFAR-FTUs huggingface dataset:
PII: S0925-4773(02)00131-4

The development of avian cutaneous appendages, feathers and scales, is known to arise from the epithelial–mesenchymal interaction. Here we show that FGF10 is associated with this developmental process as an early signal from mesenchymal cells underlying nascent cutaneous placodes. Expression of Fgf10 was detected in the mesenchymal cells underneath the developing placodes. Forced expression of Fgf10 in the femoral skin suppressed expression of Shh and a zinc finger gene snail-related (cSnR), while induced expression of Bmp2 in the interbud region, resulting in thickening of the epidermal layer. Furthermore, forced expression of Fgf10 in the foot skin caused marked ingrowings of the epidermis. The cells in the epidermal ingrowings expressed b-catenin, proliferating cell nuclear antigen, and an epidermal stem cell marker p63. These results support the idea that FGF10 is a mesenchymally derived stimulator of epidermal development through crosstalk with bone morphogenetic protein (BMP), b-catenin, and other signaling pathways. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00291-4

Small GTPases of the rho family function as signal transducer for extra-cellular stimuli to control cytoskeletal re-organization and a variety of other cellular processes including adhesion, proliferation and transcriptional regulation (Hall, A., 1998. RhoGTPases and the actin cytoskeleton. Science 279, 509±514). Usually widely expressed, their activities are tightly controlled by conformational changes induced by hydrolysis of the GTP bound molecule (Bourne H.R., Sanders D.A., 1990. The GTPase superfamily: a conserved switch for diverse cell functions. Nature 348, 125±132). Conversion of GTP to GDP relies on a rho intrinsic GTPase domain that requires GTPase activating proteins (GAPs) for potent activity (Lamarche, N., Hall. A., 1994. GAPs for rho-related GTPases. Trends Genet. 10, 436±440). Here we report on the identi®cation of a novel Drosophila GAP gene, d-CdGAPr, encoding a protein related to mammalian CdGAPs. The gene is expressed throughout development as well as in adults. Spatio-temporal transcription pattern of d-CdGAPr during embryogenesis is highly dynamic. Abundant in the pre-blastoderm embryo prior to the onset of zygotic transcription, messengers accumulate at the blastoderm posterior pole after cellularisation. During gastrulation and subsequent development, all cells accumulate low levels of d-CdGAPr RNA, while a few territories transiently display stronger expression. Sites of preferential expression include the posterior pole of the early cellular blastoderm, the neuro-ectoderm prior to neuroblast delamination, rows of epidermal cells in the most posterior part of thoracic and ®rst abdominal segments and a ring of epidermal cells at the posterior end of the embryo. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00529-9

Genes of the Sox family encode evolutionarily conserved HMG box containing transcription factors, which play key roles in various events of cell determination/differentiation during development. The total number of Sox genes in Drosophila melanogaster was estimated to be eight, after classical molecular cloning approaches and exhaustive screening of the complete Drosophila genome. Here we report the embryonic and larval expression pattern of four previously uncharacterized Sox genes, through antibody staining and in situ hybridization experiments. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
ReviewBack to the Future with Ubiquitin be eliminated for purposes of regulation or quality con -

The discovery of the ubiquitin/proteasome pathway Two papers published in 1984 by the Varshavsky laboemerged from efforts to understand why intracellular ratory revealed that the ubiquitin/proteasome pathway proteolysis, measured as the release of amino acids is the principal system for degradation of short-lived from intact cells, requires metabolic energy (Simpson, proteins in mammalian cells, setting the stage for fu1953). Key elements of the answer became clear in the ture demonstrations of this pathway’s many regulatory early 1980’s as a result of the pioneering biochemical roles. This perspective discusses the impact of those studies of Hershko and coworkers. These investigators papers and highlights some of the subsequent insights found that energy, in the form of ATP, is needed to that have led to our current appreciation of the breadth modify proteolytic substrates with ubiquitin, a highly of ubiquitin-mediated signaling. conserved 76 amino acid polypeptide that is joined to
PII: S0925-4773(02)00123-5

Patterning of the central nervous system is regulated by a signaling center located at the midbrain–hindbrain boundary (MHB), or isthmus organizer. Fibroblast growth factors secreted from the MHB are required and sufficient to direct the ordered growth and regionalization of the midbrain and anterior hindbrain. In an unbiased secretion cloning screen of Xenopus gastrula embryos we identified a novel gene, which we designated as Isthmin (xIsm) due to its prominent expression at the MHB. xIsm encodes a secreted protein of 449 amino acids containing one copy of the thrombospondin type 1 repeat (TSR). We also found orthologous Isthmin genes in human (hIsm) and mouse (mIsm), as well as a gene encoding an Isthmin-like human unknown protein (hIsm-l). The conservation of a unique carboxy-terminal region between hIsm and hIsm-l suggests that Isthmin is the founding member of a new family of secreted proteins. xIsm was strongly expressed maternally in the Xenopus egg and showed zygotic expression in the ventral blastopore lip, notochord, and MHB. Additional expression domains were detected in neural crest, ear vesicle, and developing blood islands. Interestingly, xIsm was co-expressed with Fibroblast growth factor-8 (xFgf-8) at multiple sites including the MHB, indicating that these two genes are part of a synexpression group which also includes sprouty and sef homologs. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00319-6

In vertebrates, speci®cation of the dorso±ventral axis requires Wnt signaling, which leads to formation of the Nieuwkoop center and the Spemann organizer (dorsal organizer), through the nuclear accumulation of b-catenin. Zebra®sh bozozok/dharma (boz) and squint (sqt), which encode a homeodomain protein and a Nodal-related protein, respectively, are required for the formation of the dorsal organizer. The zygotic expression of boz and sqt in the dorsal blastoderm and dorsal yolk syncytial layer (YSL) was dependent on the maternally derived Wnt signal, and their expression at the late blastula and early gastrula stages was dependent on the zygotic expression of their own genes. The dorsal organizer genes, goosecoid (gsc) and chordin (din), were ectopically expressed in wild-type embryos injected with boz or sqt RNA. The expression of gsc strictly depended on both boz and sqt while the expression of din strongly depended on boz but only partially depended on sqt and cyclops (cyc, another nodal-related gene). Overexpression of boz in embryos defective in Nodal signaling elicited the ectopic expression of din but not gsc and resulted in dorsalization, implying that boz could induce part of the organizer, independent of the Nodal proteins. Furthermore, boz; sqt and boz;cyc double mutants displayed a severely ventralized phenotype with anterior truncation, compared with the single mutants, and boz;sqt;cyc triple mutant embryos exhibited an even more severe phenotype, lacking the anterior neuroectoderm and notochord, suggesting that Boz/Dharma and the Nodal-related proteins cooperatively regulate the formation of the dorsal organizer. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00447-6

Retinoid binding proteins and nuclear receptors are expressed in the developing mouse inner ear. Here, we report that the retinaldehyde dehydrogenase 2 (Raldh2) gene, whose product is involved in the enzymatic generation of retinoic acid (RA), exhibits a restricted expression pattern during mouse inner ear ontogenesis. The Raldh2 gene is ®rst expressed at embryonic day (E) 10.5 in a V-shaped medio-dorsal region of the otocyst outer epithelium, which evolves as two separate domains upon otocyst morphogenesis. At E14.5, Raldh2 is expressed in two areas of the utricle epithelium and speci®c regions of the saccule and cochlear mesenchyme. Later, Raldh2 transcripts are restricted to two cochlear areas, the stria vascularis and Reissner membrane. Raldh2 mesenchymal expression did not correlate with migrating neural crestderived melanoblasts. These restricted expression domains may correspond to speci®c sites of RA synthesis during inner ear morphogenesis. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00545-7

Receptor protein–tyrosine phosphatases (RPTPs) are key players in Drosophila development. To study the role of RPTPs in vertebrate development, we have cloned zebrafish (zf) RPTPs, including RPTP alpha (RPTPa), RPTP sigma (RPTPs) and LAR. These three RPTPs are broadly transcribed in early development. At 24 h post fertilisation (hpf), all three genes are expressed in the nervous system in partially overlapping patterns. At 3 days post fertilisation zf-RPTPa and zf-LAR show similar expression patterns in the central nervous system (CNS), the pharyngeal arches, the pectoral fins and the spinal cord. Interestingly, zf-LAR is uniquely expressed in the neuromast cells, whereas zf-RPTPs expression is confined to the central nervous system. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(98)00213-2

The present study concerns the dynamics of multiple fixation search. We tried to gain insight into: (1) how the peripheral and foveal stimulus affect fixation duration; and (2) how fixation duration affects the peripheral target selection for saccades. We replicated the non-corroborating results of Luria and Strauss (1975) (‘Eye movements during search for coded and uncoded targets’, Perception and Psychophysics 17, 303–308) (saccades were selective), and Zelinsky (1996) (Using eye movements to assess the selectivity of search movements. Vision research 36(14), 2177–2187) (saccades were not selective), by manipulating the critical features for peripheral selection and discrimination separately. We found search to be more selective and efficient when the selection task was easy or when fixations were long-lasting. Remarkably, subjects did not increase their fixation durations when the peripheral selection task was more difficult. Only the discrimination task affected the fixation duration. This implies that the time available for peripheral target selection is determined mainly by the discrimination task. The results of the present experiment suggest that, besides the difficulty of the peripheral selection task, fixation duration is an important factor determining the selection of potential targets for eye movements. © 1999 Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(02)00328-3

Over the last decade significant advances have been made in our understanding of the molecular mechanisms that control early aspects of mammalian liver development. Studies using tissue explant cultures and molecular biology techniques as well as the analysis of transgenic and knockout mice have identified signaling molecules and transcription factors that are necessary for the onset of hepatogenesis. This review presents an overview of these studies and discusses the role of individual factors during hepatic development. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(98)00180-1

In 74 normal subjects (62 children aged 5–8 years and 12 adults), we tested the widely-held belief that visual sensitivity improves substantially during childhood. Maturation of the retino-striate pathways is generally invoked to account for age-related changes in visual sensitivity. We evaluated the extent to which attentional factors unduly emphasized the effect of age on the purely physiological mechanisms. After a specially-designed familiarization procedure, sensitivity was fully evaluated at two locations in the superior temporal field using a bracketing technique (Octopus 2000R). False-positive (FP) and false-negative (FN) catch-trials were interspersed with the sequence of stimuli. Analyses demonstrated that: (1) age affected sensitivity; and (2) the general level of attentiveness varied not only with age, but also among subjects in the same age group. We then estimated the extent to which improved visual sensitivity may reflect a concomitant evolution of vigilance. Firstly, controlled variance analyses indicated that factors for evaluating attentiveness (rate of FN responses, slope of the psychometric function at the median, and goodness of fit) were indeed much better predictors than age of the sensitivity measured. Secondly and more significantly, the grouping of subjects into homogeneous subgroups, on the basis of their attentional performance, showed that children as young as 5 years may have a visual sensitivity that is only marginally lower than that of adults. © 1999 Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(01)00384-7

Scaffold proteins play an important role in regulating signal transduction by targeting kinases and phosphatases in close proximity to their relevant substrates. SSeCKS protein has been described as a protein kinase C and A (PKC/PKA) anchoring protein as well as a PKC substrate with a tumor suppressor activity. In this study, we report the generation, via gene trapping in embryonic stem cells of mice carrying an insertion in the mouse SSeCKS gene. Through the molecular analysis of the insertion site, we show that SSeCKS contains two alternative promoters directing the synthesis of mRNAs (P1and P2-mRNA), encoding two different proteins, one of which would be a truncated form of the other. Interestingly, these RNAs are differentially expressed, P2 being found exclusively in the male germ line, while P1 exhibits a dynamic and wider pattern of expression during embryonic development and in the adult; its expression is predominant in the nervous system. Finally, we show that P1but not P2-mRNA expression is abolished by the insertion and furthermore that mice homozygous for the mutation lack SSeCKS in all tissues except the male germ cells. Nevertheless and surprisingly, these mice do not exhibit any obvious phenotype. The functional implications of these observations are discussed. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00464-6

The development of multi-cellular organisms is regulated by the ordered de®nition of gene expression programmes that govern cell proliferation and differentiation. Although differential gene activity is mainly controlled by transcription factors, it is also dependent upon the underlying chromatin structure, which can stabilize transcriptional `on' or `off' states. We have recently isolated human (SUV39H1) and mouse (Suv39h1) histone methyltransferases (HMTases) and shown that they are important regulators for the organization of repressive chromatin domains. To investigate whether a SUV39H1-induced modulation of heterochromatin would affect mammalian development, we generated transgenic mice that over-express the SUV39H1 HMTase early during embryogenesis. SUV39H1 transgenic mice are growth retarded, display a weak penetrance of skeletal transformations and are largely characterized by impaired erythroid differentiation, consistent with highest transgene expression in foetal liver. Ex vivo transgenic foetal liver cultures initially contain reduced numbers of cells in G1 but progress to immortalized erythroblasts that are compromised in executing an erythroid differentiation programme. The outgrowing SUV39H1-immortalized erythroblasts can maintain a diploid karyotype despite deregulation of several tumour suppressor proteins and dispersed distribution of the heterochromatin component HP1. Together, these data provide evidence for a role of the SUV39H1 HMTase during the mammalian development and indicate a possible function for higher-order chromatin in contributing to the balance between proliferation and differentiation potentials of progenitor cells. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
Covert Identification Over Binary-Input Discrete Memoryless Channels

This paper considers the covert identification problem in which a sender aims to reliably convey an identification (ID) message to a set of receivers via a binary-input discrete memoryless channel (BDMC), and simultaneously to guarantee that the communication is covert with respect to a warden who monitors the communication via another independent BDMC. We prove a square-root law for the covert identification problem. This states that an ID message of size <inline-formula> <tex-math notation="LaTeX">$\exp (\exp (\Theta (\sqrt {\text {n}})))$ </tex-math></inline-formula> can be transmitted over <italic>n</italic> channel uses. We then characterize the exact pre-constant in the <inline-formula> <tex-math notation="LaTeX">$\Theta (\cdot)$ </tex-math></inline-formula> notation. This constant is referred to as the covert identification capacity. We show that it equals the recently developed covert capacity in the standard covert communication problem, and somewhat surprisingly, the covert identification capacity can be achieved without any shared key between the sender and receivers. The achievability proof relies on a random coding argument with pulse-position modulation (PPM), coupled with a second stage which performs code refinements. The converse proof relies on an expurgation argument as well as results for channel resolvability with stringent input constraints.
Quantifying language changes surrounding mental health on Twitter

Mental health challenges are thought to afflict around 10% of the global population each year, with many going untreated due to stigma and limited access to services. Here, we explore trends in words and phrases related to mental health through a collection of 1- , 2-, and 3-grams parsed from a data stream of roughly 10% of all English tweets since 2012. We examine temporal dynamics of mental health language, finding that the popularity of the phrase 'mental health' increased by nearly two orders of magnitude between 2012 and 2018. We observe that mentions of 'mental health' spike annually and reliably due to mental health awareness campaigns, as well as unpredictably in response to mass shootings, celebrities dying by suicide, and popular fictional stories portraying suicide. We find that the level of positivity of messages containing 'mental health', while stable through the growth period, has declined recently. Finally, we use the ratio of original tweets to retweets to quantify the fraction of appearances of mental health language due to social amplification. Since 2015, mentions of mental health have become increasingly due to retweets, suggesting that stigma associated with discussion of mental health on Twitter has diminished with time.
Dynamical phases in a ``multifractal'' Rosenzweig-Porter model

We consider the static and the dynamical phases in a Rosenzweig-Porter (RP) random matrix ensemble with a distribution of off-diagonal matrix elements of the form of the large-deviation ansatz. We present a general theory of survival probability in such a random-matrix model and show that the averaged survival probability may decay with time as a simple exponent, as a stretch-exponent and as a power-law or slower. Correspondingly, we identify the exponential, the stretch-exponential and the frozen-dynamics phases. As an example, we consider the mapping of the Anderson localization model on Random Regular Graph onto the RP model and find exact values of the stretch-exponent \kappaκ in the thermodynamic limit. As another example we consider the logarithmically-normal RP random matrix ensemble and find analytically its phase diagram and the exponent \kappaκ. Our theory allows to describe analytically the finite-size multifractality and to compute the critical length with the exponent \nu_{MF}=1νMF=1 associated with it.
A Systematic Investigation of KB-Text Embedding Alignment at Scale

Knowledge bases (KBs) and text often contain complementary knowledge: KBs store structured knowledge that can support long range reasoning, while text stores more comprehensive and timely knowledge in an unstructured way. Separately embedding the individual knowledge sources into vector spaces has demonstrated tremendous successes in encoding the respective knowledge, but how to jointly embed and reason with both knowledge sources to fully leverage the complementary information is still largely an open problem. We conduct a large-scale, systematic investigation of aligning KB and text embeddings for joint reasoning. We set up a novel evaluation framework with two evaluation tasks, few-shot link prediction and analogical reasoning, and evaluate an array of KB-text embedding alignment methods. We also demonstrate how such alignment can infuse textual information into KB embeddings for more accurate link prediction on emerging entities and events, using COVID-19 as a case study.
The impact of the CMB on the evolution of high-z blazars

Different works have recently found an increase of the average X-ray-to-radio luminosity ratio with redshift in the blazar population. We evaluate here whether the inverse Compton interaction between the relativistic electrons within the jet and the photons of the Cosmic Microwave Background (IC/CMB) can explain this trend. Moreover, we test whether the IC/CMB model can also be at the origin of the different space density evolutions found in X-ray and radio selected blazar samples. By considering the best statistically complete samples of blazars selected in the radio or in the X-ray band and covering a large range of redshift (0.5. z. 5.5), we evaluate the expected impact of the CMB on the observed X-ray emission on each sample and then we compare these predictions with the observations. We find that this model can satisfactorily explain both the observed trend of the X-ray-to-radio luminosity ratios with redshift and the different cosmological evolutions derived from the radio and X-ray band. Finally, we discuss how currently on-going X-ray missions, like eROSITA, could help to further constrain the observed evolution at even higher redshifts (up to z∼6-7).
MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories

Simulation-based inference enables learning the parameters of a model even when its likelihood cannot be computed in practice. One class of methods uses data simulated with different parameters to infer models of the likelihood-to-evidence ratio, or equivalently the posterior function. Here we frame the inference task as an estimation of an energy function parametrized with an artificial neural network. We present an intuitive approach, named MINIMALIST, in which the optimal model of the likelihood-to-evidence ratio is found by maximizing the likelihood of simulated data. Within this framework, the connection between the task of simulation-based inference and mutual information maximization is clear, and we show how several known methods of posterior estimation relate to alternative lower bounds to mutual information. These distinct objective functions aim at the same optimal energy form and therefore can be directly benchmarked. We compare their accuracy in the inference of model parameters, focusing on four dynamical systems that encompass common challenges in time series analysis: dynamics driven by multiplicative noise, nonlinear interactions, chaotic behavior, and high-dimensional parameter space.