Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Physics of Signal Estimation in Gaussian Noise: Theory and Examples of Phase Transitions

We consider the problem of signal estimation (denoising) from a statistical mechanical perspective, using a relationship between the minimum mean square error (MMSE), of estimating a signal, and the mutual information between this signal and its noisy version. The paper consists of essentially two parts. In the first, we derive several statistical-mechanical relationships between a few important quantities in this problem area, such as the MMSE, the differential entropy, the Fisher information, the free energy, and a generalized notion of temperature. We also draw analogies and differences between certain relations pertaining to the estimation problem and the parallel relations in thermodynamics and statistical physics. In the second part of the paper, we provide several application examples, where we demonstrate how certain analysis tools that are customary in statistical physics, prove useful in the analysis of the MMSE. In most of these examples, the corresponding statistical-mechanical systems turn out to consist of strong interactions that cause phase transitions, which in turn are reflected as irregularities and discontinuities (similar to threshold effects) in the behavior of the MMSE.
Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP

Musashi1 (Msi1) is an RNA-binding protein that is highly expressed in neural stem cells. We previously reported that Msi1 contributes to the maintenance of the immature state and self-renewal activity of neural stem cells through translational repression of m-Numb. However, its translation repression mechanism has remained unclear. Here, we identify poly(A) binding protein (PABP) as an Msi1-binding protein, and find Msi1 competes with eIF4G for PABP binding. This competition inhibits translation initiation of Msi1's target mRNA. Indeed, deletion of the PABP-interacting domain in Msi1 abolishes its function. We demonstrate that Msi1 inhibits the assembly of the 80S, but not the 48S, ribosome complex. Consistent with these conclusions, Msi1 colocalizes with PABP and is recruited into stress granules, which contain the stalled preinitiation complex. However, Msi1 with mutations in two RNA recognition motifs fails to accumulate into stress granules. These results provide insight into the mechanism by which sequence-specific translational repression occurs in stem cells through the control of translation initiation.
Direct Interaction of Kindlin-3 With Integrin &agr;IIb&bgr;3 in Platelets Is Required for Supporting Arterial Thrombosis in Mice

Objective— Kindlin-3 is a critical supporter of integrin function in platelets. Lack of expression of kindlin-3 protein in patients impairs integrin &agr;IIb&bgr;3–mediated platelet aggregation. Although kindlin-3 has been categorized as an integrin-binding partner, the functional significance of the direct interaction of kindlin-3 with integrin &agr;IIb&bgr;3 in platelets has not been established. Here, we evaluated the significance of the binding of kindlin-3 to integrin &agr;IIb&bgr;3 in platelets in supporting integrin &agr;IIb&bgr;3–mediated platelet functions. Approach and Results— We generated a strain of kindlin-3 knockin (K3KI) mice that express a kindlin-3 mutant that carries an integrin-interaction defective substitution. K3KI mice could survive normally and express integrin &agr;IIb&bgr;3 on platelets similar to their wild-type counterparts. Functional analysis revealed that K3KI mice exhibited defective platelet function, including impaired integrin &agr;IIb&bgr;3 activation, suppressed platelet spreading and platelet aggregation, prolonged tail bleeding time, and absence of platelet-mediated clot retraction. In addition, whole blood drawn from K3KI mice showed resistance to in vitro thrombus formation and, as a consequence, K3KI mice were protected from in vivo arterial thrombosis. Conclusions— These observations demonstrate that the direct binding of kindlin-3 to integrin &agr;IIb&bgr;3 is involved in supporting integrin &agr;IIb&bgr;3 activation and integrin &agr;IIb&bgr;3-dependent responses of platelets and consequently contributes significantly to arterial thrombus formation.
Glacial Surface Temperatures of the Southeast Atlantic Ocean

A detailed record of sea surface temperature from sediments of the Cape Basin in the subtropical South Atlantic indicates a previously undocumented progression of marine climate change between 41 and 18 thousand years before the present (ky B.P.), during the last glacial period. Whereas marine records typically indicate a long-term cooling into the Last Glacial Maximum (around 21 ky B.P.) consistent with gradually increasing global ice volume, the Cape Basin record documents an interval of substantial temperate ocean warming from 41 to 25 ky B.P. The pattern is similar to that expected in response to changes in insolation owing to variations in Earth's tilt.
Robust absolute stability of time-varying nonlinear discrete-time systems

This paper studies the problem of robust absolute stability of a class of nonlinear discrete-time systems with time-varying matrix uncertainties of polyhedral type and multiple time-varying sector nonlinearities. By using the variational method and the Lyapunov second method, criteria for robust absolute stability are obtained in different forms for the class of systems under consideration. Specifically, we determine the parametric classes of Lyapunov functions which define the necessary and sufficient conditions of robust absolute stability. We apply the piecewise-linear Lyapunov functions of the infinity vector norm type to derive an algebraic criterion for robust absolute stability in the form of solvability conditions of a set of matrix equations. Some simple sufficient conditions of robust absolute stability are given which become necessary and sufficient for several special cases. An example is presented as an application of these results to a specific class of systems with time-varying interval matrices in the linear part.
Yeast microbiota of raptors: a possible tool for environmental monitoring.

Twenty-two raptors from a rehabilitation centre were evaluated for the presence of yeasts prior to returning them to the wild, and the recovered Candida isolates were tested for in vitro antifungal susceptibility and phospholipase production. Samples were collected from the crop/lower esophagus and cloaca. In vitro antifungal susceptibility and phospholipase production of 21 Candida strains were assessed through broth microdilution and growth on egg yolk agar respectively. Twenty-seven isolates, belonging to seven species, were recovered from 16 tested birds, with C. albicans and C. famata as the most prevalent species. Three out of 21 isolates (2 C. albicans and 1 C. tropicalis) were simultaneously resistant to fluconazole and itraconazole. As for phospholipase production, 8 (8/21) isolates (6 C. albicans, 1 C. famata and 1 C. parapsilosis) showed enzymatic activity. The most relevant finding in this study was the isolation of resistant Candida spp. from wild raptors that had never been submitted to antifungal therapy, which suggests exposure to environmental contaminants. Based on this, we propose the assessment of Candida spp. from the gastrointestinal tract of raptors as a tool for environmental monitoring.
Multilevel coding for multiple-antenna transmission

The application of powerful coding for transmission over multiple-input/multiple-output channels is discussed. The authors emphasize that as an immediate consequence of the mutual information chain rule, multilevel coding (MLC) constitutes the optimum coded modulation scheme. On the other hand, simple bit-interleaved coded modulation (BICM) is only a convenient alternative for the case of two transmit and one receive antennas when combined with orthogonal space-time block codes. Starting from MLC, the authors further propose a hybrid coded modulation scheme, which favorably combines the advantages of MLC and BICM.
Laser Doppler flowmetric determination of ureteral blood flow after ureteral access sheath placement.

BACKGROUND AND PURPOSE The ureteral access sheath has positively impacted ureteroscopy by decreasing operative times and increasing success rates. However, as previous studies have suggested that large-caliber endoscopes may cause ureteral ischemia, concern has been raised about the impact of access sheath insertion on ureteral blood flow. We sought to determine whether the access sheath compromises ureteral blood supply and, if so, causes ischemic damage to the ureter during ureteroscopic procedures. MATERIALS AND METHODS Using a swine animal model, ureteral blood flow was measured with a laser Doppler flowmeter. Eleven ureteral units were randomized into four study groups: those dilated with 10F-12F, 12F-14F, and 14F-16F access sheaths (N = 3 per group) and an undilated control group (N = 2). Blood flow measurements were obtained from the proximal ureter via laser Doppler flowmetry for 70 minutes at 5-minute intervals. Hemodynamic variability was controlled for through intraoperative heart rate and oxygen saturation monitoring, as well as a second Doppler probe that was placed on the animal's skin, from which readings were also taken every 5 minutes. Results were correlated with histopathologic findings. RESULTS The control group demonstrated little ureteral blood flow variability over the course of 70 minutes. The study groups that were dilated with sheaths, however, all showed a decrease in ureteral blood flow after access sheath insertion, with the flow in animals dilated with 12F-14F and 14F-16F sheaths dropping below 50% of baseline. This initial drop in blood flow was followed by a gradual increase from nadir toward baseline values over the course of the study. On average, the 14F-16F group reached nadir more quickly and took longer to restore its ureteral blood flow. All animals remained hemodynamically stable throughout the study, showing only minimal variability in heart rate, oxygen saturation, and skin blood flow over the 70-minute experiment. Histologically, there was no evidence of ischemic damage in any of the study groups at 72 hours. CONCLUSIONS In this animal model, the access sheath does cause a transient decrease in ureteral blood flow. Nonetheless, compensatory mechanisms of the ureteral wall restore blood flow to near-baseline rates and preserve urothelial integrity, suggesting that use of the ureteral access sheath remains a safe adjunct to flexible ureteroscopy. Because the chronic effects of the access sheath have yet to be elucidated, care must be taken in selecting an appropriate-size sheath for each individual case. Preventive measures may be available to help avoid sheath-related ureteral injury in those patients identified as high risk.
A Drosophila model for fetal alcohol syndrome disorders: role for the insulin pathway

SUMMARY Prenatal exposure to ethanol in humans results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, reduced brain size, permanent neurobehavioral abnormalities and fetal death. Here we describe the use of Drosophila melanogaster as a model for exploring the effects of ethanol exposure on development and behavior. We show that developmental ethanol exposure causes reduced viability, developmental delay and reduced adult body size. We find that flies reared on ethanol-containing food have smaller brains and imaginal discs, which is due to reduced cell division rather than increased apoptosis. Additionally, we show that, as in mammals, flies reared on ethanol have altered responses to ethanol vapor exposure as adults, including increased locomotor activation, resistance to the sedating effects of the drug and reduced tolerance development upon repeated ethanol exposure. We have found that the developmental and behavioral defects are largely due to the effects of ethanol on insulin signaling; specifically, a reduction in Drosophila insulin-like peptide (Dilp) and insulin receptor expression. Transgenic expression of Dilp proteins in the larval brain suppressed both the developmental and behavioral abnormalities displayed by ethanol-reared adult flies. Our results thus establish Drosophila as a useful model system to uncover the complex etiology of fetal alcohol syndrome.
Effects of supplemental irrigation on water consumption characteristics and grain yield in different wheat cultivars

Shortage of water resources is a major limiting factor for wheat (Triticum aestivum L.) production in the North China Plain. The objectives of this study were to evaluate the effects of supplemental irrigation (SI) on water use characteristics and grain yield of the wheat cultivars 'Jimai 22'and 'Zhouyuan 9369'. Two supplemental irrigation treatment regimens were designed based on target relative soil moisture contents in 0-140 cm soil layers at jointing rising to 75% of field capacity (FC) for each cultivar, and at anthesis rising to 65% and 75% (W1), and 70% and 80% (W2) in 2009-2010 and 2010-2011, respectively. Rain-fed (W0) treatment was used as control. Under W1, grain yield of 'Jimai 22' was 5.22% higher than that of W2, and water use efficiency (WUE) of 'Zhouyuan 9369' was 4.0% higher than that under W2. No significant differences in WUE of 'Jimai 22' and grain yield of 'Zhouyuan 9369' were observed for the two treatment regimens in 2009-2010. Grain yield and WUE in W1 were higher than those of W2 for both cultivars in 2010-2011. W1 enhanced soil water consumption compared to W2, especially in the 100-200 cm soil layers, for both cultivars in 2009-2011. Meanwhile, 'Jimai 22' showed higher soil water consumption and ET from anthesis to mature stage, which resulted in increase in grain yield and WUE of 'Jimai 22' by 8.15-21.7% and 7.75-11.73% in 2009-2010 and 2010-2011, respectively, compared with 'Zhouyuan 9369'. Thus, our results showed that SI increased the yield and WUE of 'Jimai 22' and W1 was the better treatment regimen.
T-Cell Levels Are Prognostic in Mantle Cell Lymphoma

Purpose: The purpose of this study was to investigate the impact of T-cell subsets on pathologic and clinical features including disease outcome in mantle cell lymphoma (MCL). Experimental Design: Cell populations were investigated using flow cytometry in diagnostic MCL (n = 153) and reactive (n = 26) lymph node biopsies. Levels of tumor cells, T cells, T-cell subsets, and the CD4:CD8 ratio were assessed and related to pathologic and clinical parameters. Results: MCL cases with diffuse and nodular histologic subtypes showed lower levels of T cells, especially CD4+ T cells, than those with mantle zone growth pattern. Both CD3 and CD4 levels were lower in the nodular subtype than in mantle zone (P = 0.007; P = 0.003) and in the diffuse compared with the nodular subtype (P = 0.022; P = 0.015). The CD4:CD8 ratios were inversely correlated to tumor cell proliferation (P = 0.003). Higher levels of CD3+ and CD4+ T cells and higher CD4:CD8 ratios were associated with indolent disease (P = 0.043, 0.021, and 0.003 respectively). In univariate analysis, a high CD4:CD8 ratio, but not the histologic subtype, was correlated to longer overall survival (OS). In multivariate analysis, the CD4:CD8 ratio correlated with OS independently of Mantle Cell Lymphoma International Prognostic Index (MIPI) and high p53 expression (P = 0.023). Conclusion: CD3+, CD8+, and particularly CD4+ T-cell levels are higher in indolent MCL and decrease with more aggressive histology as reflected by a diffuse growth pattern. High CD4:CD8 ratio correlated independently of other high-risk prognostic factors with longer OS, suggesting a prognostic role for T cells in MCL. Clin Cancer Res; 20(23); 6096–104. ©2014 AACR.
Newton-type algorithms for robot motion optimization

The paper presents a class of Newton-type algorithms for the optimization of robot motions that take into account the dynamics. Using techniques from the theory of Lie groups and Lie algebras, the equations of motion of a rigid multibody system can be formulated in such a way that both the first and second derivatives of the dynamic equations with respect to arbitrary joint variables can be computed analytically. The result is that one can formulate the exact gradient and Hessian of an objective function involving the dynamics, and develop efficient second-order Newton-type optimization algorithms for generating optimal robot motions. The methodology is illustrated with a nontrivial example.
Development and Stem Cells Research Article 1445 Materials and Methods Mouse Breeding

INTRODUCTION During central nervous system (CNS) development, both neurons and glia derive from a population of radial neural progenitors. SOX2, a member of the HMG box transcriptional activators (of the SOXB1 subfamily), plays an essential role in progenitor cell maintenance in the developing and adult CNS (Favaro et al. Disruption of SOX2 function in the embryonic and adult CNS results in both a loss of neural progenitor cells (NPCs) and a decrease in neurogenesis. To date, the key biological function of SOX2 required for NPC maintenance has not been elucidated. In this study, we address this question by genetically dissecting the role of SOX2 in the postnatal mouse retina. In the developing retina, six neuronal and one glial cell type are produced by retinal progenitor cells (RPCs) in a distinct temporal order that is conserved among vertebrates (Livesey and Cepko, 2001). To ensure the correct final composition of the retina with respect to the ratios of neuronal and glial cell types, a delicate balance between RPC maintenance and differentiation must be preserved throughout the course of retinogenesis. This balance is achieved through the coordinated actions of transcription factors regulating neuronal cell fate specification, such as those of the basic helix-loop-helix (bHLH) and homeobox families, and the molecular mechanisms acting to maintain the undifferentiated state of RPCs (Marquardt, 2003; Ohsawa and Kageyama, 2008). We previously demonstrated that SOX2 is essential for the maintenance of both the RPC undifferentiated state and their neurogenic potential (Matsushima et al., 2011; Taranova et al., 2006). Ablation of Sox2 in embryonic RPCs abrogates neurogenesis through the loss of key RPC characteristics: their molecular identity, morphology and proliferative and differentiation capacity. In this study we dissect the mechanism of SOX2 function in the maintenance of NPC identity. During the postnatal period, RPCs primarily give rise to rod photoreceptors, bipolar cells and Müller glia (MG) (Marquardt and Gruss, 2002; Ohsawa and Kageyama, 2008). Among these late-born cell types, MG are the only cells to maintain both an RPC-like radial morphology and gene expression profile, including expression of SOX2 (Nelson et al., 2011; Roesch et al., 2008; Taranova et al., 2006). Under homeostatic conditions, MG support neuronal function by maintaining retinal architecture and providing trophic support. However, recent evidence suggests that MG do not irreversibly exit the progenitor state, as they can re-enter the cell cycle in response to retinal injury and maintain the potential to give rise to …
Hepatitis C Virus Proteins Modulate MicroRNA Expression and Chemosensitivity in Malignant Hepatocytes

Purpose: Hepatocellular cancer (HCC) is highly resistant to chemotherapy and is associated with poor prognosis. Chronic hepatitis C virus (HCV) infection is a major cause of HCC. However, the effect of viral proteins in mediating chemosensitivity in tumor cells is unknown. We postulated that HCV viral proteins could modulate therapeutic responses by altering host cell microRNA (miRNA) expression. Experimental Design: HepG2 malignant hepatocytes were stably transfected with full-length HCV genome (Hep-394) or an empty vector (Hep-SWX). MiRNA profiling was done by using a custom microarray, and the expression of selected miRNAs was validated by real-time PCR. Protein expression was assessed by Western blotting, whereas caspase activation was assessed by a luminometric assay. Results: The IC50 to sorafenib was lower in Hep-394 compared with Hep-SWX control cells. Alterations in miRNA expression occurred with 10 miRNAs downregulated >2-fold and 23 miRNAs upregulated >2-fold in Hep-394 cells compared with controls. Of these, miR-193b was overexpressed by 5-fold in Hep-394 cells. miR-193b was predicted to target Mcl-1, an antiapoptotic protein that can modulate the response to sorafenib. The expression of Mcl-1 was decreased, and basal caspase-3/7 activity and poly ADP ribose polymerase cleavage were increased in Hep-394 cells compared with controls. Moreover, transfection with precursors to miR-193b decreased both Mcl-1 expression and the IC50 to sorafenib. Conclusions: Cellular expression of full-length HCV increases sensitivity to sorafenib by the miRNA-dependent modulation of Mcl-1 and apoptosis. Modulation of miRNA responses may be a useful strategy to enhance response to chemotherapy in HCC. Clin Cancer Res; 16(3); 957–66
Exact Minimum Codegree Threshold for K − 4-Factors

Given hypergraphs F and H, an F-factor in H is a set of vertex-disjoint copies of F which cover all the vertices in H. Let K − 4 denote the 3-uniform hypergraph with four vertices and three edges. We show that for sufficiently large n ∈ 4ℕ, every 3-uniform hypergraph H on n vertices with minimum codegree at least n/2−1 contains a K − 4-factor. Our bound on the minimum codegree here is best possible. It resolves a conjecture of Lo and Markström [15] for large hypergraphs, who earlier proved an asymptotically exact version of this result. Our proof makes use of the absorbing method as well as a result of Keevash and Mycroft [11] concerning almost perfect matchings in hypergraphs.
Gene Recognition from Questionable ORFs in Bacterial and Archaeal Genomes

Abstract The ORFs of microbial genomes in annotation files are usually classified into two groups: the first corresponds to known genes; whereas the second includes ‘putative’, ‘probable’, ‘conserved hypothetical’, ‘hypothetical’, ‘unknown’ and ‘predicted’ ORFs etc. Since the annotation is not 100% accurate, it is essential to confirm which ORF of the latter group is coding and which is not. Starting from known genes in the former, this paper describes an improved Z curve method to recognize genes in the latter. Ten-fold cross-validation tests show that the average accuracy of the algorithm is greater than 99% for recognizing the known genes in 57 bacterial and archaeal genomes. The method is then applied to recognize genes of the latter group. The likely non-coding ORFs in each of the 57 bacterial or archaeal genomes studied here are recognized and listed at the website http://tubic.tju. edu.cn/ZCURVE_C_html/non-coding.html. The working mechanism of the algorithm has been discussed in details. A computer program, called ZCURVE_C, was written to calculate a coding score called Z-curve score for ORFs in the above 57 bacterial and archaeal genomes. Coding/non-coding is simply determined by the criterion of Z-curve score > 0/Z-curve score lt; 0. A website has been set up to provide the service to calculate the Z-curve score. A user may submit the DNA sequence of an ORF to the server at http://tubic.tju. edu.cn/ZCURVE_C/Default.cgi, and the Z-curve score of the ORF is calculated and returned to the user immediately.