Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Time Course Clustering with Countably Infinite Hidden Markov Models

Most existing approaches to clustering gene expression time course data treat the different time points as independent dimensions and are invariant to permutations, such as reversal, of the experimental time course. Approaches utilizing HMMs have been shown to be helpful in this regard, but are hampered by having to choose model architectures with appropriate complexities. Here we propose for a clustering application an HMM with a countably infinite state space; inference in this model is possible by recasting it in the hierarchical Dirichlet process (HDP) framework (Teh et al. 2006), and hence we call it the HDP-HMM. We show that the infinite model outperforms model selection methods over finite models, and traditional time-independent methods, as measured by a variety of external and internal indices for clustering on two large publicly available data sets. Moreover, we show that the infinite models utilize more hidden states and employ richer architectures (e.g. state-to-state transitions) without the damaging effects of overfitting.
Crowdsourced Outcome Determination in Prediction Markets

A prediction market is a useful means of aggregating information about a future event. To function, the market needs a trusted entity who will verify the true outcome in the end. Motivated by the recent introduction of decentralized prediction markets, we introduce a mechanism that allows for the outcome to be determined by the votes of a group of arbiters who may themselves hold stakes in the market. Despite the potential conflict of interest, we derive conditions under which we can incentivize arbiters to vote truthfully by using funds raised from market fees to implement a peer prediction mechanism. Finally, we investigate what parameter values could be used in a real-world implementation of our mechanism.
Zinc Supplementation Improves Glucose Homeostasis in High Fat-Fed Mice by Enhancing Pancreatic β-Cell Function

Zinc is an essential component of the insulin granule and it possibly modulates insulin secretion and signaling. Since insulin resistance is a hallmark in the development of type 2 diabetes mellitus, this study aimed at investigating if zinc supplementation is able to improve glucose tolerance and β-cell function in a model of insulin resistance. Male C57BL/6 mice were distributed in four groups according to the diet: normal fat (NF); normal fat supplemented with ZnCl2 (NFZ); high-fat (HF); and, high-fat chow supplemented with ZnCl2 (HFZ). Intraperitoneal glucose (ipGTT) and insulin (ipITT) tolerance, glycemia, insulinemia, HOMA-IR, and HOMA-β were determined after 15 weeks in each diet. Glucose-stimulated insulin secretion (GSIS) was investigated in isolated islets. The insulin effect on glucose uptake, metabolism, and signaling was investigated in soleus muscle. ZnCl2 did not affect body mass or insulin sensitivity as assessed by ipITT, HOMA-IR, muscle glucose metabolism, and Akt and GSK3-β phosphorylation. However, glucose tolerance, HOMA-β, and GSIS were significantly improved by ZnCl2 supplementation. Therefore, ZnCl2 supplementation improves glucose homeostasis in high fat-fed mice by a mechanism that enhances β-cell function, rather than whole-body or muscle insulin sensitivity.
The effect of ADHD on the life of an individual, their family, and community from preschool to adult life

Attention deficit/hyperactivity disorder (ADHD) may affect all aspects of a child’s life. Indeed, it impacts not only on the child, but also on parents and siblings, causing disturbances to family and marital functioning. The adverse effects of ADHD upon children and their families changes from the preschool years to primary school and adolescence, with varying aspects of the disorder being more prominent at different stages. ADHD may persist into adulthood causing disruptions to both professional and personal life. In addition, ADHD has been associated with increased healthcare costs for patients and their family members.
Degradation of 1,2-dichloroethane by Ancylobacter aquaticus and other facultative methylotrophs

Cultures of the newly isolated bacterial strains AD20, AD25, and AD27, identified as strains of Ancylobacter aquaticus, were capable of growth on 1,2-dichloroethane (DCE) as the sole carbon and energy source. These strains, as well as two other new DCE utilizers, were facultative methylotrophs and were also able to grow on 2-chloroethanol, chloroacetate, and 2-chloropropionate. In all strains tested, DCE was degraded by initial hydrolytic dehalogenation to 2-chloroethanol, followed by oxidation by a phenazine methosulfate-dependent alcohol dehydrogenase and an NAD-dependent aldehyde dehydrogenase. The resulting chloroacetic acid was converted to glycolate by chloroacetate dehalogenase. The alcohol dehydrogenase was induced during growth on methanol or DCE in strain AD20, but no activity was found during growth on glucose. However, in strain AD25 the enzyme was synthesized to a higher level during growth on glucose than on methanol, and it reached levels of around 2 U/mg of protein in late-exponential-phase cultures growing on glucose. The haloalkane dehalogenase was constitutively produced in all strains tested, but strain AD25 synthesized the enzyme at a level of 30 to 40% of the total cellular protein, which is much higher than that found in other DCE degraders. The nucleotide sequences of the haloalkane dehalogenase (dhlA) genes of strains AD20 and AD25 were the same as the sequence of dhlA from Xanthobacter autotrophicus GJ10 and GJ11. Hybridization experiments showed that the dhlA genes of six different DCE utilizers were all located on an 8.3-kb EcoRI restriction fragment, indicating that the organisms may have obtained the dhlA gene by horizontal gene transmission.
Interconnection of competence, stress and CiaR regulons in Streptococcus pneumoniae: competence triggers stationary phase autolysis of ciaR mutant cells

Of the 13 two‐component signal transduction systems (TCS) identified in Streptococcus pneumoniae, two, ComDE and CiaRH, are known to affect competence for natural genetic transformation. ComD and ComE act together with the comC‐encoded competence‐stimulating peptide (CSP) and with ComAB, the CSP‐dedicated exporter, to co‐ordinate activation of genes required for differentiation to competence. Several lines of evidence suggest that the CiaRH TCS and competence regulation are interconnected, including the observation that inactivation of the CiaR response regulator derepresses competence. However, the nature of the interconnection remains poorly understood. Interpretation of previous transcriptome analyses of ciaR mutants was complicated by competence derepression in the mutants. To circumvent this problem, we have used microarray analysis to investigate the transition from non‐competence to competence in a comC‐null wild‐type strain and its ciaR derivative after the addition of CSP. This study increased the number of known CSP‐induced genes from ≈ 47 to 105 and revealed ≈ 42 genes with reduced expression in competent cells. Induction of the CiaR regulon, as well as the entire HrcA and part of the CtsR stress response regulons, was observed in wild‐type competent cells. Enhanced induction of stress response genes was detected in ciaR competent cells. In line with these observations, CSP was demonstrated to trigger growth arrest and stationary phase autolysis in ciaR cells. Taken together, these data strongly suggest that differentiation to competence imposes a temporary stress on cells, and that the CiaRH TCS is required for the cells to exit normally from the competent state.
Simulated annealing wavelet estimation via fourth-order cumulant matching

The fourth-order cumulant matching method has been developed recently for estimating a mixed-phase wavelet from a convolutional process. Matching between the trace cumulant and the wavelet moment is done in a minimum mean-squared error sense under the assumption of a non-Gaussian, stationary, and statistically independent reflectivity series. This leads to a highly nonlinear optimization problem, usually solved by techniques that require a certain degree of linearization, and that invariably converge to the minimum closest to the initial model. Alternatively, we propose a hybrid strategy that makes use of a simulated annealing algorithm to provide reliability of the numerical solutions by reducing the risk of being trapped in local minima. Beyond the numerical aspect, the reliability of the derived wavelets depends strongly on the amount of data available. However, by using a multidimensional taper to smooth the trace cumulant, we show that the method can be used even in a trace-by-trace implementation, which is very important from the point of view of stationarity and consistency. We demonstrate the viability of the method under several reflectivity models. Finally, we illustrate the hybrid strategy using marine and field real data examples. The consistency of the results is very encouraging because the improved cumulant matching strategy we describe can be effectively used with a limited amount of data.
Calcific Tendinopathy of the Rotator Cuff: Pathogenesis, Diagnosis, and Management

&NA; Calcific tendinopathy, or calcifying tendinitis, is a disease characterized by multifocal, cell-mediated calcification of living tissue. After spontaneous disappearance of the calcific deposits or, less frequently, surgical removal, the tendon reconstitutes itself. Attention to the clinical presentation and the radiologic, morphologic, and gross characteristics of the calcium deposit will facilitate differentiation between the formative phase and the resorptive phase, which is of paramount importance in the management of this disease. Should conservative treatment fail, surgical removal may be indicated during the formative phase, but only under exceptional circumstances during the resorptive phase. Aspiration and lavage of the deposit should be performed only during the latter phase.
Man is but a worm: Chordate origins

The origin of chordates remains one of the major puzzles of zoology, even after more than a century of intense scientific inquiry, following Darwin's “Origin of Species”. The chordates exhibit a unique body plan that evolved from a deuterostome ancestor some time before the Cambrian. Molecular data gathered from phylogenetics and developmental gene expression has changed our perception of the relationships within and between deuterostome phyla. Recent developmental gene expression data has shown that the chordates use similar gene families and networks to specify their anterior‐posterior, dorsal‐ventral and left‐right body axes. The anterior‐posterior axis is similarly established among deuterostomes and is determined by a related family of transcription factors, the Hox gene clusters and Wnt signaling pathways. In contrast, the dorsal‐ventral axis is inverted in chordates, compared with other nonchordate invertebrates, while still determined by expression of BMP signaling pathway members and their antagonists. Finally, left‐right asymmetries in diverse deuterostomes are determined by nodal signaling. These new data allow revised, testable hypotheses about our earliest ancestors. We present a new hypothesis for the origin of the chordates whereby the expansion of BMP during dorsal‐ventral patterning allowed the evolution of noneural ectoderm and pharyngeal gill slits on the ventral side. We conclude that “Man is but a worm…,” that our chordate ancestors were worm‐like deposit and/or filter feeders with pharyngeal slits, and an anterior tripartite unsegmented neurosensory region. genesis 46:605–613, 2008. © 2008 Wiley‐Liss, Inc.
High-fidelity simulations of unsteady civil aircraft aerodynamics: stakes and perspectives. Application of zonal detached eddy simulation

This paper provides an up-to-date survey of the use of zonal detached eddy simulations (ZDES) for unsteady civil aircraft applications as a reflection on the stakes and perspectives of the use of hybrid methods in the framework of industrial aerodynamics. The issue of zonal or non-zonal treatment of turbulent flows for engineering applications is discussed. The ZDES method used in this article and based on a fluid problem-dependent zonalization is briefly presented. Some recent landmark achievements for conditions all over the flight envelope are presented, including low-speed (aeroacoustics of high-lift devices and landing gear), cruising (engine–airframe interactions), propulsive jets and off-design (transonic buffet and dive manoeuvres) applications. The implications of such results and remaining challenges in a more global framework are further discussed.
Ablation of Hepatic Tumors through the Use of a Novel Magnetic Nanocomposite Probe: Magnetic Characterization and Finite Element Method Analysis

The authors recently proposed a novel system for thermoablation—based on nanoheating—that can potentially overcome limitations associated with previously reported techniques. The aim of this study was to evaluate the therapeutic performance of the system in the ablation of hepatic tissue, the most frequently ablated. A model nanocomposite system, maghemite nanoparticle-filled polydimethylsiloxane, was prepared, and its magnetic properties were studied as a function of nanoparticle concentration. On the basis of measured magnetic properties, a 3D finite element method (FEM) model was used to explore the development of temperature and thermal damage in nonperfused and fully perfused tissue using alternating magnetic field (AMF) parameters that are acceptable for human use. The FEM model was tested for its validity using an analytical model. The saturation magnetization increased to about 9% of the value of pure maghemite nanoparticles over the range of volume fraction (vol. %) between 1 and 5%. Lesion sizes were shown to be greatly affected by tissue perfusion and time. FEM predictions showed good agreement with results obtained with an analytical model to within 7%. Probes fabricated with magnetic nanocomposite can potentially be used to achieve reasonable lesion sizes in hepatic tissues using human-safe AMF parameters.
Determination of Heavy Metals in Young, Matured and Aged Leaves of Moringa setenopetala Tree Using Flame Atomic Absorption Spectroscopy in South Ethiopia

This study was aimed at concentration determination of some heavy metals (Cu, Pb, Fe, Zn and Cr) in Moringa stenopetala tree leaves at three growing stages (young, matured and aged). Determination was made on samples collected from Southern part of Ethiopia using flame atomic absorption spectrometry (FAAS) with acidic digestive method deployed. In the results, three of five metals (Cu, Fe and Zn) are detected but Pb and Cr was not detected by the technique. Results indicated that presence of the metals in all the three growing stages (young, matured and aged) varied. It was observed that mean concentration of iron content increases as the age of the leave increases while mean concentration of zinc decreases as the age of the leave increases. Mean copper concentration was found to be higher in matured and lower in aged leaves. However, the heavy metals lead and chromium were not detected in this experiment.
Optical properties of (ZnTiO3)/Epoxy Nanocomposite Thin films

Two layers of epoxy reinforced with nano- Zinc Tetanet (ZnTiO3) uniform thin films have been prepared using a spin coating technique on glass floors, dispersion and magnetic stirring techniques are used to prepare the nanocomposites, FTIR was employed to aid interpretation of results with a fixed thickness and proportions by weight (0Wt%,1Wt%,2Wt%,3Wt%,4Wt%) ZnTiO3additives.The optical characteristics were studied by measuring the transmittance and absorbance spectrometry as a function of the wavelength (200-1100) nanometers. The results of the transmittance were very high, and high transparency in infrared (IR) radiation was measured by the FTIR and UV-VIS measurements. The optical properties included the calculations of the energy gap; some optical constants were also carried out, which included absorption coefficient making it Suitable for applications of solar cells
High Efficiency Direct Shoot Organogenesis from Leaf Segments of Aerva lanata (L.) Juss. Ex Schult by Using Thidiazuron

An efficient protocol for direct shoot organogenesis has been developed for the medicinal plant Aerva lanata (L.) Juss. ex Schult. Regeneration was achieved from leaf segments of 20 days old in vitro plantlets raised on Murashige and Skoog (MS) medium containing 0.25–2.0 mg L−1 thiadiazuron (TDZ), 3% sucrose, and 0.8% agar. After 21 days of culture incubation, maximum number of shoot organogenesis (23.6 ± 0.16) was obtained on medium containing 1.0 mg L−1 TDZ. The shoots were able to produce in vitro flowers on medium containing 1.0 mg L−1 TDZ in combination with 0.25–0.5 mg L−1 α-naphthaleneacetic acid (NAA). Histological observation showed that the epidermal cells of the leaf explants exhibited continuous cell division led to formation of numerous dome shaped meristematic protrusions and subsequently developed into adventitious shoots. Upon transfer of shootlets to half strength MS medium containing 1.0 mg L−1 indole-3-butyric acid (IBA), around 86% of the regenerated shoots formed roots and plantlets. Rooted plants were hardened and successfully established in the soil at the survival rate of 92%. The regeneration protocol developed in this study provides an important method of micropropagation of this plant. Furthermore, this protocol may be used for a large scale production of its medicinally active compounds and genetic transformations for further improvement.
Risks in Anonymous Distributed Computing Systems

Anonymous distributed systems consist of potentially millions of heterogeneous processing nodes connected by the global Internet. These nodes can be administer ed by thousands of organizations and individuals, with no direct knowledge of each other. Several approaches have been proposed to handle the technical aspects of such systems; this paper addresses some social, ethical, and legal aspects, particularly the potential risks, to nodes both within and outside such systems. We describe the structure of anonymous distributed systems, then identify potential risks and where they occur within the structure. We then examine which risks can be addressed through existing techniques and technologies, and which require further study.
Cohesive subgroup model for graph-based text mining

A k-plex is a graph theoretic generalization of a clique, introduced in social network analysis (SNA) to model tightly knit social subgroups referred to as cohesive subgroups. Clique model was the earliest mathematical model for a cohesive subgroup, but its overly restrictive definition motivated several relaxations including the k-plex model. The models from SNA are suitable, and potentially more realistic cluster models for graph-based clustering and data mining. This article will discuss the applicability of the k-plex model and its advantages compared to the clique model. Some recent developments in integer programming based approaches to identify large k-plexes would be described and the approaches demonstrated on a text mining network.
Chicken Skin Mucosa Surrounding Adult Colorectal Adenomas is a Risk Factor for Carcinogenesis

ObjectivesTransformation of normal mucosa to colorectal adenoma could occur over a span of 5 to 20 years, whereas transformation of colorectal adenoma to colorectal cancer could take an additional 5 to 15 years. This study aims to investigate whether chicken skin mucosa (CSM) surrounding adult colorectal adenomas may be a risk factor for carcinogenesis. MethodsPatients with colorectal mucosa, colorectal adenomas without CSM, or colorectal adenomas with CSM were enrolled in this study. Immunohistochemistry and enzyme-linked immunosorbent assays were used to determine the expression levels of proliferation markers (ki-67 and COX-2) and apoptosis factors (survivin and caspase-3) in tissues. ResultsThe expression of ki-67 was significantly higher in colorectal adenomas with CSM compared with colorectal adenoma tissues (P < 0.01). Colorectal adenocarcinoma showed significantly higher levels of COX-2 protein compared with normal colorectal mucosa and colorectal adenoma tissues (P < 0.001). COX-2 expression was significantly higher in adenomas with CSM compared with normal colorectal mucosa (P < 0.001). Adenomas with CSM and adenocarcinomas exhibited significantly higher levels of survivin when compared with colorectal adenoma without CSM and normal tissues (P < 0.001). Although we found no significant difference in caspase-3 levels between adenocarcinomas and adenomas with CSM, caspase-3 expression was significantly lower in these tissues when compared with colorectal adenomas without CSM and normal mucosa (P < 0.001). ConclusionsThe biological characteristics of colorectal adenomas with CSM were different from those of colorectal adenomas without CSM. Colorectal adenomas with CSM exhibited active cell proliferation and inhibition of apoptotic pathways, suggesting an increased risk of carcinogenesis in these adenomas.
Shikonin circumvents cancer drug resistance by induction of a necroptotic death

Defect in apoptotic signaling and up-regulation of drug transporters in cancer cells significantly limits the effectiveness of cancer chemotherapy. We propose that an agent inducing non-apoptotic cell death may overcome cancer drug resistance and showed that shikonin, a naturally occurring naphthoquinone, induced a cell death in MCF-7 and HEK293 distinct from apoptosis and characterized with (a) a morphology of necrotic cell death; (b) loss of plasma membrane integrity; (c) loss of mitochondrial membrane potentials; (d) activation of autophagy as a downstream consequence of cell death, but not a contributing factor; (e) elevation of reactive oxygen species with no critical roles contributing to cell death; and (f) that the cell death was prevented by a small molecule, necrostatin-1, that specifically prevents cells from necroptosis. The characteristics fully comply with those of necroptosis, a basic cell-death pathway recently identified by Degterev et al. with potential relevance to human pathology. Furthermore, we proved that shikonin showed a similar potency toward drug-sensitive cancer cell lines (MCF-7 and HEK293) and their drug-resistant lines overexpressing P-glycoprotein, Bcl-2, or Bcl-xL, which account for most of the clinical cancer drug resistance. To our best knowledge, this is the first report to document the induction of necroptosis by a small molecular compound to circumvent cancer drug resistance. [Mol Cancer Ther 2007;6(5):1641–9]
Modulating Memory Performance in Healthy Subjects with Transcranial Direct Current Stimulation Over the Right Dorsolateral Prefrontal Cortex

Objective The role of the Dorsolateral Prefrontal Cortex (DLPFC) in recognition memory has been well documented in lesion, neuroimaging and repetitive Transcranial Magnetic Stimulation (rTMS) studies. The aim of the present study was to investigate the effects of transcranial Direct Current Stimulation (tDCS) over the left and the right DLPFC during the delay interval of a non-verbal recognition memory task. Method 36 right-handed young healthy subjects participated in the study. The experimental task was an Italian version of Recognition Memory Test for unknown faces. Study included two experiments: in a first experiment, each subject underwent one session of sham tDCS and one session of left or right cathodal tDCS; in a second experiment each subject underwent one session of sham tDCS and one session of left or right anodal tDCS. Results Cathodal tDCS over the right DLPFC significantly improved non verbal recognition memory performance, while cathodal tDCS over the left DLPFC had no effect. Anodal tDCS of both the left and right DLPFC did not modify non verbal recognition memory performance. Conclusion Complementing the majority of previous studies, reporting long term memory facilitations following left prefrontal anodal tDCS, the present findings show that cathodal tDCS of the right DLPFC can also improve recognition memory in healthy subjects.