Miracle-dz/UniFAR-FTUs huggingface dataset:
Activation by Point Mutation of Ki-ras Gene Occurring in Transfected Human Normal dna

A mutation-activated human Ki-ras gene was detected in NIH 3T3 cells transfected with high molecular weight DNA extracted from peripheral blood leukocytes of a healthy blood donor. A deoxyguanosine at position 35 of the first exon was substituted by deoxythymidine. Nevertheless, cloning and sequencing of seven independent Ki-ras first exons, isolated from the same human genomic DNA used to transfect NIH 3T3 cells, failed to reveal the expected point mutation. Since transfected DNA is susceptible to mutagenesis in mammalian cells, we hypothesize that a base substitution occurred during the transfection assay.
Matrix Factorization and Matrix Concentration

Motivated by the constrained factorization problems of sparse principal components analysis (PCA) for gene expression modeling, low-rank matrix completion for recommender systems, and robust matrix factorization for video surveillance, this dissertation explores the modeling, methodology, and theory of matrix factorization. We begin by exposing the theoretical and empirical shortcomings of standard deflation techniques for sparse PCA and developing alternative methodology more suitable for deflation with sparse “pseudo-eigenvectors. ” We then explicitly reformulate the sparse PCA optimization problem and derive a generalized deflation procedure that typically outperforms more standard techniques on real-world datasets. We next develop a fully Bayesian matrix completion framework for integrating the complementary approaches of discrete mixed membership modeling and continuous matrix factorization. We introduce two Mixed Membership Matrix Factorization (M3F) models, develop highly parallelizable Gibbs sampling inference procedures, and find that M3F is both more parsimonious and more accurate than state-of-the-art baselines on real-world collaborative filtering datasets. Our third contribution is Divide-Factor-Combine (DFC), a parallel divide-and-conquer framework for boosting the scalability of a matrix completion or robust matrix factorization algorithm while retaining its theoretical guarantees. Our experiments demonstrate the near-linear to super-linear speed-ups attainable with this approach, and our analysis shows that DFC enjoys high-probability recovery guarantees comparable to those of its base algorithm. Finally, inspired by the analyses of matrix completion and randomized factorization procedures, we show how Stein’s method of exchangeable pairs can be used to derive concentration inequalities for matrix-valued random elements. As an immediate consequence, we obtain analogues of classical moment inequalities and exponential tail inequalities for independent and dependent sums of random matrices. We moreover derive comparable concentration inequalities for self-bounding matrix functions of dependent random elements.
EVALUATING A CROSS-CULTURAL CHILDREN ’ S ONLINE BOOK COMMUNITY : SOCIABILITY , USABILITY , AND CULTURAL EXCHANGE

As an extension of the International Children’s Digital Library, the ICDLCommunities project will enable children’s communities to develop around the book collection, build tools that allow intercultural communication between children without the use of machine translation, and promote cross-cultural understanding. It will provide a supportive, safe environment for children (aged 7-11) who speak different languages and are from different cultures to come together and use activities related to books in the ICDL to provide common ground. This report presents a review of the research on children, technology, and online communities; describes an evaluation of the prototype activities and tools conducted with children in Argentina and the U.S.; and discusses the lessons learned and their implications on the design of the ICDLCommunities interface. ICDL Communities Technical Report, p. 2
Basolateral D‐glucose transport activity along the crypt‐villus axis in rat jejunum and upregulation induced by gastric inhibitory peptide and glucagon‐like peptide−2

Phloridzin‐insensitive D‐glucose uptake into enterocytes isolated sequentially from along the crypt‐villus axis showed the majority of transport activity to reside in cells from the upper third of the villus. In contrast, total postnuclear glucose transporter 2 (GLUT2) protein content of the cells was high even close to the crypt and was almost constant for the upper 80% of the villi. A 4 h lumenal perfusion in vivo with 100 mM D‐glucose prior to harvesting the enterocytes produced a 2‐ to 3‐fold increase in phloridzin‐insensitive D‐glucose uptake which extended down 70% of the villus. Vascular infusion in vivo with either 800 pM gastric inhibitory polypeptide (GIP) or glucagon‐like peptide‐2 (GLP‐2) prior to harvesting enterocytes produced the same response as lumenal glucose, while glucagon like peptide‐1 (GLP‐1) had no effect. Inclusion of 30 microM brefeldin A (BFA), an inhibitor of protein trafficking, in the lumenal perfusate produced a small, but not significant, increase in the control uptake profile along the villus in isolated enterocytes. However, BFA significantly reduced the upregulation induced by lumenal glucose and vascular GIP and blocked the stimulation produced by vascular GLP‐2. Biotinylation of surface proteins and isolation with protein A indicated that there was no change in the membrane abundance of GLUT2 after GLP‐2 treatment. These results are discussed in relation to the role of gastrointestinal peptide hormones in controlling intestinal hexose transport and the possibility of protein trafficking being involved in mediating the upregulation of GLUT2 activity in the enterocyte basolateral membrane.
Vascular Endothelial Growth Factor and Angiopoietin-1 Stimulate Postnatal Hematopoiesis by Recruitment of Vasculogenic and Hematopoietic Stem Cells

Tyrosine kinase receptors for angiogenic factors vascular endothelial growth factor (VEGF) and angiopoietin-1 (Ang-1) are expressed not only by endothelial cells but also by subsets of hematopoietic stem cells (HSCs). To further define their role in the regulation of postnatal hematopoiesis and vasculogenesis, VEGF and Ang-1 plasma levels were elevated by injecting recombinant protein or adenoviral vectors expressing soluble VEGF165, matrix-bound VEGF189, or Ang-1 into mice. VEGF165, but not VEGF189, induced a rapid mobilization of HSCs and VEGF receptor (VEGFR)2+ circulating endothelial precursor cells (CEPs). In contrast, Ang-1 induced delayed mobilization of CEPs and HSCs. Combined sustained elevation of Ang-1 and VEGF165 was associated with an induction of hematopoiesis and increased marrow cellularity followed by proliferation of capillaries and expansion of sinusoidal space. Concomitant to this vascular remodeling, there was a transient depletion of hematopoietic activity in the marrow, which was compensated by an increase in mobilization and recruitment of HSCs and CEPs to the spleen resulting in splenomegaly. Neutralizing monoclonal antibody to VEGFR2 completely inhibited VEGF165, but not Ang-1–induced mobilization and splenomegaly. These data suggest that temporal and regional activation of VEGF/VEGFR2 and Ang-1/Tie-2 signaling pathways are critical for mobilization and recruitment of HSCs and CEPs and may play a role in the physiology of postnatal angiogenesis and hematopoiesis.
The Pollutant Diethylhexyl Phthalate Regulates Hepatic Energy Metabolism via Species-Specific PPARα-Dependent Mechanisms

Background The modulation of energetic homeostasis by pollutants has recently emerged as a potential contributor to the onset of metabolic disorders. Diethylhexyl phthalate (DEHP) is a widely used industrial plasticizer to which humans are widely exposed. Phthalates can activate the three peroxisome proliferator–activated receptor (PPAR) isotypes on cellular models and induce peroxisome proliferation in rodents. Objectives In this study, we aimed to evaluate the systemic and metabolic consequences of DEHP exposure that have remained so far unexplored and to characterize the underlying molecular mechanisms of action. Methods As a proof of concept and mechanism, genetically engineered mouse models of PPARs were exposed to high doses of DEHP, followed by metabolic and molecular analyses. Results DEHP-treated mice were protected from diet-induced obesity via PPARα-dependent activation of hepatic fatty acid catabolism, whereas the activity of neither PPARβ nor PPARγ was affected. However, the lean phenotype observed in response to DEHP in wild-type mice was surprisingly abolished in PPARα-humanized mice. These species differences are associated with a different pattern of coregulator recruitment. Conclusion These results demonstrate that DEHP exerts species-specific metabolic actions that rely to a large extent on PPARα signaling and highlight the metabolic importance of the species-specific activation of PPARα by xenobiotic compounds.
Mittag-Leffler stability of fractional-order neural networks with impulses

This paper is concerned with the global Mittag-Leffler stability issue for fractional-order neural networks with impulse effects. Based on the properties of topological degree, the existence of the network equilibrium point is proved, and the expression of solution is given.An inequality for the Caputo fractional derivative, with 0 < γ < 1, is improved, which plays central roles in the investigation of the global Mittag-Leffler stability. Applying the fractional Lyapunov method with impulses, the global Mittag-Leffler stability condition is presented in terms of linear matrix inequalities (LMIs). Finally, an illustrative example is given to demonstrate the effectiveness of the theoretical results.
In situ studies of the crystallization kinetics in Sb–Ge films

The crystallization process in SbxGe1−x alloy films has been observed during in situ annealing in a transmission electron microscope. Results are presented for two films with x=0.89 (89 at. % Sb) and x=0.71 (71 at. % Sb), which lie on either side of the eutectic composition (x=0.85). In the former films radial crystals are observed to grow rapidly from discrete nuclei, whereas in the latter films the crystallization process occurs through a near‐planar front. In addition, quantitative data obtained from these experiments show that the Sb0.89Ge0. 11 films have a higher activation energy for crystal growth and a lower temperature for the nucleation of crystals. Significant differences are observed between the crystallization processes for the two films studied, with the Sb0.89Ge0. 11 film showing better potential for development as an ultrafast optical phase‐change storage medium.
In Vivo Imaging of Preferential Motor Axon Outgrowth to and Synaptogenesis at Prepatterned Acetylcholine Receptor Clusters in Embryonic Zebrafish Skeletal Muscle

Little is known about the spatial and temporal dynamics of presynaptic and postsynaptic specializations that culminate in synaptogenesis. Here, we imaged presynaptic vesicle clusters in motor axons and postsynaptic acetylcholine receptor (AChR) clusters in embryonic zebrafish to study the earliest events in synaptogenesis in vivo. Prepatterned AChR clusters are present on muscle fibers in advance of motor axon outgrowth from the spinal cord. Motor axon growth cones and filopodia are selectively extended toward and contact prepatterned AChR clusters, followed by the rapid clustering of presynaptic vesicles and insertion of additional AChRs, hallmarks of synaptogenesis. All initially formed neuromuscular synapses contain AChRs that were inserted into the membrane at the time the prepattern is present. Examination of embryos in which AChRs were blocked or clustering is absent showed that neither receptor activity or receptor protein is required for these events to occur. Thus, during initial synaptogenesis, postsynaptic differentiation precedes presynaptic differentiation, and prepatterned neurotransmitter clusters mark sites destined for synapse formation.
Comparison of Six Real-Time PCR Assays for Qualitative Detection of Cytomegalovirus in Clinical Specimens

ABSTRACT In this study, we compared the performance of six real-time PCR assays for the qualitative detection of cytomegalovirus (CMV) in clinical samples other than plasma. Two hundred specimens (respiratory [n = 72], urine [n = 67], cerebrospinal fluid [CSF] [n = 25], tissue [n = 18], amniotic fluid [n = 10], and bone marrow [n = 8]) submitted for routine testing by CMV real-time PCR analyte-specific reagents (ASR) (Roche Diagnostics, Indianapolis, IN) were also tested by a laboratory-developed test (LDT) and 4 commercially available PCR assays: EraGen Multicode (Luminex, Austin, TX), Focus Simplexa (Focus Diagnostics, Cypress, CA), Elitech MGB Alert CMV (Fisher Scientific, Hanover Park, IL), and Abbott CMV (Abbott Park, IL). Nucleic acid was extracted using the MagNA Pure system (Roche Diagnostics) and subsequently tested by each PCR method. Results were analyzed by comparing each assay to a “consensus result,” which was defined as the result obtained from at least 4 of the 6 assays. In addition to the prospective samples, 13 lower respiratory samples with known positive results by CMV shell vial were tested by each PCR method. Following testing of the 200 prospective specimens, the Abbott, Elitech, EraGen, and Focus PCR assays demonstrated a sensitivity of 100% (46/46), while the Roche analyte-specific reagents (ASR) and LDT showed sensitivities of 89% (41/46) and 98% (45/46), respectively. Percent specificities ranged from 97% (149/154) by Elitech to 100% (154/154) by the LDT. Among the 13 shell vial-positive lower respiratory samples, the percent sensitivities ranged from 69% (9/13) by Elitech to 92% (12/13) by the LDT. The Abbott, EraGen, Elitech, Focus, and LDT PCR assays performed similarly (κ ≥ 0.89) for the detection of CMV in clinical specimens and demonstrated increased sensitivity compared to the Roche ASR.
Fractures of the Talus: State of the Art

Talus fractures occur rarely but are often associated with complications and functional limitations. Urgent reduction of associated dislocations is recommended with open reduction and internal fixation of displaced fractures when adjacent soft tissue injury permits. Delayed definitive fixation may reduce the risks of wound complications and infections. Restoration of articular and axial alignment is necessary to optimize ankle and hindfoot function. Despite this, posttraumatic arthrosis occurs frequently after talar neck and body fractures, especially with comminution of the talar body. Osteonecrosis is reported in up to half of talar neck fractures, although many of these injuries will revascularize without collapse of the talar dome. Initial fracture displacement and presence of open fractures increase the risk of osteonecrosis. Talar process fractures may be subtle and easily missed on plain radiographs. Advanced imaging will provide detail to facilitate treatment planning. Level of Evidence: Therapeutic Level V. See Instructions for Authors for a complete description of levels of evidence.
Obstacle Avoidance for Kinematically Redundant Manipulators Using a Dual Neural Network

One important issue in the motion planning and control of kinematically redundant manipulators is the obstacle avoidance. In this paper, a recurrent neural network is developed and applied for kinematic control of redundant manipulators with obstacle avoidance capability. An improved problem formulation is proposed in the sense that the collisionavoidance requirement is represented by dynamically-updated inequality constraints. In addition, physical constraints such as joint physical limits are also incorporated directly into the formulation. Based on the improved problem formulation, a dual neural network is developed for the online solution to collision-free inverse kinematics problem. The neural network is simulated for motion control of the PA10 robot arm in the presence of point and window-shaped obstacle.
Ideomotor effects of pitch on continuation tapping

The ideomotor principle predicts that perception will modulate action where overlap exists between perceptual and motor representations of action. This effect is demonstrated with auditory stimuli. Previous perceptual evidence suggests that pitch contour and pitch distance in tone sequences may elicit tonal motion effects consistent with listeners’ implicit awareness of the lawful dynamics of locomotive bodies. To examine modulating effects of perception on action, participants in a continuation tapping task produced a steady tempo. Auditory tones were triggered by each tap. Pitch contour randomly and persistently varied within trials. Pitch distance between successive tones varied between trials. Although participants were instructed to ignore them, tones systematically affected finger dynamics and timing. Where pitch contour implied positive acceleration, the following tap and the intertap interval (ITI) that it completed were faster. Where pitch contour implied negative acceleration, the following tap and the ITI that it completed were slower. Tempo was faster with greater pitch distance. Musical training did not predict the magnitude of these effects. There were no generalized effects on timing variability. Pitch contour findings demonstrate how tonal motion may elicit the spontaneous production of accents found in expressive music performance.
Inhibitors of the Mitogen-Activated Protein Kinase Kinase 1/2 Signaling Pathway Clear Prion-Infected Cells from PrPSc

Prions represent a unique class of infectious agents in which the normal cellular prion protein (PrPC) is converted to an abnormal isoform (PrPSc), which accumulates in the brain and constitutes the major, if not the only, component of the infectious particle. Factors that still remain to be identified may facilitate the conversion of PrPC to PrPSc. In the present study, we first demonstrated that a growth factor of the neurotrophin family, brain-derived neurotrophic factor (BDNF), stimulates the formation of PrPSc in a gonadotropin-releasing hormone-secreting neuronal cell line (GT1-1 cells) infected with the Rocky Mountain Laboratory (RML) strain of scrapie as determined by Western blot analysis. We then observed that the prion-infected cells can be cleared from PrPSc by treatment with three inhibitors of mitogen-activated protein kinase kinase 1/2 (MEK1/2) [1,4-diamino-2,3-dicyano-1,4-bis(o-aminophenylmercapto)butadiene and 2-(2-amino-3-methyoxyphenyl)-4H-1-benzopyran-4-one, as well as α-[amino[(4-aminophenyl)thio]methylene]-2-(trifluoromethyl) benzeneacetonitrile, which passes the blood–brain barrier], a component of one of the intracellular signaling pathways activated by BDNF. The MEK1/2 inhibitors were also efficient in clearing PrPSc from prion-infected GT1-1 cells stimulated to accumulate high levels of PrPSc by enhanced serum concentrations in the medium or by the use of a serum-free neuron-specific neurobasal medium. PrPSc did not reappear in the cultures within 5 weeks after completion of treatment. We conclude that inhibitors of the MEK1/2 pathway can efficiently and probably irreversibly clear PrPSc from prion-infected cells. The MEK pathway may therefore be a suitable target for therapeutic intervention in prion diseases.
An equilibrium model of wealth distribution $ Neng Wang

I present an explicitly solved equilibrium model for the distribution of wealth and income in an incomplete-markets economy. I first propose a self-insurance model with an inter-temporally dependent preference [Uzawa, H. 1968. Time preference, the consumption function, and optimal asset holdings. In: Wolfe, J.N. (Ed.), Value, Capital, and Growth: Papers in Honour of Sir John Hicks. Edinburgh University Press, Edinburgh, pp. 485–504]. I then derive an analytical consumption rule which captures stochastic precautionary saving motive and generates stationary wealth accumulation. Finally, I provide a complete characterization for the equilibrium crosssectional distribution of wealth and income in closed form by developing a recursive formulation for the moments of the distribution of wealth and income. Using this recursive formulation, I show that income persistence and the degree of wealth mean reversion are the main determinants of wealthincome correlation and relative dispersions of wealth to income, such as skewness and kurtosis ratios between wealth and income. r 2006 Elsevier B.V. All rights reserved. JEL classification: D91; E21
Nanocarriers for Transmucosal Vaccine Delivery

Immunization has been realized as one of the most cost effective methods of controlling microbial infections. Currently, the most widely employed means of vaccine delivery includes intramuscular injection which is effective against pathogens invading via the systemic route. The antibody titers do not extend to mucosal or serosal sites which are also the portals of entry for invading pathogens. Mucosal means of delivery comes as viable alternatives. The oral route for mucosal vaccination has not been successful in presenting an- tigens to the body. Acidic environment and inactivating enzymes of the GI tract degrade the antigen before it is presented to the M-cells of Peyer's patches. Nanocarrier based vaccines however, can help to overcome the problems associated with mucosal delivery. These car- riers have shown to improve the bioavailability, act as adjuvant to provoke a stronger immune response while being targeted to associated tissues, leading to improved success of vaccination which inculcates interest of nanotechnology in vaccination. This review encompasses a wide range of nanocarriers that have been of interest.
Camouflaging an Object from Many Viewpoints

We address the problem of camouflaging a 3D object from the many viewpoints that one might see it from. Given photographs of an object's surroundings, we produce a surface texture that will make the object difficult for a human to detect. To do this, we introduce several background matching algorithms that attempt to make the object look like whatever is behind it. Of course, it is impossible to exactly match the background from every possible viewpoint. Thus our models are forced to make trade-offs between different perceptual factors, such as the conspicuousness of the occlusion boundaries and the amount of texture distortion. We use experiments with human subjects to evaluate the effectiveness of these models for the task of camouflaging a cube, finding that they significantly outperform naïve strategies.
Cognitive Alexithymia Is Associated with the Degree of Risk for Psychosis

Alexithymia is a personality construct denoting emotion processing problems. It has been suggested to encompass two dimensions: a cognitive and affective dimension. The cognitive dimension is characterized by difficulties in identifying, verbalizing and analyzing emotions, while the affective dimension reflects the level of emotional arousal and imagination. Alexithymia has been previously proposed as a risk factor for developing psychosis. More specifically, the two alexithymia dimensions might be differentially related to the vulnerability for psychosis. Therefore, we examined the two dimensions of alexithymia, measured with the BVAQ in 94 siblings of patients with schizophrenia, 52 subjects at ultra-high risk (UHR) for developing psychosis, 38 patients with schizophrenia and 109 healthy controls. The results revealed that siblings and patients had higher levels of cognitive alexithymia compared to controls. In addition, subjects at UHR for psychosis had even higher levels of cognitive alexithymia compared to the siblings. The levels of affective alexithymia in siblings and patients were equal to controls. However, UHR individuals had significantly lower levels of affective alexithymia (i.e. higher levels of emotional arousal and fantasizing) compared to controls. Alexithymia was further related to subclinical levels of negative and depressive symptoms. These findings indicate that alexithymia varies parametrically with the degree of risk for psychosis. More specifically, a type-II alexithymia pattern, with high levels of cognitive alexithymia and normal or low levels of affective alexithymia, might be a vulnerability factor for psychosis.