Miracle-dz/UniFAR-FTUs huggingface dataset:
Autoregulation and Heterogeneity in Expression of Human Cripto-1

Cripto-1 (CR-1) is involved in various processes in embryonic development and cancer. Multiple pathways regulate CR-1 expression. Our present work demonstrates a possible positive feedback circuit where CR-1 induces its own expression. Using U-87 MG cells treated with exogenous CR-1, we show that such induction involves ALK4/SMAD2/3 pathway. Stochasticity in gene expression gives rise to heterogeneity in expression in genetically identical cells. Positive feedback increases such heterogeneity and often gives rise to two subpopulations of cells, having higher and lower expression of a gene. Using flow cytometry, we show that U-87 MG cells have a minuscule subpopulation with detectable expression of CR-1. Induction of CR-1 expression, by exogenous CR-1, increases the size of this CR-1 positive subpopulation. However, even at very high dose, most of the cells remain CR-1 negative. We show that population behavior of CR-1 induction has a signature similar to bimodal expression expected in a transcriptional circuit with positive feedback. We further show that treatment of U-87 MG cells with CR-1 leads to higher expression of drug efflux protein MDR-1 in the CR-1 positive subpopulation, indicating correlated induction of these two proteins. Positive feedback driven heterogeneity in expression of CR-1 may play crucial role in phenotypic diversification of cancer cells.
An H∞ methodology for position control of 6-DoF Cable-Driven Parallel Robots

This paper proposes an H∞ methodology for position control of 6-DoF Cable-Driven Parallel Robots, which is then applied to the redundant 6-DoF cable-robot INCA with 8 cables. The issue is to control a non-linear coupled MIMO system with constrained states. The control scheme is composed of two cascade parts: position and force control. The position is controlled in the operational space, making use of the end-effector pose measured by a vision-tracking system, where a four-blocks H∞ design scheme with finely adjusted weighting filters ensures good trajectories tracking and disturbances rejection properties while handling properly the non-linear and coupling effects. The force control allows then to generate the control inputs that maintain the cables under feasible tensions. The methodology is evaluated by simulations with a model of the INCA 6D robot.
Large Scale Correlation Clustering Optimization

Clustering is a fundamental task in unsupervised learning. The focus of this paper is the Correlation Clustering functional which combines positive and negative affinities between the data points. The contribution of this paper is two fold: (i) Provide a theoretic analysis of the functional. (ii) New optimization algorithms which can cope with large scale problems (>100K variables) that are infeasible using existing methods. Our theoretic analysis provides a probabilistic generative interpretation for the functional, and justifies its intrinsic "model-selection" capability. Furthermore, we draw an analogy between optimizing this functional and the well known Potts energy minimization. This analogy allows us to suggest several new optimization algorithms, which exploit the intrinsic "model-selection" capability of the functional to automatically recover the underlying number of clusters. We compare our algorithms to existing methods on both synthetic and real data. In addition we suggest two new applications that are made possible by our algorithms: unsupervised face identification and interactive multi-object segmentation by rough boundary delineation.
Analytical approximations of bulk and shear moduli for dry rock based on the differential effective medium theory

Differential effective medium theory has been applied to determine the elastic properties of porous media. The ordinary differential equations for bulk and shear moduli are coupled and it is more difficult to obtain accurate analytical formulae about the moduli of dry porous rock. In this paper, in order to decouple these equations we first substitute an analytical approximation for the dry‐rock modulus ratio into the differential equation and derive analytical solutions of the bulk and shear moduli for dry rock with three specific pore shapes: spherical pores, needle‐shaped pores and penny‐shaped cracks. Then, the validity of the analytical approximations is tested by integrating the full differential effective medium equation numerically. The analytical formulae give good estimates of the numerical results over the whole porosity range for the cases of the three given pore shapes. These analytical formulae can be further simplified under the assumption of small porosity. The simplified formulae for spherical pores are the same as Mackenzie's equations. The analytical formulae are relatively easy to analyse the relationship between the elastic moduli and porosity or pore shapes and can be used to invert some rock parameters such as porosity or pore aspect ratio. The predictions of the analytical formulae for experimental data show that the formulae for penny‐shaped cracks are suitable to estimate the elastic properties of micro‐crack rock such as granite, they can be used to estimate the crack aspect ratio while the crack porosity is known and also to estimate the crack porosity evolution with pressure if the crack aspect ratio is given.
On the design of MIMO-NOMA downlink and uplink transmission

In this paper, a novel MIMO-NOMA framework for downlink and uplink transmission is proposed by applying the concept of signal alignment. By using stochastic geometry, closed-form analytical results are developed to facilitate the performance evaluation of the proposed framework for randomly deployed users and interferers. The impact of different power allocation strategies, such as fixed power allocation and cognitive radio inspired power allocation, on the performance of MIMO-NOMA is also investigated. Computer simulation results are provided to demonstrate the performance of the proposed framework and the accuracy of the developed analytical results.
The future of microarray technology: networking the genome search

In recent years microarray technology has been increasingly used in both basic and clinical research, providing substantial information for a better understanding of genome‐environment interactions responsible for diseases, as well as for their diagnosis and treatment. However, in genomic research using microarray technology there are several unresolved issues, including scientific, ethical and legal issues. Networks of excellence like GA2LEN may represent the best approach for teaching, cost reduction, data repositories, and functional studies implementation.
Hypergraph Models of Playlist Dialects

Playlist generation is an important task in music information retrieval. While previous work has treated a playlist collection as an undifferentiated whole, we propose to build playlist models which are tuned to specific categories or dialects of playlists. Toward this end, we develop a general class of flexible and scalable playlist models based upon hypergraph random walks. To evaluate the proposed models, we present a large corpus of categorically annotated, user-generated playlists. Experimental results indicate that category-specific models can provide substantial improvements in accuracy over global playlist models.
Immunohistochemical studies of Na+/D-glucose cotransporters in the intestine and kidney of Squalus acanthias and Leucoraja erinacea

In preceding studies different characteristics for the Na/D-glucose cotransport in the kidneys of the little skate (Leucoraja erinacea) and the spiny dogfish (Squalus acanthias) were detected. The transporter in the skate showed a high affinity for D-glucose (Km=0.12 mM) and an apparent coupling ratio of 2 Na to 1 D-glucose, whereas the affinity of the shark transporter was much lower (Km=1.90 mM) and the coupling ratio was determined as 1:1. It was therefore suggested that Na-dependent uptake of glucose in the skate is carried out by SGLT1, whereas SGLT2 is in charge of the Na/Dglucose cotransport in the dogfish, because these transporters display the aforementioned transport characteristics in mammals. We have earlier cloned the corresponding genes from the shark and skate kidney. Comparison of the DNA sequences revealed that the shark transporter has a high homology to SGLT2, while the skate sequence is strongly homologous to SGLT1. Furthermore we detected expression of SGLT1 in the skate intestine by RT-PCR, but no expression of any SGLT in the shark intestine. To investigate these species-specific characteristics of Na-dependent glucose uptake in more detail, we generated polyclonal antibodies in rabbits against different extracellular loops of the cloned transporters (see Althoff et al., this bulletin).
Dark Matter RNA: Existence, Function, and Controversy

The mysteries surrounding the ∼97–98% of the human genome that does not encode proteins have long captivated imagination of scientists. Does the protein-coding, 2–3% of the genome carry the 97–98% as a mere passenger and neutral “cargo” on the evolutionary path, or does the latter have biological function? On one side of the debate, many commentaries have referred to the non-coding portion of the genome as “selfish” or “junk” DNA (Orgel and Crick, 1980), while on the other side, authors have argued that it contains the real blueprint for organismal development (Penman, 1995; Mattick, 2003), and the mechanisms of developmental complexity. Thus, this question could be referred to without much exaggeration as the most important issue in genetics today.
Comparative evaluation of the E test, agar dilution, and broth microdilution for testing susceptibilities of Helicobacter pylori strains to 20 antimicrobial agents

The Epsilometer test (E test; AB Biodisk, Solna, Sweden), a new quantitative technique for the determination of antimicrobial susceptibility, was compared to reference methods (agar dilution and broth microdilution) for the antimicrobial susceptibility testing of Helicobacter pylori. Seventy-one H. pylori strains isolated from patients with duodenal ulcers were tested against 20 antimicrobial agents. The E test and the agar dilution method were carried out on Mueller-Hinton agar; the broth microdilution method was performed with Mueller-Hinton broth. The E-test results showed excellent correlation with the agar dilution results, with 91.3 and 98.8% agreement within 1 and 2 log2 dilution steps, respectively, in a total of 1,350 tests. The correlation between the E-test results and the broth microdilution results was slightly higher, with 91.6 and 99.1% agreement within 1 and 2 log2 dilution steps, respectively, in a total of 1,317 tests. There were six major errors and two very major errors by the metronidazole E test compared to the results obtained by reference methods. Excellent agreement between E-test, agar dilution, and broth microdilution results was found for resistance to erythromycin (8%), clarithromycin (6%), and tetracycline (6%). Our results confirm that the E test is comparable to standardized methods for susceptibility testing. Therefore, the E test is a reliable and alternative method for testing H. pylori susceptibility to a wide range of antimicrobial agents in clinical practice.
Caregiver Perspectives on Safety in Home Dementia Care

Home safety is a significant problem for caregivers of people with Alzheimer's disease and other dementias. This focus group study is designed to gain insight into caregivers' experiences of managing safety issues and to explore application of the transtheoretical model of health behavior change (TTM) to this problem, toward development of interventions to improve safety care. Caregivers identified safety problems and management strategies, as well as barriers and factors facilitating management, that can help guide the development of interventions. Caregivers described different stages of adopting actions to prevent accidents and injuries consistent with the TTM. The TTM warrants further study for understanding how to help caregivers make changes to promote safe care.
Modeling NMR chemical shifts: crystal potential derived point charge (CPPCh) model to calculate solid state effects on 31P chemical shifts tensors

Center for High Performance Computing, University of Utah, Salt Lake City, UT 84112, US. *M. B. Ferraro: marta@df.uba. ar**J. C. Facelli: facelli@chpc.utah. eduReceived: 9 April 2000 / Accepted: 10 October 2000 / Published: 13 October 2000Abstract: This paper presents a new method to calculate solid-state effects on NMR chemi-cal shifts. Using full crystal potentials, this new method (CPPCh) eliminates the need to ar-bitrarily select the point charges that are included in the calculations of the NMR chemicalshieldings to take into account intermolecular effects. By eliminating the arbitrary selectionof the point charges, the method provides a mechanism to systematically improve the simu-lation of intermolecular effects on chemical shielding calculations.This new method has been applied to the calculation of the
Finding Gait in Space and Time

We describe an approach to characterize the signatures generated by walking humans in spatio-temporal domain. To describe the computational model for this periodic pattern, we take the mathematical theory of geometry group theory, which is widely used in crystallographic structure research. Both empirical and theoretical analyses prove that spatio-temporal helical patterns generated by legs belong to the Frieze Groups because they can be characterized by a repetitive motif along the direction of walking. The theory is applied to an automatic detection-and-tracking system capable of counting heads and handling occlusion by recognizing such patterns. Experimental results for videos acquired from both static and moving ground sensors are presented. Our algorithm demonstrates robustness to non-rigid human deformation as well as background clutter
Perception of Neighborhood Problems, Health Behaviors, and Diabetes Outcomes Among Adults With Diabetes in Managed Care

OBJECTIVE—Recent data suggest that residential environment may influence health behaviors and outcomes. We assessed whether perception of neighborhood problems was associated with diabetes behaviors and outcomes. RESEARCH DESIGN AND METHODS—This cross-sectional analysis included 7,830 diabetic adults enrolled in Translating Research Into Action for Diabetes, a study of diabetes care and outcomes in managed care settings. Perception of neighborhood problems was measured using a summary score of participants’ ratings of crime, trash, litter, lighting at night, and access to exercise facilities, transportation, and supermarkets. Outcomes included health behaviors and clinical outcomes. Hierarchical regression models were used to account for clustering of patients within neighborhoods and to adjust for objective neighborhood socioeconomic status (percentage living in poverty) and potential individual-level confounders (age, sex, race/ethnicity, education, income, comorbidity index, and duration of diabetes). RESULTS—After adjustment, residents of neighborhoods in the lowest tertile (most perceived problems) reported higher rates of current smoking (15 vs. 11%) than those in the highest tertile and had slightly lower participation in any weekly physical activity (95 vs. 96%). In addition, their blood pressure control was worse (25 vs. 31% <130/80 mmHg), and their Short Form 12 scores were slightly lower (44 vs. 46 units for emotional well-being and 43 vs. 44 units for physical well-being); all P < 0.01. CONCLUSIONS—Neighborhood problems were most strongly associated with more smoking and higher blood pressure, both of which have significant implications for cardiovascular risk. Potential mechanisms that explain these associations should be further explored in longitudinal studies.
Cancer Biomarker Discovery: Lectin-Based Strategies Targeting Glycoproteins

Biomarker discovery can identify molecular markers in various cancers that can be used for detection, screening, diagnosis, and monitoring of disease progression. Lectin-affinity is a technique that can be used for the enrichment of glycoproteins from a complex sample, facilitating the discovery of novel cancer biomarkers associated with a disease state.
Maximal quotient rational reconstruction: an almost optimal algorithm for rational reconstruction

Let n/d ∈ Q, m be a positive integer and let u = n/d mod m. Thus $u$ is the image of a rational number modulo m. The rational reconstruction problem is; given u and m find n/d. A solution was first given by Wang in 1981. Wang's algorithm outputs n/d when m > 2 M2 where M = max(|n|,d). Because of the wide application of this algorithm in computer algebra, several authors have investigated its practical efficiency and asymptotic time complexity.In this paper we present a new solution which is almost optimal in the following sense; with controllable high probability, our algorithm will output n/d when m is a modest number of bits longer than 2 |n| d. This means that in a modular algorithm where m is a product of primes, the modular algorithm will need one or two primes more than the minimum necessary to reconstruct n/d; thus if |n| ⇐ d or d ⇐ |n| the new algorithm saves up to half the number of primes. Further, our algorithm will fail with high probability when m < 2 |n| d.
Plan and operation of the NHANES II Mortality Study, 1992.

OBJECTIVES The NHANES II Mortality Study is a prospective study of adult participants examined in the second National Health and Nutrition Examination Survey (NHANES II) conducted between 1976 and 1980. It was designed to investigate the association between factors measured at baseline and mortality. The methods used in the study are described and assessed in this report. METHODS The vital status of NHANES II participants who were 30-75 years of age at their examination was ascertained after 12-16 years. Vital status was assessed by searching the National Death Index and the Social Security Administration Death Master File for deaths occurring in the United States. Causes of death were obtained from the National Center for Health Statistics Multiple Cause of Death file or death certificates. To assess how well mortality was ascertained, the survival of the cohort after 5 and 10 years was compared to that of the U.S. population during the same period. RESULTS As of December 31, 1992, 23.2 percent of the 9,250 cohort members were found to be deceased. The remaining 76.8 percent that were not found to be deceased may be assumed to be alive for analytic purposes. Cumulative survival probabilities for the cohort were generally higher than probabilities calculated from U.S. life table data. Although some differences were expected, these data suggest that after 10 years of follow-up using passive methods, mortality may have been under ascertained for the cohort. Discrepancies between the survival patterns for NHANES II cohort and U.S. vital statistics were larger for black than for white participants, indicating that ascertainment of mortality was poorer among black participants. Researchers using the NHANES II Mortality Study, 1992 data should be aware of these study limitations.
A diagnostic ATPG for delay faults based on genetic algorithms

This paper presents a GA-based technique to generate diagnostic-oriented delay tests for logic circuits. The aim is to produce a test sequence for a given circuit such that any couple of non-equivalent delay faults is distinguished by at least one rest pair belonging to the test sequence. For this purpose, we decided to preferably use a simulation-based approach with a directed search mechanism rather than developing a new deterministic ATPG. An appropriate fitness function that ranks population members according to their diagnostic capabilities has been defined, and genetic operators allowing a population to evolve during successive generations are presented. In order to have a diagnostic program providing near-optimal solutions, we combined the GA-based technique proposed in this paper with an existing post test diagnostic method for delay faults. Experimental results show that the genetic approach is effective for solving our diagnostic test generation problem, and point out the fact that the GA performs very well in comparison to a random test method.
The Effects of Discourse Cues on Garden Path Processing

We report a self-paced reading study that investigated gardenpath sentences like While the boy washed {a/the} dog barked loudly and While the man hunted {a/the} deer ran into the woods. In such sentences, the critical noun phrase (dog, deer) tends to be misparsed as an object of the preceding verb, and has to be re-analyzed as a subject of the following clause when the disambiguating verb (e.g. barked, ran) is encountered. To better understand how discourse level information guides realtime processing, we build on earlier corpus work in linguistics which found a relationship between syntactic function and information status: Entities in subject position tend to be already-mentioned (old/given) information and definite, while entities in object position are typically new information and indefinite. We investigated whether the information status of the ambiguous noun influences the extent of processing difficulty, and whether this effect also depends on the argument structure of the first verb. Results from self-paced reading showed that information status matters when processing the ambiguous NP after optionally transitive verbs (e.g. hunt) but not after reflexive absolute verbs (e.g. wash). These results suggest that access to discourse-level representations during reanalysis of the noun phrase is modulated by verb argument structure.
Synergism between upregulation of Rab7 and inhibition of autophagic degradation caused by mycoplasma facilitates intracellular mycoplasma infection

Following fusion of a mycoplasma with a host cell membrane, the inserted components of mycoplasma may then be transported through the endocytic pathway. However, the effects of mycoplasmas on the host cell endomembrane system are largely unknown. In this study, mycoplasma-induced changes in the dynamics of endocytic and autophagic systems were investigated. Endocytosis and autophagy are two major processes involved in the survival of intracellular prokaryotic pathogens. It was found that, immediately following infection, mycoplasmas induce endocytosis in the host cell; however, in the long term the mycoplasmas suppress turnover of the components of the endocytic pathway. Immunofluorescence microscopy revealed that Rab7 and LC3-II are recruited to the intracellular mycoplasma-containing compartments. Western blot analysis and quantitative reverse transcription-polymerase chain reaction (qPCR) showed that mycoplasmas increase expression of Rab7 by upregulating transcription, but increase levels of LC3-II and p62 by post-translational regulation. Furthermore, it was demonstrated that mycoplasma infection causes inhibition of autophagic degradation of LC3-II and p62. In addition, it was found that upregulation of Rab7 and inhibition of autophagic degradation synergistically contributes to intracellular mycoplasma accumulation. In conclusion, these findings suggest that mycoplasmas may manipulate host cell endosomal and autophagic systems in order to facilitate intracellular infection.