Miracle-dz/UniFAR-FTUs huggingface dataset:
pathMap: a path-based mapping tool for long noisy reads with high sensitivity

Abstract With the rapid development of single-molecule sequencing (SMS) technologies, the output read length is continuously increasing. Mapping such reads onto a reference genome is one of the most fundamental tasks in sequence analysis. Mapping sensitivity is becoming a major concern since high sensitivity can detect more aligned regions on the reference and obtain more aligned bases, which are useful for downstream analysis. In this study, we present pathMap, a novel k-mer graph-based mapper that is specifically designed for mapping SMS reads with high sensitivity. By viewing the alignment chain as a path containing as many anchors as possible in the matched k-mer graph, pathMap treats chaining as a path selection problem in the directed graph. pathMap iteratively searches the longest path in the remaining nodes; more candidate chains with high quality can be effectively detected and aligned. Compared to other state-of-the-art mapping methods such as minimap2 and Winnowmap2, experiment results on simulated and real-life datasets demonstrate that pathMap obtains the number of mapped chains at least 11.50% more than its closest competitor and increases the mapping sensitivity by 17.28% and 13.84% of bases over the next-best mapper for Pacific Biosciences and Oxford Nanopore sequencing data, respectively. In addition, pathMap is more robust to sequence errors and more sensitive to species- and strain-specific identification of pathogens using MinION reads.
Characterization of the Human QT Interval: Novel Distribution‐Based Assessment of the Repolarization Effects of Moxifloxacin

The authors have previously demonstrated rate‐independent QT variability in the dog and cynomolgus monkey, where the QT associated with any RR was a normally distributed value that was accurately evaluated as the distribution mean. The present study investigated the rate‐independent characteristics of the human QT. Digital electrocardiographs (1000 Hz) were collected for 24 hours in 51 patients (thorough QT study) and analyzed by computer. Distribution‐based analysis was applied to the placebo and moxifloxacin (400 mg) arms to characterize the nature of the QT interval and to assess the efficacy of distribution‐based analysis for QTc determination. Novel statistics using continuous means and bootstrapped 95% confidence intervals were developed to facilitate QT analysis. Machine‐read QT values were compared with core laboratory semiautomated values for verification. RR intervals demonstrated repetitive protocol‐dependent variations (50–250 milliseconds); QT intervals were normally distributed, spanning 60 to 100 milliseconds for each RR interval. Distribution‐based analysis detected a moxifloxacin response identical to semiautomated analysis, but with reduced variability and improved statistical power, where n = 12 satisfied the ICH E14 criteria for a positive control. Distribution‐based analysis has the potential to provide a universal method for clinical QT heart rate correction, enabling accurate detection of QT changes when limited numbers of volunteers are exposed to drug.
Horizontal Transfer of Bacterial Symbionts: Heritability and Fitness Effects in a Novel Aphid Host

ABSTRACT Members of several bacterial lineages are known only as symbionts of insects and move among hosts through maternal transmission. Such vertical transfer promotes strong fidelity within these associations, favoring the evolution of microbially mediated effects that improve host fitness. However, phylogenetic evidence indicates occasional horizontal transfer among different insect species, suggesting that some microbial symbionts retain a generalized ability to infect multiple hosts. Here we examine the abilities of three vertically transmitted bacteria from the Gammaproteobacteria to infect and spread within a novel host species, the pea aphid, Acyrthosiphon pisum. Using microinjection, we transferred symbionts from three species of natural aphid hosts into a common host background, comparing transmission efficiencies between novel symbionts and those naturally infecting A. pisum. We also examined the fitness effects of two novel symbionts to determine whether they should persist under natural selection acting at the host level. Our results reveal that these heritable bacteria vary in their capacities to utilize A. pisum as a host. One of three novel symbionts failed to undergo efficient maternal transmission in A. pisum, and one of the two efficiently transmitted bacteria depressed aphid growth rates. Although these findings reveal that negative fitness effects and low transmission efficiency can prevent the establishment of a new infection following horizontal transmission, they also indicate that some symbionts can overcome these obstacles, accounting for their widespread distributions across aphids and related insects.
Sugar Sensing and Sugar-Mediated Signal Transduction in Plants

Information concerning the sugar status of plant cells is of great importance during all stages of the plant life cycle. The availability of or lack of sugars triggers many metabolic and developmental responses, and it is not surprising, therefore, that sugars profoundly affect the expression of a large number of genes (for review, see Koch, 1996; Graham, 1996). Sugar sensing occurs at the level of individual cells and the responses of such cells must be integrated at the tissue, organ, and plant level. Therefore, sugar-induced signals will interact with other sensing and signaling pathways. The mechanisms used by plant cells to sense sugars and to process this information are essentially unknown, and only recently are these questions being addressed experimentally. This lack of knowledge contrasts with the situation in yeast and bacteria, in which the molecular and physiological analysis of mutants have yielded extensive information about sugar perception (Trumbly, 1992; Ronne, 1995; Saier et al., 1995).
Synthetic Phosphopeptides Enable Quantitation of the Content and Function of the Four Phosphorylation States of Phospholamban in Cardiac Muscle*

Background: Phosphorylation of phospholamban regulates cardiac calcium transport, but the content and function of the four phosphorylation states of phospholamban are unknown. Results: Synthetic phosphopeptides solved both problems. Conclusion: The phosphorylation states were quantified in normal and hypertrophic pig hearts, and each has a distinct effect on calcium transport. Significance: This information is needed for improved diagnosis and treatment of heart failure. We have studied the differential effects of phospholamban (PLB) phosphorylation states on the activity of the sarcoplasmic reticulum Ca-ATPase (SERCA). It has been shown that unphosphorylated PLB (U-PLB) inhibits SERCA and that phosphorylation of PLB at Ser-16 or Thr-17 relieves this inhibition in cardiac sarcoplasmic reticulum. However, the levels of the four phosphorylation states of PLB (U-PLB, P16-PLB, P17-PLB, and doubly phosphorylated 2P-PLB) have not been measured quantitatively in cardiac tissue, and their functional effects on SERCA have not been determined directly. We have solved both problems through the chemical synthesis of all four PLB species. We first used the synthetic PLB as standards for a quantitative immunoblot assay, to determine the concentrations of all four PLB phosphorylation states in pig cardiac tissue, with and without left ventricular hypertrophy (LVH) induced by aortic banding. In both LVH and sham hearts, all phosphorylation states were significantly populated, but LVH hearts showed a significant decrease in U-PLB, with a corresponding increase in the ratio of total phosphorylated PLB to U-PLB. To determine directly the functional effects of each PLB species, we co-reconstituted each of the synthetic peptides in phospholipid membranes with SERCA and measured calcium-dependent ATPase activity. SERCA inhibition was maximally relieved by P16-PLB (the most highly populated PLB state in cardiac tissue homogenates), followed by 2P-PLB, then P17-PLB. These results show that each PLB phosphorylation state uniquely alters Ca2+ homeostasis, with important implications for cardiac health, disease, and therapy.
The Role of Organizational Culture and Process-Structure in Marketing Intelligence: Perspective of IT Professionals

The presented study seeks to explore the factors impacting MI of select consumer durable organizations and to know the strength of their relationship. The intention is the development of a scale and to find the role of organizational culture and process-structure in generating MI. Survey method is used to collect the responses of IT professionals of select consumer durable companies. Data from IT professionals of consumer durable companies from Northern region of India has been collected. The principles of reliability, validity, sensitivity in the design of scale and linear regression technique have been applied to know the strength of the relationship between organizational culture and process-structure on MI. This study advances the understanding of intelligence generation in an organization that is further used in marketing applications by investigating relationships among elements of intelligence.
Feasibility Study of MongoDB and Radio Frequency Identification Technology in Asset Tracking System

Taking into consideration the real time situation specifically the higher academic institutions, small, medium to large companies, public to private sectors and the remaining sectors, do experience the inventory or asset shrinkages due to theft, loss or even inventory tracking errors. This happening is due to a zero or poor security systems and measures being taken and implemented in their organizations. Henceforth, implementing the Radio Frequency Identification (RFID) technology into any manual or existing webbased system or web application can simply deter and will eventually solve certain major issues to serve better data retrieval and data access. Having said, this manual or existing system can be enhanced into a mobile-based system or application. In addition to that, the availability of internet connections can aid better services of the system. Such involvement of various technologies resulting various privileges to individuals or organizations in terms of accessibility, availability, mobility, efficiency, effectiveness, real-time information and also security. This paper will look deeper into the integration of mobile devices with RFID technologies with the purpose of asset tracking and control. Next, it is to be followed by the development and utilization of MongoDB as the main database to store data and its association with RFID technology. Finally, the development of a web based system which can be viewed in a mobile based formation with the aid of Hypertext Preprocessor (PHP), MongoDB, Hyper-Text Markup Language 5 (HTML5), Android, JavaScript and AJAX programming language. Keywords—RFID, asset tracking system, MongoDB, NoSQL.
Structure–Function analysis of secreted frizzled‐related protein‐1 for its Wnt antagonist function

Secreted frizzled‐related proteins (sFRPs) are glycoproteins that are recognized as Wnt antagonists. To identify the functional domains that are involved in Wnt antagonist function, several sFRP‐1 mutants and sFRP‐1/sFRP‐2 chimeras were generated. These mutants were characterized in an optimized T‐cell factor (TCF)‐luciferase based assay in U2OS human osteosarcoma cells. Deletions of the sFRP‐1 cysteine rich domain (CRD) lead to the complete loss of Wnt antagonist function. A region between amino acids 73–86 within the second loop of the CRD of sFRP‐1 was necessary for the optimal Wnt inhibitory function. Within this region, a conserved tyrosine residue played a critical role, and its change to neutral or polar amino acids lead to decreased Wnt inhibitory activity. The sFRP‐1/sFRP‐2 chimeras with the netrin domain of sFRP‐1 replaced by corresponding sFRP‐2 sequences showed 40–70% loss of Wnt antagonist function. The sFRP‐1/sFRP‐2 chimera with the replacement of C‐terminal 19 amino acids of sFRP‐1 with 11 amino acids of sFRP‐2 resulted in 70% loss of activity indicating that carboxyl‐terminal region of sFRP‐1 is important for its Wnt inhibitory activity. The structure–function analysis studies of sFRP‐1 clearly demonstrate the interaction of several functional domains for its optimal Wnt antagonist function. J. Cell. Biochem. 102: 1519–1528, 2007. © 2007 Wiley‐Liss, Inc.
Fast and Robust: Hexapedal Robots via Shape Deposition Manufacturing

Robots to date lack the robustness and performance of even the simplest animals when operating in unstructured environments. This observation has prompted an interest in biomimetic robots that take design inspiration from biology. However, even biomimetic designs are compromised by the complexity and fragility that result from using traditional engineering materials and manufacturing methods. We argue that biomimetic design must be combined with structures that mimic the way biological structures are composed, with embedded actuators and sensors and spatially-varied materials. This proposition is made possible by a layered-manufacturing technology called shape deposition manufacturing (SDM). We present a family of hexapedal robots whose functional biomimetic design is made possible by SDM's unique capabilities and whose fast (over four body-lengths per second) and robust (traversal over hip-height obstacles) performance begins to compare to that seen in nature. We describe the design and fabrication of the robots and we present the results of experiments that focus on their performance and locomotion dynamics.
Gene expression in peripheral blood mononuclear cells from children with diabetes.

OBJECTIVE We hypothesized that type 1 diabetes (T1D) is accompanied by changes in gene expression in peripheral blood mononuclear cells due to dysregulation of adaptive and innate immunity, counterregulatory responses to immune dysregulation, insulin deficiency, and hyperglycemia. RESEARCH DESIGN AND METHODS Microarray analysis was performed on peripheral blood mononuclear cells from 43 patients with newly diagnosed T1D, 12 patients with newly diagnosed type 2 diabetes (T2D), and 24 healthy controls. One- and 4-month follow-up samples were obtained from 20 of the T1D patients. RESULTS Microarray analysis identified 282 genes differing in expression between newly diagnosed T1D patients and controls at a false discovery rate of 0.05. Changes in expression of IL1B, early growth response gene 3, and prostaglandin-endoperoxide synthase 2 resolved within 4 months of insulin therapy and were also observed in T2D, suggesting that they resulted from hyperglycemia. With use of a knowledge base, 81 of 282 genes could be placed within a network of interrelated genes with predicted functions including apoptosis and cell proliferation. IL1B and the MYC oncogene were the most highly connected genes in the network. IL1B was highly overexpressed in both T1D and T2D, whereas MYC was dysregulated only in T1D. CONCLUSION T1D and T2D likely share a final common pathway for beta-cell dysfunction that includes secretion of IL-1beta and prostaglandins by immune effector cells, exacerbating existing beta-cell dysfunction, and causing further hyperglycemia. The results identify several targets for disease-modifying therapy of diabetes and potential biomarkers for monitoring treatment efficacy.
1 Micron-Resolution Particle Image Velocimetry

During the past five years, significant progress has been made in the development and application of micron-resolution Particle Image Velocimetry (μPIV). Developments of the technique have extended typical spatial resolutions of PIV from order 1-mm to order 1-μm. These advancements have been obtained as a result of novel improvements in instrument hardware and post processing software. Theory describing the limits of in-plane and out-of-plane spatial resolution are presented. The basis of the theory for in-plane spatial resolution extends the original work of Adrian & Yao (1985). The theory for out-of-plane spatial resolution closely follows the recent work of Olsen & Adrian (2000a). The desire for high spatial resolution dictates that the flow tracing particles typically range between 200 – 700 nm in diameter. The effect of Brownian forces on particle motion is discussed in detail. Guidelines are given to determine optimal particle size and to estimate particle flow following fidelity. Advances in post processing algorithm provide improvements in velocity accuracy and spatial resolution. The correlation-averaging algorithm increases the effective particle concentration, while maintaining sufficiently low particle concentration in the working fluid. Central difference interrogation provides second order accurate estimates of velocity, which becomes important in regions containing high spatial variations in velocity. These post-processing techniques are particularly useful in challenging micro length scales, and can also be extended to macroscopic flows. The utility of μPIV is demonstrated by applying it to flows in microchannels, micronozzles, BioMEMS, and flow around cells. While the technique was initially developed for microscale velocity measurements, it has been extended to measure wall positions with tens of nanometers resolution, the deformation of hydrogels, micro-particle thermometry, infrared-PIV, and particle tracking velocimetry.
Low Truncation Error and Area Efficient Multiplier for Cryptographic Applications

Multipliers play a vital role in many cryptographic applications like elliptic curve cryptography, RSA and other algorithms. The direct truncation of least significant part of the product leads to large error in the resultant product when fixed width output is the requirement. This paper proposes a truncation error minimizing logic which greatly reduces truncation error. Truncation error minimizing logic has been inserted in the least significant part of full length Baugh Wooley multiplier and Modified Booth Recoding multiplier and the results are compared.VHDL simulation shows that the truncation error is reduced up to 68% compared with direct truncated multiplier and involves lesser number of gates when compared to full length multipliers. It is also found that the total power consumed by these multipliers is only half the amount consumed by full length multiplier. Also Baugh Wooley multiplier performs better than Modified Booth Recoding multiplier.
Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro

The evolution of an 851-bp segment of the human immunodeficiency virus type 1 (HIV-1) genome encoding the nef open reading frame and U3/R elements of the long terminal repeat has been followed over a 4-year period in vivo and in vitro. The population of viral sequences at any given time was established by sequencing cloned polymerase chain reaction products. The samples studied were derived from the same man for whom a detailed analysis of the tat gene was previously described (A. Meyerhans, R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, L. Morfeldt-Manson, B. Asjö, and S. Wain-Hobson, Cell 58:901-910, 1989). Once again in vitro culture resulted in the selection of minor forms. Over a 4-year period in vivo, there was no obvious selection for, or outgrowth of, any particular nef or U3/R sequence. Few defective nef protein sequences were observed, which argues against nef acting as a negative regulatory factor. Although no functionally defective promoter/trans-activation-responsive elements were identified, the transactivation efficiencies varied between 0.2 and 2 times that of the control. The sequence encoding the most efficient trans-activation-responsive region did not outgrow others. The extreme genetic heterogeneity of the different samples of the locus, either in vivo or in vitro, indicates that there is no such thing as a single, distinct HIV sequence. It is suggested that different HIV-1 loci evolve independently, recombination being responsible for their uncoupling.
Análise de conteúdo em pesquisas de Psicologia

The study focuses the application of the content analysis method in empirical research in psychology, according to the technical procedures identified under that methodology. It presents in the first place a brief discussion on the variations in CA and an analysis of the scientific validation criteria that support the method practice. Then it describes the most frequent modes of uses of the CA, extracted from a review conducted in 83 articles published between 2004 and 2009 in six psychology journals in Brazil. The selected journals were classified as A1 and A2 in a triennial assessment for the CAPES periodicals (2007- 2009), and were retrieved from the Scielo base of journals. The final discussion highlights the evaluation assessment of methodological rigor accuracy associated to the practice of the method, suggesting clear information about the CA approach, implementation of the CA and careful explanation of the steps and technical procedures adopted in data analysis.
Pulsed Electromagnetic Fields Increase the Rate of Rat Liver Regeneration after Partial Hepatectomy

Abstract Pulsed extremely low-frequency electromagnetic fields interact with rat liver regeneration following partial hepatectomy when delivered to the rats immediately after the operation and every 12 hr thereafter. This interaction results first in an increased ornithine decarboxylase activity, an enzyme used as an early marker of cell growth. The rate of labeled thymidine incorporation into DNA is also increased by the treatments with magnetic fields during the early phases of liver regeneration. Glycogen depletion and lipid accumulation, two well-known early peculiar phenomena of liver regeneration following partial hepatectomy, are quantitatively decreased by the treatments with electromagnetic fields. The recovery to normal glycogen and lipid contents is completed within 5 days after surgery, instead of 7 days as found in control rats.
Market Bubbles and Chrashes

Episodes of market crashes have fascinated economists for centuries. Although many academics, practitioners and policy makers have studied questions related to collapsing asset price bubbles, there is little consensus yet about their causes and effects. This review and essay evaluates some of the hypotheses offered to explain the market crashes that often follow asset price bubbles. Starting from historical accounts and syntheses of past bubbles and crashes, we put the problem in perspective with respect to the development of the efficient market hypothesis. We then present the models based on heterogeneous agents and the limits to arbitrage that prevent rational agents from bursting bubbles before they inflate. Then, we explore another set of explanations of why rational traders would be led to actually profit from and surf on bubbles, by anticipating the behavior of noise traders or by realizing the difficulties in synchronizing their actions. We then end by discussing a complex system approach of social imitation leading to collective market regimes like herding and the phenomenon of bifurcation (or phase transition) that rationalize what crash can occur in unstable market regimes. The key insight is that diagnosing bubbles may be feasible when taking into account the positive feedback mechanisms that give rise to transient "super-exponential" price growth, the bubbles.