Miracle-dz/UniFAR-FTUs huggingface dataset:
How does cell size regulation affect population growth

The proliferation of a growing microbial colony is well characterized by the population growth rate. However, at the single-cell level, isogenic cells often exhibit different cell-cycle durations. For evolutionary dynamics, it is thus important to establish the connection between the population growth rate and the heterogeneous single-cell generation time. Existing theories often make the assumption that the generation times of mother and daughter cells are independent. However, it has been shown that to maintain a bounded cell size distribution, cells that grow exponentially at the single-cell level need to adopt cell size regulation, leading to a negative correlation of mother-daughter generation time. In this work, we construct a general framework to describe the population growth in the presence of size regulation. We derive a formula for the population growth rate, which only depends on the variability of single-cell growth rate, independent of other sources of noises. Our work shows that a population can enhance the population growth by reducing the growth rate variability, which may be the reason for the mild growth rate variability observed in many microorganisms.
Advances in computational and statistical diffusion MRI

Computational methods are crucial for the analysis of diffusion magnetic resonance imaging (MRI) of the brain. Computational diffusion MRI can provide rich information at many size scales, including local microstructure measures such as diffusion anisotropies or apparent axon diameters, whole‐brain connectivity information that describes the brain's wiring diagram and population‐based studies in health and disease. Many of the diffusion MRI analyses performed today were not possible five, ten or twenty years ago, due to the requirements for large amounts of computer memory or processor time. In addition, mathematical frameworks had to be developed or adapted from other fields to create new ways to analyze diffusion MRI data. The purpose of this review is to highlight recent computational and statistical advances in diffusion MRI and to put these advances into context by comparison with the more traditional computational methods that are in popular clinical and scientific use. We aim to provide a high‐level overview of interest to diffusion MRI researchers, with a more in‐depth treatment to illustrate selected computational advances.
A 12-bit 210-MS/s 5.3-mW pipelined-SAR ADC with a passive residue transfer technique

A 210 MS/s dual-channel 12-bit analog-to-digital converter (ADC) employing a pipelined successive approximation (SAR) architecture is presented. The ADC is partitioned into 3 stages with passive residue transferring between the 1st and the 2nd stages and active residue amplification between the 2nd and the 3rd stages. The ADC consumes 5.3 mW from a 1-V supply and achieves an SNDR of 63.48 dB at a 5-MHz input and 60.1 dB near Nyquist-rate.
Experimental Mouse Model of Lumbar Ligamentum Flavum Hypertrophy

Lumbar spinal canal stenosis (LSCS) is one of the most common spinal disorders in elderly people, with the number of LSCS patients increasing due to the aging of the population. The ligamentum flavum (LF) is a spinal ligament located in the interior of the vertebral canal, and hypertrophy of the LF, which causes the direct compression of the nerve roots and/or cauda equine, is a major cause of LSCS. Although there have been previous studies on LF hypertrophy, its pathomechanism remains unclear. The purpose of this study is to establish a relevant mouse model of LF hypertrophy and to examine disease-related factors. First, we focused on mechanical stress and developed a loading device for applying consecutive mechanical flexion-extension stress to the mouse LF. After 12 weeks of mechanical stress loading, we found that the LF thickness in the stress group was significantly increased in comparison to the control group. In addition, there were significant increases in the area of collagen fibers, the number of LF cells, and the gene expression of several fibrosis-related factors. However, in this mecnanical stress model, there was no macrophage infiltration, angiogenesis, or increase in the expression of transforming growth factor-β1 (TGF-β1), which are characteristic features of LF hypertrophy in LSCS patients. We therefore examined the influence of infiltrating macrophages on LF hypertrophy. After inducing macrophage infiltration by micro-injury to the mouse LF, we found excessive collagen synthesis in the injured site with the increased TGF-β1 expression at 2 weeks after injury, and further confirmed LF hypertrophy at 6 weeks after injury. Our findings demonstrate that mechanical stress is a causative factor for LF hypertrophy and strongly suggest the importance of macrophage infiltration in the progression of LF hypertrophy via the stimulation of collagen production.
Protein-protein interaction analysis of distinct molecular pathways in two subtypes of colorectal carcinoma

The aim of this study was to identify the molecular events that distinguish serrated colorectal carcinoma (SCRC) from conventional colorectal carcinoma (CCRC) through differential gene expression, pathway and protein-protein interaction (PPI) network analysis. The GSE4045 and GSE8671 microarray datasets were downloaded from the Gene Expression Omnibus database. We identified the genes that are differentially expressed between SCRC and normal colon tissues, CCRC and healthy tissues, and between SCRC and CCRC using Student’s t-tests and Benjamini-Hochberg (BH) multiple testing corrections. The differentially expressed genes (DEGs) were then mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and their enrichment for specific pathways was investigated using the Database for Annotation, Visualization and Integrated Discovery (DAVID) tool with a significance threshold of 0.1. Analysis of the potential interactions between the protein products of 220 DEGs (between CCRC and SCRC) was performed by constructing a PPI network using data from the high performance RDF database (P<0.1). The interaction between pathways was also analyzed in CCRC based on the PPI network. Our study identified thousands of genes differentially expressed in SCRC and CCRC compared to healthy tissues. The DEGs in SCRC and CCRC were enriched in cell cycle, DNA replication, and base excision repair pathways. The proteasome pathway was significantly enriched in SCRC but not in CCRC after BH adjustment. The PPI network showed that tumour necrosis factor receptor-associated factor 6 (TRAF6) and atrophin 1 (ATN1) were the most central genes in the network, with respective degrees of node predicted at 90 and 88. In conclusion, the preoteasome pathway was shown to be specifically enriched in SCRC. Furthermore, TRAF6 and ATN1 may be promising biomarkers for the distinction between serrated and conventional CRC.
A NOVEL WIRELESS NETWORK BASED MOBILE E-BUISINESS GENERAL ARCHITECTURE

The upcoming mobile and ubiquitous computing world will need new forms of information sharing and services collaboration between mobile devices, thus to support mobile commerce applications. In this paper, an general mobile business architecture(GMBA: General Mobile Business Architecture) was presented, which can be used in hybrid network environment with wireless network for GMBA. General mobile business architecture relies on wireless peer-to-peer communication model to provide mobile business services. More than 6 major main blocks of the GMBA are defined and the responsibility of each of them is described. In order to illustrate the validation of proposed GMBA, a mobile commerce services application based on GMBA was created, which contains several main blocks of GMBA to perform a particular task promotion mobile service for store vendors among wireless device holders in an reasonable moving area with mutual one-hop radio reachable distance.
Control of posture in patients with neurologically asymptomatic HIV infection and patients with beginning HIV-1-related encephalopathy.

OBJECTIVE Stance control measurements (sway velocity, sway area, and postural reflexes) were performed in 36 patients with neurologically asymptomatic human immunodeficiency virus infection (HIV) and in 10 patients with beginning HIV type 1 (HIV-1)-related encephalopathy. All recordings were performed using a movable platform system. OBSERVATIONS Static posturography and postural reflexes revealed pathologic results in patients with beginning HIV-1-related encephalopathy and in about 25% of patients with nonsymptomatic HIV infection in comparison with age- and sex-matched control subjects. CONCLUSIONS Postural control is well preserved in early HIV infection; thus, it is not an appropriate measure for detecting subclinical deficits, but disturbances of postural control seem to be one of the first neurological abnormalities in patients with beginning HIV-1-related encephalopathy.
In vitro and in vivo differentiation into B cells, T cells, and myeloid cells of primitive yolk sac hematopoietic precursor cells expanded > 100-fold by coculture with a clonal yolk sac endothelial cell line.

The yolk sac, first site of hematopoiesis during mammalian development, contains not only hematopoietic stem cells but also the earliest precursors of endothelial cells. We have previously shown that a nonadherent yolk sac cell population (WGA+, density < 1.077, AA4.1+) can give rise to B cells, T cells and myeloid cells both in vitro and in vivo. We now report on the ability of a yolk sac-derived cloned endothelial cell line (C166) to provide a suitable microenvironment for expansion of these early precursor cells. Single day 10 embryonic mouse yolk sac hematopoietic stem cells wer expanded > 100 fold within 8 days by coculture with irradiated C166 cells. Colony-forming ability was retained for at least three passages in vitro, with retention of the ability to differentiate into T-cell, B-cell, and myeloid lineages. Stem cell properties were maintained by a significant fraction of nonadherent cells in the third passage, although these stem cells expressed a somewhat more mature cell surface phenotype than the initial yolk sac stem cells. When reintroduced into adult allogeneic immunocompromised (scid) hosts, they were able to give rise to all of the leukocyte lineages, including T cells, B cells, and myeloid cells. We conclude that yolk sac endothelial cells can support the stable proliferation of multipotential hematopoietic stem cells, thus generating adequate numbers of cells for study of the mechanisms involved in their subsequent development and differentiation, for in vivo hematopoietic restitution, and for potential use as a vehicle for gene transfer.
THE RELATIONSHIP BETWEEN SECONDARY SCHOOL STUDENTS' DYSFUNCTIONAL ATTITUDES AND THEIR HUMAN VALUES

The aim of this research is to investigate secondary school students' dysfunctional attitudes and their human values. The study has a correlational research design. The sample consisted of 547 students studying at various secondary schools. Two scales were used for data collection; a Human Values Scale developed by Dilmac (2007) and a Dysfunctional Attitudes Scale developed by Weissman and Beck and translated into Turkish by Şahin and Şahin (1991). The findings indicated that four factors of the Dysfunctional Attitudes Scale and six factors of the human values scale were related. Moreover, the factors of the human values scale were found to explain the perfectionist attitude, need for approval, autonomous attitude and tentative attitude factors of the dysfunctional attitudes scale.
Hierarchical Fast Clustering Method for fMRI Feature Reconstruction

In order to solve the feature reconstruction problem of fMRI time series, hierarchical fast clustering method (HFCM) is proposed. The reconstruction of features can be thought as finding the task-related region of interest (ROI) in the human brain fMRI in order to eliminate information redundary. HFCM takes advantage of optimizing the hierarchical structure and tuning weights of different kind of distances. Comparing with the existing reconstruction methods, e.g. K-means and t-test, HFCM saves more than 62% running time, on condition of ensuring the precision of task-related estimating.
The NOESIS open source framework for network data mining

NOESIS is a software framework for the development of data mining techniques for networked data. As an open source project, released under a BSD license, NOESIS intends to provide the necessary infrastructure for solving complex network data mining problems. Currently, it includes a large collection of popular network-related data mining techniques, including the analysis of network structural properties, community detection algorithms, link scoring and prediction methods, and network visualization techniques. The design of NOESIS tries to facilitate the development of parallel algorithms using solid object-oriented design principles and structured parallel programming. NOESIS can be used as a stand-alone application, as many other network analysis packages, and can be included, as a lightweight library, in domain-specific data mining applications and systems.
One- and Two-Way Decode-and-Forward Relaying for Wireless Multiuser MIMO Networks

In this paper, we propose multiuser multiple-input multiple-ouput (MIMO) one-and two-way relaying protocols. Several wireless MIMO node pairs are establishing either unidirectional or bidirectional transmission links via a single decode-and-forward MIMO relay without causing interference to each other. For both half-duplex two-phase relaying protocols, the relay separates messages of different node pairs spatially by using zero-forcing based methods, whereas, in order to cancel the interference within the bidirectional links, XOR preceding followed by self-interference cancellation is employed. Both sum rate and maxmin fairness optimizations, as well as quality-of-service assurance, are considered for the design of the precoders at the relay. The corresponding optimization algorithms for both one-and two-way relaying have been developed using semideflnite programming, which consider the intersection of multiple access and broadcast phases' rate regions.
Developing a tissue‐engineered model of the human bronchiole

Scientists are always looking for new tools to better mimic human anatomy and physiology, especially to study chronic respiratory disease. Airway remodelling is a predominant feature in asthma and occurs in conjunction with chronic airway inflammation. Both the inflammatory and repair processes alter the airway wall which is marked by anatomical, physiological and functional changes. A tissue‐engineered model of bronchiole remodelling presents a novel approach to investigating the initiation and progression of airway remodelling. By developing a unique bioreactor system, cylindrical‐shaped bronchioles constructed from well‐characterized human lung primary cells have been engineered and examined with a much greater control over experimental variables. We have grown human bronchioles composed of fibroblasts, airway smooth muscle cells, small airway epithelial cells and extracellular matrices. The various cell types are in close proximity to one another for cell–cell signalling and matrix interactions. The cylindrical geometry of the tissue applies radial distension for mechanotransduction and the air interface provides a natural environment for the epithelial cells. Optimal cell density, extracellular matrix concentration and media composition were determined. Immunohistochemistry verified bronchiole phenotypic stability. Quiescence was gauged by protein expression which verified a change in phenotype after the initial fabrication stage and implementation of the air interface. A fabrication timeline was devised for repeatable bronchiole fabrication and to understand tissue contraction and cell‐seeding duration. The stability of the bronchiole structures and their cellular composition lends these bronchioles to study cell–cell interactions and remodelling events while maintaining in vivo geometrical dimensions and relationships. Copyright © 2010 John Wiley & Sons, Ltd.
The intention-to-treat principle: a primer for the orthopaedic surgeon.

Randomization in clinical trials reduces bias. Its intent is to generate groups of patients that are comparable with each other before starting a study. As a result, both known and unknown patient factors that may affect the outcome under investigation are balanced between the treatment groups, minimizing the risk of differences between the two groups at the onset of the trial. This helps to ensure that differences in outcomes observed between the groups are the result of the intervention. Anything that compromises the balance of these factors may introduce bias into the results1,2. If an imbalance between the groups skews the results in favor of one intervention over the other, this can lead to a biased study. Therefore, a randomized, double-blinded, placebo-controlled (when appropriate) trial with intention-to-treat analysis is considered to be the highest level of evidence in clinical research. This provides the clearest insight into the effect of the intervention being studied by controlling for as many factors as possible. Intention-to-treat analysis compares study groups in terms of the treatment to which they were randomly allocated, irrespective of the treatment they actually received2-4. If subjects do not receive the treatment to which they were originally randomized, they are in violation of the study protocol. There are several examples of protocol violation, including crossover from one treatment group to another, patients lost to follow-up, and inclusion of patients who should not have been included. Regardless of protocol violation, intention-to-treat analysis is done according to the originally assigned treatment groups because this helps to preserve the value of randomization. Some investigators exclude from analysis any participants who violate the study protocol (e.g., those who cross over, are lost to follow-up, or have insufficient follow-up). This is known as per-protocol analysis2. Patients …
Secondary structure and mutational analysis of the ribosomal frameshift signal of rous sarcoma virus1

Abstract Expression of the Gag-Pol polyprotein of Rous sarcoma virus (RSV) requires a −1 ribosomal frameshifting event at the overlap region of the gag and pol open reading frames. The signal for frameshifting is composed of two essential mRNA elements; a slippery sequence (AAAUUUA) where the ribosome changes reading frame, and a stimulatory RNA structure located immediately downstream. This RNA is predicted to be a complex stem-loop but may also form an RNA pseudoknot. We have investigated the structure of the RSV frameshift signal by a combination of enzymatic and chemical structure probing and site-directed mutagenesis. The stimulatory RNA is indeed a complex stem-loop with a long stable stem and two additional stem-loops contained as substructures within the main loop region. The substructures are not however required for frameshifting. Evidence for an additional interaction between a stretch of nucleotides in the main loop and a region downstream to generate an RNA pseudoknot was obtained from an analysis of the frameshifting properties of RSV mutants translated in the rabbit reticulocyte lysate in vitro translation system. Mutations that disrupted the predicted pseudoknot-forming sequences reduced frameshifting but when the mutations were combined and should re-form the pseudoknot, frameshifting was restored to a level approaching that of the wild-type construct. It was also observed that the predicted pseudoknot-forming regions had reduced sensitivity to cleavage by the single-stranded probe imidazole. Overall, however, the structure probing data indicate that the pseudoknot interaction is weak and may form transiently. In comparison to other characterised RNA structures present at viral frameshift signals, the RSV stimulator falls into a novel group. It cannot be considered to be a simple hairpin-loop yet it is distinct from other well characterised frameshift-inducing RNA pseudoknots in that the overall contribution of the RSV pseudoknot to frameshifting is less dramatic.
Millimeter-wave MIMO radar system using L-shaped Tx and Rx arrays

This paper proposes L-shaped Tx and Rx arrays for MIMO Radar, which enable to enhance azimuth and elevation angular resolution to the maximum under the limitation on the number of the array elements. The proposed L-shaped Tx and Rx arrays include unequally spacing between array elements to be minimum redundancy array on the virtual Rx array, and 2D array interpolation on the Rx virtual array is proposed in order to suppress sidelobes in 2D angular profiles. Computer simulation and experimental measurements have been done for verification. Consequently, our work proves the effectiveness of the proposed MIMO radar array to enhance angular resolution in MIMO radar systems.
Homocysteine, 5,10-methylenetetrahydrofolate reductase 677C>T polymorphism, nutrient intake, and incident cardiovascular disease in 24,968 initially healthy women.

BACKGROUND Hyperhomocysteinemia has been associated with a higher risk of cardiovascular disease (CVD) in epidemiological studies, but recent trials have failed to show a benefit of lowering homocysteine. To address this apparent paradox, we explored whether interaction between genetic and dietary factors related to homocysteine metabolism contributes to CVD risk. METHODS We evaluated the associations of homocysteine, methylenetetrahydrofolate reductase (MTHFR) 677C>T genotype, and dietary intake of folate/B-vitamins with subsequent CVD events in 24 968 apparently healthy white American women followed for 10 years. Plasma homocysteine was measured using an enzymatic assay. MTHFR genotype was determined with a multiplex PCR using biotinylated primers. RESULTS In unadjusted analyses, homocysteine showed moderately strong linear associations with CVD, with hazard ratios (95% CI) comparing top with bottom quintiles for total CVD of 1.92 (1.55-2.37), myocardial infarction 2.32 (1.52-3.54), and ischemic stroke 2.25 (1.45-3.50), all P(trend) <0.001. These ratios were markedly attenuated after adjusting for traditional risk factors and socioeconomic status to 1.08 (0.86-1.36), P(trend) = 0.12; 1.20 (0.76-1.87), P(trend) = 0.14; and 1.21 (0.75-1.94), P(trend) = 0.50, respectively. Homocysteine was associated with MTHFR genotype (1.4 micromol/L higher homocysteine for TT vs CC, P <0.001) and inversely with intake of folate, vitamin B(2), B(6), and B(12), all P(trend) <0.001. However, there was no association of MTHFR genotype or dietary folate/B-vitamins with CVD. In addition, there were no gene-diet or gene-homocysteine interactions in relation to CVD. CONCLUSIONS In this large-scale prospective study, the association of homocysteine with CVD was markedly attenuated after adjusting for risk factors and was not modified by MTHFR 677C>T or intake of folate or B-vitamins.