Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated CAD for Nodule Detection for Magnetic Resonance Image Contrast

-------------------------------------------------------------------ABSTRACT--------------------------------------------------------------Contrast is a measure of the variation in intensity or gray value in a specified region of an image. In all applications concerning image acquisition, followed by processing of images, successful pre-processing is of the essence. Every sensor has its own characteristics, but in general the quality of the acquired MR image is fairly poor. Overall grayscale intensity variations, poor contrast and noisy background are the frequently encountered issues. The Rational Unsharp Masking method is the one introduced here to improve the quality of the MR image. It is demonstrated, that the proposed method has much reduced noise sensitivity than another polynomial operator, Cubic Unsharp masking and number of approaches devised to improve the perceived quality of an image. This algorithm has been tested for various slices of axial, sagittal and coronal sections of MR image. The results confirm the ability of the algorithm to produce better quality images, helpful to have effective diagnosis.
TMUNSW: Identification of Disorders and Normalization to SNOMED-CT Terminology in Unstructured Clinical Notes

Unstructured clinical notes are rich sources for valuable patient information. Information extraction techniques can be employed to extract this valuable information, which in turn can be used to discover new knowledge. Named entity recognition and normalization are the basic tasks involved in information extraction. In this paper, identification of disorder named entities and the mapping of identified disorder entities to SNOMED-CT terminology using UMLS Metathesaurus is presented. A supervised linear chain conditional random field model based on sets of features to predict disorder mentions is used in conjunction with MetaMap to identify and normalize disorders. Error analysis conclude that recall of the developed system can be significantly increased by adding more features during model development and also by using a frame based approach for handling disjoint entities.
Effects of proteasome inhibitors MG132, ZL3VS and AdaAhx3L3VS on protein metabolism in septic rats

Proteasome inhibitors are novel therapeutic agents for the treatment of cancer and other severe disorders. One of the possible side effects is influencing the metabolism of proteins. The aim of our study was to evaluate the influence of three proteasome inhibitors MG132, ZL3VS and AdaAhx3L3VS on protein metabolism and leucine oxidation in incubated skeletal muscle of control and septic rats. Total proteolysis was determined according to the rates of tyrosine release into the medium during incubation. The rates of protein synthesis and leucine oxidation were measured in a medium containing L‐[1‐14C]leucine. Protein synthesis was determined as the amount of L‐[1‐14C]leucine incorporated into proteins, and leucine oxidation was evaluated according to the release of 14CO2 during incubation. Sepsis was induced in rats by means of caecal ligation and puncture. MG132 reduced proteolysis by more than 50% and protein synthesis by 10–20% in the muscles of healthy rats. In septic rats, proteasome inhibitors, except ZL3VS, decreased proteolysis in both soleus and extensor digitorum longus (EDL) muscles, although none of the inhibitors had any effect on protein synthesis. Leucine oxidation was increased by AdaAhx3L3VS in the septic EDL muscle and decreased by MG132 in intact EDL muscle. We conclude that MG132 and AdaAhx3L3VS reversed protein catabolism in septic rat muscles.
The Morningside Initiative: Collaborative Development of a Knowledge Repository to Accelerate Adoption of Clinical Decision Support

The Morningside Initiative is a public-private activity that has evolved from an August, 2007, meeting at the Morningside Inn, in Frederick, MD, sponsored by the Telemedicine and Advanced Technology Research Center (TATRC) of the US Army Medical Research Materiel Command. Participants were subject matter experts in clinical decision support (CDS) and included representatives from the Department of Defense, Veterans Health Administration, Kaiser Permanente, Partners Healthcare System, Henry Ford Health System, Arizona State University, and the American Medical Informatics Association (AMIA). The Morningside Initiative was convened in response to the AMIA Roadmap for National Action on Clinical Decision Support and on the basis of other considerations and experiences of the participants. Its formation was the unanimous recommendation of participants at the 2007 meeting which called for creating a shared repository of executable knowledge for diverse health care organizations and practices, as well as health care system vendors. The rationale is based on the recognition that sharing of clinical knowledge needed for CDS across organizations is currently virtually non-existent, and that, given the considerable investment needed for creating, maintaining and updating authoritative knowledge, which only larger organizations have been able to undertake, this is an impediment to widespread adoption and use of CDS. The Morningside Initiative intends to develop and refine (1) an organizational framework, (2) a technical approach, and (3) CDS content acquisition and management processes for sharing CDS knowledge content, tools, and experience that will scale with growing numbers of participants and can be expanded in scope of content and capabilities. Intermountain Healthcare joined the initial set of participants shortly after its formation. The efforts of the Morningside Initiative are intended to serve as the basis for a series of next steps in a national agenda for CDS. It is based on the belief that sharing of knowledge can be highly effective as is the case in other competitive domains such as genomics. Participants in the Morningside Initiative believe that a coordinated effort between the private and public sectors is needed to accomplish this goal and that a small number of highly visible and respected health care organizations in the public and private sector can lead by example. Ultimately, a future collaborative knowledge sharing organization must have a sustainable long-term business model for financial support.
Sequential and Adaptive Learning Algorithms for M-Estimation

The M-estimate of a linear observation model has many important engineering applications such as identifying a linear system under non-Gaussian noise. Batch algorithms based on the EM algorithm or the iterative reweighted least squares algorithm have been widely adopted. In recent years, several sequential algorithms have been proposed. In this paper, we propose a family of sequential algorithms based on the Bayesian formulation of the problem. The basic idea is that in each step we use a Gaussian approximation for the posterior and a quadratic approximation for the log-likelihood function. The maximum a posteriori (MAP) estimation leads naturally to algorithms similar to the recursive least squares (RLSs) algorithm. We discuss the quality of the estimate, issues related to the initialization and estimation of parameters, and robustness of the proposed algorithm. We then develop LMS-type algorithms by replacing the covariance matrix with a scaled identity matrix under the constraint that the determinant of the covariance matrix is preserved. We have proposed two LMS-type algorithms which are effective and low-cost replacement of RLS-type of algorithms working under Gaussian and impulsive noise, respectively. Numerical examples show that the performance of the proposed algorithms are very competitive to that of other recently published algorithms.
Exploring the short-sleep obesity association in young children

There is strong and consistent epidemiological evidence that short sleep duration is associated with increased risk of obesity from early childhood. Childhood obesity and inadequate sleep have negative consequences for health and well-being, and the ability to target both of these public health concerns with a novel obesity intervention involving sleep extension is appealing; yet little is known about the mechanisms linking short sleep with obesity. In adults, hormonal mechanisms have been proposed; in young children, behavioural mechanisms and parenting are likely to be involved. Furthermore, the wider social and cultural determinants of short sleep and obesity should be incorporated into sleep-obesity research. This study aimed to explore some aspects of the sleep-obesity link in preschool children, using an exploratory design with a mixture of quantitative and qualitative methods, and applying an evolutionary medicine perspective. Participants were 109 3-year-old children and their parents in Stockton-on-Tees. Children’s sleep (validated by actigraphy), food intake and activity over 4 days/5 nights were assessed by parental diary report, and body composition was measured. Parents’ attitudes were explored using semi-structured interviews. Combined daytime and nighttime sleep duration was associated with central fat. Alternate parenting strategies were identified, based on regulation and consistency (routine-led), or child-governance and lack of regulation (routine-free). Building on the trends identified and the literature reviewed, I propose two hypotheses to explain the short sleep-obesity link in young children: the Behavioural Mechanisms Hypothesis (dietary and activity behaviours mediate or confound the association), and the Parental Confounding Hypothesis (parenting strategies, which vary with SES, impact on both children’s sleep duration and obesity risk). Parenting impacts children’s health by either limiting or facilitating discordance between children’s experiences in evolutionarily novel environments, and their biological make-up. I conclude that sleep-based obesity interventions should consider the wider context of children’s behaviours, particularly strategies of parenting.
Burkholderia cepacia Genomovar III Is a Common Plant-Associated Bacterium

ABSTRACT A polyphasic taxonomic study involving DNA-DNA hybridization, whole-cell protein electrophoresis, and 16S ribosomal DNA sequence analysis revealed that a group of Burkholderia cepacia-like organisms isolated from the rhizosphere or tissues of maize, wheat, and lupine belong to B. cepacia genomovar III, a genomic species associated with “cepacia syndrome” in cystic fibrosis patients. The present study also revealed considerable protein electrophoretic heterogeneity within this species and demonstrated that the B. cepacia complex consists of two independent phylogenetic lineages.
Modeling mouse and human development using organoid cultures

In vitro three-dimensional (3D) cultures are emerging as novel systems with which to study tissue development, organogenesis and stem cell behavior ex vivo. When grown in a 3D environment, embryonic stem cells (ESCs) self-organize into organoids and acquire the right tissue patterning to develop into several endoderm- and ectoderm-derived tissues, mimicking their in vivo counterparts. Tissue-resident adult stem cells (AdSCs) also form organoids when grown in 3D and can be propagated in vitro for long periods of time. In this Review, we discuss recent advances in the generation of pluripotent stem cell- and AdSC-derived organoids, highlighting their potential for enhancing our understanding of human development. We will also explore how this new culture system allows disease modeling and gene repair for a personalized regenerative medicine approach. Summary: This Review discusses recent advances in the generation of ESC- and adult stem cell-derived organoids in order to understand the development of endoderm-derived organs in human and to develop therapeutic strategies for repair.
CYP 2 C 9 and UGT 1 A 6 Genotypes Modulate the Protective Effect of Aspirin on Colon Adenoma Risk 1

Regular use of nonsteroidal anti-inflammatory drugs (NSAIDs) has a protective effect on the incidence of colon neoplasia. However, polymorphisms in NSAID-metabolizing enzymes may alter this effect. NSAIDs, particularly aspirin, are glucuronidated by UGT1A6 and some classes of NSAIDs are also metabolized by cytochrome P450 (CYP) 2C9. Both of these enzymes have slow-metabolizing, variant forms. We tested the hypothesis that the slow alleles of these enzymes can modify the inverse association between NSAIDs and colon neoplasia in the Minnesota Cancer Prevention Research Unit (CPRU) adenomatous polyp case-control study. CYP2C9and UGT1A6genotypes were determined for 474 adenoma cases and 563 controls. NSAID use was inversely associated with adenoma risk [odds ratio (OR), 0.63; 95% confidence interval (CI), 0.44–0.90 for aspirin; and OR, 0.50; 95% CI, 0.31–0.82 for nonaspirin NSAID]. However, this association was absent in aspirin users who carried theCYP2C9 variant alleles (OR, 0.88; 95% CI, 0.51–1.53) or who were homozygous wild-type UGT1A6 (OR, 0.86; 95% CI, 0.50–1.50). Carriers of both of these alleles who use aspirin were also not at reduced risk of adenomatous polyps (OR, 1.59; 95% CI, 0.68–3.73). The variants of these enzymes did not influence the association between nonaspirin NSAIDs and adenoma risk. These data indicate that the effectiveness of chemopreventive drugs can be modulated by the genotype of metabolizing enzymes.
Abelson Helper Integration Site-1 Gene Variants on Major Depressive Disorder and Bipolar Disorder

Objective The present study aimed to explore whether 4 single nucleotide polymorphisms (SNPs) within the AHI1 gene could be associated with major depressive disorder (MD) and bipolar disorder (BD), and whether they could predict clinical outcomes in mood disorders. Methods One hundred and eighty-four (184) patients with MD, 170 patients with BD and 170 healthy controls were genotyped for 4 AHI1 SNPs (rs11154801, rs7750586, rs9647635 and rs9321501). Baseline and final clinical measures for MD patients were assessed through the Hamilton Rating Scale for Depression (HAM-D). Allelic and genotypic frequencies in MD and BD subjects were compared with those of each disorder and healthy group using the χ2 statistics. Repeated measures ANOVA was used to test possible influences of SNPs on treatment efficacy. Results The rs9647635 A/A was more represented in subjects with BD as compared with MD and healthy subjects together. The rs9647635 A/A was also more presented in patients with MD than in healthy subjects. With regard to the allelic analysis, rs9647635 A allele was more represented in subjects with BD compared with healthy subjects, while it was not observed between patients with MD and healthy subjects. Conclusion Our findings provide potential evidence of an association between some variants of AHI1 and mood disorders susceptibility but not with clinical outcomes. However, we will need to do more adequately-powered and advanced association studies to draw any conclusion due to clear limitations.
RAPID: Reliable Probabilistic Dissemination in Wireless Ad-Hoc Networks

In this paper, we propose a novel reliable probabilistic dissemination protocol, RAPID, for mobile wireless ad-hoc networks that tolerates message omissions, node crashes, and selfish behavior. The protocol employs a combination of probabilistic forwarding with deterministic corrective measures. The forwarding probability is set based on the observed number of nodes in each one-hop neighborhood, while the deterministic corrective measures include deterministic gossiping as well as timer based corrections of the probabilistic process. These aspects of the protocol are motivated by a theoretical analysis that is also presented in the paper, which explains why this unique protocol design is inherent to ad-hoc networks environments. Since the protocol only relies on local computations and probability, it is highly resilient to mobility and failures. The paper includes a detailed performance evaluation by simulation. We compare the performance and the overhead of RAPID with the performance of other probabilistic approaches. Our results show that RAPID achieves a significantly higher node coverage with a smaller overhead.
Learning with two sites of synaptic integration

Since the classical work of D O Hebb 1949 The Organization of Behaviour (New York: Wiley) it is assumed that synaptic plasticity solely depends on the activity of the pre- and the post-synaptic cells. Synapses influence the plasticity of other synapses exclusively via the post-synaptic activity. This confounds effects on synaptic plasticity and neuronal activation and, thus, makes it difficult to implement networks which optimize global measures of performance. Exploring solutions to this problem, inspired by recent research on the properties of apical dendrites, we examine a network of neurons with two sites of synaptic integration. These communicate in such a way that one set of synapses mainly influences the neurons' activity; the other set gates synaptic plasticity. Analysing the system with a constant set of parameters reveals: (1) the afferents that gate plasticity act as supervisors, individual to every cell. (2) While the neurons acquire specific receptive fields the net activity remains constant for different stimuli. This ensures that all stimuli are represented and, thus, contributes to information maximization. (3) Mechanisms for maximization of coherent information can easily be implemented. Neurons with non-overlapping receptive fields learn to fire correlated and preferentially transmit information that is correlated over space. (4) We demonstrate how a new measure of performance can be implemented: cells learn to represent only the part of the input that is relevant to the processing at higher stages. This criterion is termed ‘relevant infomax’.
Quantifying the limits of unidirectional ultrashort optical pulse propagation

In this paper we explore the limits of the unidirectional pulse propagation equation (UPPE) in general nonlinear media. Our main aim is to investigate under which physical conditions two-way propagation becomes significant, and leads to a breakdown of the unidirectional approximation. Using a spectral constraint appearing in the derivation of UPPE we derive a first correction which renormalizes the forward-propagating amplitude. This correction is the main result of our paper and we investigate its effects through numerical simulations.
Spatial Regulation of Exocytic Site and Vesicle Mobilization by the Actin Cytoskeleton

Numerous studies indicate a role for the actin cytoskeleton in secretion. Here, we have used evanescent wave and widefield fluorescence microscopy to study the involvement of the actin cytoskeleton in secretion from PC12 cells. Secretion was assayed as loss of ANF-EmGFP in widefield mode. Under control conditions, depolarization induced secretion showed two phases: an initial rapid rate of loss of vesicular cargo (tau = 1.4 s), followed by a slower, sustained drop in fluorescence (tau = 34.1 s). Pretreatment with Latrunculin A changed the kinetics to a single exponential, slightly faster than the fast component of control cells (1.2 s). Evanescent wave microscopy allowed us to examine this at the level of individual events, and revealed equivalent changes in the rates of vesicular arrival at the plasma membrane immediately following and during the sustained phase of release. Co-transfection of mCherry labeled β-actin and ANF-EmGFP demonstrated that sites of exocytosis had an inverse relationship with sites of actin enrichment. Disruption of visualized actin at the membrane resulted in the loss of specificity of exocytic site.
Kisspeptin-54 stimulates gonadotropin release most potently during the preovulatory phase of the menstrual cycle in women.

CONTEXT Kisspeptin, the endogenous ligand of the G protein-coupled receptor 54, is a key regulator of the hypothalamo-pituitary-gonadal (HPG) axis. GPR54-null mice exhibit reproductive dysfunction, and exogenous kisspeptin potently stimulates the HPG axis in rodents, primates, and human males. The effects of kisspeptin administration to human females are unknown. OBJECTIVE Our objective was to investigate the effects of kisspeptin on LH release during the menstrual cycle in female volunteers. DESIGN Bolus sc kisspeptin-54 was administered to female volunteers, and plasma gonadotropins were measured. SETTING The study took place at a hospital clinical research facility. VOLUNTEERS Subjects were healthy female volunteers with regular menstrual cycles. INTERVENTION 1) Volunteers received a sc bolus injection of kisspeptin-54 (0, 0.2, 0.4, 0.8, 1.6, 3.2, and 6.4 nmol/kg; n = 3-4 per dose) in the follicular phase; and 2) volunteers (n = 8) received a sc bolus injection of either kisspeptin-54 (0.4 nmol/kg) or saline in random order during each phase of the menstrual cycle. MAIN OUTCOME MEASURES Plasma gonadotropins were measured. RESULTS 1) Kisspeptin-54 caused a dose-dependent increase in mean LH over time at doses from 0.2-6.4 nmol/kg. 2) Kisspeptin-54 increased plasma LH compared with saline injection in all phases of the cycle. The effect of kisspeptin was greatest in the preovulatory phase and least in the follicular phase of the cycle [mean increase in LH over baseline (IU/liter) +/- sem for follicular phase was 0.12 +/- 0.17; preovulatory phase, 20.64 +/- 2.91 (P < 0.001 vs. follicular phase); luteal phase, 2.17 +/- 0.79 (P < 0.01 vs. follicular phase)]. CONCLUSION Elevation of plasma kisspeptin in human females potently stimulates LH release in the preovulatory phase and provides a novel mechanism for manipulation of the HPG axis in women.
Hesitation and interrogative Swedish intonation

This paper presents the results of a perception experiment designed to investigate the contribution of a pre-focal hesitation pause, delayed focal peak and a raised F0 range for signaling interrogative mode in Swedish. The results support the hypothesis that a pause strengthens the interpretation of a focal peak delay as signaling question intonation. The results are discussed in terms of a framework of biological codes for universal meanings of intonation proposed by Gussenhoven.
Cancer‐testis antigen expression and its epigenetic modulation in acute myeloid leukemia

Cancer‐testis antigens (CTA) represent attractive targets for tumor immunotherapy. However, a broad picture of CTA expression in acute myeloid leukemia (AML) is missing. CTA expression was analyzed in normal bone marrow (BM) as well as in AML cell lines before and after treatment with demethylating agents and/or histone acetylase inhibitors. Presence of selected CTA with a strictly tumor‐restricted expression was then determined in samples of patients with AML before and after demethylating therapy. Screening AML cell lines for the expression of 20 CTA, we identified six genes (MAGE‐A3, PRAME, ROPN1, SCP‐1, SLLP1, and SPO11) with an AML‐restricted expression. Analyzing the expression of these CTA in blast‐containing samples from AML patients (N = 64), we found all samples to be negative for MAGE‐A3 and SPO11 while a minority of patients expressed ROPN1 (1.6%), SCP‐1 (3.1%), or SLLP1 (9.4%). The only CTA expressed in substantial proportion of patients (53.1%) was PRAME. Following demethylating treatment with 5′‐aza‐2′‐deoxycytidine, we observed an increased or de novo expression of CTA, in particular of SSX‐2, in AML cell lines. In AML patients, we detected increased expression of PRAME and induction of SSX‐2 after demethylating therapy with 5‐azacytidine. With the exception of PRAME, CTA are mostly absent from AML blasts. However, demethylating treatment induces strong expression of CTA, particularly of SSX‐2, in vitro and in vivo. Therefore, we propose that CTA‐specific immunotherapy for AML should preferentially target PRAME and/or should be combined with the application of demethylating agents opening the perspective for alternative targets like CTA SSX‐2. Am. J. Hematol. , 2011. © 2011 Wiley‐Liss, Inc.