Miracle-dz/UniFAR-FTUs huggingface dataset:
Multipoint linkage disequilibrium mapping using case‐control designs

Case‐control study has been and continues to be one of the most popular designs in epidemiology. More recently, this design has been adopted to test for candidate genes when searching for disease genetic etiology. In this report, we present a multipoint linkage disequilibrium (LD) mapping approach with the focus on estimating the location of the target trait locus. It builds upon a representation, which shows that the difference between a case and a control in probabilities of carrying the target allele of a marker is proportional to that of the trait locus and that the proportionality factor is simply a measure of LD between the trait locus and the marker. Our method has the desired properties that (1) there is no need to specify phases of genotypic data with multiple markers, (2) it provides an estimate of location of the disease locus along with sampling uncertainty to help investigators to narrow chromosomal regions, and (3) a single test statistic is provided to test for LD in the framed region rather than testing the hypothesis one marker at a time. Our simulation work suggests that the proposed method performs well in terms of bias and coverage probability. Extension of the proposed method to account for confounding and genetic heterogeneity is discussed. We apply the proposed method to a published case‐control data set for cystic fibrosis. Genet. Epidemiol. 29:365–376, 2005. © 2005 Wiley‐liss, Inc.
Altered Protein Expression Profiles in Umbilical Veins: Insights into Vascular Dysfunctions of the Children Born after In Vitro Fertilization1

ABSTRACT Cardiovascular dysfunction and remodeling have been found in some children conceived by in vitro fertilization (IVF). However, the underlying mechanisms remain unclear. In this study, the retrospective investigation showed that the blood pressure of IVF-conceived Chinese children was higher than that of naturally conceived (NC) children at ages 3–13 yr. We analyzed the expression profile of proteins in the umbilical veins of IVF and NC newborns by proteomic techniques. Using iTRAQ (isobaric tags for relative and absolute quantitation), 47 differentially expressed proteins (DEPs) were identified by feature selection in IVF umbilical veins compared with NC. Ingenuity Pathway Analysis, which is used to explore the signaling pathways of DEPs, revealed that these DEPs played important roles in vascular system development and carbon metabolism, implying that these DEPs might be potential candidates for further exploration of the mechanism(s) of vascular dysfunction in IVF children. We found that the serum estradiol (E2) level in the cord blood of IVF newborns was significantly higher than that of NC newborns. High concentrations of E2 induced alteration of lumican and vimentin expression in human umbilical vein endothelial cells, which was consistent with the proteomic results. These findings suggested that abnormal expression of proteins in umbilical veins might be related to the cardiovascular dysfunction and remodeling in IVF offspring. In conclusion, our data for the first time reveal the protein expression profile in blood vessels of IVF offspring and provide information for further mechanism study and evaluation of risks of cardiovascular abnormality in IVF children.
Integrating Inertial Sensors with GPS for Vehicle Dynamics Control

ABSTRACT This paper demonstrates a method of estimating several key vehicle states – sideslip angle, longitudinal velocity, roll and grade – by combining automotive grade inertial sensors with a Global Positioning System (GPS) receiver. Kinematic Kalman filters that are independent of uncertain vehicle parameters integrate the inertial sensors with GPS to provide high update estimates of the vehicle states and the sensor biases. Using a twoantenna GPS system, the effects of pitch and roll on the measurements can be quantified and are demonstrated to be quite significant in sideslip angle estimation. Employing the same GPS system as an input to the estimator, this paper develops a method that compensates for roll and pitch effects to improve the accuracy of the vehicle state and sensor bias estimates. In addition, calibration procedures for the sensitivity and crosscoupling of inertial sensors are provided to further reduce measurement error. The resulting state estimates compare well to the results from calibrated models and Kalman filter predictions and are clean enough to use in vehicle dynamics control systems without additional filtering.
Sliding mode reference conditioning for coordination in swarms of non-identical multi-agent systems

A novel approach is proposed for coordination of swarms of dynamical systems in order to provide them with a desired collective behavior. The approach is based on the sliding mode reference conditioning technique as local interaction handler among neighbor systems. Neighbor systems become connected when a virtual constraint between them is violated, leading to a time-varying switching topology for the connections in the swarm. The approach addresses the problem of coordinating dynamical systems with possibly different dynamics (e.g. linear and nonlinear, different orders, constraints, etc.), assuming there is no leader. The main idea is to shape the systems local feasible references in order to keep them coordinated. Coordination is understood as invariance of a set defined by some aimed relationship among the references. This implies considering the local goals, the systems constraints and the achievable performances as well. To show the applicability of the approach, the problem of coordinating a swarm of different dynamical systems with control saturations is addressed as a particular case.
A pilot study of l-arginine supplementation on functional capacity in peripheral arterial disease

Peripheral arterial disease (PAD) impairs walking capacity and is often associated with a profound endothelial vasodilator dysfunction, characterized by reduced bioactivity and/or synthesis of endothelium-derived nitric oxide (NO). Previous studies have suggested that dietary supplementation of L-arginine, the precursor of NO, improves endothelium-dependent vasodilation, limb blood flow and walking distance. However, these studies have been small, and have used large intravenous doses of L-arginine. The optimal dose of L-arginine has not been determined. Accordingly, this pilot study was conducted to establish the lowest effective oral dose of L-arginine to improve walking distance in preparation for the definitive study. Patients with PAD and intermittent claudication (n = 80) participated in this study. Eligibility criteria included: (1) ankle-brachial index (ABI) at rest ≤0.90; (2) post-exercise reduction in ABI ≥25%; and (3) difference in absolute claudication distance of ≤25% between two consecutive treadmill tests. Treadmill testing was performed using the Skinner-Gardner protocol and community-based walking was assessed using the walking impairment questionnaire. Patients were randomly assigned to oral doses of 0, 3, 6 or 9 g of L-arginine daily in three divided doses for 12 weeks. Treadmill testing was performed prior to administration of the study drug and again after 12 weeks of treatment. The study drug was well tolerated, with no significant adverse effects of L-arginine therapy. The safety laboratory studies were unremarkable, except for a statistically significant reduction in hematocrit in the L-arginine-treated groups. There was no significant difference observed in absolute claudication distance between the groups. However, a trend was observed for a greater increase in walking distance in the group treated with 3 g L-arginine daily, and there was a trend for an improvement in walking speed in patients treated with L-arginine. This pilot study provided data for safety, for power calculation and for dosing for the larger definitive trial that is now underway.
Looking for balance between promoting adult separation anxiety disorder and overlooking it

A response by Silove and Manica-vasagar (2013) to my commentary about separation anxiety disorder (SAD) in adults (Starcevic, 2013) is a welcome contribution to a debate on several important issues. This com-mentary aims to correct an apparent misreading of my earlier commentary and shed more light on the underlying issues.First, there is no doubt that sepa-ration anxiety is an important compo -nent of human development and that it can play a role in the development of psychopathology. According to Silove and Manicavasagar (2013), my view is that separation anxiety ‘
Secretion, and Binding Properties Antimicrobial Activity, Localization, Bovine Peptidoglycan Recognition Protein-S:

Peptidoglycan (PGN) recognition proteins (PGRPs) are pattern recognition molecules of innate immunity that are conserved from insects to humans. Various PGRPs are reported to have diverse functions: they bind bacterial molecules, digest PGN, and are essential to the Toll pathway in Drosophila . One family member, bovine PGN recognition protein-S (bPGRP-S), has been found to bind and kill microorganisms in a PGN-independent manner, raising questions about the identity of the bPGRP-S ligand. Addressing this, we have determined the binding and microbicidal properties of bPGRP-S in a range of solutions approximating physiologic conditions. In this study we show that bPGRP-S interacts with other bacterial components, including LPS and lipoteichoic acid, with higher afﬁnities than for PCP, as determined by their abilities to inhibit bPGRP-S-mediated killing of bacteria. Where and how PGRPs act in vivo is not yet clear. Using Immunogold electron microscopy, PGRP-S was localized to the dense/large granules of naive neutrophils, which contain the oxygen-independent bactericidal proteins of these cells, and to the neutrophil phagolysosome. In addition, Immunogold staining and secretion studies demonstrate that neutrophils secrete PGRP-S when exposed to bacteria. Bovine PGRP-S can mediate direct lysis of heat-killed bacteria; however, PGRP-S-mediated killing of bacteria is independent of this activity. Evidence that bPGRP-S has multiple activities and afﬁnity to several bacterial molecules challenges the assumption that the PGRP family of proteins recapitulates the evolution of TLRs. Mammalian PGRPs do not have a single antimicrobial activity against a narrow range of target organisms; rather, they are generalists in their afﬁnity and activity. The Journal of Immunology, 2006, 176: 1154–1162.
Active FOXO1 Is a Key Determinant of Isoform-Specific Progesterone Receptor Transactivation and Senescence Programming

Progesterone promotes differentiation coupled to proliferation and prosurvival in the breast, but inhibits estrogen-driven growth in the reproductive tract and ovaries. Herein, it is demonstrated, using progesterone receptor (PR) isoform-specific ovarian cancer model systems, that PR-A and PR-B promote distinct gene expression profiles that differ from PR-driven genes in breast cancer cells. In ovarian cancer models, PR-A primarily regulates genes independently of progestin, while PR-B is the dominant ligand-dependent isoform. Notably, FOXO1 and the PR/FOXO1 target gene p21 (CDKN1A) are repressed by PR-A, but induced by PR-B. In the presence of progestin, PR-B, but not PR-A, robustly induced cellular senescence via FOXO1-dependent induction of p21 and p15 (CDKN2B). Chromatin immunoprecipitation (ChIP) assays performed on PR isoform–specific cells demonstrated that while each isoform is recruited to the same PRE-containing region of the p21 promoter in response to progestin, only PR-B elicits active chromatin marks. Overexpression of constitutively active FOXO1 in PR-A–expressing cells conferred robust ligand-dependent upregulation of the PR-B target genes GZMA, IGFBP1, and p21, and induced cellular senescence. In the presence of endogenous active FOXO1, PR-A was phosphorylated on Ser294 and transactivated PR-B at PR-B target genes; these events were blocked by the FOXO1 inhibitor (AS1842856). PR isoform–specific regulation of the FOXO1/p21 axis recapitulated in human primary ovarian tumor explants treated with progestin; loss of progestin sensitivity correlated with high AKT activity. Implications: This study indicates FOXO1 as a critical component for progesterone signaling to promote cellular senescence and reveals a novel mechanism for transcription factor control of hormone sensitivity. Mol Cancer Res; 14(2); 141–62. ©2015 AACR.
Keyword Search With Access Control Over Encrypted Cloud Data

In this paper, we study the problem of keyword search with access control (KSAC) over encrypted data in cloud computing. We first propose a scalable framework where user can use his attribute values and a search query to locally derive a search capability, and a file can be retrieved only when its keywords match the query and the user’s attribute values can pass the policy check. Using this framework, we propose a novel scheme called KSAC, which enables keyword search with access control over encrypted data. KSAC utilizes a recent cryptographic primitive called hierarchical predicate encryption to enforce fine-grained access control and perform multi-field query search. Meanwhile, it also supports the search capability deviation, and achieves efficient access policy update as well as keyword update without compromising data privacy. To enhance the privacy, KSAC also plants noises in the query to hide users’ access privileges. Intensive evaluations on real-world dataset are conducted to validate the applicability of the proposed scheme and demonstrate its protection for user’s access privilege.
Imitation and primitive symbol acquisition of humanoids by the integrated mimesis loop

Mimesis is a primitive learning framework and origins of human intelligence. We have developed a behavior acquisition and understanding system based on the mimesis. This system is able to abstract observed others' behaviors into conceptual symbols, to recognize others' behavior using the primitive symbols, and to generate self motion patterns using the primitive symbols. In this paper, we mention the integration of mimesis loop which is the acquisition and development system based on mimesis, and confirmation of the feasibility against whole body motions on virtual humanoids.
Why Rescue the Administrative Data Version of the “Failure to Rescue” Quality Indicator

I ust as continuous quality improvement is needed for the highly complex world of health I care delivery, measurement of quality itself merits continual examination. With the price tag for health care rising and increased public awareness of medical error, pressures continue to mount for ways to efficiently measure the outcomes of health care. An alphabet soup of organizations are developing, evaluating, and implementing such measures for a variety of purposes. However, without sound validation studies and careful interpretation of their implications, the science of measurement and the appropriate usage of measures are stymied. Therefore, the validation study by Horwitz et al, conducted with members of the University HealthSystem Consortium (UHC), is a welcome addition to the scientific literature. This editorial offers a careful examination of the study and its implications, so that the sound bites inevitably culled from its analysis and conclusions do not obscure the essential truths. Drawing from a familiar metaphor the baby and the bathwater the voices that quickly seize any reason to dismiss an indicator, must be averted to preserve that which is particularly valuable in the tub: (1) the concept of failure to rescue (FTR), (2) use of administrative data, (3) chart review validation, and (4) prudent interpretation of the validation study.
Modular design for in vivo optical imaging and ultrasound treatment in the murine brain

Simultaneous optical imaging and ultrasound exposure to the brain is challenging due to geometric constraints. We demonstrate sonication through the ventral surface of the mouse, leaving the dorsal aspect free for imaging. Ultrasound components are integrated into a commercial multiphoton microscope, and animals are imaged during ultrasound-induced blood-brain barrier disruption
A Brief Measure of Narcissism Among Female Juvenile Delinquents and Community Youths: The Narcissistic Personality Inventory–13

Research on narcissism has a long tradition, but there is limited knowledge regarding its application among female youth, especially for forensic samples of incarcerated female youth. Drawing on 377 female adolescents (103 selected from forensic settings and 274 selected from school settings) from Portugal, the current study is the first to examine simultaneously the psychometric properties of a brief version of the Narcissistic Personality Inventory (NPI-13) among females drawn from incarcerated and community settings. The results support the three-factor structure model of narcissism after the removal of one item due to its low factor loading. Internal consistency, convergent validity, and discriminant validity showed promising results. In terms of criterion-related validity, significant associations were found with criterion-related variables such as age of criminal onset, conduct disorder, crime severity, violent crimes, and alcohol and drug use. The findings provide support for use of the NPI-13 among female juveniles.
Minimum clone size for estimating normal reproductive capacity of cultured cells.

Abstract The end-points used for estimating the survival of irradiated mammalian cells are discussed. The single-cell cloning method as used for monolayer cultures in vitro is a much less demanding criterion of survival than those used for mammalian cells growing in vivo and also for suspension cultures in vitro. Comparisons were made of the survival levels of HeLa cells in monolayer culture and P388F lymphoma cells in suspension culture, using the end-points of clone-forming ability and backward extrapolation from growth curves. With the monolayer cultures the usual minimum clone size is 50 cells and with this criterion much higher levels of survival were found in comparison with those from growth curves. This discrepancy could be removed when a larger minimum clone size was used for the end-point. With the suspension cultures the levels of survival obtained from agar clones were in agreement with those from growth curves. The minimum agar clone size was already larger than 50 cells and survival was asse.
Systemic Risk in Interbanking Networks

We develop a mean field model of interbanking borrowing and lending activities. Each bank borrows from or lends to other counterparties at an idiosyncratic rate, and is exposed to sudden shocks affecting the level of its monetary reserves. Using weak convergence analysis, we provide an explicit characterization of the measure-valued process associated with a large interbanking system. We use the limit process to construct law of large number approximations for systemic indicators assessing average distance to default and measuring the total volume of interbanking activities. We illustrate the predictive power and accuracy of our framework via a detailed numerical analysis, showing that indicators are sensitive to lending preferences, volatility, and occurrences of negative events.
Compact Resonators for Permittivity Reconstruction of Biological Tissues

In this paper, a patch resonator is proposed for non-invasive measurement of dielectric properties of biological tissues. Resonator is operating at 2.4 GHz when placed on tissue. The patch resonator is simulated in HFSS with four layered tissue mimicking material (skin, fat, blood, muscle) placed on top. The electrical properties of blood layer is decreased and the change in S parameters is tracked. Effective dielectric properties of the tissue is reconstructed from simulated S parameter response of the resonator.
High incidence of N and K‐Ras activating mutations in multiple myeloma and primary plasma cell leukemia at diagnosis

Using allele‐specific amplification method (ARMS), a highly sensitive one‐stage allele‐specific PCR, we have evaluated the incidence of NRAS and KRAS2 activating mutations (codons 12, 13, and 61) in 62 patients with either monoclonal gammopathy of undetermined significance (MGUS) or multiple myeloma (MM), primary plasma‐cell leukemia (P‐PCL), and also in human myeloma cell lines (HMCL). NRAS and/or KRAS2 mutations were found in 54.5% of MM at diagnosis (but in 81% at the time of relapse), in 50% of P‐PCL, and in 50% of 16 HMCL. In contrast, the occurrence of such mutations was very low in MGUS and indolent MM (12.50%). Of note, KRAS2 mutations were always more frequent than NRAS. The validity of the technique was assessed by direct sequencing of cell lines and of some patients. Multiple mutations found in two patients were confirmed by subcloning exon PCR amplification products, testing clones with our method, and sequencing them. Thus, these early mutations could play a major role in the oncogenesis of MM and P‐PCL. Hum Mutat 18:212–224, 2001. © 2001 Wiley‐Liss, Inc.
Is empathy associated with a self‐ascribed sense of meaning among resident physicians working with patients nearing the end of life on a hematology‐oncology ward?

Empathy decline duringmedical training has beenwell documented and is associated with elevated distress levels among trainees. Physicians and physicians in training are at risk of potential traumatization by the difficult patient scenarios they encounter, such as the patient deaths that affect them adversely. Resilience may ameliorate distress but may not necessarily enhance empathy. Unfortunately, a standard method for teaching empathy to physician trainees has not been found. At the same time, meaning‐centered therapy has been shown to increase patient and caregiver coping and decrease distress as they become accustomed to having cancer. A potential therapeutic intervention to enhance meaning in the work of residents as they face difficult patient situations has not been explored previously. Encountering a sense of meaning in loss (eg, death) can be empowering for people who are encountering overwhelming and de‐stabilizing situations. Although medical training is not usually considered an “overwhelming” situation, trauma can be experienced vicariously, which may lead to a decline in empathy. An association between physician‐in‐training ascribed meaning from vicarious trauma (eg, patient deaths) and empathy has not been explored previously. This study sought to understand if the ability to find meaning in the clinical situations that residents face might be associated with empathy. If so, finding meaning in difficult clinical situations may counteract empathy decline among medical trainees.
Infrastructure-free tactical situational awareness (INTACT)

The objective of the INTACT project is to analyze and develop methods for infrastructure–free simultaneous localization and mapping (SLAM) and context recognition for tactical situational awareness. Most important research questions are how an accurate and reliable SLAM system may be obtained using a single camera, multiple inertial sensors and ranging equipment, and how good situational awareness the equipment provides. All measurements will be collected using only equipment attached to the user. Indoor environments are selected as a specific research environment, because localization is most challenging in those areas, but all results are well suited also for urban and for some extent for all outdoor environments. The project addresses applications aimed for soldiers, but the methods developed will serve the needs of e.g. police, border guards and rescue personnel as well.