Miracle-dz/UniFAR-FTUs huggingface dataset:
Essential Role for Prolyl Hydroxylase Domain Protein 2 in Oxygen Homeostasis of the Adult Vascular System

Background— Prolyl hydroxylase domain (PHD) proteins, including PHD1, PHD2, and PHD3, mediate oxygen-dependent degradation of hypoxia-inducible factor (HIF)-α subunits. Although angiogenic roles of hypoxia-inducible factors are well known, the roles of PHDs in the vascular system remain to be established. Methods and Results— We evaluated angiogenic phenotypes in mice carrying targeted disruptions in genes encoding different PHD isoforms. Although Phd1−/− and Phd3−/− mice did not display apparent angiogenic defects, broad-spectrum conditional knockout of Phd2 led to hyperactive angiogenesis and angiectasia. Blood vessels in PHD2-deficient mice were highly perfusable. Furthermore, examination of medium-sized vessels in subendocardial layer in the heart demonstrated successful recruitment of vascular smooth muscle cells. Surprisingly, increased vascular growth was independent of local efficiency of Phd2 disruption. Mice carrying significant Phd2 disruption in multiple organs, including the liver, heart, kidney, and lung, displayed excessive vascular growth not only in these organs but also in the brain, where Phd2 disruption was very inefficient. More surprisingly, increased accumulation of hypoxia-inducible factor-1α and angiectasia in the liver were not accompanied by corresponding increases in hepatic expression of Vegfa or angiopoietin-1. However, the serum vascular endothelial growth factor-A level was significantly increased in PHD2-deficient mice. Conclusions— PHD2, but not PHD1 and PHD3, is a major negative regulator for vascular growth in adult mice. Increased angiogenesis in PHD2-deficient mice may be mediated by a novel systemic mechanism.
Response to Radioiodine Therapy for Thyrotoxicosis: Disparate Outcomes for an Indigenous Population

Despite 70 years of experience treating thyrotoxic patients with radioiodine not all patients are successfully treated by a single dose. Multiple factors predicting radioiodine efficacy have been reported. The aim of this study was to assess whether ethnicity was associated with radioiodine response. A retrospective review was performed of patients who received radioiodine therapy for thyrotoxicosis from 1 January 2008 to 31 December 2010 and had follow-up available of a minimum of 12 months. 224 patients were included, 82.4% female, and 63.7% had Graves's disease. Radioiodine failed in 21.5% of patients overall, with a higher failure rate in the indigenous population (35.2%). When controlling for other influencing factors by logistic regression, there continued to be an increased risk for the indigenous group (OR 2.82) and those treated with antithyroid drugs following radioiodine (OR 2.04). Younger age was also associated with an increased risk of failing radioiodine therapy (OR 0.97 for each year of age). Cure rates following radioiodine were lower for indigenes independent of factors known to affect radioiodine outcome. This is the first report demonstrating ethnicity as a possible independent variable for radioiodine efficacy. Further work is needed to investigate the cause of this difference.
STELLAR KINEMATIC CONSTRAINTS ON GALACTIC STRUCTURE MODELS REVISITED: BAR AND SPIRAL ARM RESONANCES

We study the phase space available to the local stellar distribution using a Galactic potential consistent with several recent observational constraints. We find that the induced phase space structure has several observable consequences. The spiral arm contribution to the kinematic structure in the solar neighborhood may be as important as the one produced by the Galactic bar. We suggest that some of the stellar kinematic groups in the solar neighborhood, such as the Hercules structure and the kinematic branches, can be created by the dynamical resonances of self-gravitating spiral arms and not exclusively by the Galactic bar. A structure coincident with the Arcturus kinematic group is developed when a hot stellar disk population is considered, which introduces a new perspective on the interpretation of its extragalactic origin. A bar-related resonant mechanism can modify this kinematic structure. We show that particles in the dark matter disk-like structure predicted by recent lambda cold dark matter galaxy formation experiments, with similar kinematics to the thick disk, are affected by the same resonances, developing phase space structures or dark kinematic groups that are independent of the Galaxy assembly history and substructure abundance. We discuss the possibility of using the stellar phase space groups as constraints to nonaxisymmetric models of the Milky Way structure.
Wireless sensors in agriculture and food industry — Recent development and future perspective

This paper presents an overview on recent development of wireless sensor technologies and standards for wireless communications as applied to wireless sensors. Examples of wireless sensors and sensor networks applied in agriculture and food production for environmental monitoring, precision agriculture, M2M-based machine and process control, building and facility automation and RFID-based traceability systems are given. The paper also discusses advantages of wireless sensors and obstacles that prevent their fast adoption. Finally, based on an analysis of market growth, the paper discusses future trend of wireless sensor technology development in agriculture and food industry. © 2005 Elsevier B.V. All rights reserved.
Staphylococcal Cassette Chromosome mec (SCCmec) Typing of Methicillin-Resistant Staphylococcus aureus Strains Isolated in 11 Asian Countries: a Proposal for a New Nomenclature for SCCmec Elements

ABSTRACT A description of staphylococcal cassette chromosome mec (SCCmec) elements carried by 615 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in 11 Asian countries is reported, and a novel nomenclatural system based on their structures is proposed. The 615 strains were classified as type 3A (370 strains), type 2A (207 strains), type 2B (32 strains), type 1B (1 strain), and nontypeable (5 strains). The previously reported type III SCCmec (DDBJ/EMBL/GenBank accession no. AB037671) carried by the MRSA strain 85/2082 was ascertained to be composed of two SCC elements, type 3A SCCmec and SCCmercury. PCR analysis indicated that 310 of 370 type 3A SCCmec strains carried both SCC elements. These strains were prevalent in eight countries: Thailand, Sri Lanka, Indonesia, Vietnam, Philippines, Saudi Arabia, India, and Singapore. The remaining 60 type 3A SCCmec strains differed with respect to the left extremity polymorphism or to the presence of ccrC. Among these, two were identified as carrying only type 3A SCCmec elements, but their left extremities differed. Type 2A SCCmec strains predominated in Korea and Japan, although the frequency of the presence of ant(4′)-1 gene downstream of mecA varied (53% for Korean strains; 93% for Japanese strains). Various SCCmec elements were identified in the tested strains, and limited numbers were identified by their multilocus sequence typing genotypes. These data suggest that numerous MRSA clones are disseminated in Asian hospitals, and these consist of minor clones that are presumed to have arisen locally and major clones that are presumed to have been introduced from other countries.
Can REDD+ Help the Conservation of Restricted-Range Island Species? Insights from the Endemism Hotspot of São Tomé

REDD+ aims to offset greenhouse gas emissions through “Reduced Emissions from Deforestation and forest Degradation”. Some authors suggest that REDD+ can bring additional benefits for biodiversity, namely for the conservation of extinction-prone restricted-range species. Here, we assess this claim, using São Tomé Island (Democratic Republic of São Tomé and Príncipe) as a case study. We quantified the abundance of bird and tree species, and calculated the aboveground carbon stocks across a gradient of land-use intensity. We found a strong spatial congruence between carbon and the presence and abundance of endemic species, supporting the potential of REDD+ to protect these taxa. We then assessed if REDD+ could help protect the forests of São Tomé and Príncipe. To do so, we used OSIRIS simulations to predict country-level deforestation under two different REDD+ designs. These simulations showed that REDD+ could promote the loss of forests in São Tomé and Príncipe through leakage. This happened even when additional payments for biodiversity were included in the simulations, and despite São Tomé and Príncipe having the fourth highest carbon stocks per land area and the second highest biodiversity values according to the OSIRIS database. These results show weaknesses of OSIRIS as a planning tool, and demonstrate that the benefits that REDD+ might bring for biodiversity are strongly dependent on its careful implementation. We recommend that payment for ecosystem services programmes such as REDD+ develop safeguards to ensure that biodiversity co-benefits are met and perverse outcomes are avoided across all tropical countries. In particular, we advise specific safeguards regarding the conservation of extinction-prone groups, such as island restricted-range species.
Origin and Nature of Spontaneous Shape Fluctuations in “Small” Nanoparticles

Normally chemically inert materials such as Au have been found to be catalytically active in the form of particles whose size is about 1 nm. Direct and indirect observations of various types of metal nanoparticles (NPs) in this size range, under catalytically relevant conditions for fuel-cell operation and catalysis, have indicated that such “small” particles can exhibit large spontaneous shape fluctuations and significant changes in shape and chemical activity in response to alterations in environmental conditions. NPs also normally exhibit facile coalescence when in proximity, impacting their stability and reactivity in applications. We perform molecular dynamics simulations on Ni nanoparticles, a commonly used NP in catalytic applications and carbon nanotube growth, in the ≈1 nm size regime where large-scale shape fluctuations have been observed experimentally. An analysis of the large-scale shape fluctuations observed in our simulations of these “small” NPs indicates that they are accompanied by collective motion of Ni atoms through the NP center, and we quantify these dynamic structures and their impact on NP shape. In contrast, stringlike collective atomic motion is confined to the NP interfacial region of NPs having a diameter greater than a few nanometers, and correspondingly, the overall NP shape remains roughly spherical, a case studied in our prior Ni NP simulations. Evidently, the large spontaneous NP shape fluctuations reflect a change in character of the collective atomic dynamics when the NPs become critically small in size.
Activity-dependent gene regulation in neurons: energy coupling and a novel biosensor

v PREFACE vii TABLE OF CONTENTS viii LIST OF TABLES xi LIST OF FIGURES xii LIST OF ABBREVIATIONS xiv CHAPTER I: INTRODUCTION 1 A. Neuronal activity and energy metabolism 1 1. Energy metabolism: a coordination between two genomes 1 2. Nuclear-encoded regulators of mitochondrial biogenesis: NRF-1 and PGC-1α . 2 2.1 NRF1 2 2.2 PGC-1α and NRF-1 in neurons 5 B. Epilepsy 8 1. General classification 8 2. Treatment 10 3. Temporal lobe epilepsy (TLE) and animal models 16 3.1 Pilocarpine model of TLE 17 3.2 BDNF signaling and epilepsy 18 ix 3.3 GABARs and epilepsy 20 3.4 β1 subunit-containing GABARs 22 3.5 Transcription of the β1 subunit gene 24 C. CREB and activity-dependent gene expression 25 1. Post-translational modification 25 2. Models for CREB-mediated gene regulation 28 3. Potential mechanisms in the attenuation of CREB signaling 30 CHAPTER II: MATERIALS AND METHODS 32 A. Cell culture 32 B. Chromatin immunoprecipitation (ChIP) 33 C. Electrophoretic mobility shift (EMSA) and supershift assay 34 D. Preparation of nuclear protein extracts 34 E. Molecular subcloning 35 F. DNA Sequencing 38 G. Transfections for transient mammalian cell expression 39 H. Promoter luciferase reporter assays 40 I. Assays for protein determination 41 J. Quantitative reverse-transcription PCR (qRT-PCR) 42 K. RNA interference 43 L. Western blot analysis 44 M. Bioluminescence imaging 45
Surviving rather than thriving: Understanding the experiences of women coaches using a theory of gendered social well-being

In shifting our gaze to the sociological impact of being in the minority, the purpose of this study was to substantiate a model of gendered social well-being to appraise women coaches’ circumstances, experiences and challenges as embedded within the social structures and relations of their profession. This is drawn on in-depth interviews with a sample of head women coaches within the UK. The findings demonstrate that personal lives, relationships, social and family commitments were sidelined by many of the participants in order to meet the expectations of being a (woman) coach. We locate these experiences in the organisational practices of high performance sport which hinder women coaches from having meaningful control over their lives. The complexities of identity are also revealed through the interplay of gender with (dis)ability, age and whiteness as evidence of hegemonic femininity within the coaching profession. Consequently, for many women, coaching is experienced as a ‘developmental dead-end’.
Atorvastatin at Reperfusion Reduces Myocardial Infarct Size in Mice by Activating eNOS in Bone Marrow-Derived Cells

Background The current study was designed to test our hypothesis that atorvastatin could reduce infarct size in intact mice by activating eNOS, specifically the eNOS in bone marrow-derived cells. C57BL/6J mice (B6) and congenic eNOS knockout (KO) mice underwent 45 min LAD occlusion and 60 min reperfusion. Chimeric mice, created by bone marrow transplantation between B6 and eNOS KO mice, underwent 40 min LAD occlusion and 60 min reperfusion. Mice were treated either with vehicle or atorvastatin in 5% ethanol at a dose of 10 mg/kg IV 5 min before initiating reperfusion. Infarct size was evaluated by TTC and Phthalo blue staining. Results Atorvastatin treatment reduced infarct size in B6 mice by 19% (p<0.05). In eNOS KO vehicle-control mice, infarct size was comparable to that of B6 vehicle-control mice (p = NS). Atorvastatin treatment had no effect on infarct size in eNOS KO mice (p = NS). In chimeras, atorvastatin significantly reduced infarct size in B6/B6 (donor/recipient) mice and B6/KO mice (p<0.05), but not in KO/KO mice or KO/B6 mice (p = NS). Conclusions The results demonstrate that acute administration of atorvastatin significantly reduces myocardial ischemia/reperfusion injury in an eNOS-dependent manner, probably through the post-transcriptional activation of eNOS in bone marrow-derived cells.
Analysis of the Tradeoff between Delay and Source Rate in Multiuser Wireless Systems

This work addresses the limits on the information that can be transmitted over the wireless channel under the conditions stated by the MAC layer: a selected scheduling discipline and an ensured level of QoS. Based on the effective bandwidth theory, the joint influence of the channel fading, the data outsourcing process, and the scheduling discipline in the QoS metrics are studied. We obtain a closed-form expression of the vector of attainable users' rates for several scheduling algorithms, representing the maximum constant rate that the uth user can transmit under the selected discipline and fulfilling a target Bit Error Rate (BER) and the delay constraint given by the pair , where is the target delay and is the probability of exceeding .
The Kick-In System: A Novel Rapid Knock-In Strategy

Knock-in mouse models have contributed tremendously to our understanding of human disorders. However, generation of knock-in animals requires a significant investment of time and effort. We addressed this problem by developing a novel knock-in system that circumvents several traditional challenges by establishing stem cells with acceptor elements enveloping a particular genomic target. Once established, these acceptor embryonic stem (ES) cells are efficient at directionally incorporating mutated target DNA using modified Cre/lox technology. This is advantageous, because knock-ins are not restricted to one a priori selected variation. Rather, it is possible to generate several mutant animal lines harboring desired alterations in the targeted area. Acceptor ES cell generation is the rate-limiting step, lasting approximately 2 months. Subsequent manipulations toward animal production require an additional 8 weeks, but this delimits the full period from conception of the genetic alteration to its animal incorporation. We call this system a “kick-in” to emphasize its unique characteristics of speed and convenience. To demonstrate the functionality of the kick-in methodology, we generated two mouse lines with separate mutant versions of the voltage-dependent potassium channel Kv7.2 (Kcnq2): p.Tyr284Cys (Y284C) and p.Ala306Thr (A306T); both variations have been associated with benign familial neonatal epilepsy. Adult mice homozygous for Y284C, heretofore unexamined in animals, presented with spontaneous seizures, whereas A306T homozygotes died early. Heterozygous mice of both lines showed increased sensitivity to pentylenetetrazole, possibly due to a reduction in M-current in CA1 hippocampal pyramidal neurons. Our observations for the A306T animals match those obtained with traditional knock-in technology, demonstrating that the kick-in system can readily generate mice bearing various mutations, making it a suitable feeder technology toward streamlined phenotyping.
Earth X-ray albedo for cosmic X-ray background radiation in the 1–1000 keV band

We present calculations of the reflection of the cosmic X-ray background (CXB) by the Earth’s atmosphere in the 1‐1000 keV energy range. The calculations include Compton scattering and X-ray fluorescent emission and are based on a realistic chemical composition of the atmosphere. Such calculations are relevant for CXB studies using the Earth as an obscuring screen (as was recently done by INTEGRAL). The Earth’s reflectivity is further compared with that of the Sun and the Moon ‐ the two other objects in the Solar system subtending a large solid angle on the sky, as needed for CXB studies.
Computing classic closeness centrality, at scale

Closeness centrality, first considered by Bavelas (1948), is an importance measure of a node in a network which is based on the distances from the node to all other nodes. The classic definition, proposed by Bavelas (1950), Beauchamp (1965), and Sabidussi (1966), is (the inverse of) the average distance to all other nodes. We propose the first highly scalable (near linear-time processing and linear space overhead) algorithm for estimating, within a small relative error, the classic closeness centralities of all nodes in the graph. Our algorithm applies to undirected graphs, as well as for centrality computed with respect to round-trip distances in directed graphs. For directed graphs, we also propose an efficient algorithm that approximates generalizations of classic closeness centrality to outbound and inbound centralities. Although it does not provide worst-case theoretical approximation guarantees, it is designed to perform well on real networks. We perform extensive experiments on large networks, demonstrating high scalability and accuracy.
A formal framework for design and analysis of human-machine interaction

Automated systems are increasingly complex, making it hard to design interfaces for human operators. Human-machine interaction (HMI) errors like automation surprises are more likely to appear and lead to system failures or accidents. In previous work, we studied the problem of generating system abstractions, called mental models, that facilitate system understanding while allowing proper control of the system by operators as defined by the full-control property. Both the domain and its mental model have Labelled Transition Systems (LTS) semantics, and we proposed algorithms for automatically generating minimal mental models as well as checking full-control. This paper presents a methodology and an associated framework for using the above and other formal method based algorithms to support the design of HMI systems. The framework can be used for modelling HMI systems and analysing models against HMI vulnerabilities. The analysis can be used for validation purposes or for generating artifacts such as mental models, manuals and recovery procedures. The framework is implemented in the JavaPathfinder model checker. Our methodology is demonstrated on two examples, an existing benchmark of a medical device, and a model generated from the ADEPT toolset developed at NASA Ames. Guidelines about how ADEPT models can be translated automatically into JavaPathfinder models are also discussed.
Efficient Constraint Monitoring Using Adaptive Thresholds

Detecting constraint violations in large-scale distributed systems has recently attracted plenty of attention from the research community due to its varied applications (security, network monitoring, etc.). Communication efficiency of these systems is a critical concern and determines their practicality. In this paper, we introduce a new set of methods called non-zero slack schemes to implement distributed SUM queries efficiently. We show, both analytically and empirically, that these methods can lead to a considerable reduction in the amount of communication. We propose three adaptive non-zero slack schemes that adapt to changing data distributions; our best scheme is a lightweight reactive scheme that probabilistically adjusts local constraints based on the occurrence of certain events (using only a periodic probability estimation). We conduct an extensive experimental study using real-life and synthetic data sets, and show that our non-zero slack schemes incur significantly less communication overhead compared to the state of the art zero slack scheme (over a 60% savings).
Trajectories of maternal mental health: a prospective study of mothers of infants with congenital heart defects from pregnancy to 36 months postpartum.

OBJECTIVE To chart mothers' trajectories of mental health from pregnancy to 36 months postpartum in order to investigate the association between infants' congenital heart defects (CHD) and compromised maternal mental health. METHODS Mothers of infants with mild, moderate, or severe CHD (n = 141) and mothers (n = 36,437) enrolled in the Norwegian Mother and Child Cohort Study were assessed at regular intervals from pregnancy up to 36 months postpartum, including measurements at 6 and 18 months, using an 8-item version of the Hopkins Symptom Checklist-25. RESULTS Mean score trajectories of SCL-8 for mothers of infants with severe CHD deviated significantly from cohort controls 6, 18, and 36 months postpartum, indicating heightened symptoms of depression and anxiety. CONCLUSIONS Mothers of infants with severe CHD are at risk of compromised mental health from delivery to 36 months postpartum. Strain due to CHD-related interventions is identified as a possible partial mediator of the distress.
Coxeter group actions on the complement of hyperplanes and special involutions

We consider both standard and twisted action of a (real) Coxeter group $G$ on the complement $\mathcal M_G$ to the complexified reflection hyperplanes by combining the reflections with complex conjugation. We introduce a natural geometric class of special involutions in $G$ and give explicit formulae which describe both actions on the total cohomology $H^*(\mathcal M_G, {\mathbb C})$ in terms of these involutions. As a corollary we prove that the corresponding twisted representation is regular only for the symmetric group $S_n$, the Weyl groups of type $D_{2m+1}$, $E_6$ and dihedral groups $I_2 (2k+1). $ We discuss also the relations with the cohomology of Brieskorn's braid groups.