bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlas2 Cloud: a framework for personal genome analysis in the cloud
Authors: Evani Uday S , Challis Danny , Yu Jin , Jackson Andrew R , Paithankar Sameer , Bainbridge Matthew N , Jakkamsetti Adinarayana , Pham Peter , Coarfa Cristian , Milosavljevic Aleksandar , Yu Fuli 
Published: October 2012

Abstract

Background
Until recently, sequencing has primarily been carried out in large genome centers which have invested heavily in developing the computational infrastructure that enables genomic sequence analysis. The recent advancements in next generation sequencing (NGS) have led to a wide dissemination of sequencing technologies and data, to highly diverse research groups. It is expected that clinical sequencing will become part of diagnostic routines shortly. However, limited accessibility to computational infrastructure and high quality bioinformatic tools, and the demand for personnel skilled in data analysis and interpretation remains a serious bottleneck. To this end, the cloud computing and Software-as-a-Service (SaaS) technologies can help address these issues.

Results
We successfully enabled the Atlas2 Cloud pipeline for personal genome analysis on two different cloud service platforms: a community cloud via the Genboree Workbench, and a commercial cloud via the Amazon Web Services using Software-as-a-Service model. We report a case study of personal genome analysis using our Atlas2 Genboree pipeline. We also outline a detailed cost structure for running Atlas2 Amazon on whole exome capture data, providing cost projections in terms of storage, compute and I/O when running Atlas2 Amazon on a large data set.

Conclusions
We find that providing a web interface and an optimized pipeline clearly facilitates usage of cloud computing for personal genome analysis, but for it to be routinely used for large scale projects there needs to be a paradigm shift in the way we develop tools, in standard operating procedures, and in funding mechanisms.
Mathematical modeling and stability analysis of macrophage activation in left ventricular remodeling post-myocardial infarction
Authors: Wang Yunji , Yang Tianyi , Ma Yonggang , Halade Ganesh V , Zhang Jianqiu , Lindsey Merry L , Jin Yu-Fang 
Published: October 2012

AbstractBackgroundAbout 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macrophages: classically activated macrophages which contribute to extracellular matrix destruction and alternatively activated macrophages which contribute to extracellular matrix construction. Though experimental results have shown the transitions between these two types of macrophages, little is known about the dynamic progression of macrophages activation. Therefore, the objective of this study is to analyze macrophage activation patterns post-MI.ResultsWe have collected experimental data from adult C57 mice and built a framework to represent the regulatory relationships among cytokines and macrophages. A set of differential equations were established to characterize the regulatory relationships for macrophage activation in the left ventricle post-MI based on the physical chemistry laws. We further validated the mathematical model by comparing our computational results with experimental results reported in the literature. By applying Lyaponuv stability analysis, the established mathematical model demonstrated global stability in homeostasis situation and bounded response to myocardial infarction.ConclusionsWe have established and validated a mathematical model for macrophage activation post-MI. The stability analysis provided a possible strategy to intervene the balance of classically and alternatively activated macrophages in this study. The results will lay a strong foundation to understand the mechanisms of left ventricular remodelling post-MI.
Dengue hemorrhagic fever and severe thrombocytopenia in a patient on mandatory anticoagulation; balancing two life threatening conditions; a case report
Authors: Gamakaranage Champika , Rodrigo Chaturaka , Samarawickrama Sincy , Wijayaratne Dilushi , Jayawardane Malaka , Karunanayake Panduka , Jayasinghe Saroj 
Published: October 2012

Abstract

Background
Managing a severe dengue infection is a challenge specially when complicated by other comorbidities. We report a patient with dengue haemorrhagic fever and spontaneous bleeding who required mandatory anticoagulation for a prosthetic mitral valve replacement. This is the first case report in published literature describing this therapeutic dilemma.

Case presentation
A fifty one year old Sri Lankan woman was diagnosed with dengue haemorrhagic fever with bleeding manifestations. During the critical phase of her illness, the platelet count dropped to 5,000/ɥl. She was also on warfarin 7 mg daily following a prosthetic mitral valve insertion. In managing the patient, the risk of bleeding had to be balanced against the risk of valve thrombosis without anticoagulation. Warfarin was withheld when the platelet count dropped to 100,000/ɥl and restarted when it recovered above 50,000/ɥl. The patient was off anticoagulation for 10 days.

Conclusions
We managed this patient with close observation and continuous risk benefit assessments of management decisions. However, experience with one patient cannot be generalized to others. Therefore, it is essential that clinicians share their experiences in managing such difficult patients.
Hypofractionated stereotactic radiotherapy of limited brain metastases: a single-centre individualized treatment approach
Authors: Märtens Bettina , Janssen Stefan , Werner Martin , Frühauf Jörg , Christiansen Hans , Bremer Michael , Steinmann Diana 
Published: October 2012

Abstract

Background
We retrospectively report treatment results of our single-centre experience with hypofractionated stereotactic radiotherapy (hfSRT) of limited brain metastases in primary and recurrence disease situations. Our aim was to find the most effective and safe dose concept.

Methods
From 04/2006 to 12/2010, 75 patients, with 108 intracranial metastases, were treated with hfSRT. 52 newly diagnosed metastases (48%), without up-front whole brain radiotherapy (WBRT), received hfSRT as a primary treatment. 56 metastases (52%) received a prior WBRT and were treated in this study in a recurrence situation. Main fractionation concepts used for primary hfSRT were 6-7x5 Gy (61.5%) and 5x6 Gy (19.2%), for recurrent hfSRT 7-10x4 Gy (33.9%) and 5-6x5 Gy (33.9%).

Results
Median overall survival (OS) of all patients summed up to 9.1 months, actuarial 6-and 12-month-OS was 59% and 35%, respectively. Median local brain control (LC) was 11.9 months, median distant brain control (DC) 3.9 months and intracranial control (IC) 3.4 months, respectively. Variables with significant influence on OS were Gross Tumour Volume (GTV) (p = 0.019), the biological eqivalent dose (calculated on a 2 Gy single dose, EQD2, α/β = 10) < and ≥ median of 39 Gy (p = 0.012), extracerebral activity of the primary tumour (p < 0.001) and the steroid uptake during hfSRT (p = 0.03). LC was significantly influenced by the EQD2, ≤ and > 35 Gy (p = 0.004) in both uni- and multivariate Cox regression analysis. Median LC was 14.9 months for EQD2 >35 Gy and 3.4 months for doses ≤35 Gy, respectively. Early treatment related side effects were usually mild. Nevertheless, patients with a EQD2 >35 Gy had higher rates of toxicity (31%) than ≤35 Gy (8.3%, p=0.026).

Conclusion
Comparing different dose concepts in hfSRT, a cumulative EQD2 of ≥35 Gy seems to be the most effective concept in patients with primary or recurrent limited brain metastases. Despite higher rates of only mild toxicity, this concept represents a safe treatment option.
Substrate cycles in Penicillium chrysogenum quantified by isotopic non-stationary flux analysis
Authors: Zhao Zheng , ten Pierick Angela , de Jonge Lodewijk , Heijnen Joseph J , Wahl S Aljoscha 
Published: October 2012

AbstractBackgroundPenicillium chrysogenum, the main production strain for penicillin-G, has a high content of intracellular carbohydrates, especially reduced sugars such as mannitol, arabitol, erythritol, as well as trehalose and glycogen. In previous steady state13C wash-in experiments a delay of labeling enrichments in glycolytic intermediates was observed, which suggests turnover of storage carbohydrates. The turnover of storage pools consumes ATP which is expected to reduce the product yield for energy demanding production pathways like penicillin-G.ResultsIn this study, a13C labeling wash-in experiment of 1 hour was performed to systematically quantify the intracellular flux distribution including eight substrate cycles. The experiments were performed using a mixed carbon source of 85% CmolGlc/CmolGlc+EtOHlabeled glucose (mixture of 90% [1-13C1] and 10% [U-13C6]) and 15% ethanol [U-13C2]. It was found, that (1) also several extracellular pools are enriched with13C labeling rapidly (trehalose, mannitol, and others), (2) the intra- to extracellular metabolite concentration ratios were comparable for a large set of metabolites while for some carbohydrates (mannitol, trehalose, and glucose) the measured ratios were much higher.ConclusionsThe fast enrichment of several extracellular carbohydrates and a concentration ratio higher than the ratio expected from cell lysis (2%) indicate active (e.g. ATP consuming) transport cycles over the cellular membrane. The flux estimation indicates, that substrate cycles account for about 52% of the gap in the ATP balance based on metabolic flux analysis.
Spin injection in n-type resonant tunneling diodes
Authors: Orsi Gordo Vanessa , Herval Leonilson KS , Galeti Helder VA , Gobato Yara Galvão , Brasil Maria JSP , Marques Gilmar E , Henini Mohamed , Airey Robert J 
Published: October 2012

Abstract
We have studied the polarized resolved photoluminescence of n-type GaAs/AlAs/GaAlAs resonant tunneling diodes under magnetic field parallel to the tunnel current. Under resonant tunneling conditions, we have observed two emission lines attributed to neutral (X) and negatively charged excitons (X−). We have observed a voltage-controlled circular polarization degree from the quantum well emission for both lines, with values up to −88% at 15 T at low voltages which are ascribed to an efficient spin injection from the 2D gases formed at the accumulation layers.
Self-adapting root-MUSIC algorithm and its real-valued formulation for acoustic vector sensor array
Authors: Wang Peng , Zhang Guo-jun , Xue Chen-yang , Zhang Wen-dong , Xiong Ji-jun 
Published: October 2012

Abstract
In this paper, based on the root-MUSIC algorithm for acoustic pressure sensor array, a new self-adapting root-MUSIC algorithm for acoustic vector sensor array is proposed by self-adaptive selecting the lead orientation vector, and its real-valued formulation by Forward-Backward(FB) smoothing and real-valued inverse covariance matrix is also proposed, which can reduce the computational complexity and distinguish the coherent signals. The simulation experiment results show the better performance of two new algorithm with low Signal-to-Noise (SNR) in direction of arrival (DOA) estimation than traditional MUSIC algorithm, and the experiment results using MEMS vector hydrophone array in lake trails show the engineering practicability of two new algorithms.
Preclinical Alzheimer disease: identification of cases at risk among cognitively intact older individuals
Authors: Lazarczyk Maciej J , Hof Patrick R , Bouras Constantin , Giannakopoulos Panteleimon 
Published: October 2012

Abstract
Since the first description of the case of Auguste Deter, presented in Tübingen in 1906 by Alois Alzheimer, there has been an exponential increase in our knowledge of the neuropathological, cellular, and molecular foundation of Alzheimer's disease (AD). The concept of AD pathogenesis has evolved from a static, binary view discriminating cognitive normality from dementia, towards a dynamic view that considers AD pathology as a long-lasting morbid process that takes place progressively over years, or even decades, before the first symptoms become apparent, and thus operating in a continuum between the two aforementioned extreme states. Several biomarkers have been proposed to predict AD-related cognitive decline, initially in cases with mild cognitive impairment, and more recently in cognitively intact individuals. These early markers define at-risk individuals thought to be in the preclinical phase of AD. However, the clinical relevance of this preclinical phase remains controversial. The fate of such individuals, who are cognitively intact, but positive for some early AD biomarkers, is currently uncertain at best. In this report, we advocate the point of view that although most of these preclinical cases will evolve to clinically overt AD, some appear to have efficient compensatory mechanisms and virtually never develop dementia. We critically review the currently available early AD markers, discuss their clinical relevance, and propose a novel classification of preclinical AD, designating these non-progressing cases as 'stable asymptomatic cerebral amyloidosis'.
The placental analogue and the pattern of sexual reproduction in the cheilostome bryozoan Bicellariella ciliata (Gymnolaemata)
Authors: Moosbrugger Martin , Schwaha Thomas , Walzl Manfred G , Obst Matthias , Ostrovsky Andrew N 
Published: October 2012

AbstractBackgroundMatrotrophy or extraembryonic nutrition – transfer of nutrients from mother to embryo during gestation – is well known and thoroughly studied among vertebrates, but still poorly understood in invertebrates. The current paper focuses on the anatomy and ultrastructure of the oogenesis and placentotrophy as well as formation of the brood chamber (ovicell) in the cheilostome bryozoanBicellariella ciliata(Linnaeus, 1758). Our research aimed to combine these aspects of the sexual reproduction into an integral picture, highlighting the role of the primitive placenta-like system in the evolution of bryozoan reproductive patterns.ResultsFollicular and nutrimentary provisioning of the oocyte occur during oogenesis. Small macrolecithal oocytes are produced, and embryos are nourished in the ovicell via a simple placental analogue (embryophore). Every brooding episode is accompanied by the hypertrophy of the embryophore, which collapses after larval release. Nutrients are released and uptaken by exocytosis (embryophore) and endocytosis (embryo). Embryos lack specialized area for nutrient uptake, which occurs through the whole epidermal surface. The volume increase between the ripe oocyte and the larva is ca. 10-fold.ConclusionsThe ovicell is a complex organ (not a special polymorph as often thought) consisting of an ooecium (protective capsule) and an ooecial vesicle (plugging the entrance to the brooding cavity) that develop from the distal and the fertile zooid correspondingly. Combination of macrolecithal oogenesis and extraembryonic nutrition allows attributingB. ciliatato species with reproductive pattern IV. However, since its oocytes are small, this species represents a previously undescribed variant of this pattern, which appears to represent a transitional state from the insipient matrotrophy (with large macrolecithal eggs) to substantial one (with small microlecithal ones). Altogether, our results substantially added and corrected the data obtained by the previous authors, providing a new insight in our understanding of the evolution of matrotrophy in invertebrates.
Proton therapy versus photon radiation therapy for the management of a recurrent desmoid tumor of the right flank: a case report
Authors: Kil Whoon Jong , Nichols R Charles , Kilkenny John W , Huh Soon Y , Ho Meng Wei , Gupta Pratibha , Marcus Robert B , Indelicato Daniel J 
Published: October 2012

Abstract
Desmoid tumors are benign mesenchymal tumors with a strong tendency for local recurrence after surgery. Radiotherapy improves local control following incomplete resection, but nearby organs at risk may limit the dose to the target volume. The patient in this report presented with a recurrent desmoid tumor of the right flank and underwent surgery with microscopically positive margins. Particular problems presented in this case included that the tumor bed was situated in close proximity to the liver and the right kidney and that the right kidney was responsible for 65% of the patient’s renal function. Intensity-modulated radiation therapy plans delivering 54 Gy necessarily exposed the right kidney to a V18 of 98% and the liver to a V30 of 55%. Proton therapy plans significantly reduced the right kidney V18 to 32% and the liver V30 to 28%. In light of this, the proton plan was utilized for treatment of this patient. Proton therapy was tolerated without gastrointestinal discomfort or other complaints. Twenty-four months after initiation of proton therapy, the patient is without clinical or radiographic evidence of disease recurrence. In this setting, the improved dose distribution associated with proton therapy allowed for curative treatment of a patient who arguably could not have been safely treated with intensity-modulated radiation therapy or other methods of conventional radiotherapy.
Design of optimal solvent for extraction of bio–active ingredients from six varieties of Medicago sativa
Authors: Caunii Angela , Pribac George , Grozea Ioana , Gaitin Dorin , Samfira Ionel 
Published: October 2012

Abstract

Background
Extensive research has been performed worldwide and important evidences were collected to show the immense potential of plants used in various traditional therapeutic systems. The aim of this work is to investigate the different extracting solvents in terms of the influence of their polarity on the extracting ability of bioactive molecules (phenolic compounds) from the M. sativa flowers.

Results
The total phenolic content of samples was determined using the Folin Ciocalteu (FC) procedure and their antioxidant activity was assayed through in vitro radical decomposing activity using the radical DPPH° assay (IUPAC name for DPPH is (phenyl)–(2,4,6–trinitrophenyl) iminoazanium). The results showed that water was better than methanol and acetic acid for extracting bioactive compounds, in particular for total phenolic compounds from the flowers of alfalfa. The average content of bioactive molecules in methanol extract was 263.5±1.02 mg GAE/100g of dry weight lyophilized extract. The total phenolic content of the tested plant extracts was highly correlated with the radical decomposing activity. However, all extracts were free–radical inhibitors, but the water extract was more potent than the acetic and the methanol ones. The order of inhibitor effectiveness (expressed by IC50) proved to be: water extract (0.924mg/mL) > acetic acid extract (0.154mg/mL) > methanol (0.079mg/mL). The profiles of each extract (fingerprint) were characterized by FT–MIR spectroscopy.

Conclusions
The present study compares the fingerprint of different extracts of the M. sativa flowers, collected from the wild flora of Romania. The total phenolic content of the tested plant extracts was highly correlated with the radical decomposing activity. The dependence of the extract composition on the solvent polarity (acetic acid vs. methanol vs. water) was revealed by UV–VIS spectrometry and Infrared fingerprint.
Multimodality cardiac imaging of a ventricular septal rupture post myocardial infarction: a case report
Authors: Dhaliwal Surinder , Ducas Robin , Shuangbo Liu , Horne David , Lee John , Hussain Farrukh , Kirkpatrick Iain DC , Jassal Davinder S 
Published: October 2012

Abstract

Background
Ventricular septal rupture (VSR), a mechanical complication following an acute myocardial infarction (MI), is thought to result from coagulation necrosis due to lack of collateral reperfusion. Although the gold standard test to confirm left-to-right shunting between ventricular cavities remains invasive ventriculography, two-dimensional transthoracic echocardiography (TTE) with color flow Doppler and cardiac MRI (CMR) are reliable tests for the non-invasive diagnosis of VSR.

Case presentation
A 62-year-old Caucasian female presented with a late case of a VSR post inferior MI diagnosed by multimodality cardiac imaging including TTE, CMR and ventriculography.

Conclusion
We review the presentation, diagnosis and management of VSR post MI.
Eating lizards: a millenary habit evidenced by Paleoparasitology
Authors: Sianto Luciana , Teixeira-Santos Isabel , Chame Marcia , Chaves Sergio M , Souza Sheila M , Ferreira Luiz Fernando , Reinhard Karl , Araujo Adauto 
Published: October 2012

Abstract

Background
Analyses of coprolites have contributed to the knowledge of diet as well as infectious diseases in ancient populations. Results of paleoparasitological studies showed that prehistoric groups were exposed to spurious and zoonotic parasites, especially food-related. Here we report the findings of a paleoparasitological study carried out in remote regions of Brazil’s Northeast.

Findings
Eggs of Pharyngodonidae (Nematoda, Oxyuroidea), a family of parasites of lizards and amphibians, were found in four human coprolites collected from three archaeological sites. In one of these, lizard scales were also found.

Conclusions
Through the finding of eggs of Pharyngodonidae in human coprolites and reptile
scales in one of these, we have provided evidence that humans have consumed reptiles at least 10,000 years ago. This food habit persists to modern times in remote regions of Brazil’s Northeast. Although Pharyngodonidae species are not known to infect humans, the consumption of raw or undercooked meat from lizards and other reptiles may have led to transmission of a wide range of zoonotic agents to humans in the past.
The existence and uniqueness of solutions to boundary value problems of fractional difference equations
Authors: Pan Yuanyuan , Han Zhenlai , Sun Shurong , Huang Zhiqing 
Published: October 2012

Abstract
In this paper, we study the existence and uniqueness of solutions for the boundary value problem

−

Δ

ν
−
μ

ν

y
(
t
)
=
f
(
t
,
y
(
t
+
ν
−
1
)
)
,

Δ

i

y
(
ν
−
N
)
=
0
,

i
∈
{
0
,
…
,
N
−
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}
,

Δ

N
−
2

y
(
ν
−
N
)
=
g
(
y
)
,

Δ

ν
−
N

μ

y
(
b
+
M
+
ν
−
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)
=
0
,

where

ν
≥
2
,
1
≤
μ
<
ν
,
f
:
{
0
,
·
·
·
,
b
+
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}
×
R
→
R

is continuous, and nonnegative for

y
≥
0
,
g
:
C
(
[
ν
−
N
,
·
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,
b
+
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+
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]
,
R
)

is a given function. We give a representation for the solution to this problem, and we prove the existence and uniqueness of solution to this problem by contraction mapping theorem and Brouwer theorem.