bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meat Juice Serology and Improved Food Chain Information as Control Tools for Pork‐Related Public Health Hazards
Authors: Felin E. , Jukola E. , Raulo S. , Fredriksson‐Ahomaa M. 
Published: December 2014

SummaryThe seroprevalence of Salmonella spp., pathogenic Yersinia spp., Toxoplasma gondii and Trichinella spp. was studied in 1353 finishing pigs from 259 farms that were allocated according to farm types: large fattening farms (≥1000 pig places), small fattening farms (< 1000 pig places) and farrow‐to‐finish farms. The antibodies were analysed with commercial ELISA kits in meat juice samples that were collected at Finnish slaughterhouses. Salmonella antibodies were rare (3% of pigs, 14% of farms) when the cut‐off optical density (OD) value 0.2 was used. Antibodies to pathogenic Yersinia spp. and T. gondii were detected in 57% of pigs and 85% of farms (OD ≥0.3) and in 3% of pigs and 9% of farms (OD ≥0.15), respectively. No antibodies to Trichinella spp. were detected (OD ≥0.3). The European Food Safety Authority (EFSA) considers Salmonella spp., Yersinia enterocolitica, T. gondii and Trichinella spp. as the most relevant biological hazards in the context of meat inspection of pigs. The seroprevalence of these important zoonotic pathogens was low in Finland, except that of Yersinia. The seroprevalence of Toxoplasma was significantly higher in pigs originating from small‐scale fattening farms (P < 0.05). Strong positive correlation was observed at the animal level between Salmonella and Yersinia seropositivity and between Salmonella and Toxoplasma seropositivity (P < 0.05). We suggest that these results reflect the level and importance of biosecurity measures applied on the farms. Meat juice serology at slaughter is a useful tool for targeting measures to control these pathogens. The information obtained from analyses should be used as part of the food chain information (FCI).
Image reconstructions from super‐sampled data sets with resolution modeling in PET imaging
Authors: Li Yusheng , Matej Samuel , Metzler Scott D. 
Published: December 2014

Purpose:Spatial resolution in positron emission tomography (PET) is still a limiting factor in many imaging applications. To improve the spatial resolution for an existing scanner with fixed crystal sizes, mechanical movements such as scanner wobbling and object shifting have been considered for PET systems. Multiple acquisitions from different positions can provide complementary information and increased spatial sampling. The objective of this paper is to explore an efficient and useful reconstruction framework to reconstruct super‐resolution images from super‐sampled low‐resolution data sets.Methods:The authors introduce a super‐sampling data acquisition model based on the physical processes with tomographic, downsampling, and shifting matrices as its building blocks. Based on the model, we extend the MLEM and Landweber algorithms to reconstruct images from super‐sampled data sets. The authors also derive a backprojection‐filtration‐like (BPF‐like) method for the super‐sampling reconstruction. Furthermore, they explore variant methods for super‐sampling reconstructions: the separate super‐sampling resolution‐modeling reconstruction and the reconstruction without downsampling to further improve image quality at the cost of more computation. The authors use simulated reconstruction of a resolution phantom to evaluate the three types of algorithms with different super‐samplings at different count levels.Results:Contrast recovery coefficient (CRC) versus background variability, as an image‐quality metric, is calculated at each iteration for all reconstructions. The authors observe that all three algorithms can significantly and consistently achieve increased CRCs at fixed background variability and reduce background artifacts with super‐sampled data sets at the same count levels. For the same super‐sampled data sets, the MLEM method achieves better image quality than the Landweber method, which in turn achieves better image quality than the BPF‐like method. The authors also demonstrate that the reconstructions from super‐sampled data sets using a fine system matrix yield improved image quality compared to the reconstructions using a coarse system matrix. Super‐sampling reconstructions with different count levels showed that the more spatial‐resolution improvement can be obtained with higher count at a larger iteration number.Conclusions:The authors developed a super‐sampling reconstruction framework that can reconstruct super‐resolution images using the super‐sampling data sets simultaneously with known acquisition motion. The super‐sampling PET acquisition using the proposed algorithms provides an effective and economic way to improve image quality for PET imaging, which has an important implication in preclinical and clinical region‐of‐interest PET imaging applications.
Adaptive Coding of Orofacial and Speech Actions in Motor and Somatosensory Spaces with and without Overt Motor Behavior
Authors: Sato Marc , Vilain Coriandre , Lamalle Laurent , Grabski Krystyna 
Published: December 2014

Abstract
Studies of speech motor control suggest that articulatory and phonemic goals are defined in multidimensional motor, somatosensory, and auditory spaces. To test whether motor simulation might rely on sensory–motor coding common with those for motor execution, we used a repetition suppression (RS) paradigm while measuring neural activity with sparse sampling fMRI during repeated overt and covert orofacial and speech actions. RS refers to the phenomenon that repeated stimuli or motor acts lead to decreased activity in specific neural populations and are associated with enhanced adaptive learning related to the repeated stimulus attributes. Common suppressed neural responses were observed in motor and posterior parietal regions in the achievement of both repeated overt and covert orofacial and speech actions, including the left premotor cortex and inferior frontal gyrus, the superior parietal cortex and adjacent intraprietal sulcus, and the left IC and the SMA. Interestingly, reduced activity of the auditory cortex was observed during overt but not covert speech production, a finding likely reflecting a motor rather an auditory imagery strategy by the participants. By providing evidence for adaptive changes in premotor and associative somatosensory brain areas, the observed RS suggests online state coding of both orofacial and speech actions in somatosensory and motor spaces with and without motor behavior and sensory feedback.
Cortical Representations Sensitive to the Number of Perceived Auditory Objects Emerge between 2 and 4 Months of Age: Electrophysiological Evidence
Authors: Folland Nicole A. , Butler Blake E. , Payne Jennifer E. , Trainor Laurel J. 
Published: December 2014

Abstract
Sound waves emitted by two or more simultaneous sources reach the ear as one complex waveform. Auditory scene analysis involves parsing a complex waveform into separate perceptual representations of the sound sources [Bregman, A. S. Auditory scene analysis: The perceptual organization of sounds. London: MIT Press, 1990]. Harmonicity provides an important cue for auditory scene analysis. Normally, harmonics at integer multiples of a fundamental frequency are perceived as one sound with a pitch corresponding to the fundamental frequency. However, when one harmonic in such a complex, pitch-evoking sound is sufficiently mistuned, that harmonic emerges from the complex tone and is perceived as a separate auditory object. Previous work has shown that the percept of two objects is indexed in both children and adults by the object-related negativity component of the ERP derived from EEG recordings [Alain, C., Arnott, S. T., & Picton, T. W. Bottom–up and top–down influences on auditory scene analysis: Evidence from event-related brain potentials. Journal of Experimental Psychology: Human Perception and Performance, 27, 1072–1089, 2001]. Here we examine the emergence of object-related responses to an 8% harmonic mistuning in infants between 2 and 12 months of age. Two-month-old infants showed no significant object-related response. However, in 4- to 12-month-old infants, a significant frontally positive component was present, and by 8–12 months, a significant frontocentral object-related negativity was present, similar to that seen in older children and adults. This is in accordance with previous research demonstrating that infants younger than 4 months of age do not integrate harmonic information to perceive pitch when the fundamental is missing [He, C., Hotson, L., & Trainor, L. J. Maturation of cortical mismatch mismatch responses to occasional pitch change in early infancy: Effects of presentation rate and magnitude of change. Neuropsychologia, 47, 218–229, 2009]. The results indicate that the ability to use harmonic information to segregate simultaneous sounds emerges at the cortical level between 2 and 4 months of age.
Neural Correlates of Fixation Duration during Real-world Scene Viewing: Evidence from Fixation-related (FIRE) fMRI
Authors: Henderson John M. , Choi Wonil 
Published: December 2014

Abstract
During active scene perception, our eyes move from one location to another via saccadic eye movements, with the eyes fixating objects and scene elements for varying amounts of time. Much of the variability in fixation duration is accounted for by attentional, perceptual, and cognitive processes associated with scene analysis and comprehension. For this reason, current theories of active scene viewing attempt to account for the influence of attention and cognition on fixation duration. Yet almost nothing is known about the neurocognitive systems associated with variation in fixation duration during scene viewing. We addressed this topic using fixation-related fMRI, which involves coregistering high-resolution eye tracking and magnetic resonance scanning to conduct event-related fMRI analysis based on characteristics of eye movements. We observed that activation in visual and prefrontal executive control areas was positively correlated with fixation duration, whereas activation in ventral areas associated with scene encoding and medial superior frontal and paracentral regions associated with changing action plans was negatively correlated with fixation duration. The results suggest that fixation duration in scene viewing is controlled by cognitive processes associated with real-time scene analysis interacting with motor planning, consistent with current computational models of active vision for scene perception.
Study of Snow Dynamics at Subgrid Scale in Semiarid Environments Combining Terrestrial Photography and Data Assimilation Techniques
Authors: Pimentel Rafael , Herrero Javier , Zeng Yijian , Su Zhongbo , Polo María J. 
Published: December 2014

Abstract
Snow cover simulation is a complex task in mountain regions because of its highly irregular distribution. GIS-based calculations of snowmelt–accumulation models must deal with nonnegligible scale effects below cell size, which may result in unsatisfactory predictions depending on the study scale. Terrestrial photography, whose scales can be adapted to the study problem, is a cost-effective technique, capable of reproducing snow dynamics at subgrid scale. A series of high-frequency images were combined with a mass and energy model to reproduce snow evolution at cell scale (30 m × 30 m) by means of the assimilation of the snow cover fraction observation dataset obtained from terrestrial photography in the Sierra Nevada, southern Spain. The ensemble transform Kalman filter technique is employed. The results show the convenience of adopting a selective depletion curve parameterization depending on the succession of accumulation–melting cycles in the snow season in these highly variable environments. A reduction in the error for snow depth to 50% (from 463.87 to 261.21 mm and from 238.22 to 128.50 mm) is achieved if the appropriate curve is selected.
Improving the quality of tracheostomy care
Authors: Zhu Hannah , Das Preety , Woodhouse Ralph , Kubba Haytham 
Published: December 2014

Educational aimsTo understand the current challenges in the care of tracheostomy patientsTo understand principles of quality improvement collaboration and how this can improve the quality of care for tracheostomy patientsSummaryThe UK National Confidential Enquiry into Patient Outcomes and Death illustrates that there remains significant morbidity and mortality relating to patients with a tracheostomy, with much preventable harm. Challenges include the inherent complexity of the patient's underlying condition, wide variations in tracheostomy management, variable delivery of education for staff, patients and families, and difficult coordination of care between such a variety of individuals involved in performing, managing and ultimately removing tracheostomies.Quality-improvement collaboratives are groups of institutions with a common purpose who work together to drive positive change. They help support clinicians in developing skills and teams necessary to design and sustain quality-improvement cycles. They are a cost-effective way of rapidly disseminating improvement strategies and engaging in shared learning across institutions around the world. The Global Tracheostomy Collaborative aims to improve quality of care and outcomes through five interdependent key drivers: coordinated multidisciplinary team care, education, institution-wide protocols, family and patient-centred care, and metrics and outcomes using a specifically designed database.
Male-specific Y-linked transgene markers to enhance biologically-based control of the Mexican fruit fly, Anastrepha ludens(Diptera: Tephritidae)
Authors: Meza J Salvador , Schetelig Marc F , Zepeda-Cisneros C Silvia , Handler Alfred M 
Published: December 2014

Abstract
Background
Reliable marking systems are critical to the prospective field release of transgenic insect strains. This is to unambiguously distinguish released insects from wild insects in the field that are collected in field traps, and tissue-specific markers, such as those that are sperm-specific, have particular uses such as identifying wild females that have mated with released males. For tephritid fruit flies such as the Mexican fruit fly, Anastrepha ludens, polyubiquitin-regulated fluorescent protein body markers allow transgenic fly identification, and fluorescent protein genes regulated by the spermatocyte-specific β2-tubulin promoter effectively mark sperm. For sterile male release programs, both marking systems can be made male-specific by linkage to the Y chromosome.

Results
An A. ludens wild type strain was genetically transformed with a piggyBac vector, pBXL{PUbnlsEGFP, Asβ2tub-DsRed.T3}, having the polyubiquitin-regulated EGFP body marker, and the β2-tubulin-regulated DsRed.T3 sperm-specific marker. Autosomal insertion lines effectively expressed both markers, but a single Y-linked insertion (YEGFP strain) expressed only PUbnlsEGFP. This insertion was remobilized by transposase helper injection, which resulted in three new autosomal insertion lines that expressed both markers. This indicated that the original Y-linked Asβ2tub-DsRed.T3 marker was functional, but specifically suppressed on the Y chromosome. The PUbnlsEGFP marker remained effective however, and the YEGFP strain was used to create a sexing strain by translocating the wild type allele of the black pupae (bp+) gene onto the Y, which was then introduced into the bp- mutant strain. This allows the mechanical separation of mutant female black pupae from male brown pupae, that can be identified as adults by EGFP fluorescence.

Conclusions
A Y-linked insertion of the pBXL{PUbnlsEGFP, Asβ2tub-DsRed.T3} transformation vector in A. ludens resulted in male-specific expression of the EGFP fluorescent protein marker, and was integrated into a black pupae translocation sexing strain (T(YEGFP/bp+), allowing the identification of male adults when used in sterile male release programs for population control. A unique observation was that expression of the Asβ2tub-DsRed.T3 sperm-specific marker, which was functional in autosomal insertions, was specifically suppressed in the Y-linked insertion. This may relate to the Y chromosomal regulation of male-specific germ-line genes in Drosophila.
Iron is essential for living!
Authors: Lasocki Sigismond , Gaillard Thomas , Rineau Emmanuel 
Published: December 2014

AbstractIron as an element is a double-edged sword, essential for living but also potentially toxic through the generation of oxidative stress. The recent study by Chen and colleagues in Critical Care reminds us of this elegantly. In a mouse model of acute lung injury, they showed that silencing hepcidin (the master regulator of iron metabolism) locally in airway epithelial cells aggravates lung injury by increasing the release of iron from alveolar macrophages, which in turn enhances pulmonary bacterial growth and reduces the macrophages’ killing properties. This work underscores that hepcidin acts not only systematically (as a hormone) but also locally for iron metabolism regulation. This opens areas of research for sepsis treatment but also for iron deficiency or anaemia treatment, since the local and systemic iron regulation appear to be independent.
A practical approach to goal-directed echocardiography in the critical care setting
Authors: Walley Patricia E , Walley Keith R , Goodgame Ben , Punjabi Vivek , Sirounis Demetrios 
Published: December 2014

AbstractUrgent cardiac ultrasound examination in the critical care setting is clinically useful. Application of goal-directed echocardiography in this setting is quite distinct from typical exploratory diagnostic comprehensive echocardiography, because the urgent critical care setting mandates a goal-directed approach. Goal-directed echocardiography most frequently aims to rapidly identify and differentiate the cause(s) of hemodynamic instability and/or the cause(s) of acute respiratory failure. Accordingly, this paper highlights 1) indications, 2) an easily memorized differential diagnostic framework for goal-directed echocardiography, 3) clinical questions that must be asked and answered, 4) practical issues to allow optimal image capture, 5) primary echocardiographic views, 6) key issues addressed in each view, and 7) interpretation of findings within the differential diagnostic framework. The most frequent indications for goal-directed echocardiography include 1) the spectrum of hemodynamic instability, shock, and pulseless electrical activity arrest and 2) acute respiratory failure. The differential diagnostic categories for hemodynamic instability can be remembered using the mnemonic ‘SHOCK’ (for Septic, Hypovolemic, Obstructive, Cardiogenic, and (K) combinations/other kinds of shock). RESP-F (for exacerbation of chronic Respiratory disease, pulmonary Embolism, ST changes associated with cardiac or pericardial disease, Pneumonia, and heart Failure) can be used for acute respiratory failure. The goals of goal-directed echocardiography in the unstable patient are: assessing global ventricular systolic function, identifying marked right ventricular and left ventricular enlargement, assessing intravascular volume, and the presence of a pericardial effusion. In an urgent or emergent setting, it is recommended to go directly to the best view, which is frequently the subcostal or apical view. The five views are the subcostal four-chamber view, subcostal inferior vena cava view, parasternal long axis view, parasternal short axis view, and the apical four chamber view. Always interpret goal-directed echocardiographic findings in the context of clinically available hemodynamic information. When goal-directed echocardiography is insufficient or when additional abnormalities are appreciated, order a comprehensive echocardiogram. Goal-directed echocardiography and comprehensive echocardiography are not to be used in conflict with each other.
TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator
Authors: Tsai Ya-Ping , Chen Hsiao-Fan , Chen Sung-Yuan , Cheng Wei-Chung , Wang Hsei-Wei , Shen Zih-Jie , Song Chunxiao , Teng Shu-Chun , He Chuan , Wu Kou-Juey 
Published: December 2014

Abstract
Background
Hypoxia induces the epithelial-mesenchymal transition, EMT, to promote cancer metastasis. In addition to transcriptional regulation mediated by hypoxia-inducible factors, HIFs, other epigenetic mechanisms of gene regulation, such as histone modifications and DNA methylation, are utilized under hypoxia. However, whether DNA demethylation mediated by TET1, a DNA dioxygenase converting 5-methylcytosine, 5mC, into 5-hydroxymethylcytosine, 5hmC, plays a role in hypoxia-induced EMT is largely unknown.

Results
We show that TET1 regulates hypoxia-responsive gene expression. Hypoxia/HIF-2α regulates the expression of TET1. Knockdown of TET1 mitigates hypoxia-induced EMT. RNA sequencing and 5hmC sequencing identified the set of TET1-regulated genes. Cholesterol metabolic process genes are among the genes that showed high prevalence and statistical significance. We characterize one of the genes, INSIG1 (insulin induced gene 1), to confirm its expression and the 5hmC levels in its promoter. Knockdown of INSIG1 also mitigates hypoxia-induced EMT. Finally, TET1 is shown to be a transcriptional co-activator that interacts with HIF-1α and HIF-2α to enhance their transactivation activity independent of its enzymatic activity. TET1 acts as a co-activator to further enhance the expression of INSIG1 together with HIF-2α. We define the domain in HIF-1α that interacts with TET1 and map the domain in TET1 that confers transactivation to a 200 amino acid region that contains a CXXC domain. The TET1 catalytically inactive mutant is capable of rescuing hypoxia-induced EMT in TET1 knockdown cells.

Conclusions
These findings demonstrate that TET1 serves as a transcription co-activator to regulate hypoxia-responsive gene expression and EMT, in addition to its role in demethylating 5mC.
Low frequency of paleoviral infiltration across the avian phylogeny
Authors: Cui Jie , Zhao Wei , Huang Zhiyong , Jarvis Erich D , Gilbert M Thomas P , Walker Peter J , Holmes Edward C , Zhang Guojie 
Published: December 2014

Abstract
Background
Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small genomes may enable important insights into the patterns and processes of endogenous viral element evolution.

Results
Through a systematic screening of the genomes of 48 species sampled across the avian phylogeny we reveal that birds harbor a limited number of endogenous viral elements compared to mammals, with only five viral families observed: Retroviridae, Hepadnaviridae, Bornaviridae, Circoviridae, and Parvoviridae. All nonretroviral endogenous viral elements are present at low copy numbers and in few species, with only endogenous hepadnaviruses widely distributed, although these have been purged in some cases. We also provide the first evidence for endogenous bornaviruses and circoviruses in avian genomes, although at very low copy numbers. A comparative analysis of vertebrate genomes revealed a simple linear relationship between endogenous viral element abundance and host genome size, such that the occurrence of endogenous viral elements in bird genomes is 6- to 13-fold less frequent than in mammals.

Conclusions
These results reveal that avian genomes harbor relatively small numbers of endogenous viruses, particularly those derived from RNA viruses, and hence are either less susceptible to viral invasions or purge them more effectively.