bluuebunny/crossref_metadata_2025_split huggingface dataset:
ALBIRA: A small animal PET/SPECT/CT imaging system
Authors: Sánchez F. , Orero A. , Soriano A. , Correcher C. , Conde P. , González A. , Hernández L. , Moliner L. , Rodríguez‐Alvarez M. J. , Vidal L. F. , Benlloch J. M. , Chapman S. E. , Leevy W. M. 
Published: April 2013

Purpose:The authors have developed a trimodal PET/SPECT/CT scanner for small animal imaging. The gamma ray subsystems are based on monolithic crystals coupled to multianode photomultiplier tubes (MA‐PMTs), while computed tomography (CT) comprises a commercially available microfocus x‐ray tube and a CsI scintillator 2D pixelated flat panel x‐ray detector. In this study the authors will report on the design and performance evaluation of the multimodal system.Methods:X‐ray transmission measurements are performed based on cone‐beam geometry. Individual projections were acquired by rotating the x‐ray tube and the 2D flat panel detector, thus making possible a transaxial field of view (FOV) of roughly 80 mm in diameter and an axial FOV of 65 mm for the CT system. The single photon emission computed tomography (SPECT) component has a dual head detector geometry mounted on a rotating gantry. The distance between the SPECT module detectors can be varied in order to optimize specific user requirements, including variable FOV. The positron emission tomography (PET) system is made up of eight compact modules forming an octagon with an axial FOV of 40 mm and a transaxial FOV of 80 mm in diameter. The main CT image quality parameters (spatial resolution and uniformity) have been determined. In the case of the SPECT, the tomographic spatial resolution and system sensitivity have been evaluated with a99mTc solution using single‐pinhole and multi‐pinhole collimators. PET and SPECT images were reconstructed using three‐dimensional (3D) maximum likelihood and ordered subset expectation maximization (MLEM and OSEM) algorithms developed by the authors, whereas the CT images were obtained using a 3D based FBP algorithm.Results:CT spatial resolution was 85μm while a uniformity of 2.7% was obtained for a water filled phantom at 45 kV. The SPECT spatial resolution was better than 0.8 mm measured with a Derenzo‐like phantom for a FOV of 20 mm using a 1‐mm pinhole aperture collimator. The full width at half‐maximum PET radial spatial resolution at the center of the field of view was 1.55 mm. The SPECT system sensitivity for a FOV of 20 mm and 15% energy window was 700 cps/MBq (7.8 × 10−2%) using a multi‐pinhole equipped with five apertures 1 mm in diameter, whereas the PET absolute sensitivity was 2% for a 350–650 keV energy window and a 5 ns timing window. Several animal images are also presented.Conclusions:The new small animal PET/SPECT/CT proposed here exhibits high performance, producing high‐quality images suitable for studies with small animals. Monolithic design for PET and SPECT scintillator crystals reduces cost and complexity without significant performance degradation.
Twentieth-Century Oceanic Carbon Uptake and Storage in CESM1(BGC)*
Authors: Long Matthew C. , Lindsay Keith , Peacock Synte , Moore J. Keith , Doney Scott C. 
Published: April 2013

Abstract
Ocean carbon uptake and storage simulated by the Community Earth System Model, version 1–Biogeochemistry [CESM1(BGC)], is described and compared to observations. Fully coupled and ocean-ice configurations are examined; both capture many aspects of the spatial structure and seasonality of surface carbon fields. Nearly ubiquitous negative biases in surface alkalinity result from the prescribed carbonate dissolution profile. The modeled sea–air CO2 fluxes match observationally based estimates over much of the ocean; significant deviations appear in the Southern Ocean. Surface ocean pCO2 is biased high in the subantarctic and low in the sea ice zone. Formation of the water masses dominating anthropogenic CO2 (Cant) uptake in the Southern Hemisphere is weak in the model, leading to significant negative biases in Cant and chlorofluorocarbon (CFC) storage at intermediate depths. Column inventories of Cant appear too high, by contrast, in the North Atlantic. In spite of the positive bias, this marks an improvement over prior versions of the model, which underestimated North Atlantic uptake. The change in behavior is attributable to a new parameterization of density-driven overflows. CESM1(BGC) provides a relatively robust representation of the ocean–carbon cycle response to climate variability. Statistical metrics of modeled interannual variability in sea–air CO2 fluxes compare reasonably well to observationally based estimates. The carbon cycle response to key modes of climate variability is basically similar in the coupled and forced ocean-ice models; however, the two differ in regional detail and in the strength of teleconnections.
Characteristics of Landfalling Atmospheric Rivers Inferred from Satellite Observations over the Eastern North Pacific Ocean
Authors: Matrosov Sergey Y. 
Published: April 2013

Abstract
Narrow elongated regions of moisture transport known as atmospheric rivers (ARs), which affect the West Coast of North America, were simultaneously observed over the eastern North Pacific Ocean by the polar-orbiting CloudSat and Aqua satellites. The presence, location, and extent of precipitation regions associated with ARs and their properties were retrieved from measurements taken at 265 satellite crossings of AR formations during the three consecutive cool seasons of the 2006–09 period. Novel independent retrievals of AR mean rain rate, precipitation regime types, and precipitation ice region properties from satellite measurements were performed. Relations between widths of precipitation bands and AR thicknesses (as defined by the integrated water vapor threshold of 20 mm) were quantified. Precipitation regime partitioning indicated that “cold” precipitation with a significant amount of melting precipitating ice and “warm” rainfall conditions with limited or no ice in the atmospheric column were observed, on average, with similar frequencies, though the cold rainfall fraction had an increasing trend as AR temperature decreased. Rain rates were generally higher for the cold precipitation regime. Precipitating ice cloud and rainfall retrievals indicated a significant correlation between the total ice amounts and the resultant rain rate. Observationally based statistical relations were derived between the boundaries of AR precipitation regions and integrated water vapor amounts and between the total content of precipitating ice and rain rate. No statistically significant differences of AR properties were found for three different cool seasons, which were characterized by differing phases of El Niño–Southern Oscillation.
A case of neonatal tetanus presented within 24 hours of life
Authors: Chatterjee Sayan , Hemram Sunil , Bhattacharya Subhasish , Khuntdar Bidyut Kumar 
Published: April 2013

Summary Neonatal tetanus is still prevalent in developing countries such as India. Generally, neonatal tetanus is seen in babies of unimmunized mothers beyond the second day of life. A neonate presented to us on the 4th hour of birth with a periumbilical ulcer. The baby's antenatal and birth history was uneventful. The mother had been immunized against tetanus. At presentation, the baby was active, alert and sucking normally. Avery small ulcer was noted below the umbilicus. Subsequently, the baby developed rigidity and a tonic spasm of its body with recurrent seizures from the 18th hour of its birth and by 21st hour. It also had a full blown clinical picture of neonatal tetanus including: masseter spasm; generalized rigidity; a high pitched cry: and intermittent opisthotonos posturing. An ulcer gradually enlarged to 5 × 4 cm and a swab from ulcer showed Clostridium tetani (both on Gram staining and culture). A review of the published literature did not reveal any case that had presented so early. Therefore, this is probably the first case of neonatal tetanus being reported within the 21st hour of birth.
Paediatric head injuries in the Kwazulu-Natal Province of South Africa: a developing country perspective
Authors: Okyere-Dede Ebenezer K , Nkalakata Munyaradzi C , Nkomo Tshepo , Hadley G P , Madiba Thandinkosi E 
Published: April 2013

Summary We investigated the causes, management and outcome of head injuries in paediatric patients admitted to the paediatric surgery unit at King Edward VIII Hospital overa 3-year period, from 1999 to 2001. There were 506 patients (331 male; M:F ratio 2:1) and the mean age was 71.99 +36.8 months (2 weeks to 180 months). The injuries were due to: motor vehicle crashes (324); falls (121); assault (30); inadvertent injury (23); and unknown (11). Forty-nine patients (9%) were admitted with a Glasgow Coma Scale ≤8. The most common intracranial pathology on computed tomography was: intracranial haematoma/haemorrhage (44); contusion (16); and brain oedema (10). Nineteen patients (3.4%) underwent neurosurgical intervention and the rest were managed conservatively. Eighteen died in hospital (3.6%). The mean hospital stay was 5 ± 12 days. Twenty-three patients (4.5%) were discharged with neurological sequelae. Few paediatric patients are admitted with severe head injury: the majority from blunt injury caused by motor vehicle crashes. Management mainly requires simple neurological observation in a general ward with a surprisingly good prognosis. Specific protocols for paediatric head injuries have been proposed based on these findings.
Pure cerebellitis due to scrub typhus: a unique case report
Authors: Karanth Suman S , Gupta Anurag , Prabhu Mukhyaprana 
Published: April 2013

Summary We report the case of a 24-year old Indian man who presented with: high fever; drowsiness; an eschar and gross cerebellar dysfunction with horizontal gaze nystagmus; ataxic speech; and truncal ataxia. Scrub typhus was diagnosed by serological tests. This is the first case of a pure cerebellar involvement as the only manifestation of scrub typhus in the published literature.
Percutaneous needle aspiration in uncomplicated amebic liver abscess: a randomized trial
Authors: Bammigatti Chanaveerappa , Ramasubramanian NS , Kadhiravan Tamilarasu , Das Ashok Kumar 
Published: April 2013

Summary Amoebic liver abscess develops in less than 1% of patients with amoebaisis and metronidazole is the drug of choice for the treatment of amebic liver abscess. Abscesses of less than 5 cm can be treated with metronidazole alone. However, abscesses of more than 10 cm must undergo ultrasound guided percutaneous needle aspiration along with metronidazole. The role of percutaneous needle aspiration in abscesses of 5 to 10 cm is not clear. Fifty-seven patients with a solitary, right lobe, uncomplicated amoebic liverabscess of 5–10 cm were randomized to receive either metronidazole alone (control group; n = 29) or ultrasound guided percutaneous needle aspiration along with metronidazole (intervention group; n = 28). Although the resolution of pain and fever occurred earlier in the intervention group (27 h and 17 h, respectively) than the control group (48 h and 30 h, respectively), the difference was not statistically significant ( P = 0.16 and 0.48, respectively). There were no deaths during the study period and treatment failure, complications (rupture of abscess), days to normalization of leukocytosis and duration of hospitalization were similar in both groups. Ultrasound guided percutaneous needle aspiration along with metronidazole was no better than metronidazole alone in the management of uncomplicated, solitary, right lobe amoebic liver abscess of 5 to 10 cm.
Lymphatic filariasis elimination programme in Andaman and Nicobar Islands, India: drug coverage and compliance post eight rounds of MDA
Authors: Sunish I P , Shriram A N , Sivan A , Kartick C , Saha B P , Vijayachari P 
Published: April 2013

Summary Lymphatic filariasis (LF) is endemic in the Andaman and Nicobar islands, including the lone foci for a diurnally sub-periodic form of Wuchereria bancrofti in the Nancowry group of islands. A programme to eliminate LF was launched in 2004 by the Directorate of Health Services, Andaman and Nicobar Administration which involved a single annual mass drug administration (MDA) using diethylcarbamazine (DEC) with albendazole. So far, eight rounds of MDA have been implemented through the Public Health Care network. The pattern of antifilarial drug distribution and compliance achieved in the on-going LF elimination programme in these islands has been assessed. This is the first systematic effort undertaken in these remote islands to assess the coverage and compliance with the LF elimination programme. This study covered 900 households in each of the 3 districts. There were a largest number of side effects in the Nicobar district (6.4%). Non-consumption of drugs ranged from 18.6% (Nicobar) to 42% (North and Middle Andaman). A survey revealed that almost 95.3% of the respondents had heard about MDA from the drug distributors. Therefore, the distributors should be involved in programmes designed to educate the community at risk of acquiring filarial infection and the possible side effects of the drugs.
VaccImm: simulating peptide vaccination in cancer therapy
Authors: von Eichborn Joachim , Woelke Anna Lena , Castiglione Filippo , Preissner Robert 
Published: April 2013

Abstract

Background
Despite progress in conventional cancer therapies, cancer is still one of the leading causes of death in industrial nations. Therefore, an urgent need of progress in fighting cancer remains. A promising alternative to conventional methods is immune therapy. This relies on the fact that low-immunogenic tumours can be eradicated if an immune response against them is induced. Peptide vaccination is carried out by injecting tumour peptides into a patient to trigger a specific immune response against the tumour in its entirety. However, peptide vaccination is a highly complicated treatment and currently many factors like the optimal number of epitopes are not known precisely. Therefore, it is necessary to evaluate how certain parameters influence the therapy.

Results
We present the VaccImm Server that allows users to simulate peptide vaccination in cancer therapy. It uses an agent-based model that simulates peptide vaccination by explicitly modelling the involved cells (immune system and cancer) as well as molecules (antibodies, antigens and semiochemicals). As a new feature, our model uses real amino acid sequences to represent molecular binding sites of relevant immune cells. The model is used to generate detailed statistics of the population sizes and states of the single cell types over time. This makes the VaccImm web server well suited to examine the parameter space of peptide vaccination in silico. VaccImm is publicly available without registration on the web at http://bioinformatics.charite.de/vaccimm; all major browsers are supported.

Conclusions
The VaccImm Server provides a convenient way to analyze properties of peptide vaccination in cancer therapy. Using the server, we could gain interesting insights into peptide vaccination that reveal the complex and patient-specific nature of peptide vaccination.
Exome sequencing of senescence-accelerated mice (SAM) reveals deleterious mutations in degenerative disease-causing genes
Authors: Tanisawa Kumpei , Mikami Eri , Fuku Noriyuki , Honda Yoko , Honda Shuji , Ohsawa Ikuro , Ito Masafumi , Endo Shogo , Ihara Kunio , Ohno Kinji , Kishimoto Yuki , Ishigami Akihito , Maruyama Naoki , Sawabe Motoji , Iseki Hiroyoshi , Okazaki Yasushi , Hasegawa-Ishii Sanae , Takei Shiro , Shimada Atsuyoshi , Hosokawa Masanori , Mori Masayuki , Higuchi Keiichi , Takeda Toshio , Higuchi Mitsuru , Tanaka Masashi 
Published: April 2013

AbstractBackgroundSenescence-accelerated mice (SAM) are a series of mouse strains originally derived from unexpected crosses between AKR/J and unknown mice, from which phenotypically distinct senescence-prone (SAMP) and -resistant (SAMR) inbred strains were subsequently established. Although SAMP strains have been widely used for aging research focusing on their short life spans and various age-related phenotypes, such as immune dysfunction, osteoporosis, and brain atrophy, the responsible gene mutations have not yet been fully elucidated.ResultsTo identify mutations specific to SAMP strains, we performed whole exome sequencing of 6 SAMP and 3 SAMR strains. This analysis revealed 32,019 to 38,925 single-nucleotide variants in the coding region of each SAM strain. We detectedOgg1p.R304W andMbd4p.D129N deleterious mutations in all 6 of the SAMP strains but not in the SAMR or AKR/J strains. Moreover, we extracted 31 SAMP-specific novel deleterious mutations. In all SAMP strains except SAMP8, we detected a p.R473W missense mutation in theLdb3gene, which has been associated with myofibrillar myopathy. In 3 SAMP strains (SAMP3, SAMP10, and SAMP11), we identified a p.R167C missense mutation in thePrxgene, in which mutations causing hereditary motor and sensory neuropathy (Dejerine-Sottas syndrome) have been identified. In SAMP6 we detected a p.S540fs frame-shift mutation in theIl4ragene, a mutation potentially causative of ulcerative colitis and osteoporosis.ConclusionsOur data indicate that different combinations of mutations in disease-causing genes may be responsible for the various phenotypes of SAMP strains.
A multistep genomic screen identifies new genes required for repair of DNA double-strand breaks in Saccharomyces cerevisiae
Authors: McKinney Jennifer Summers , Sethi Sunaina , Tripp Jennifer DeMars , Nguyen Thuy N , Sanderson Brian A , Westmoreland James W , Resnick Michael A , Lewis L Kevin 
Published: April 2013

Abstract

Background
Efficient mechanisms for rejoining of DNA double-strand breaks (DSBs) are vital because misrepair of such lesions leads to mutation, aneuploidy and loss of cell viability. DSB repair is mediated by proteins acting in two major pathways, called homologous recombination and nonhomologous end-joining. Repair efficiency is also modulated by other processes such as sister chromatid cohesion, nucleosome remodeling and DNA damage checkpoints. The total number of genes influencing DSB repair efficiency is unknown.

Results
To identify new yeast genes affecting DSB repair, genes linked to gamma radiation resistance in previous genome-wide surveys were tested for their impact on repair of site-specific DSBs generated by in vivo expression of EcoRI endonuclease. Eight members of the RAD52 group of DNA repair genes (RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, MRE11 and XRS2) and 73 additional genes were found to be required for efficient repair of EcoRI-induced DSBs in screens utilizing both MATa and MATα deletion strain libraries. Most mutants were also sensitive to the clastogenic chemicals MMS and bleomycin. Several of the non-RAD52 group genes have previously been linked to DNA repair and over half of the genes affect nuclear processes. Many proteins encoded by the protective genes have previously been shown to associate physically with each other and with known DNA repair proteins in high-throughput proteomics studies. A majority of the proteins (64%) share sequence similarity with human proteins, suggesting that they serve similar functions.

Conclusions
We have used a genetic screening approach to detect new genes required for efficient repair of DSBs in Saccharomyces cerevisiae. The findings have spotlighted new genes that are critical for maintenance of genome integrity and are therefore of greatest concern for their potential impact when the corresponding gene orthologs and homologs are inactivated or polymorphic in human cells.
RIC-3 differentially modulates α4β2 and α7 nicotinic receptor assembly, expression, and nicotine-induced receptor upregulation
Authors: Dau Alejandro , Komal Pragya , Truong Mimi , Morris Geoff , Evans Gareth , Nashmi Raad 
Published: April 2013

AbstractBackgroundRecent work has shown that the chaperoneresistant toinhibitors of acetylcholinesterase (RIC-3) is critical for the folding, maturation and functional expression of a variety of neuronal nicotinic acetylcholine receptors. α7 nicotinic receptors can only assemble and functionally express in select lines of cells, provided that RIC-3 is present. In contrast, α4β2 nicotinic receptors can functionally express in many cell lines even without the presence of RIC-3. Depending on the cell line, RIC-3 has differential effects on α4β2 receptor function – enhancement in mammalian cells but inhibition inXenopusoocytes. Other differences between the two receptor types include nicotine-induced upregulation. When expressed in cell lines, α4β2 receptors readily and robustly upregulate with chronic nicotine exposure. However, α7 nicotinic receptors appear more resistant and require higher concentrations of nicotine to induce upregulation. Could the coexpression of RIC-3 modulate the extent of nicotine-induced upregulation not only for α7 receptors but also α4β2 receptors? We compared and contrasted the effects of RIC-3 on assembly, trafficking, protein expression and nicotine-induced upregulation on both α7 and α4β2 receptors using fluorescent protein tagged nicotinic receptors and Förster resonance energy transfer (FRET) microscopy imaging.ResultsRIC-3 increases assembly and cell surface trafficking of α7 receptors but does not alter α7 protein expression in transfected HEK293T cells. In contrast, RIC-3 does not affect assembly of α4β2 receptors but increases α4 and β2 subunit protein expression. Acute nicotine (30 min exposure) was sufficient to upregulate FRET between α4 and β2 subunits. Surprisingly, when RIC-3 was coexpressed with α4β2 receptors nicotine-induced upregulation was prevented. α7 receptors did not upregulate with acute nicotine in the presence or absence of RIC-3.ConclusionsThese results provide interesting novel data that RIC-3 differentially regulates assembly and expression of different nicotinic receptor subunits. These results also show that nicotine-mediated upregulation of α4β2 receptors can be dynamically regulated by the presence of the chaperone, RIC-3. This could explain a novel mechanism why high affinity α4β2 receptors are upregulated in specific neuronal subtypes in the brain and not others.