bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fungi associated with drug recalls and rare disease outbreaks
Authors: Ahearn Donald G , Doyle Stulting R 
Published: August 2014

AbstractFungi rarely cause disease outbreaks associated with use of microbe-contaminated drugs. These rare episodes typically involve a restricted spectrum of common environmental species with relatively low virulence, rather than classical pathogens. Review of data involving over-the-counter contact lens solutions and prescription drug-related recalls revealed six episodes during the past decade with significant adverse health and financial impact (including loss of vision and death). Contaminations involved fungi mostly identified with the genera Aspergillus, Exserohilum, Fusarium, Paecilomyces, and Rhizopus. These organisms are noted for their capacity to produce resistant morphotypes (chlamydoconidia, ascospores) under various adverse conditions, generally with temperature survival/tolerances markedly in excess of maximal growth temperatures. High constituent levels of melanin, trehalose and heat-shock proteins facilitate differential survival of morphotypes following exposures to toxic chemicals and temperatures above 80 °C. Adverse environmental factors that induce resistant morphotypes are suggested to occur more readily in situ than during in vitro testing. Rare unexplained, sporadic drug contamination episodes with select thermotolerant fungi may relate, in part, to resistant dormant stages.
Fatty Acid Profiles of Virgin Olive Oils from the Five Olive‐Growing Zones of Extremadura (Spain)
Authors: Martínez Manuel , Fuentes Manuel , Franco Nieves , Sánchez Jacinto , de Miguel Concepción 
Published: August 2014

AbstractIn this study, 278 samples of virgin olive oil from 40 mills belonging to five olive‐growing zones of Extremadura were evaluated according to their fatty acid composition. An analysis of variance of the fatty acid contents, and their principal group subtotals and ratios revealed significant differences at the 95 % confidence level between zones. Means were compared using Tukey's HSD test (p < 0.05). A discriminant analysis, taking the zone as the grouping variable and the different fatty acids and their ratios as independent variables, explained nearly 90 % of the variance with the first two functions. The model correctly classified 88.8 % of the analysed samples into their proper olive‐growing zone. Validation against an extra test set of 30 samples resulted in 90 % being correctly classified; the results of the discriminant analysis were therefore considered to be validated. A two‐dimensional graphical representation of the different groups studied using the first two resulting canonical discriminant functions clearly showed the Sierra Norte of Cáceres and Vegas del Guadiana each to be clearly separated from the rest and from each other, while the other three zones—Siberia, Serena and Tierra de Barros—overlapped considerably.
Early life arsenic exposure and brain dopaminergic alterations in rats
Authors: Chandravanshi Lalit P. , Shukla Rajendra K. , Sultana Sarwat , Pant Aditya B. , Khanna Vinay K. 
Published: August 2014

AbstractRecently, we found that early life exposure to arsenic at low doses resulted to cause brain cholinergic deficits and exhibited a trend of recovery on withdrawal of arsenic exposure. In continuation to this, the present study has been carried out to assess the impact of low level arsenic exposure on brain dopaminergic system and associated behavior in developing rats and investigate if neurobehavioral changes are recovered or persistent. Early life exposure (PD22–PD59) to arsenic (2 or 4 mg/kg body weight, p.o.) in rats resulted to increase the motor activity on PD60, compared to controls. The hyperactivity in arsenic exposed rats was found to be linked with increase in the binding of DA‐D2 receptors (38%, 56%), mRNA expression of DAR‐D2 receptor gene (68%, 97%) and expression of tyrosine hydroxylase protein (1.93, 2.73‐fold) in the corpus striatum as compared to controls on PD60. Exposure to arsenic enhanced generation of ROS (47%, 84%) and was associated with decrease in the mitochondrial membrane potential (13.3%, 15.33%), activity of mitochondrial complexes and increased oxidative stress. Disruption in the expression of pro‐apoptotic, anti‐apoptotic and stress marker proteins was also distinct in the corpus striatum of arsenic exposed rats. The severity of changes in the behavioral and neurochemical endpoints were found to persist in rats exposed to arsenic at high dose and exhibited a trend of recovery at low dose on withdrawal of arsenic exposure on PD90. Early life arsenic exposure appears to be critical and vulnerable as development of dopamine receptors continues during this period.
Reliability of Magnetic Resonance Imaging Assessment of Rotator Cuff: The ROW Study
Authors: Jain Nitin B. , Collins Jamie , Newman Joel S. , Katz Jeffrey N. , Losina Elena , Higgins Laurence D. 
Published: August 2014

AbstractBackgroundPhysiatrists encounter patients with rotator cuff disorders, and imaging is frequently an important component of their diagnostic assessment. However, there is a paucity of literature on the reliability of magnetic resonance imaging (MRI) assessment between shoulder specialists and musculoskeletal radiologists.ObjectiveWe assessed inter‐ and intrarater reliability of MRI characteristics of the rotator cuff.DesignCross‐sectional secondary analyses in a prospective cohort study.SettingAcademic tertiary care centers.PatientsSubjects with shoulder pain were recruited from orthopedic and physiatry clinics.MethodsTwo shoulder‐fellowship–trained physicians (a physiatrist and a shoulder surgeon) jointly performed a blinded composite MRI review by consensus of 31 subjects with shoulder pain. Subsequently, MRI was reviewed by one fellowship‐trained musculoskeletal radiologist.Main Outcome MeasurementsWe calculated the Cohen kappa coefficients and percentage agreement among the 2 reviews (composite review of 2 shoulder specialists versus that of the musculoskeletal radiologist). Intrarater reliability was assessed among the shoulder specialists by performing a repeated blinded composite MRI review. In addition to this repeated composite review, only one of the physiatry shoulder specialists performed an additional review.ResultsInterrater reliability (shoulder specialists versus musculoskeletal radiologist) was substantial for the presence or absence of tear (kappa 0.90 [95% confidence interval {CI}, 0.72‐1.00]), tear thickness (kappa 0.84 [95% CI, 0.70‐0.99]), longitudinal size of tear (kappa 0.75 [95% CI, 0.44‐1.00]), fatty infiltration (kappa 0.62 [95% CI, 0.45‐0.79]), and muscle atrophy (kappa 0.68 [95% CI, 0.50‐0.86]). There was only fair interrater reliability of the transverse size of tear (kappa 0.20 [95% CI, 0.00‐0.51]). The kappa for intrarater reliability was high for tear thickness (0.88 [95% CI, 0.72‐1.00]), longitudinal tear size (0.61 [95% CI, 0.22‐0.99]), fatty infiltration (0.89 [95% CI, 0.80,‐0.98]), and muscle atrophy (0.87 [95% CI, 0.76‐0.98]). Intrarater reliability for the individual shoulder specialist was similar to that of the composite reviews.ConclusionsThere was high interrater and intrarater reliability for most findings on shoulder MRI. Analysis of our data supports the reliability of MRI assessment by shoulder specialists for rotator cuff disorders.
Modified midfacial translocation for access to ventral skull base tumours
Authors: Hussain A , Shakeel M , Vallamkondu V , Kamel M 
Published: August 2014

AbstractObjective:To describe our technical modifications of midfacial translocation for access to the nasopharynx, and anterior, central and lateral skull base.Design:Retrospective chart review of a prospective case series.Setting:Department of Otolaryngology-Head and Neck Surgery, Aberdeen Royal Infirmary, Scotland, UK.Methods:Along with demographics, other parameters studied were adequacy of exposure, completeness of resection, aesthetic outcome and complications. Our main outcome measures included adequacy of exposure, partial or total resection of tumour, aesthetic outcome, and complications related to surgical technique.Results:A total of 48 patients underwent modified midfacial translocation at our institution for nasopharyngeal, parapharyngeal, and anterior, central and lateral skull base tumours. In all cases, the exposure was deemed to be adequate. Two patients developed wound dehiscence in previously irradiated fields. Other incisions healed very well and the aesthetic outcome was regarded as satisfactory.Conclusion:Modified midfacial translocation is based on the principle of temporary craniofacial disassembly for access to the skull base. Our modifications offer adequate access and a better aesthetic outcome. All incisions are placed through the aesthetic sub units of the nose with preservation of the lip. Preservation of the bony piriform aperture prevents airway compromise.
Thoracic Spondylodiscitis Caused by Methicillin-resistant Staphylococcus aureus as a Superinfection of Pulmonary Tuberculous Granuloma in an Immunocompetent Patient: A Case Report
Authors: Donnarumma Pasquale , Tarantino Roberto , Palmarini Valeria , De Giacomo Tiziano , Delfini Roberto 
Published: August 2014

Study Design Case report. Objective To describe a very rare case of an immunocompetent man who underwent surgery for thoracic spondylodiscitis caused by methicillin-resistant Staphylococcus aureus (MRSA) that developed as a superinfection of a pulmonary tuberculous granuloma. Methods Posterior decompression and pedicle screw vertebral fixation were followed by T5–T6 anterior somatotomy with implant of an expandable mesh and lateral plating as symptoms worsened. During the anterior approach, an atypical resection of the left lower lobe was also performed. Results A tuberculous granuloma was detected on histology. Ziehl-Neelsen stain confirmed the diagnosis. Culture also detected MRSA. Conclusions Early medical management is the first choice for spondylodiscitis to eradicate the infection and alleviate pain. Immobilization of the affected spine segments can protect the patient from vertebral collapse and from the appearance of neurologic deficits. Surgery is suggested if there are compressive effects on the spinal cord, spinal epidural abscess, vertebral collapse, and deformity. We decided to remove the abscess and to restore the anterior column using an anterior approach. Moreover, in this case, an anterior approach allowed us to identify the etiology of the lesion and to determine the best chemotherapy regimen.
Theaflavins enhance intestinal barrier of Caco-2 Cell monolayers through the expression of AMP-activated protein kinase-mediated Occludin, Claudin-1, and ZO-1
Authors: Park Ha-Young , Kunitake Yuri , Hirasaki Naoto , Tanaka Mitsuru , Matsui Toshiro 
Published: August 2014

Abstract
We investigated the effect of theaflavins (TFs) on membrane barrier of Caco-2 cells. For fluorescein-transport experiments, the apparent permeability (Papp) of fluorescein in Caco-2 cells pretreated with 20 μM TFs were significantly decreased compared with that in untreated cells. Although the respective monomeric catechins did not show any Papp reduction, purpurogallin pretreatment resulted in a significant Papp reduction similar to that of TF-3′-O-gallate (TF3′G) pretreatment. This indicates that the benzotropolone moiety may play a crucial role in the Papp reduction or tight junction (TJ)-closing effect induced by TFs. In TF-3′-O-gallate-pretreated Caco-2 cells, fluorescein transport was completely restored by compound C (AMPK inhibitor). In addition, TF3′G significantly increased both the mRNA and protein expression of TJ-related proteins (occludin, claudin-1, and ZO-1) as well as the phosphorylation of AMPK. It was, thus, concluded that TFs could enhance intestinal barrier function by increasing the expression of TJ-related proteins through the activation of AMPK in Caco-2 cells.
Frameshift alignment: statistics and post-genomic applications
Authors: Sheetlin Sergey L. , Park Yonil , Frith Martin C. , Spouge John L. 
Published: August 2014

Abstract
Motivation: The alignment of DNA sequences to proteins, allowing for frameshifts, is a classic method in sequence analysis. It can help identify pseudogenes (which accumulate mutations), analyze raw DNA and RNA sequence data (which may have frameshift sequencing errors), investigate ribosomal frameshifts, etc. Often, however, only ad hoc approximations or simulations are available to provide the statistical significance of a frameshift alignment score.
Results: We describe a method to estimate statistical significance of frameshift alignments, similar to classic BLAST statistics. (BLAST presently does not permit its alignments to include frameshifts.) We also illustrate the continuing usefulness of frameshift alignment with two ‘post-genomic’ applications: (i) when finding pseudogenes within the human genome, frameshift alignments show that most anciently conserved non-coding human elements are recent pseudogenes with conserved ancestral genes; and (ii) when analyzing metagenomic DNA reads from polluted soil, frameshift alignments show that most alignable metagenomic reads contain frameshifts, suggesting that metagenomic analysis needs to use frameshift alignment to derive accurate results.
Availability and implementation: The statistical calculation is available in FALP ( http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/index/software.html ), and giga-scale frameshift alignment is available in LAST ( http://last.cbrc.jp/falp ).
Contact: spouge@ncbi.nlm.nih.gov or martin@cbrc.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
Authors: Keane Michael , Craig Thomas , Alföldi Jessica , Berlin Aaron M. , Johnson Jeremy , Seluanov Andrei , Gorbunova Vera , Di Palma Federica , Lindblad-Toh Kerstin , Church George M. , de Magalhães João Pedro 
Published: August 2014

Abstract
Motivation: The naked mole rat ( Heterocephalus glaber ) is an exceptionally long-lived and cancer-resistant rodent native to East Africa. Although its genome was previously sequenced, here we report a new assembly sequenced by us with substantially higher N50 values for scaffolds and contigs.
Results: We analyzed the annotation of this new improved assembly and identified candidate genomic adaptations which may have contributed to the evolution of the naked mole rat’s extraordinary traits, including in regions of p53, and the hyaluronan receptors CD44 and HMMR (RHAMM). Furthermore, we developed a freely available web portal, the Naked Mole Rat Genome Resource ( http://www.naked-mole-rat.org ), featuring the data and results of our analysis, to assist researchers interested in the genome and genes of the naked mole rat, and also to facilitate further studies on this fascinating species.
Availability and implementation: The Naked Mole Rat Genome Resource is freely available online at http://www.naked-mole-rat.org . This resource is open source and the source code is available at https://github.com/maglab/naked-mole-rat-portal .
Contact: jp@senescence.info
Protein–protein binding affinity prediction from amino acid sequence
Authors: Yugandhar K. , Gromiha M. Michael 
Published: August 2014

Abstract
Motivation: Protein–protein interactions play crucial roles in many biological processes and are responsible for smooth functioning of the machinery in living organisms. Predicting the binding affinity of protein–protein complexes provides deep insights to understand the recognition mechanism and identify the strong binding partners in protein–protein interaction networks.
Results: In this work, we have collected the experimental binding affinity data for a set of 135 protein–protein complexes and analyzed the relationship between binding affinity and 642 properties obtained from amino acid sequence. We noticed that the overall correlation is poor, and the factors influencing affinity depends on the type of the complex based on their function, molecular weight and binding site residues. Based on the results, we have developed a novel methodology for predicting the binding affinity of protein–protein complexes using sequence-based features by classifying the complexes with respect to their function and predicted percentage of binding site residues. We have developed regression models for the complexes belonging to different classes with three to five properties, which showed a correlation in the range of 0.739–0.992 using jack-knife test. We suggest that our approach adds a new aspect of biological significance in terms of classifying the protein–protein complexes for affinity prediction.
Availability and implementation: Freely available on the Web at http://www.iitm.ac.in/bioinfo/PPA_Pred/
Contact: gromiha@iitm.ac.in
Supplementary information: Supplementary data are available at Bioinformatics online.
Human structural proteome-wide characterization of Cyclosporine A targets
Authors: Hu Gang , Wang Kui , Groenendyk Jody , Barakat Khaled , Mizianty Marcin J. , Ruan Jishou , Michalak Marek , Kurgan Lukasz 
Published: August 2014

Abstract
Motivation: Off-target interactions of a popular immunosuppressant Cyclosporine A (CSA) with several proteins besides its molecular target, cyclophilin A, are implicated in the activation of signaling pathways that lead to numerous side effects of this drug.
Results: Using structural human proteome and a novel algorithm for inverse ligand binding prediction, ILbind, we determined a comprehensive set of 100+ putative partners of CSA. We empirically show that predictive quality of ILbind is better compared with other available predictors for this compound. We linked the putative target proteins, which include many new partners of CSA, with cellular functions, canonical pathways and toxicities that are typical for patients who take this drug. We used complementary approaches (molecular docking, molecular dynamics, surface plasmon resonance binding analysis and enzymatic assays) to validate and characterize three novel CSA targets: calpain 2, caspase 3 and p38 MAP kinase 14. The three targets are involved in the apoptotic pathways, are interconnected and are implicated in nephrotoxicity.
Contact: lkurgan@ece.ualberta.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Merging of multi-string BWTs with applications
Authors: Holt James , McMillan Leonard 
Published: August 2014

Abstract
Motivation : The throughput of genomic sequencing has increased to the point that is overrunning the rate of downstream analysis. This, along with the desire to revisit old data, has led to a situation where large quantities of raw, and nearly impenetrable, sequence data are rapidly filling the hard drives of modern biology labs. These datasets can be compressed via a multi-string variant of the Burrows–Wheeler Transform (BWT), which provides the side benefit of searches for arbitrary k -mers within the raw data as well as the ability to reconstitute arbitrary reads as needed. We propose a method for merging such datasets for both increased compression and downstream analysis.
Results : We present a novel algorithm that merges multi-string BWTs in O(LCS×N) time where LCS is the length of their longest common substring between any of the inputs, and N is the total length of all inputs combined (number of symbols) using O(N×log2(F)) bits where F is the number of multi-string BWTs merged. This merged multi-string BWT is also shown to have a higher compressibility compared with the input multi-string BWTs separately. Additionally, we explore some uses of a merged multi-string BWT for bioinformatics applications.
Availability and implementation : The MSBWT package is available through PyPI with source code located at https://code.google.com/p/msbwt/ .
Contact : holtjma@cs.unc.edu
Local Fields of the Hippocampus: More than Meets the Eye
Authors: Agarwal Gautam 
Published: August 2014

A standard methodology in systems neuroscience is to establish correlations between the brain and the world. These correlations have been robustly observed when probing the activity of single neurons. For example, there are cells that activate vigorously when subjects are presented with images of certain celebrities (e.g. the “Jennifer Aniston” neuron, Quiroga et al., 2005). While single neuron measurements provide remarkable insights into the functional specificity of different brain areas, it remains unclear how single cell activity arises from, and contributes to, the collective activity of brain networks. New technologies allow for the simultaneous recording of spikes from hundreds of cells, yet we are still far from observing entire neuronal circuits in action.An alternative approach in monitoring neuronal populations is to measure local field potentials (LFPs). These potentials arise from the coordinated activity of thousands of nearby neurons. LFPs often exhibit oscillations of various frequencies, which correlate with different states of awareness, such as alertness, relaxation, or drowsiness. However, establishing correlations between LFPs and specific behavioral events can be challenging, because the contributions of different neurons to the LFP usually cannot be distinguished. In this chapter, we examine LFPs recorded from the rat hippocampus. At first glance, these LFPs appear to bear little relation to the subject’s changing environment. However, through appropriate signal processing, we find that carried in the structure of the LFP is a remarkably precise stream of information (Agarwal et al., 2014).
Neuronal control of locomotor handedness in Drosophila
Authors: Buchanan Sean M. , Kain Jamey S. , de Bivort Benjamin L. 
Published: August 2014

AbstractHandedness in humans – better performance using either the left or right hand – is personally familiar, moderately heritable1, and regulated by many genes2, including those involved in general body symmetry3. But behavioral handedness, i.e. lateralization, is a multifaceted phenomenon. For example, people display clockwise or counter-clockwise biases in their walking behavior that is uncorrelated to their hand dominance4,5, and lateralized behavioral biases have been shown in species as disparate as mice (paw usage6), octopi (eye usage7), and tortoises (side rolled on during righting8). However, the mechanisms by which asymmetries are instilled in behavior are unknown, and a system for studying behavioral handedness in a genetically tractable model system is needed. Here we show thatDrosophila melanogasterflies exhibit striking variability in their left-right choice behavior during locomotion. Very strongly biased "left-handed" and "right-handed" individuals are common in every line assayed. The handedness of an individual persists for its lifetime, but is not passed on to progeny, suggesting that mechanisms other than genetics determine individual handedness. We use theDrosophilatransgenic toolkit to map a specific set of neurons within the central complex that regulates the strength of behavioral handedness within a line. These findings give insights into choice behaviors and laterality in a simple model organism, and demonstrate that individuals from isogenic populations reared under experimentally identical conditions nevertheless display idiosyncratic behaviors.