bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of complications associated with standard and totally tubeless percutaneous nephrolithotomy according to modified Clavien grading: A multicenter retrospective study
Authors: Karakoyunlu Nihat , Ekici Musa , Yesil Suleyman , Zengin Kursad , Goktug Goksel , Ozok Ugur 
Published: October 2014

AbstractThe aim of this study was to compare the complications of standard and totally tubeless percutaneous nephrolithotomy (PCNL) based on the modified Clavien complication grading system. We retrospectively evaluated the complications of 290 consecutive patients who had undergone standard or totally tubeless PCNL at four institutes between January 2010 and August 2012 based on the modified Clavien scale. The totally tubeless cases were classified as Group 1 and the cases to which a Malecot re‐entry catheter was applied were classified as Group 2. The postoperative complications were recorded according to the modified Clavien complication grading system. Statistically significant differences were observed only in the first‐degree injury class between the two groups based on the modified Clavien classification. The requirement for blood transfusion and prolonged percutaneous access site leakage were more frequent in Group 2, but these differences were not statistically significant. We also performed a pain evaluation by monitoring postoperative analgesia demands. In Group 1, the analgesic demand rates in the 1st and 6th postoperative hours were 64.6% and 31.5%, respectively. In Group 2, the analgesic demand rates were 87.5% and 58.75% in the 1st and 6th postoperative hours, respectively. The mean ± standard deviation of analgesic doses in the first 6 hours was 0.96 ± 0.7 and 1.46 ± 0.6 in Groups 1 and 2, respectively. These differences were statistically significant. Based on our results, we can conclude that the tubeless technique has fewer complications, improved postoperative patient comfort, shorter hospitalization times, and a reduced need for analgesics, suggesting that tubeless PCNL should be the standard approach. For suitable cases, this technique may be used safely as the standard PCNL approach.
Resolving the polyphyletic nature ofPyricularia(Pyriculariaceae)
Authors: Klaubauf S. , Tharreau D. , Fournier E. , Groenewald J.Z. , Crous P.W. , de Vries R.P. , Lebrun M.-H. 
Published: October 2014

Species ofPyricularia(magnaporthe-like sexual morphs) are responsible for major diseases on grasses.Pyricularia oryzae(sexual morphMagnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, whilePyricularia grisea(sexual morphMagnaporthe grisea) is responsible for foliar diseases ofDigitaria.Magnaporthe salvinii, M. poaeandM. rhizophilaproduce asexual spores that differ from those ofPyricularia sensu strictothat has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation.Magnaporthe salviniiwas recently allocated toNakataea, whileM. poaeandM. rhizophilawere placed inMagnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species ofPyricularia s. str.belong to a monophyletic clade that includes allP. oryzae/P. griseaisolates tested, defining thePyriculariaceae,which is sister to theOphioceraceae, representing two novel families. These clades are clearly distinct from species belonging to theGaeumannomyces pro parte/Magnaporthiopsis/Nakataeageneric complex that are monophyletic and define theMagnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated toMagnaporthaceaeandPyriculariaceae. Pyricularia oryzae/P. griseaisolates cluster into two related clades. Host plants such asEleusine, Oryza,SetariaorTriticumwere exclusively infected by isolates fromP. oryzae, while some host plant such asCenchrus, Echinochloa, Lolium, PennisetumorZingiberwere infected by differentPyriculariaspecies. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate conidium morphology ofP. grisea/P. oryzaeis restricted toPyriculariaandNeopyricularia, while most other genera have obclavate to more ellipsoid 2-septate conidia. Some related genera (Deightoniella, Macgarvieomyces) have evolved 1-septate conidia. Therefore, conidium morphology cannot be used as taxonomic criterion at generic level without phylogenetic data. We also identified 10 novel genera, and seven novel species. A re-evaluation of generic and species concepts withinPyriculariaceaeis presented, and novelties are proposed based on morphological and phylogenetic data.
Summary of the Snowmastodon Project Special VolumeA high-elevation, multi-proxy biotic and environmental record of MIS 6–4 from the Ziegler Reservoir fossil site, Snowmass Village, Colorado, USA
Authors: Miller Ian M. , Pigati Jeffrey S. , Scott Anderson R. , Johnson Kirk R. , Mahan Shannon A. , Ager Thomas A. , Baker Richard G. , Blaauw Maarten , Bright Jordon , Brown Peter M. , Bryant Bruce , Calamari Zachary T. , Carrara Paul E. , Cherney Michael D. , Demboski John R. , Elias Scott A. , Fisher Daniel C. , Gray Harrison J. , Haskett Danielle R. , Honke Jeffrey S. , Jackson Stephen T. , Jiménez-Moreno Gonzalo , Kline Douglas , Leonard Eric M. , Lifton Nathaniel A. , Lucking Carol , McDonald H. Gregory , Miller Dane M. , Muhs Daniel R. , Nash Stephen E. , Newton Cody , Paces James B. , Petrie Lesley , Plummer Mitchell A. , Porinchu David F. , Rountrey Adam N. , Scott Eric , Sertich Joseph J.W. , Sharpe Saxon E. , Skipp Gary L. , Strickland Laura E. , Stucky Richard K. , Thompson Robert S. , Wilson Jim 
Published: October 2014

AbstractIn North America, terrestrial records of biodiversity and climate change that span Marine Oxygen Isotope Stage (MIS) 5 are rare. Where found, they provide insight into how the coupling of the ocean–atmosphere system is manifested in biotic and environmental records and how the biosphere responds to climate change. In 2010–2011, construction at Ziegler Reservoir near Snowmass Village, Colorado (USA) revealed a nearly continuous, lacustrine/wetland sedimentary sequence that preserved evidence of past plant communities between ~140 and 55 ka, including all of MIS 5. At an elevation of 2705 m, the Ziegler Reservoir fossil site also contained thousands of well-preserved bones of late Pleistocene megafauna, including mastodons, mammoths, ground sloths, horses, camels, deer, bison, black bear, coyotes, and bighorn sheep. In addition, the site contained more than 26,000 bones from at least 30 species of small animals including salamanders, otters, muskrats, minks, rabbits, beavers, frogs, lizards, snakes, fish, and birds. The combination of macro- and micro-vertebrates, invertebrates, terrestrial and aquatic plant macrofossils, a detailed pollen record, and a robust, directly dated stratigraphic framework shows that high-elevation ecosystems in the Rocky Mountains of Colorado are climatically sensitive and varied dramatically throughout MIS 5.
Neck Pain following Laminoplasty
Authors: Mesfin Addisu , Park Moon-Soo , Piyaskulkaew Chaiwat , Chuntarapas Tapanut , Song Kwang Sup , Kim Han Jo , Riew K. Daniel 
Published: October 2014

Study Design Retrospective evaluation of prospectively collected data. Objective To compare preoperative and postoperative neck pain following laminoplasty using the Neck Disability Index (NDI). Methods Seventy-two patients undergoing laminoplasty from 2006 to 2009 at a single institution were identified. Thirty-four patients with a minimum 1-year follow-up who completed preoperative, 6-week, and 1-year postoperative NDI questionnaires were enrolled. Demographic data and surgical data including estimated blood loss (EBL), length of surgery, number of laminoplasty levels, complications, and length of hospitalization were collected. Results Mean age was 62 years (range: 34 to 88), mean follow-up was 17 months (range: 12 to 31), and there were 21 men and 13 women. Diagnoses were cervical spondylotic myelopathy ( n = 26), ossification of the posterior longitudinal ligament ( n = 6), and central cord syndrome ( n = 2). Mean EBL was 120 mL (range: 50 to 200), and mean surgical time was 152 minutes (range: 70 to 240). Average number of laminoplasty levels was 3 (range: 1 to 5). The open door technique was used, and 24/34 (71%) did not have laminoplasty at C3 and C7. No intraoperative complications were noted, and average hospital stay was 1.6 days (range: 1 to 7). Significant improvement in NDI total score was noted at 1 year ( p < 0.002) and in NDI pain score at 6 weeks ( p < 0.028) and 1 year ( p < 0.007) postoperatively. Conclusions Patients having laminoplasty experienced significant improvement in NDI pain subscore and NDI total scores at a minimum of 1 year postoperatively.
Bone Scans Are Reliable for the Identification of Lumbar Disk and Facet Pathology
Authors: Malham Gregory M. , Parker Rhiannon M. , Ballok Zita E. , Goss Ben , Diwan Ashish D. , Uribe Juan S. 
Published: October 2014

Study Design Surgeon survey. Objective To evaluate the reliability of bone single-photon emission computed tomography (SPECT) versus bone SPECT images co-registered with computed tomography (bone SPECT-CT) by analyzing interobserver agreement for identification of the anatomical location of technetium99m-labeled oxidronate uptake in the lumbar disk and/or facet joint. Methods Seven spine surgeons interpreted 20 bone scans: 10 conventional black-and-white tomograms (bone SPECT) and 10 color-graded bone SPECT-CT scans. Each surgeon was asked to identify the location of any diagnostically relevant uptake in the disk and/or facet joint between L1 and S1. Reliability was evaluated using the free-marginal kappa statistic, and the level of agreement was assessed using the Landis and Koch interpretation. Results Conventional bone SPECT scans and bone SPECT-CT scans were reliable for the identification of diagnostically relevant uptake, with bone SPECT-CT having higher reliability (kappa = 0.72) than bone SPECT alone (0.59). Bone SPECT and bone SPECT-CT were also reliable in identifying disk pathology, with kappa values of 0.72 and 0.81, respectively. However, bone SPECT-CT was more reliable (0.81) than bone SPECT (0.60) when identifying facet disease. Conclusions For the identification of disk pathology, it is reasonable to use either conventional bone SPECT or bone SPECT-CT; however, bone SPECT-CT is more reliable for facet joint pathology.
First Confirmed Metastatic Adamantinoma of the Spine: Case Report and Literature Review
Authors: Morales Ciancio Ruben A. , Gasbarrini Alessandro , Boriani Stefano , Gambarotti Marco 
Published: October 2014

Study Design Case report and literature review. Objective To present the first case of metastatic adamantinoma of the spine with immunohistochemical confirmation and an updated literature review. Summary of Background Data Spinal metastatic disease could be difficult to diagnose because of the multiple differential diagnoses involved. Spinal surgeons must be aware of unusual primary extra-axial tumors that metastasize to the spine because in certain cases the primary surgery must determine the prognosis of this lesion. Methods We present a fully documented case of a middle-aged man with tibial adamantinoma who developed spine metastasis, confirmed by immunohistochemistry. A literature review was done. Results Based on clinical, imaging, and pathology findings, we provide evidence for the first proven metastatic adamantinoma of the spine, adding this condition to the long list of differential diagnoses of secondary spinal disease. Conclusions Adamantinoma is a very rare bone tumor representing ∼1% of primary bone tumors. Spinal metastatic adamantinoma with immunohistochemical confirmation has not been described previously. Due to the lack of specific image findings or serum markers and multiple differential diagnoses, biopsy with immunohistochemical confirmation is mandatory, because “en block resection” might prove to be curative treatment.
Fully quantum state-resolved inelastic scattering of NO(X) + Kr: Differential cross sections and product rotational alignment
Authors: Brouard M. , Chadwick H. , Gordon S. D. S. , Hornung B. , Nichols B. , Kłos J. , Aoiz F. J. , Stolte S. 
Published: October 2014

Fully quantum state selected and resolved inelastic scattering of NO(X) by krypton has been investigated. Initial Λ-doublet state selection is achieved using an inhomogeneous hexapole electric field. Differential cross sections and even-moment polarization dependent differential cross sections have been obtained at a collision energy of 514 cm−1 for both spin-orbit and parity conserving and changing collisions. Experimental results are compared with those obtained from quantum scattering calculations and are shown to be in very good agreement. Hard shell quantum scattering calculations are also performed to determine the effects of the different parts of the potential on the scattering dynamics. Comparisons are also made with the NO(X) + Ar system.
The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes
Authors: Mérai Zsuzsanna , Chumak Nina , García-Aguilar Marcelina , Hsieh Tzung-Fu , Nishimura Toshiro , Schoft Vera K. , Bindics János , Ślusarz Lucyna , Arnoux Stéphanie , Opravil Susanne , Mechtler Karl , Zilberman Daniel , Fischer Robert L. , Tamaru Hisashi 
Published: October 2014

Significance
Centromeres are the fundamental unit required for segregation of chromosomes during mitosis and meiosis, and they are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). In contrast to the relatively well-known process of de novo assembly of CenH3 at centromeres, little is known of how CenH3 is actively removed, leading to centromere disassembly, an essential biological process during the life of a cell. This study describes the process of centromere disassembly, demonstrating that it occurs via an active, proteolytic mechanism, which is also linked to major changes in chromosome dynamics: chromatin decondensation and bulk rRNA gene activation.
Antihypertensive Drug Class and Adherence: An Electronic Monitoring Study
Authors: Moise Nathalie , Schwartz Joseph , Bring Rachel , Shimbo Daichi , Kronish Ian M. 
Published: October 2014

Abstract

BACKGROUND
Medication adherence is essential to optimizing blood pressure (BP) control. Prior research has demonstrated differences in pharmacy refill patterns according to antihypertensive drug class. No prior study has assessed the association between drug class and day-to-day adherence.

METHODS
Between 2011 and 2014, we enrolled a convenience sample of 149 patients with persistently uncontrolled hypertension from two inner-city clinics and concurrently measured adherence of up to four antihypertensive medications using electronic pillboxes during the interval between two primary care visits. The main outcome was mean percent of days adherent to each drug. Mixed effects regression analyses were used to assess the association between drug class and adherence adjusting for age, gender, race, ethnicity, education, health insurance, coronary artery disease, heart failure, chronic kidney disease, diabetes, number of medications, days monitored, and dosing frequency.

RESULTS
The mean age was 64 years; 72% women, 75% Hispanic, 88% prescribed ≥1 BP medication. In unadjusted analyses, adherence was lower for beta-blockers (70.9%) compared to angiotensin receptor blocking agents (75.0%, P = 0.11), diuretics (75.9%, P &lt; 0.001), calcium channel blockers (77.6%, P &lt; 0.001) and angiotensin-converting enzyme inhibitors (78.0%, P &lt; 0.0001). In the adjusted analysis, only dosing frequency (P = 0.0001) but not drug class (P = 0.71) was associated with medication adherence.

CONCLUSIONS
Antihypertensive drug class was not associated with electronically measured adherence after accounting for dosing frequency amongst patients with uncontrolled hypertension. Low adherence to beta-blockers may have been due to the common practice of prescribing multiple daily dosing. Providers may consider using once daily formulations to optimize adherence and should assess adherence among all treated patients with uncontrolled hypertension.
MP-GeneticSynth: inferring biological network regulations from time series
Authors: Castellini Alberto , Paltrinieri Daniele , Manca Vincenzo 
Published: October 2014

Summary: MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis.
Availability and implemention: Source code, binaries, documentation (including quick start guide and videos) and case studies are freely available at http://mplab.sci.univr.it/plugins/mpgs/index.html.
Contact: castellini@mpimp-golm.mpg.de
iDoComp: a compression scheme for assembled genomes
Authors: Ochoa Idoia , Hernaez Mikel , Weissman Tsachy 
Published: October 2014

Motivation: With the release of the latest next-generation sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing a Human has dropped to a mere $4000. Thus we are approaching a milestone in the sequencing history, known as the $1000 genome era, where the sequencing of individuals is affordable, opening the doors to effective personalized medicine. Massive generation of genomic data, including assembled genomes, is expected in the following years. There is crucial need for compression of genomes guaranteed of performing well simultaneously on different species, from simple bacteria to humans, which will ease their transmission, dissemination and analysis. Further, most of the new genomes to be compressed will correspond to individuals of a species from which a reference already exists on the database. Thus, it is natural to propose compression schemes that assume and exploit the availability of such references.
Results: We propose iDoComp, a compressor of assembled genomes presented in FASTA format that compresses an individual genome using a reference genome for both the compression and the decompression. In terms of compression efficiency, iDoComp outperforms previously proposed algorithms in most of the studied cases, with comparable or better running time. For example, we observe compression gains of up to 60% in several cases, including H.sapiens data, when comparing with the best compression performance among the previously proposed algorithms.
Availability: iDoComp is written in C and can be downloaded from: http://www.stanford.edu/~iochoa/iDoComp.html (We also provide a full explanation on how to run the program and an example with all the necessary files to run it.).
Contact: iochoa@stanford.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
RETRACTED: LFQC: a lossless compression algorithm for FASTQ files
Authors: Pathak Sudipta , Rajasekaran Sanguthevar 
Published: October 2014

Abstract

Motivation
Next-generation sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole-genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large Fastq files using innovative compression techniques.

Results
We introduce a new lossless non-reference-based fastq compression algorithm named lossless FastQ compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz, fqzcomp, G-SQZ, SCALCE, Quip, DSRC, DSRC-LZ etc. This comparison reveals that our algorithm achieves better compression ratios. The improvement obtained is up to 225%. For example, on one of the datasets (SRR065390_1), the average improvement (over all the algorithms compared) is 74.62%.

Availability and implementation
The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/FastqPrograms.zip.
Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization
Authors: Lekschas Fritz , Stachelscheid Harald , Seltmann Stefanie , Kurtz Andreas 
Published: October 2014

Summary: Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to the subcellular level and visualising expression profiles by means of semantically annotated anatomical illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users.
Availability and implementation: The Semantic Body Browser is a JavaScript web application that is freely available at http://sbb.cellfinder.org. The source code is provided on https://github.com/flekschas/sbb.
Contact: sbb@cellfinder.org
A novel representation of genomic sequences for taxonomic clustering and visualization by means of self-organizing maps
Authors: Delgado Soledad , Morán Federico , Mora Antonio , Merelo Juan Julián , Briones Carlos 
Published: October 2014

Motivation: Self-organizing maps (SOMs) are readily available bioinformatics methods for clustering and visualizing high-dimensional data, provided that such biological information is previously transformed to fixed-size, metric-based vectors. To increase the usefulness of SOM-based approaches for the analysis of genomic sequence data, novel representation methods are required that automatically and bijectively transform aligned nucleotide sequences into numeric vectors, dealing with both nucleotide ambiguity and gaps derived from sequence alignment.Results: Six different codification variants based on Euclidean space, just like SOM processing, have been tested using two SOM models: the classical Kohonen’s SOM and growing cell structures. They have been applied to two different sets of sequences: 32 sequences of small sub-unit ribosomal RNA from organisms belonging to the three domains of life, and 44 sequences of the reverse transcriptase region of the pol gene of human immunodeficiency virus type 1 belonging to different groups and sub-types. Our results show that the most important factor affecting the accuracy of sequence clustering is the assignment of an extra weight to the presence of alignment-derived gaps. Although each of the codification variants shows a different level of taxonomic consistency, the results are in agreement with sequence-based phylogenetic reconstructions and anticipate a broad applicability of this codification method.Contact: sole@eui.upm.esSupplementary information: Supplementary Data are available at Bioinformatics online.