bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical and Radiographic Outcomes After Pedicle Subtraction Osteotomy According to Surgeon's Experience
Authors: Choi Ho Yong , Hyun Seung-Jae , Kim Ki-Jeong , Jahng Tae-Ahn , Kim Hyun-Jib 
Published: October 2016

Study Design.
Retrospective case series.

Objective.
The aim of this study was to evaluate and compare the surgical, radiographic, and clinical outcomes of pedicle subtraction osteotomy (PSO) according to surgeon's experience.

Summary of Background Data.
Although PSO has been widely used to correct spinal deformities, it still remains technically demanding procedure with high complications.

Methods.
Comparative analysis of 40 consecutive patients treated with lumbar PSOs was performed. According to time period, the former and latter 20 patients were divided into group 1 and group 2, respectively. Patients’ demographic data, operative, radiographic/clinical outcomes, and complications were compared between the groups.

Results.
Baseline characteristics and preoperative radiographic parameters were not different between the groups. Significant reductions of operative time (569.6 vs. 392.0 minutes, P = 0.000), surgical bleeding (1777.5 vs. 949.5 mL, P = 0.002), and transfused volume of red blood cell (1232.6 vs. 864.1 mL, P = 0.041) in group 2 were observed. Postoperative sagittal vertical axis was significantly different between the groups (40.1 and –3.6 mm, groups 1 and 2, respectively, P = 0.008), and the difference was sustained to the ultimate follow-up (59.4 vs. 13.2 mm, P = 0.003). There was a difference regarding the amount of curve correction by PSO, which was significantly greater in group 2 (25.7° vs. 35.8°, P = 0.023). Intraoperative complications (7 vs. 1, P = 0.019) were significantly lower in group 2. Total complications (20 vs. 10, P = 0.070), postoperative transient neurologic deficit (2 vs. 1), and revision surgery (4 vs. 3) were also lower in group 2, without statistical significance. The amount of the improvement of SRS-22 score was not different between the groups (P = 0.395).

Conclusion.
PSO may be performed in patients with fixed sagittal imbalance with an acceptable rate of complications after about 20 cases. With acquisition of surgical experiences, surgeons could perform PSO more effectively and safely.

Level of Evidence: 4
Lumbar Fusion in Utah Workers’ Compensation Patients
Authors: Cuneo Jessica G. , DeBerard M. Scott , Wheeler Anthony J. 
Published: October 2016

Study Design.
This study was a retrospective-cohort design involving a review of patient medical and cost records and a 2-year postsurgery follow-up outcome survey.

Objective.
To evaluate the functional and cost outcomes associated with recent lumbar fusion surgeries in Utah workers and compare these outcomes with a comparable prior study cohort.

Summary of Background Data.
Lumbar fusion performed on injured workers has dramatically increased over the past 2 decades and this likely coincided with the increased use of more advanced surgical instrumentation. Considering the recent changes in lumbar fusion surgery, there is a need to identify how patient outcomes have changed among injured workers.

Materials and Methods.
Retrospective chart review and 2-year postsurgery follow-up survey of patient outcomes were performed. Postsurgical outcomes for this sample were compared with established norms for back pain patients and a previous cohort of compensated lumbar fusion patients obtained from Workers’ Compensation Fund of Utah.

Results.
The current cohort evidenced a solid fusion rate of 89% and significant increase in the use of surgical instrumentation, particularly titanium fusion cages. Despite increased solid fusion rates, injured workers who have undergone lumbar fusion in Utah demonstrated equivalent and in some cases worse outcomes than those documented a decade ago. Specifically, there were significant increases in back pain dysfunction and narcotic medication usage in the current versus the past cohort. Medical and compensation costs for compensated lumbar fusion patients in Utah also significantly increased since the mid-1990s.

Conclusion.
Over the past decade, injured workers who have undergone lumbar fusion in Utah showed an increase in solid fusion rates and costs without a corresponding improvement in patient outcomes.

Level of Evidence.
3
Necrotizing Infundibular Crystalline Folliculitis (NICF) Induced by Anti-Tumoral Therapies: Report of 2 Cases
Authors: Fattouh Kinda , Collet-Benzaquen Diane , Provensal Anne M. , Desseigne Françoise , Castillo Christine , Combemale Patrick , de la Fouchardière Arnaud 
Published: October 2016

Abstract:
Necrotizing Infundibular Crystalline Folliculitis (NICF) is rare entity of unknown pathogenesis presenting as follicular crystalline papules arising in seborrheic areas. We report 2 cases of NICF in patients under targeted therapy for metastatic adenocarcinoma. In one case, the lesions reappeared cyclically every 3 weeks after each injection and in the other case, lesions persisted until disruption of the continuous oral therapy. Punch-biopsies demonstrated folliculitis with a plugging crystalline material associated with either bacteria or yeast. These are the first descriptions of drug-induced NICF.
Lymphocyte–monocyte ratio at admission predicts possible outcomes in patients with acute-on-chronic liver failure
Authors: Zhu ShaoMing , Waili Yulituzi , Qi XiaoTing , Chen YueMei , Lou YuFeng 
Published: October 2016

Background
The lymphocyte–monocyte ratio (LMR) in the peripheral blood is suggested to be a potential biomarker for predicting the clinical outcomes of several diseases. We aimed to evaluate the relative efficiency of LMR for predicting 3-month mortality in patients with acute-on-chronic liver failure (AoCLF).

Patients and methods
In this study, 74 chronic hepatitis B patients, 90 AoCLF patients, and 70 healthy controls were followed up for 4 months. The primary endpoint was 3-month in-hospital mortality. Hematological and virological parameters as well as liver biochemistry were determined using blood samples ordered upon admission. A panel of clinical and biochemical variables were analyzed for potential associations with outcomes using Cox proportional hazards and multiple regression models.

Results
A significantly lower LMR was detected in AoCLF patients than in healthy controls and chronic hepatitis B groups (both P=0.001). The LMR inversely correlated with model for end-stage liver disease scores, and a lower LMR was associated with increased 3-month mortality. Multivariate analysis suggested that both LMR and model for end-stage liver disease scores were independent predictors of 3-month mortality (P<0.01).

Conclusion
A low LMR measured at admission is predictive of a poor prognosis in AoCLF patients.
Modelling coffee leaf rust risk in Colombia with climate reanalysis data
Authors: Bebber Daniel P. , Castillo Ángela Delgado , Gurr Sarah J. 
Published: October 2016

Many fungal plant diseases are strongly controlled by weather, and global climate change is thus likely to have affected fungal pathogen distributions and impacts. Modelling the response of plant diseases to climate change is hampered by the difficulty of estimating pathogen-relevant microclimatic variables from standard meteorological data. The availability of increasingly sophisticated high-resolution climate reanalyses may help overcome this challenge. We illustrate the use of climate reanalyses by testing the hypothesis that climate change increased the likelihood of the 2008–2011 outbreak of Coffee Leaf Rust (CLR,Hemileia vastatrix) in Colombia. We develop a model of germination and infection risk, and drive this model using estimates of leaf wetness duration and canopy temperature from the Japanese 55-Year Reanalysis (JRA-55). We model germination and infection as Weibull functions with different temperature optima, based upon existing experimental data. We find no evidence for an overall trend in disease risk in coffee-growing regions of Colombia from 1990 to 2015, therefore, we reject the climate change hypothesis. There was a significant elevation in predicted CLR infection risk from 2008 to 2011 compared with other years. JRA-55 data suggest a decrease in canopy surface water after 2008, which may have helped terminate the outbreak. The spatial resolution and accuracy of climate reanalyses are continually improving, increasing their utility for biological modelling. Confronting disease models with data requires not only accurate climate data, but also disease observations at high spatio-temporal resolution. Investment in monitoring, storage and accessibility of plant disease observation data are needed to match the quality of the climate data now available.This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
Ploidy dynamics and evolvability in fungi
Authors: Wertheimer Noa Blutraich , Stone Neil , Berman Judith 
Published: October 2016

Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge
Authors: Gow Neil A. R. , Netea Mihai G. 
Published: October 2016

Fungi cause more than a billion skin infections, more than 100 million mucosal infections, 10 million serious allergies and more than a million deaths each year. Global mortality owing to fungal infections is greater than for malaria and breast cancer and is equivalent to that owing to tuberculosis (TB) and HIV. These statistics evidence fungal infections as a major threat to human health and a major burden to healthcare budgets worldwide. Those patients who are at greatest risk of life-threatening fungal infections include those who have weakened immunity or have suffered trauma or other predisposing infections such as HIV. To address these global threats to human health, more research is urgently needed to understand the immunopathology of fungal disease and human disease susceptibility in order to augment the advances being made in fungal diagnostics and drug development. Here, we highlight some recent advances in basic research in medical mycology and fungal immunology that are beginning to inform clinical decisions and options for personalized medicine, vaccine development and adjunct immunotherapies.This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
Food system consequences of a fungal disease epidemic in a major crop
Authors: Godfray H. Charles J. , Mason-D'Croz Daniel , Robinson Sherman 
Published: October 2016

Fungal diseases are major threats to the most important crops upon which humanity depends. Were there to be a major epidemic that severely reduced yields, its effects would spread throughout the globalized food system. To explore these ramifications, we use a partial equilibrium economic model of the global food system (IMPACT) to study a hypothetical severe but short-lived epidemic that reduces rice yields in the countries affected by 80%. We modelled a succession of epidemic scenarios of increasing severity, starting with the disease in a single country in southeast Asia and ending with the pathogen present in most of eastern Asia. The epidemic and subsequent crop losses led to substantially increased global rice prices. However, as long as global commodity trade was unrestricted and able to respond fast enough, the effects on individual calorie consumption were, to a large part, mitigated. Some of the worse effects were projected to be experienced by poor net-rice importing countries in sub-Saharan Africa, which were not affected directly by the disease but suffered because of higher rice prices. We critique the assumptions of our models and explore political economic pressures to restrict trade at times of crisis. We finish by arguing for the importance of ‘stress-testing’ the resilience of the global food system to crop disease and other shocks.
This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
Mitigating amphibian chytridiomycoses in nature
Authors: Garner Trenton W. J. , Schmidt Benedikt R. , Martel An , Pasmans Frank , Muths Erin , Cunningham Andrew A. , Weldon Che , Fisher Matthew C. , Bosch Jaime 
Published: October 2016

Amphibians across the planet face the threat of population decline and extirpation caused by the disease chytridiomycosis. Despite consensus that the fungal pathogens responsible for the disease are conservation issues, strategies to mitigate their impacts in the natural world are, at best, nascent. Reducing risk associated with the movement of amphibians, non-amphibian vectors and other sources of infection remains the first line of defence and a primary objective when mitigating the threat of disease in wildlife. Amphibian-associated chytridiomycete fungi and chytridiomycosis are already widespread, though, and we therefore focus on discussing options for mitigating the threats once disease emergence has occurred in wild amphibian populations. All strategies have shortcomings that need to be overcome before implementation, including stronger efforts towards understanding and addressing ethical and legal considerations. Even if these issues can be dealt with, all currently available approaches, or those under discussion, are unlikely to yield the desired conservation outcome of disease mitigation. The decision process for establishing mitigation strategies requires integrated thinking that assesses disease mitigation options critically and embeds them within more comprehensive strategies for the conservation of amphibian populations, communities and ecosystems.
This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
Mice deficient ofMycsuper-enhancer region reveal a differential control mechanism between normal and pathological growth
Authors: Dave Kashyap , Sur Inderpreet , Yan Jian , Zhang Jilin , Kaasinen Eevi , Zhong Fan , Blaas Leander , Li Xiaoze , Månsson Robert , Taipale Jussi 
Published: October 2016

AbstractThe gene desert upstream of theMyconcogene on chromosome 8q24 contains susceptibility loci for several major forms of human cancer, including cancers of breast, prostate, and colon. The region shows high conservation between human and mouse and contains multipleMYCenhancers that are activated in tumor cells. However, the role of this region in normal development has not been addressed. Here we show that a 538 kb deletion of the entireMYCupstream super-enhancer region in mice results in 50 to 80% decrease inMYCexpression in multiple tissues. The mice are viable and show no overt phenotype. However, they are resistant to tumorigenesis, and most normal cells isolated from them grow slowly in culture. Consistently, deletion of the 8q24 super-enhancer region perturbs Myc targets only in cultured cells, but notin vivo. These results reveal that only cells whose Myc activity is increased by serum or oncogenic driver mutations depend on the 8q24 super-enhancer region, and indicate that targeting the activity of this element is a promising strategy of cancer chemoprevention and therapy.
Characterization of Dependencies Between Growth and Division in Budding Yeast
Authors: Mayhew Michael B. , Iversen Edwin S. , Hartemink Alexander J. 
Published: October 2016

AbstractCell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeastSaccharomyces cerevisiae, this coordination or ‘size control’ appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G1prior to cell division commitment. Beyond this point, cells are presumed to complete S/G2/M at similar rates and in a size-independent manner. As such, studies of dependence between growth and division have focused on G1. Moreover, coordination between growth and division has commonly been analyzedwithinthe cycle of a single cell without accounting for correlations in growth and division characteristicsbetweencycles of related cells. In a comprehensive analysis of three published time-lapse microscopy datasets, we analyze both intra-and inter-cycle dependencies between growth and division, revisiting assumptions about the coordination between these two processes. Interestingly, we find evidence (1) that S/G2/M durations are systematically longer in daughters than in mothers, (2) of dependencies between S/G2/M and size at budding that echo the classical G1dependencies, and, (3) in contrast with recent bacterial studies, of negative dependencies between size at birth and size accumulated during the cell cycle. In addition, we develop a novel hierarchical model to uncover inter-cycle dependencies, and we find evidence for such dependencies in cells growing in sugar-poor environments. Our analysis highlights the need for experimentalists and modelers to account for new sources of cell-to-cell variation in growth and division, and our model provides a formal statistical framework for the continued study of dependencies between biological processes.
The molecular mechanism of the type IVa pilus motors
Authors: McCallum Matthew , Tammam Stephanie , Khan Ahmad , Burrows Lori L. , Howell P. Lynne 
Published: October 2016

ABSTRACTType IVa pili are protein filaments essential for virulence in many bacterial pathogens; they extend and retract from the surface of bacterial cells to pull the bacteria forward with unprecedented force. They are used for attachment, swarming and twitching motility, biofilm formation, up-regulation of other virulence factors, and natural competence. The pilus is assembled by the motor subcomplex which consists of the inner membrane protein PilC and the cytoplasmic ATPase PilB. How PilB catalyzes this process is unknown, due in part to the lack of high-resolution structural information. Phylogenetic analysis of PilB-like ATPases, including GspE, PilT, BfpD, FlaI, and archaeal GspE2 revealed highly conserved residues essential for function in this family of ATPases. Here we report the structure of the core ATPase domains ofGeobacter metalloreducensPilB bound to ADP and the non-hydrolysable ATP analogue, AMPPNP, at 3.4 and 2.3Å, respectively. Importantly, these structures were determined in non-saturating nucleotide conditions, revealing important differences in nucleotide binding between chains. Analysis of these differences revealed the sequential turnover of nucleotide by the chains, and the corresponding domain movements. Our data indicate a clockwise rotation of movement in PilB, which would support the assembly of a right-handed helical pilus. Conversely, our analysis suggests a counterclockwise rotation in PilT that would enable right-handed pilus disassembly. The proposed model provides insight into how this family of ATPases can power pilus extension and retraction with extraordinary forces.
Ontology-based workflow extraction from texts using word sense disambiguation
Authors: Halioui Ahmed , Valtchev Petko , Diallo Abdoulaye Baniré 
Published: October 2016

AbstractThis paper introduces a method for automatic workflow extraction from texts using Process-Oriented Case-Based Reasoning (POCBR). While the current workflow management systems implement mostly different complicated graphical tasks based on advanced distributed solutions (e.g.cloud computing and grid computation), workflow knowledge acquisition from texts using case-based reasoning represents more expressive and semantic cases representations. We propose in this context, an ontology-based workflow extraction framework to acquire processual knowledge from texts. Our methodology extends classic NLP techniques to extract and disambiguate tasks in texts. Using a graph-based representation of workflows and a domain ontology, our extraction process uses a context-based approach to recognize workflow components : data and control flows. We applied our framework in a technical domain in bioinformatics : i.e. phylogenetic analyses. An evaluation based on workflow semantic similarities on a gold standard proves that our approach provides promising results in the process extraction domain. Both data and implementation of our framework are available in :http://labo.bioinfo.uqam.ca/tgrowler.
Automatic identification of informative regions with epigenomic changes associated to hematopoiesis
Authors: Carrillo-de-Santa-Pau Enrique , Juan David , Pancaldi Vera , Were Felipe , Martin-Subero Ignacio , Rico Daniel , Valencia Alfonso ,   on behalf of The BLUEPRINT Consortium
Published: October 2016

AbstractHematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify forty-two human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability:https://github.com/david-juan/ChromDet