bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lymph node metastasis can be determined by just tumor depth and lymphovascular invasion in early gastric cancer patients after endoscopic submucosal dissection
Authors: Goto Atsushi , Nishikawa Jun , Hideura Eizaburou , Ogawa Ryo , Nagao Misato , Sasaki Sho , Kawasato Ryo , Hashimoto Shinichi , Okamoto Takeshi , Ogihara Hiroyuki , Hamamoto Yoshihiko , Sakaida Isao 
Published: October 2017

Purpose
Endoscopic submucosal dissection (ESD) is a minimally invasive treatment for early gastric cancer (EGC) with negligible risk of lymph node metastasis (LNM). When a patient is determined to have noncurative resection after ESD, additional surgical resection with lymph node dissection is recommended. Previous studies report that LNM is found in about 10% of these patients. It may be possible to avoid unnecessary surgical resection by selecting patients properly. We aimed to clarify the risk factors associated with LNM in EGC patients who underwent ESD and to develop a highly accurate diagnostic algorithm for LNM.

Patients and methods
Among 1005 patients with EGC who underwent ESD, 423 patients who could be followed up for more than 3 years after treatment or who underwent additional surgical resection were examined. We used the leave-one-out method to explore the combination of predictive factors of LNM and differentiated LNM by a unique classifier.

Results
Curative resection was achieved in 322 patients, whereas noncurative resection was achieved in 101 patients. In the noncurative resection group, LNM occurred in eight patients with additional surgical resection and one patient during follow-up. The combination of depth of invasion, lymphatic, and venous invasion showed the highest diagnostic performance and could differentiate LNM with 100% sensitivity, 86% specificity, and 86% diagnostic accuracy.

Conclusion
More than 500 μm submucosal invasion and lymphatic and venous invasion will be useful in assessing LNM after ESD for patients with EGC. When these three factors are not observed, follow-up alone might be appropriate and it may be possible to reduce unnecessary surgical resection.
Infection by HTLV-1 Is Associated With High Levels of Proinflammatory Cytokines in HIV-HCV–Coinfected Patients
Authors: Brites Carlos , Abrahão Marcos , Bozza Patrícia , Netto Eduardo M. , Lyra André , Bahia Fabianna 
Published: October 2017

Objectives:
HIV, hepatitis C virus (HCV), and human T-cell lymphotropic virus type 1 (HTLV-1) share the same routes of infection, making coinfection by these viruses a frequent finding in endemic areas. However, there is scarce information on the clinical/immunological consequences of triple infection. Coinfection by HTLV-1 is able to modulate cytokine's production in patients with HIV, but there are no data on the immune response of HIV-HCV-HTLV-1–infected patients.

Methods:
We compared the plasma levels of 25 different cytokines in patients with HIV-HCV, according to their serostatus to HTLV-1 infection. Eligible patients should be on stable highly active antiretroviral therapy and have undetectable HIV-1 plasma viral load for, at least, 12 months. Cytokines levels were also evaluated by CD4+ cells count, rates of sustained virological response (SVR) to previous HCV treatment, frequency of spontaneous HCV clearance, and HCV/IFN-λ3 genotypes.

Results:
Twenty-five patients (15 coinfected by HIV and HCV, 10 coinfected by HIV, HCV, and HTLV-1) were evaluated. Among the triply infected group, 3 had undetectable HCV viremia (spontaneous clearance). All but one remaining patients were previously treated for HCV, with similar SVR rates (∼29%). Cytokines levels did not differ per HCV/IFN-λ3 genotypes, mean CD4+ cells count, age, sex, or SVR. However, patients coinfected by HTLV-1 showed significantly higher levels of IL-1b, IL-2, TNF-α, IFN-γ, MIP-1α, RANTES, and interferon-induced protein 10 (IP-10) than HIV-HCV–coinfected ones. Patients presenting HCV spontaneous clearance had the highest levels of cytokines.

Conclusions:
Coinfection by HTLV-1 increases the plasma levels of proinflammatory cytokines of patients with HIV-HCV and can influence the outcomes of coinfected patients.
One-Stage Treatment of Giant Condylar Osteoma: Alloplastic Total Temporomandibular Joint Replacement Aided by Digital Templates
Authors: Xu Xin , Ma Hailong , Jin Shufang 
Published: October 2017

Objectives:
To introduce the surgical techniques and evaluate the effect of alloplastic total temporomandibular joint (TMJ) replacement aided by digital templates in giant condylar osteoma.

Methods:
Three patients with giant condylar osteoma were enrolled in this study. The maximal mouth opening was 1.9 cm on average. All the patients were underwent the computed tomography scan (slice thickness 1 mm) and the data were imported to Proplan 1.3 software for 3-dimensional bony segmentation and reconstruction. Osteotomy line and digital template according the 3-dimensional measurement were designed. All the joints were replaced with Biomet standard prosthesis under general anesthesia.

Results:
All the operations were successfully performed. The follow-up period was from 6 to 18 months (average, 12 months). Pain relief of the joint and mouth-opening improvement were significant in 3 patients. No infection or loosening the prostheses was occurred. The occlusal relationship kept stable in all patients.

Conclusions:
Total TMJ replacement with standard prosthesis is a good strategy for TMJ reconstruction after giant condylar osteoma excision. The joint pain and the mouth-opening limitation resulted from giant condylar osteoma were markedly improved. Long-term effect remains to be evaluated based on a long-term follow-up.
Perioperative Blood Loss and Transfusion in Craniosynostosis Surgery
Authors: Park Chang , Wormald Justin , Miranda Benjamin H. , Ong Juling , Hare Alison , Eccles Simon 
Published: October 2017

Abstract
Craniosynostosis has an incidence of 1 in 2000 to 2500 live births and may be corrected through several methods including total calvarial remodeling and frontal orbital advancement remodeling. Blood loss during craniosynostosis surgery can be substantial, ranging from 20% to 500% of total circulating volume with a high associated risk of transfusion-related adverse events. The authors performed a retrospective analysis of all patients undergoing surgery for craniosynostosis at a tertiary pediatric craniofacial center with a focus on blood loss and subsequent transfusion.
The authors reviewed 40 patients with craniosynostosis >16 years at a single-center. Data on perioperative blood loss and transfusion were obtained, including pre-, intra-, and postoperative hemoglobin, hematocrit, and use of tranexamic acid. The authors calculated estimated percentage of circulating red cell volume lost and transfused.
The majority of patients had sagittal synostosis and underwent total calvarial remodeling (n = 20); the rest underwent frontal orbital advancement remodeling (n = 19) or lambdoid correction (n = 1). The average estimated volume red cell loss was 77% of circulating volume and 90% of patients received blood transfusion with an average 88.3% transfusion of circulating red cell volume. Longer operative time, younger age, and lower weight predisposed to >50% blood volume transfusion (P = 0.032, <0.005, <0.005 respectively).
This single-center observational study reports red cell volume loss and volume of transfusion in children undergoing surgical correction of craniosynostosis. Red cell volume loss was comparative to that in the literature and in this cohort longer operative time, younger age, and lower weight predisposed to >50% blood volume transfusion.
Two Isometric Yoga Poses Reduce the Curves in Degenerative and Adolescent Idiopathic Scoliosis
Authors: Fishman Loren M. , Groessl Erik J. , Bernstein Paul 
Published: October 2017

Objective:
Efficacy of 2 yoga poses for degenerative scoliosis (DS) and adolescent idiopathic scoliosis (AIS).

Subjects and Methods:
Retrospective study of 49 DS and 25 AIS patients with initial Cobb angles less than 120° (DS) and less than 75° (AIS) performing side plank daily, with lumbar and thoracolumbar curves' convex side inferior. In complex curves, the half-moon pose was added. Outcome measure included Cobb angles after mean 5.8 and 9.4 months, respectively.

Results:
Mean lumbar/thoracolumbar improvement: 23.7% (P < .00) in DS, 34.2% (P = .001) in AIS. Thoracic curves improved 27.6% (P = .001) and 20.3% (P = .004): 2.5% per month and 3.5% per month, respectively.

Conclusions:
These yoga poses may reduce scoliosis in DS and AIS.
Effects of Dance and of Tai Chi on Functional Mobility, Balance, and Agility in Parkinson Disease
Authors: Mazzarin Camila Monteiro , Valderramas Silvia Regina , de Paula Ferreira Manoela , Tiepolo Eleonora , Guérios Lara , Parisotto Daniele , Israel Vera Lúcia 
Published: October 2017

Introduction:
Parkinson disease has symptoms that can be reduced by integrative therapy.

Objective:
To verify the integrative therapy effects with motion mobility, balance, and agility in people with Parkinson disease.

Methods:
A systematic review with meta-analysis was performed for randomized, nonrandomized, and semirandomized controlled trials.

Results:
A total of 122 studies were found, with 9 being selected, for people with Parkinson disease. The intervention varied from 2 weeks to 12 months, with dance and Tai Chi.

Conclusion:
The dance and Tai Chi brought no significant differences in balance and agility. Tai Chi improved mobility compared with other therapies.
Fast-SG: An alignment-free algorithm for hybrid assembly
Authors: Di Genova Alex , Ruz Gonzalo A. , Sagot Marie-France , Maass Alejandro 
Published: October 2017

ABSTRACTLong read sequencing technologies are the ultimate solution for genome repeats, allowing near reference level reconstructions of large genomes. However, long read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods which combine short and long read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. In this paper, we propose a new method, called FAST-SG, which uses a new ultra-fast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. FAST-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how FAST-SG outperforms the state-of-the-art short read aligners when building the scaffolding graph, and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using FAST-SG with shallow long read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878).
The dynamics of preferential host switching: host phylogeny as a key predictor of parasite prevalence and distribution
Authors: Engelstädter Jan , Fortuna Nicole Z. 
Published: October 2017

AbstractThis preprint has been reviewed and recommended byPeer Community In Evolutionary Biology(https://doi.org/10.24072/pci.evolbiol.100049).New parasites commonly arise through host-shifts, where parasites from one host species jump to and become established in a new host species. There is much evidence that the probability of host-shifts decreases with increasing phylogenetic distance between donor and recipient hosts, but the consequences of such preferential host switching remain little explored. We develop a mathematical model to investigate the dynamics of parasite host-shifts in the presence of this phylogenetic distance effect. Host trees evolve under a stochastic birth-death process and parasites co-evolve concurrently on those trees, undergoing host-shifts, co-speciation and extinction. Our model indicates that host trees have a major influence on these dynamics. This applies both to individual trees that evolved under the same stochastic process and to sets of trees that evolved with different macroevolutionary parameters. We predict that trees consisting of a few large clades of host species and those with fast species turnover should harbour more parasites than trees with many small clades and those that diversify more slowly. Within trees, large clades should exhibit a higher infection frequency than small clades. We discuss our results in the light of recent cophylogenetic studies in a wide range of host-parasite systems, including the intracellular bacteriumWolbachia.
Interrelationship of photoperiod and feed utilization on growth and reproductive performance in the Red eyed orange molly (Poecilia sphenops)
Authors: Zutshi Bela , Singh Aradhana 
Published: October 2017

AbstractLight is a major environmental factors that synchronize all life-stages of fish, from body growth to sexual maturation. The objective of this research is to enhance the growth and reproductive performance in the test fish, red eyed orange molly (Poecilia sphenops) exposed to standardized manipulated photoperiod. In present study, growth and gonadal development of the test fish with an average initial weight (0.52g) and an average total length (3.2cm) exposed to two photoperiods (18L:6D and 10L:14D) at constant light intensity (1500 lx) for a period of 60 days was investigated. The fish were fed with formulated feed twice a day as per 10% of body weight. During a long day photoperiod (18L:6D) significant increase in growth parameters such as, weight gain (2.2 ± 0.04), feed conversion ratio (8.9 ± 0.004) and specific growth rate (1.2 ± 0% day-1) was observed. Mean gonadosomatic index (GSI) in female (30.4± 0.11) and male fish (2.0 ± 0.17) was also significantly higher in long-day photoperiod followed by short day photoperiod (10L:14D). The results confirm that manipulated long-day photoperiod induced somatic growth and enhanced gonadal development in P. sphenops without causing any stress.SummaryThis work is novel to research field since photoperiodic effect on Poecilia sphenops, a live-bearer fish under artificial environmental conditions resulted in enhanced growth and reproductive performance with fry production.
Large conformational changes in FtsH create an opening for substrate entry
Authors: Carvalho Vanessa , Kieffer Roland , de Lange Nick , Engel Andreas , Aubin-Tam Marie-Eve 
Published: October 2017

AbstractAAA+ proteases are degradation machines, which exploit ATP hydrolysis to unfold protein substrates and translocate them through a central pore towards a degradation chamber. FtsH, a bacterial membrane-anchored AAA+ protease, plays a vital role in membrane protein quality control. Although cytoplasmic structures are described, the full-length structure of bacterial FtsH is unknown, and the route by which substrates reach the central pore remains unclear. We use electron microscopy to determine the 3D map of the full-lengthAquifex aeolicusFtsH hexamer. Moreover, detergent solubilisation induces the formation of fully active FtsH dodecamers, which consist of two FtsH hexamers in a single detergent micelle. FtsH structures reveal that the cytosolic domain can tilt with respect to the membrane. A flexible linker of ~20 residues between the second transmembrane helix and the cytosolic domain permits the observed large tilting movements, thereby facilitating the entry of substrate proteins towards the central pore for translocation.
Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits
Authors: Bertaux François , Marguerat Samuel , Shahrezaei Vahid 
Published: October 2017

AbstractThe cell division rate, size, and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cycle dynamics. We have modelled stochastic gene expression inside growing and dividing cells to study the effect of division rates on noise in mRNA and protein expression. We use assumptions and parameters relevant toEscherichia coli, for which abundant quantitative data are available. We find that coupling of transcription, but not translation rates to the rate of cell division can result in protein concentration and noise homeostasis across conditions. Interestingly, we find that the increased cell size at fast division rates, observed inE. colid other unicellular organisms, buffers noise levels even for proteins with decreased expression at faster growth. We then investigate the functional importance of these regulations using gene regulatory networks that exhibit bi-stability and oscillations. We find that network topology affects robustness to changes in division rate in complex and unexpected ways. In particular, a simple model of persistence, based on global physiological feedback, predicts increased proportion of persistors cells at slow division rates. Altogether, our study reveals how cell size regulation in response to cell division rate could help controlling gene expression noise. It also highlights that understanding of circuits’ robustness across growth conditions is key for the effective design of synthetic biological systems.
Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data
Authors: Köksal Ali Sinan , Beck Kirsten , Cronin Dylan R. , McKenna Aaron , Camp Nathan D. , Srivastava Saurabh , MacGilvray Matthew E. , Bodík Rastislav , Wolf-Yadlin Alejandro , Fraenkel Ernest , Fisher Jasmin , Gitter Anthony 
Published: October 2017

AbstractAdvances in proteomics reveal that pathway databases fail to capture the majority of cellular signaling activity. Our mass spectrometry study of the dynamic epidermal growth factor (EGF) response demonstrates that over 89% of significantly (de)phosphorylated proteins are excluded from individual EGF signaling maps, and 63% are absent from all annotated pathways. We present a computational method, the Temporal Pathway Synthesizer (TPS), to discover missing pathway elements by modeling temporal phosphoproteomic data. TPS uses constraint solving to exhaustively explore all possible structures for a signaling pathway, eliminating structures that are inconsistent with protein-protein interactions or the observed phosphorylation event timing. Applied to our EGF response data, TPS connects 83% of the responding proteins to receptors and signaling proteins in EGF pathway maps. Inhibiting predicted active kinases supports the TPS pathway model. The TPS algorithm is broadly applicable and also recovers an accurate model of the yeast osmotic stress response.
A toolbox of anti-mouse and rabbit IgG secondary nanobodies
Authors: Pleiner Tino , Bates Mark , Görlich Dirk 
Published: October 2017

AbstractPolyclonal anti-IgG secondary antibodies are essential tools for many molecular biology techniques and diagnostic tests. Their animal-based production is, however, a major ethical problem. Here, we introduce a sustainable alternative, namely nanobodies against all mouse IgG subclasses and rabbit IgG. They can be produced at large scale in E. coli and could thus make secondary antibody-production in animals obsolete. Their recombinant nature allows fusion with affinity tags or reporter enzymes as well as efficient maleimide chemistry for fluorophore-coupling. We demonstrate their superior performance in Western Blotting, both in peroxidase- and fluorophore-linked form. Their site-specific labeling with multiple fluorophores creates bright imaging reagents for confocal and super-resolution microscopy with much smaller label displacement than traditional secondary antibodies. They also enable simpler and faster immunostaining protocols and even allow multi-target localization with primary IgGs from the same species and of the same class.
A State Representation for Reinforcement Learning and Decision-Making in the Orbitofrontal Cortex
Authors: Schuck Nicolas W. , Wilson Robert , Niv Yael 
Published: October 2017

AbstractDespite decades of research, the exact ways in which the orbitofrontal cortex (OFC) influences cognitive function have remained mysterious. Anatomically, the OFC is characterized by remarkably broad connectivity to sensory, limbic and subcortical areas, and functional studies have implicated the OFC in a plethora of functions ranging from facial processing to value-guided choice. Notwithstanding such diversity of findings, much research suggests that one important function of the OFC is to support decision making and reinforcement learning. Here, we describe a novel theory that posits that OFC’s specific role in decision-making is to provide an up-to-date representation of task-related information, called a state representation. This representation reflects a mapping between distinct task states and sensory as well as unobservable information. We summarize evidence supporting the existence of such state representations in rodent and human OFC and argue that forming these state representations provides a crucial scaffold that allows animals to efficiently perform decision making and reinforcement learning in high-dimensional and partially observable environments. Finally, we argue that our theory offers an integrating framework for linking the diversity of functions ascribed to OFC and is in line with its wide ranging connectivity.
The role of product innovation on export behavior of firms
Authors: Tavassoli Sam 
Published: October 2017

Purpose
The purpose of this paper is to analyze the role of innovation on the export behavior of firms.

Design/methodology/approach
Using two waves of Swedish Community Innovation Survey merged with register data on firm-level, the authors estimate the influence of the innovation output and innovation input of firms on their export propensity and intensity.

Findings
The authors find that the innovation output of firms (measured as sales due to innovative products) has a positive and significant effect on their subsequent export behavior, particularly on export intensity. The results also show that there is no direct effect of innovation input (innovative efforts) on export behavior.

Originality/value
This is one of the first paper that clearly distinguishes between input and output parts of innovation process and empirically investigate their differentiated impact on export behavior of a representative sample of firms in an entire economy.