bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accessory Mental Foramen and Maxillofacial Surgery
Authors: Rahpeyma Amin , Khajehahmadi Saeedeh 
Published: October 2017

Abstract
Accessory mental foramens should be considered in surgical procedures performed in mandibular body and symphysis. Location and content of these foramina has significant impact on the result of surgery.
Lip numbness is the catastrophic result if these foramina are violated while their content is nerves that carry sensory inputs from lower lip. Examples of interferences with dental implant, orthognathic, and periapical surgeries are presented and it is discussed in which conditions they complicate oral surgical procedures.
Timed Up and Go Test Performance as an Indicator of Fall History in Institutionalized Elderly
Authors: Millán-Calenti José C. , Núñez-Naveira Laura , Lorenzo-López Laura , Rodríguez-Villamil José L. , Muñoz-Mendoza Carmen L. , Cabañero-Martínez M. José , Cabrero-García Julio , Maseda Ana 
Published: October 2017

Background:
Ageing is associated with sensory and physical declines and falling risk.

Objective:
To determine the association between 3 performance-based mobility tests and fall history.

Methods:
Fifty participants' mobility was assessed by Timed Up and Go (TUG) and 4- and 6-m walking tests (WT).

Results:
The TUG performance correlated with 4- and 6-m WT performance, and performance on 4-m WT positively correlated with 6-m WT. Only TUG performance showed a strong relationship to fall history.

Conclusions:
Performance tests could indicate the presence of fall history in the institutionalized older adults; the TUG being the most suitable compared with other common WT.
The Effect of Early Progressive Resistive Exercise Therapy on Balance Control of Patients With Total Knee Arthroplasty
Authors: Yousefian Molla Razieh , Sadeghi Heydar , Kahlaee Amir Hossein 
Published: October 2017

Background and Purpose:Although total knee arthroplasty (TKA) is a common treatment for severe osteoarthritis, high risks of fall and balance loss are the main complications of this procedure. While multiple rehabilitation protocols have been suggested for TKA, efficacy of early resistive exercise therapy aimed at improving balance has not yet been thoroughly investigated.Methods:In this double-blind randomized controlled trial study, 40 patients with severe osteoarthritis, sampled by a simple convenient method, were randomly assigned into either “control” group or “early resistive exercise” group. After TKA surgery, both groups attended a routine rehabilitation program while the experimental group received extra early resistive exercises. Static, semidynamic, and dynamic balance were assessed by the Sharpened Romberg (SRBT), Star Excursion (SEBT), and Berg (BBT) balance tests prior to surgery, after the rehabilitation process (seventh week), and at a 2-week later follow-up time (ninth week).Results:At the end of the seventh and ninth weeks, in both groups all 3 balance scores were significantly enhanced comparing the baseline scores (P< .001). The experimental group had significantly higher scores than the control group in SRBT, SEBT, and BBT after the intervention and at the follow-up time (P< .001).Discussion and Conclusions:The findings of this study showed that rehabilitation following TKA is accompanied by balance (static, semidynamic, and dynamic) improvement, and this improvement is greater among patients participating in an early resistive exercise regimen. Early progressive resistive exercise in addition to routine physical therapy may lead to better balance performance than routine physical therapy and might be incorporated into the postoperative physical therapy of these patients. Further studies with longer follow-up periods are needed to confirm these results.
Central vertigo
Authors: Choi Jeong-Yoon , Lee Seung-Han , Kim Ji-Soo 
Published: October 2017

Purpose of review
This review considers recent advances in central vertigo in terms of clinical and laboratory features and pathophysiology.

Recent findings
Strokes presenting dizziness–vertigo are more likely to be associated with a misdiagnosis in the emergency setting. The risk of future strokes after discharge is higher in patients diagnosed with peripheral vertigo than in control patients. Strokes and transient ischemic attacks account for one-quarter of acute transient vestibular syndrome. Diagnosis of acute combined central and peripheral vestibulopathy such as anterior inferior cerebellar artery infarction requires additional consideration whenever applying the HINTS (head impulse test, direction-changing gaze-evoked nystagmus, and test of skew). Heat illness and metronidazole have been recognized as new causes of central vestibulopathy. Some new findings have also been added to the clinical and laboratory features of central vertigo.

Summary
Central vertigo is a heterogeneous group of disorders with diverse clinical spectrums. An integrated approach based on understanding of clinical features, laboratory findings, speculated mechanisms, and limitations of current diagnostic tests will lead to better clinical practice.
Unstable Population Dynamics in Obligate Co-Operators
Authors: Halloway Abdel , Malone Margaret A. , Brown Joel S. 
Published: October 2017

AbstractCooperation significantly impacts a species’ population dynamics as individuals choose others to associate with based upon fitness opportunities. Models of these dynamics typically assume that individuals can freely move between groups. Such an assumption works well for facultative co-operators (e.g. flocking birds, schooling fish, and swarming locusts) but less so for obligate co-operators (e.g. canids, cetaceans, and primates). With obligate co-operators, the fitness consequences from associations are stronger compared to facultative co-operators. Consequently, individuals within a group should be more discerning and selective over their associations, rejecting new members and even removing current members. Incorporating such aspects into population models may better reflect obligately cooperative species. In this paper, we create and analyze a model of the population dynamics of obligate co-operators. In our model, a behavioral game determines within-group population dynamics that then spill over into between-group dynamics. Our analysis shows that group number increases when population dynamics are stable, but additional groups lead to unstable population dynamics and an eventual collapse of group numbers. Using a more general analysis, we identify a fundamental mismatch between the stability of the behavioral dynamics and the stability of the population dynamics. When one is stable, the other is not. Our results suggest that group turnover may be inherent to the population dynamics of obligate co-operators. The instability arises from a non-chaotic deterministic process, and such dynamics should be predictable and testable.
N-acetyl-2-aminofluorene (AAF) processing in adult rat hepatocytes in primary culture occurs by high-affinity low-velocity and low-affinity high-velocity AAF metabolite-forming systems
Authors: Koch K.S. , Moran T. , Shier W.T. , Leffert H.L. 
Published: October 2017

AbstractN-acetyl-2-aminofluorene (AAF) is a procarcinogen used widely in physiological investigations of chemical hepatocarcinogenesis. Its metabolic pathways have been described extensively, yet little is known about its biochemical processing, growth cycle expression and pharmacological properties inside living hepatocytes ‒ the principal cellular targets of this hepatocarcinogen. In this report, primary monolayer adult rat hepatocyte cultures and high specific-activity [ring G-3H]-N-acetyl-2-aminofluorene were used to extend previous observations of metabolic activation of AAF by highly differentiated, proliferation-competent hepatocytes in long-term cultures. AAF metabolism proceeded by zero-order kinetics. Hepatocytes processed significant amounts of procarcinogen (≈12 μg AAF/106cells/day). Five ring-hydroxylated and one deacylated species of AAF were secreted into the culture media. Extracellular metabolite levels varied during the growth cycle (days 0-13), but their rank quantitative order was time invariant: 5-OH-AAF > 7-OH-AAF > 3-OH-AAF > N-OH-AAF > aminofluorene (AF) > 1-OH-AAF. Lineweaver-Burk analyses revealed two principal classes of metabolism: System I (high-affinity and low-velocity), Km[APPARENT]= 1.64 × 10−7M and VMAX[APPARENT]= 0.1 nmols/106cells/day; and, System II (low-affinity and high-velocity), Km[APPARENT]= 3.25 × 10−5M and VMAX[APPARENT]= 1000 nmols/106cells/day. A third system of metabolism of AAF to AF, with Km[APPARENT]and VMAX[APPARENT]constants of 9.6 × 10−5M and 4.7 nmols/106cells/day, was also observed. Evidence provided in this report and its companion paper suggests selective roles and intracellular locations for System I- and System II-mediated AAF metabolite formation during hepatocarcinogenesis, although some of the molecules and mechanisms responsible for multi-system processing remain to be fully defined.
Characterization of a Novel Model of Overuse-Induced Calcific Achilles Tendinopathy in Mice: Contralateral Tendinopathy Following Unilateral Tenotomy
Authors: Wang Liang , Zhang Jie , Yin Gang-hui , Zhang Zhong-min , Chen Tian-yu , Jin Jian , Lai Ping-lin , Huang Bin , Yan Bo , Chen Yu-hui , Jin Da-di , Huang Min-jun 
Published: October 2017

AbstractObjectiveTo develop a simple but reproducible overuse induced animal model of Achilles tendinopathy in mice for better understanding the underlying mechanism and prevention of calcific Achilles tendinopathy.Methods80 C57/B6 mice (8-9 weeks old) were employed and randomly divided into control group and experimental group. Unilateral Achilles tenotomy was performed on the right hindlimb of experiment group. After 12 weeks, the onset of Achilles tedinopathy in the contralateral Achilles tendon was determined by radiological assessment, histological analysis, electron microscopy observation and biomechanical test.ResultsThe onset of calcific Achilles tendinopathy in contralateral Achilles tendon was confirmed after 12 weeks unilateral tenotomy. The contralateral Achilles tendon of experimental group was characterized as hypercelluarity, neovascularization and fused collagen fiber disarrangement, compared to the control group. Importantly, intratendon endochondral ossification and calcaneus deformity was featured in contralateral Achilles tendon. Additionally, poor biomechanical properties in the contralateral Achilles tendon revealed the incidence of Achilles tedinopathy.ConclusionWe hereby introduce a novel simple but reproducible spontaneous contralateral calcific Achilles tendinopathy model in mice, which represents the overuse conditions during the tendinopathy development in human-beings. It should be a useful tool to further study the underlying pathogenesis of calcific Achilles tendinopathy.
Marine cyanolichens from different littoral zones are associated with distinct bacterial communities
Authors: West Nyree J. , Parrot Delphine , Fayet Claire , Grube Martin , Tomasi Sophie , Suzuki Marcelino T. 
Published: October 2017

AbstractThe microbial diversity and function of terrestrial lichens has been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen speciesLichina pygmaeaandLichina confinis, and the maritime chlorolichen speciesXanthoria aureolawhich occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. TheL. confinisandL. pygmaeacommunities were significantly different from those of the maritimeXanthoria aureolalichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notablySphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the twoLichinaspecies were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes generaRubricoccus, TunicatimonasandLewinella, suggesting an important role of these species in the marineLichinalichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.
Preovulatory oocyte aging in mice affects fertilization rate and embryonic genome activation
Authors: Demond Hannah , Dankert Debora , Grümmer Ruth , Horsthemke Bernhard 
Published: October 2017

AbstractDelayed ovulation, or preovulatory aging, can seriously compromise the developmental competence of oocytes. In the present study, we have investigated the effect of preovulatory aging on preimplantation embryos. Delaying ovulation with the gonadotropin releasing hormone (GnRH) antagonist Cetrorelix led to a decline in 2-cell rate from 76 to 46%. From control mice, an average of 17 embryos per mouse was retrieved. This number decreased to a mean of 5 embryos per mouse after preovulatory aging, suggesting that fertilization is impaired by aging. For analysis of zygotic genome activation, 2-cell embryos were incubated with BrUTP, which was incorporated into nascent RNA and detected by immunohistochemistry. A 2.85-fold increase in fluorescence intensity was detected after aging, pointing to a precocious activation of the genome. A possible effect of preovulatory aging on genomic imprint maintenance was investigated at the 8-cell stage. Deep amplicon bisulfite sequencing ofIgf2r,Snrpn,H19andPou5f1showed no significant changes between embryos derived from preovulatory-aged oocytes and control embryos, indicating stable imprint maintenance throughout epigenetic reprogramming. We conclude that preovulatory aging of the oocyte affects fertilization and embryonic genomic activation.
Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors
Authors: Manheimer Kathryn B. , Patel Nihir , Richter Felix , Gorham Joshua , Tai Angela C. , Homsy Jason , Boskovski Marko T. , Parfenov Michael , Goldmuntz Elizabeth , Chung Wendy K. , Brueckner Martina , Tristani-Firouzi Martin , Srivastava Deepak , Seidman Jonathan G. , Seidman Christine E. , Gelb Bruce D. , Sharp Andrew J. 
Published: October 2017

AbstractMultiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs). Using our Mendelian Error Method (MEM), we identified 127 deletions (inherited and de novo) in 2,601 WES trios from the Pediatric Cardiac Genomics Consortium, with a validation rate of 88% by digital droplet PCR. MEM identified additional de novo deletions compared to XHMM, and also identified sample switches, DNA contamination, a significant enrichment of 15q11.2 deletions compared to controls and eight cases of uniparental disomy. We applied MEM to WGS data from the Genome In A Bottle Ashkenazi trio and identified deletions with 97% specificity. MEM provides a robust, computationally inexpensive method for identifying deletions, and an orthogonal approach for verifying deletions called by other tools.
mobsim: An R package for the simulation and measurement of biodiversity across spatial scales
Authors: May Felix , Gerstner Katharina , McGlinn Dan , Xiao Xiao , Chase Jonathan M. 
Published: October 2017

Abstract1. Estimating biodiversity and its changes in space and time poses serious methodological challenges. First, there has been a long debate on how to quantify biodiversity, and second, measurements of biodiversity change are scale-dependent. Therefore comparisons of biodiversity metrics between communities are ideally carried out across scales. Simulation can be used to study the utility of biodiversity metrics across scales, but most approaches are system specific and plagued by large parameter spaces and therefore cumbersome to use and interpret. However, realistic spatial biodiversity patterns can be generated without reference to ecological processes, which suggests a simple simulation framework could provide an important tool for ecologists.2. Here, we present the R package mobsim that allows users to simulate the abundances and the spatial distribution of individuals of different species. Users can define key properties of communities, including the total numbers of individuals and species, the relative abundance distribution, and the degree of spatial aggregation. Furthermore, the package provides functions that derive biodiversity patterns from simulated communities, or from observed data, as well as functions that simulate different sampling designs.3. We show several example applications of the package. First, we illustrate how species rarefaction and accumulation curves can be used to disentangle changes in the fundamental biodiversity components: (i) total abundance, (ii) relative abundance distribution, (iii) and species aggregation. Second, we demonstrate how mobsim can be used to assess the performance of species-richness estimators. The latter indicates how spatial aggregation challenges classical non-spatial species-richness estimators.4. mobsim allows the simulation and analysis of a large range of biodiversity scenarios and sampling designs in an efficient and comprehensive way. The simplicity and control provided by the package can also make it a useful didactic tool. The combination of controlled simulations and their analysis will facilitate a more rigorous interpretation of real world data that exhibit sampling effects and scale-dependence.
Structural robustness of mammalian transcription factor networks reveals plasticity across development
Authors: Caldu-Primo JL , Alvarez-Buylla ER , Davila-Velderrain J 
Published: October 2017

ABSTRACTNetwork biology aims to understand cell behavior through the analysis of underlying complex biomolecular networks. Inference of condition-specific interaction networks from epigenomic data enables the characterization of the structural plasticity that regulatory networks can acquire in different tissues of the same organism. From this perspective, uncovering specific patterns of variation by comparing network structure among tissues could provide insights into systems-level mechanisms underlying cell behavior. Following this idea, here we propose an empirical framework to analyze mammalian tissue-specific networks, focusing on characterizing and contrasting their structure and behavior in response to perturbations. We structurally represent the state of the cell/tissue by condition specific transcription factor networks generated using chromatin accessibility data, and we profile their systems behavior in terms of the structural robustness against random and directed perturbations. Using this framework, we unveil the structural heterogeneity existing among tissues at different levels of differentiation. We uncover a novel and conserved systems property of regulatory networks underlying embryonic stem cells (ESCs): in contrast to terminally differentiated tissues, the promiscuous regulatory connectivity of ESCs produces a globally homogeneous network resulting in increased structural robustness. Possible biological consequences of this property are discussed.
A physical model of cell metabolism
Authors: Fernandez-de-Cossio-Diaz Jorge , Vazquez Alexei 
Published: October 2017

AbstractCell metabolism is characterized by three fundamental energy demands to sustain cell maintenance, to trigger aerobic fermentation and to achieve maximum metabolic rate. Here we report a physical model of cell metabolism that explains the origin of these three energy scales. Our key hypothesis is that the maintenance energy demand is rooted on the energy expended by molecular motors to fluidize the cytoplasm and counteract molecular crowding. Using this model and independent parameter estimates we make predictions for the three energy scales that are in quantitative agreement with experimental values. The model also recapitulates the dependencies of cell growth with extracellular osmolarity and temperature. This theory brings together biophysics and cell biology in a tractable model that can be applied to understand key principles of cell metabolism.
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample
Authors: Olohan Lisa , Gardiner Laura-Jayne , Lucaci Anita , Steuernagel Burkhard , Wulff Brande , Kenny John , Hall Neil , Hall Anthony 
Published: October 2017

AbstractBackgroundBread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq.ResultsOur method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat.ConclusionWe present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses.