bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perioperative Outcomes, Complications, and Efficacy of Robotic-Assisted Prolapse Repair: A Single Institution Study of 196 Patients
Authors: Gupta Priyanka , Ehlert Michael , Bartley Jamie , Gilleran Jason , Killinger Kim A. , Boura Judith A. , Nagaraju Pradeep , Fischer Melissa 
Published: September 2017

Introduction
Abdominal pelvic organ prolapse repair is efficacious for uterovaginal and apical prolapse. We describe the safety and efficacy of robotic prolapse repair in a large teaching institution.

Methods
Consecutive robotic-assisted prolapse repairs at a single institution between 2006 and 2014 were retrospectively reviewed for patient characteristics, operative information, and outcomes.

Results
A total of 196 women (mean age, 61 ± 9 years) underwent robotic prolapse repair (189 sacrocolpopexy, 6 sacrohysteropexy, 1 enterocele repair). Concomitant procedures included hysterectomy (88), midurethral sling (84), and/or Burch colposuspension (7). Mean odds ratio time was 242 ± 69.9 minutes, and median length of stay was 1 day. Intraoperative complications were as follows: cystotomy (4), vaginotomy (4), conversion to open (2), bowel injury/aborted (1), adhesions/aborted (1), and ureteral injury (1). Women with complications had greater blood loss than those without complications (P = 0.0015). Immediate (<30 days) postoperative complications were rare: port-site hernia (2), discitis (1), ileus (1), and ulnar neuropraxia (3). At median follow-up of 9 months (range, 0–85 months), 14 women had recurrent grade 3 prolapse, and 4 had grade 2 apical prolapse. Nine of 14 women had additional prolapse repair at a mean of 9.5 ± 6.3 months. Vaginal mesh exposure was detected in 12 (6.3%) of 192 women. There were 6 procedures for mesh exposure and 2 procedures for exposed sutures. One mesh erosion into the bladder required open excision.

Conclusions
In this large series of robotic prolapse repair, complications are infrequent. Short-term apical outcomes are excellent. Few women required additional compartment repairs within 1 year with 6% rate of mesh exposure.
Evidence of semantic processing impairments in behavioural variant frontotemporal dementia and Parkinson's disease
Authors: Cousins Katheryn A.Q. , Grossman Murray 
Published: September 2017

Purpose of review
Category-specific impairments caused by brain damage can provide important insights into how semantic concepts are organized in the brain. Recent research has demonstrated that disease to sensory and motor cortices can impair perceptual feature knowledge important to the representation of semantic concepts. This evidence supports the grounded cognition theory of semantics, the view that lexical knowledge is partially grounded in perceptual experience and that sensory and motor regions support semantic representations. Less well understood, however, is how heteromodal semantic hubs work to integrate and process semantic information.

Recent findings
Although the majority of semantic research to date has focused on how sensory cortical areas are important for the representation of semantic features, new research explores how semantic memory is affected by neurodegeneration in regions important for semantic processing. Here, we review studies that demonstrate impairments to abstract noun knowledge in behavioural variant frontotemporal degeneration (bvFTD) and to action verb knowledge in Parkinson's disease, and discuss how these deficits relate to disease of the semantic selection network.

Summary
Findings demonstrate that semantic selection processes are supported by the left inferior frontal gyrus (LIFG) and basal ganglia, and that disease to these regions in bvFTD and Parkinson's disease can lead to categorical impairments for abstract nouns and action verbs, respectively.
Update on tauopathies
Authors: Lebouvier Thibaud , Pasquier Florence , Buée Luc 
Published: September 2017

Purpose of review
The purpose of this review is to provide an update on the role of tau beyond the stabilization of microtubules and on the clinical, pathological, diagnostic and therapeutic aspects of tauopathies.

Recent findings
Beyond its function as a microtubule-associated tau protein, tau is also involved in gene regulation, signal transduction and metabolism. Experimental models allow for the development of new diagnostic and therapeutic tools. Tauopathies encompass different disorders that may manifest with various clinical syndromes. Differential diagnosis with other proteinopathies is still challenging. Cerebrospinal fluid biomarkers and radiotracers were extensively studied in the last year. Although diagnostic accuracy remains deceiving in non-Alzheimer's disease tauopathies, positron emission tomography tau tracers could be used to monitor disease progression.

Summary
Despite the advent of novel therapeutic approaches and the increasing number of clinical trials in tauopathies, accurate clinical diagnosis is still an unmet need and better tau biomarkers are still desperately needed. Although primary taupathies are rare and heterogeneous disorders, their combined prevalence and the importance of tau disorder in Alzheimer's disease and secondary tauopathies makes research on tauopathy a priority – because it could benefit many patients.
Pathways of DNA unlinking: A story of stepwise simplification
Authors: Stolz Robert , Yoshida Masaaki , Brasher Reuben , Flanner Michelle , Ishihara Kai , Sherratt David J. , Shimokawa Koya , Vazquez Mariel 
Published: September 2017

AbstractInEscherichia coliDNA replication yields interlinked chromosomes. Controlling topological changes associated with replication and returning the newly replicated chromosomes to an unlinked monomeric state is essential to cell survival. In the absence of the topoisomerase topoIV, the site-specific recombination complex XerCD-dif-FtsK can remove replication links by local reconnection. We previously showed mathematically that there is a unique minimal pathway of unlinking replication links by reconnection while stepwise reducing the topological complexity. However, the possibility that reconnection preserves or increases topological complexity is biologically plausible. In this case, are there other unlinking pathways? Which is the most probable? We consider these questions in an analytical and numerical study of minimal unlinking pathways. We use a Markov Chain Monte Carlo algorithm with Multiple Markov Chain sampling to model local reconnection on 491 different substrate topologies, 166 knots and 325 links, and distinguish between pathways connecting a total of 881 different topologies. We conclude that the minimal pathway of unlinking replication links that was found under more stringent assumptions is the most probable. We also present exact results on unlinking a 6-crossing replication link. These results point to a general process of topology simplification by local reconnection, with applications going beyond DNA.
seq-seq-pan: Building a computational pan-genome data structure on whole genome alignment
Authors: Jandrasits Christine , Dabrowski Piotr W , Fuchs Stephan , Renard Bernhard Y 
Published: September 2017

AbstractBackgroundThe increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference. There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods. At the same time, this representation needs to be easily accessible and extendable to account for the constant change of available genomes.ResultsWe introduce seq-seq-pan, a framework that provides methods for adding or removing new genomes from a set of aligned genomes and uses these to construct a whole genome alignment. Throughout the sequential workflow the alignment is optimized for generating a representative linear presentation of the aligned set of genomes, that enables its usage for annotation and in downstream analyses.ConclusionsBy providing dynamic updates and optimized processing, our approach enables the usage of whole genome alignment in the field of pan-genomics. In addition, the sequential workflow can be used as a fast alternative to existing whole genome aligners. seq-seq-pan is freely available athttps://gitlab.com/groups/rki_bioinformatics
Inferring the selection window in antimicrobial resistance using deep mutational scanning data and biophysics-based fitness models
Authors: Dasmeh Pouria , Ton Anh-Tien , Quach Caroline , Serohijos Adrian W.R. 
Published: September 2017

AbstractMutant-selection window (MSW) hypothesis in antimicrobial resistance implies a range for antimicrobial concentration that promotes selection of single-step resistant mutants. Since the inception and experimental verification, MSW has been at the forefront of strategies to minimize development of antimicrobial resistance (AR). Setting the upper and lower limits of MSW requires an understanding of the dependence of selection coefficient of arising mutations to antimicrobial concentration. In this work, we employed a biophysics-based and experimentally calibrated fitness model to estimate MSW in the case of Ampicillin and Cefotaxime resistance in E.coli TEM-1 beta lactamase. In line with experimental observations, we show that selection is active at very low levels of antimicrobials. Furthermore, we elucidate the dependence of MSW to catalytic efficiency of mutants, fraction of mutants in the population and discuss the role of population genetic parameters such as population size and mutation rate. Altogether, our analysis and formalism provide a predictive model of MSW with direct implications in the design of dosage strategies.
Systematic Mutagenesis of Serine Hydroxymethyltransferase Reveals an Essential Role in Nematode Resistance
Authors: Kandoth Pramod K. , Liu Shiming , Prenger Elizabeth , Ludwig Andrew , Lakhssassi Naoufal , Heinz Robert , Zhou Zhou , Howland Amanda , Gunther Joshua , Eidson Samantha , Dhroso Andi , LaFayette Peter , Tucker Donna , Johnson Sarah , Anderson James , Alaswad Alaa , Cianzio Silvia R. , Parrott Wayne A. , Korkin Dmitry , Meksem Khalid , Mitchum Melissa G. 
Published: September 2017

Abstract
Rhg4 is a major genetic locus that contributes to soybean cyst nematode (SCN) resistance in the Peking-type resistance of soybean (Glycine max), which also requires the rhg1 gene. By map-based cloning and functional genomic approaches, we previously showed that the Rhg4 gene encodes a predicted cytosolic serine hydroxymethyltransferase (GmSHMT08); however, the novel gain of function of GmSHMT08 in SCN resistance remains to be characterized. Using a forward genetic screen, we identified an allelic series of GmSHMT08 mutants that shed new light on the mechanistic aspects of GmSHMT08-mediated resistance. The new mutants provide compelling genetic evidence that Peking-type rhg1 resistance in cv Forrest is fully dependent on the GmSHMT08 gene and demonstrates that this resistance is mechanistically different from the PI 88788-type of resistance that only requires rhg1. We also demonstrated that rhg1-a from cv Forrest, although required, does not exert selection pressure on the nematode to shift from HG type 7, which further validates the bigenic nature of this resistance. Mapping of the identified mutations onto the SHMT structural model uncovered key residues for structural stability, ligand binding, enzyme activity, and protein interactions, suggesting that GmSHMT08 has additional functions aside from its main enzymatic role in SCN resistance. Lastly, we demonstrate the functionality of the GmSHMT08 SCN resistance gene in a transgenic soybean plant.
Parametric finite element modeling and tooth contact analysis of spur and helical gears including profile and lead modifications
Authors: Wang Yanzhong , Liu Yang , Tang Wen , Liu Peng 
Published: September 2017

Purpose
The finite element method has been increasingly applied in stress, thermal and dynamic analysis of gear transmissions. Preparing the models with different design and modification parameters for the finite element analysis is a time-consuming and highly skilled burden.

Design/methodology/approach
To simplify the preprocessing work of the analysis, a parametric finite element modeling method for spur and helical gears including profile and lead modification is developed. The information about the nodes and elements is obtained and exported into the finite element software to generate the finite element model of the gear automatically.

Findings
By using the three-dimensional finite element tooth contact analysis method, the effects of tooth modifications on the transmission error and contact stress of spur and helical gears are presented.

Originality/value
The results demonstrate that the proposed method is useful for verifying the modification parameters of spur and helical gears in the case of deformations and misalignments.
The transgenerational transmission of refugee trauma: family functioning and children’s psychosocial adjustment
Authors: Dalgaard Nina Thorup , Montgomery Edith 
Published: September 2017

PurposeThe purpose of this paper is to explore the role of family functioning in the transgenerational transmission of trauma in a sample of 30 refugee families with traumatized parents and children without a history of direct trauma exposure from the Middle East.Design/methodology/approachBased on qualitative analyses of interview material, families were evaluated using theoretically derived dimensions of family functioning and placed in descriptive categories according to family cohesion, family flexibility, family roles, family coping, stressor pile-up, and marital problems. The association between these descriptive categories of family functioning and the child’s mental health as measured by the Strengths and Difficulties Questionnaire (SDQ) was explored using point-biserial correlations, correlations, and multiple regression analyses.FindingsIn all, 22 percent of the variance in children’s SDQ scores could be predicted by whether or not the family experienced a pile-up of stressors and whether or not the family was characterized by role reversal between parents and children. Furthermore, a statically significant association was established between a total measure of adaptive family functioning and lower scores on the SDQ.Originality/valueThese findings suggest that the transgenerational transmission of trauma may be associated with family functioning and have implications for interventions at several levels.
Universal opt-out screening for hepatitis C virus (HCV) within correctional facilities is an effective intervention to improve public health
Authors: Morris Meghan D. , Brown Brandon , Allen Scott A. 
Published: September 2017

Purpose
Worldwide efforts to identify individuals infected with the hepatitis C virus (HCV) focus almost exclusively on community healthcare systems, thereby failing to reach high-risk populations and those with poor access to primary care. In the USA, community-based HCV testing policies and guidelines overlook correctional facilities, where HCV rates are believed to be as high as 40 percent. This is a missed opportunity: more than ten million Americans move through correctional facilities each year. Herein, the purpose of this paper is to examine HCV testing practices in the US correctional system, California and describe how universal opt-out HCV testing could expand early HCV detection, improve public health in correctional facilities and communities, and prove cost-effective over time.

Design/methodology/approach
A commentary on the value of standardizing screening programs across facilities by mandating all facilities (universal) to implement opt-out testing policies for all prisoners upon entry to the correctional facilities.

Findings
Current variability in facility-level testing programs results in inconsistent testing levels across correctional facilities, and therefore makes estimating the actual number of HCV-infected adults in the USA difficult. The authors argue that universal opt-out testing policies ensure earlier diagnosis of HCV among a population most affected by the disease and is more cost-effective than selective testing policies.

Originality/value
The commentary explores the current limitations of selective testing policies in correctional systems and provides recommendations and implications for public health and correctional organizations.
Modelling critical risk factors for Indian construction project using interpretive ranking process (IRP) and system dynamics (SD)
Authors: Mhatre Tanmay Nitin , Thakkar J.J. , Maiti J. 
Published: September 2017

Purpose
The purpose of this paper is to employ an integrated approach of interpretive ranking process (IRP) and system dynamics (SD) for modelling the key risk factors for a typical construction project.

Design/methodology/approach
The risk parameters and performance measures applicable in the construction industry have been identified through extensive literature review and discussions with experts from the construction industry. Based on the literature review, a questionnaire was designed and 64 responses were considered. The list of 20 risk parameters and 32 performance measures relevant for a construction industry is reduced to five risk factors and five performance measure factors using factor analysis. IRP modelling is employed to examine the contextual relationships among risk factors and to rank them with respect to performance measure factors. Subsequently, the results of IRP model were utilised as inputs to SD analysis. The SD analysis is conducted for two models, namely, risk factor model and risk variable model to understand the impact of interventions offered by project management team on risk reduction and mitigation.

Findings
The developed IRP model shows that the risk factor dimension “construction management” has a high likeliness to occur during the construction phase.

Research limitations/implications
The research demonstrates an application of proposed approach for a typical construction environment and hence the results cannot be generalised.

Originality/value
This research addresses real life complexities in construction project by modelling critical risk factors using an integrate approach of IRP and SD. The proposed approach would facilitate project managers to devise appropriate risk mitigation strategies for a construction project.
Long-term regional house prices cycles. A city-based index for Italy
Authors: Gabrielli Laura , Taltavull de La Paz Paloma , Ortuño Padilla Armando 
Published: September 2017

PurposeThis paper aims to present the dynamics of housing prices in Italian cities based on unpublished data with regional details from the late 1960s, half-yearly base, for all main Italian cities measuring the average prices for three city dimensions: city centre, sub-centres and outskirts or suburbs. It estimates the Italian long-term house price index, city based in real terms, and shows a combination of methods to deal with large time-series data.Design/methodology/approachThis paper builds long-term cycles based on the city (real) data by estimating the common components of cointegrated time series and extracting the unobservable signals to build real house price index for sub-regions in Italy. Three different econometric methodologies are used: Johansen cointegration test and VAR models to identify the long-term pattern of prices at the estimated aggregate level; principal components to obtain the common (permanent and transitory) components; and signal extraction in ARIMA time series–model-based approach method to extract the unobserved time signals.FindingsResults show three long-term cycle-trends during the period and identify several one-direction causal non-permanent relationships among house prices from different Italian areas. There is no evidence of convergence among regional’s house prices suggesting that the Italian housing prices converge inside the local market with only short diffusion effects at larger regional level.Research limitations/implicationsData are measured as the average price in squared meters, and the resulting index is not quality controlled.Practical implicationsThe long-term trends on housing prices serve to implement further research and know deeply the evolution of Italian housing prices.Originality/valueThis paper contains new and unknown information about the evolution of housing prices in Italian regions and cities.
The effect of school performance on property values: a literature review and a case study
Authors: Fleishman Larisa , Fogel Nir , Fridman Israela , Shif Yaffa 
Published: September 2017

PurposeThis paper, a pioneering one in the Israeli context, aims to augment the research literature on school quality and housing prices by examining the effect of primary-school performance on local property values. It focuses on the main question whether the release of students’ test scores offered households a new source of information with which they could evaluate the quality of schools, thereby affecting local housing markets.Design/methodology/approachSeveral models that examine a variety of transactions, schools and locality characteristics that affect house prices are estimated. Using different administrative sources of information, a wide array of socioeconomic characteristics of students, parents and homebuyers, as well as locality features, is constructed and merged. This information, combined with students’ scores on Meitzav exams (standardized student achievement tests) in 2009-2012 and house prices, illuminates the relationship between student achievements and the prices of houses purchased within the defined attendance zones.FindingsStudent achievements, mainly in the state education system, are found to have a positive and statistically significant effect on housing prices. Accurate information published about a certain school that showed much stronger achievements than those yielded by information attainable about the same school before school-level publication, does contribute to boost house prices in the post-publication period. The socioeconomic background of the students’ parents was found to have a significant effect on house prices. The premium for housing value is much higher in the most prestigious, prime demand districts, in which the housing supply is limited and the housing price level is higher than in that the peripheral districts.Originality/valueThis study not only breaks new ground in the Israeli context but also contributes to the existing literature, by investigating the relation between publishing students’ scores and property values near the same schools, on a national scale. Given that the housing price dynamics and the spatial differentiation of housing stock are extremely hot issues in many European cities, the results of this study could serve as an important tool for better understanding the housing price responses to market incentives, resulting in specific patterns in local housing markets. This paper could be thus applicable in housing policy outline, urban design and planning.