bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Evaluation of Iodine-125 Radioactive Seed Localization and Wire Localization for Resection of Breast Lesions
Authors: Tran Vi Thuy , David Julie , Patocskai Erica , Zummo-Soucy Mathieu , Younan Rami , Lalonde Lucie , Labelle Maude , El Khoury Mona , Robidoux André , Trop Isabelle 
Published: September 2017

Purpose Radioactive seed localization (RSL) uses a titanium seed labeled with iodine-125 energy for surgery of nonpalpable breast lesions. RSL facilitates radiology–surgery scheduling and allows for improved oncoplasty compared with wire localization (WL). The purpose of this work was to compare the 2 techniques. Methods We performed a retrospective study of all breast lesions operated with RSL between February 2013 and March 2015 at our university institution, and compared with an equivalent number of surgeries performed with a single WL. Imaging and pathology reports were reviewed for information on guidance mode, accuracy of targeting, nature of excised lesion, size and volume of surgical specimen, status of margins, and reinterventions. Results A total of 254 lesions (247 women) were excised with RSL and compared with 257 lesions (244 women) whose surgery was guided by WL. Both groups were comparable in lesion pathology, guidance mode for RSL or WL positioning, and accuracy of targeting (98% correct). Mean delay between biopsy and surgery was 84 days for RSL versus 103 after WL ( P = .04). No differences were noted after RSL or WL for surgical specimen mean weight, largest diameter, and volume excised. For malignancies, the rate of positive margins was comparable (2.8%-3%), with 5 of 10 women in the RSL group who underwent a second surgery displaying residual malignancy compared with 3 of 9 women in the WL group. Conclusions RSL is safe and accurate, and has comparable surgical endpoints to WL. Because RSL offers flexible scheduling and facilitated oncoplasty, RSL may replace WL for resection of nonpalpable single breast lesions.
Hyperbaric oxygenation alleviates chronic constriction injury (CCI)-induced neuropathic pain and inhibits GABAergic neuron apoptosis in the spinal cord
Authors: Fu Huiqun , Li Fenghua , Thomas Sebastian , Yang Zhongjin 
Published: September 2017

Abstract

Background and aims
Dysfunction of GABAergic inhibitory controls contributes to the development of neuropathic pain. We examined our hypotheses that (1) chronic constriction injury (CCI)-induced neuropathic pain is associated with increased spinal GABAergic neuron apoptosis, and (2) hyperbaric oxygen therapy (HBO) alleviates CCI-induced neuropathic pain by inhibiting GABAergic neuron apoptosis.

Methods
Male rats were randomized into 3 groups: CCI, CCI+HBO and the control group (SHAM). Mechanical allodynia was tested daily following CCI procedure. HBO rats were treated at 2.4 atmospheres absolute (ATA) for 60 min once per day. The rats were euthanized and the spinal cord harvested on day 8 and 14 post-CCI. Detection of GABAergic cells and apoptosis was performed. The percentages of double positive stained cells (NeuN/GABA), cleaved caspase-3 or Cytochrome C in total GABAergic cells or in total NeuN positive cells were calculated.

Results
HBO significantly alleviated mechanical allodynia. CCI-induced neuropathic pain was associated with significantly increased spinal apoptotic GABA-positive neurons. HBO considerably decreased these spinal apoptotic cells. Cytochrome-C-positive neurons and cleaved caspase-3-positive neurons were also significantly higher in CCI rats. HBO significantly decreased these positive cells. Caspase-3 mRNA was also significantly higher in CCI rats. HBO reduced mRNA expression of caspase-3.

Conclusions
CCI-induced neuropathic pain was associated with increased apoptotic GABAergic neurons induced by activation of key proteins of mitochondrial apoptotic pathways in the dorsal horn of the spinal cord. HBO alleviated CCI-induced neuropathic pain and reduced GABAergic neuron apoptosis. The beneficial effect of HBO may be via its inhibitory role in CCI-induced GABAergic neuron apoptosis by suppressing mitochondrial apoptotic pathways in the spinal cord.

Implications
Increased apoptotic GABAergic neurons induced by activation of key proteins of mitochondrial apoptotic pathways in the dorsal horn of the spinal cord is critical in CCI-induced neuropathic pain. The inhibitory role of HBO in GABAergic neuron apoptosis suppresses ongoing neuropathic pain.
Calcium intake and the associations with faecal fat and energy excretion, and lipid profile in a free-living population
Authors: Kjølbæk Louise , Lorenzen Janne K. , Larsen Lesli H. , Astrup Arne 
Published: September 2017

AbstractThe aim of the present study was to investigate the associations between the habitual Ca intake and faecal fat and energy excretion as well as blood lipid profile in free-living normal-weight and overweight individuals. The participants were enrolled for an 8-d period where data from a 7-d diet registration (days 1–7), a 5-d faeces collection (days 3–7), a 2-d urine collection (days 5–7), and anthropometric measurements and a fasting blood sample (day 8) were collected. Analyses showed that dietary Ca intake (g/10 MJ per d) was positively associated with excretion of faecal fat (P = 0·004) and energy (P = 0·031) when adjusted for BMI, age, sex and intake of Ca-containing supplements. However, after adjustment for intake of fibre, the effect of Ca intake disappeared. Nevertheless, total cholesterol (CHOL) and LDL-CHOL concentrations were associated negatively with Ca intake (β−0·62 (95 % CI −0·96, −0·28) mmol/l,P < 0·001, andβ−0·49 (95 % CI −0·78, −0·20) mmol/l,P = 0·001, respectively, per 1000 mg/10 MJ per d increase in Ca intake). In conclusion, incorporation of Ca-rich food products in a habitual diet was associated with reduced total CHOL and LDL-CHOL concentrations, which may lower the risk of CVD in the long term.
Adjunctive antimicrobial chemotherapy based on hydrogen peroxide photolysis for non-surgical treatment of moderate to severe periodontitis: a randomized controlled trial
Authors: Kanno Taro , Nakamura Keisuke , Ishiyama Kirika , Yamada Yasutomo , Shirato Midori , Niwano Yoshimi , Kayaba Chie , Ikeda Koji , Takagi Airi , Yamaguchi Takuhiro , Sasaki Keiichi 
Published: September 2017

AbstractTreatment of severe periodontitis with non-surgical therapy remains challenging in dentistry. The present study aimed to evaluate the clinical efficacy of hydrogen peroxide (H2O2) photolysis-based antimicrobial chemotherapy adjunctively performed with root debridement (RD) for moderate to severe periodontitis. A randomized controlled trial was conducted that included 53 patients with 142 test teeth. The test teeth were randomly assigned to one of three treatment groups: Group 1, RD + H2O2 photolysis; Group 2, RD followed by administration of a local drug delivery system (minocycline chloride gel); or Group 3, RD alone. Clinical and microbiological examination were performed for up to 12 weeks following treatment. Probing pocket depth (PPD) and bleeding on probing (BoP) were improved after each treatment session. At 12 weeks, Group 1 had achieved significantly lower PPDs than the other groups, though there were no significant differences in BoP between Group 1 and the other groups. Counts of Porphyromonas gingivalis, a known periodontal pathogen, in Group 1 were significantly lower than those in Group 3, and were comparable to those in Group 2. Therefore, it is suggested that H2O2 photolysis treatment can be used as a novel adjunctive antimicrobial chemotherapy for non-surgical periodontal treatment.
Use of Rheumatic Scores to Guide Therapeutic Decisions in Patients with Ankylosing Spondylitis: Results of a Multicentre Study in Germany
Authors: Hillebrecht C. , Wolff B. , Kleine H. , Baerwald C. , Kuipers J. 
Published: September 2017

Abstract
Summary Background Rheumatology practice has seen an increasing development and use of scores to assess disease activity, loss of physical function, quality of life and radiographic damage. Study results, in particular for rheumatoid arthritis, demonstrate that target-oriented treatment concepts using scores lead to improved treatment results (Treat-to-Target).
Objective To review how frequently scores are used in daily rheumatological practice to assess disease activity, loss of physical function and treatment response in patients with ankylosing spondylitis and how much treatment decisions are influenced by the use of these scores.
Methods A Germany-wide prospective multicentre study 74 sites (61 rheumatologists in private practice and 13 hospital-based rheumatologists) documented the use of scores for assessing disease activity, treatment response, quality of life and imaging results in patients with ankylosing spondylitis (AS) (18–83 years) over 3 consecutive visits. A total of 1 476 fully evaluable visits of 492 patients [326 (66.26%) men and 166 (33.74%) women] were recorded.
Results The most commonly used scores were BASDAI (n=1.134, 84% of all visits) and BASFI (n=500, 37.5%). At least one score was calculated in 1.335 visits (90.45%); a combination of several scores was calculated in 748 visits (50.68%). Only in 141 visits (9.55%) no scores were calculated at all. Scores were used independently of patients’ age, duration of treatment, medication, and treatment changes and region of the participating rheumatologist. Scores recording treatment response (ASAS response) or quality of life were recorded in a few cases only. The average influence of a score on a treatment decision was 5.67 on a scale from 0 to 10.
Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest
Authors: Mills Richard J. , Titmarsh Drew M. , Koenig Xaver , Parker Benjamin L. , Ryall James G. , Quaife-Ryan Gregory A. , Voges Holly K. , Hodson Mark P. , Ferguson Charles , Drowley Lauren , Plowright Alleyn T. , Needham Elise J. , Wang Qing-Dong , Gregorevic Paul , Xin Mei , Thomas Walter G. , Parton Robert G. , Nielsen Lars K. , Launikonis Bradley S. , James David E. , Elliott David A. , Porrello Enzo R. , Hudson James E. 
Published: September 2017

Significance
Engineered cardiac muscle can be used to promote the structural and functional maturation of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs). However, previous studies have not yet produced cardiac tissues with metabolic and proliferative maturation. Here, we develop a 96-well screening platform and screen for cardiac maturation conditions in engineered cardiac muscle. We found that simulating the postnatal switch in metabolic substrates from carbohydrates to fatty acids promoted a switch in metabolism, DNA damage response, and cell cycle arrest in hPSC-CM. Our study shows that this mechanism can be harnessed to enhance the maturation of human hPSC-CM and cardiac tissues, which has major implications for stem cell sciences, drug discovery, and regenerative medicine.
IL-4–producing B cells regulate T helper cell dichotomy in type 1- and type 2-controlled diseases
Authors: Hurdayal Ramona , Ndlovu Hlumani H. , Revaz-Breton Mélanie , Parihar Suraj P. , Nono Justin Komguep , Govender Melissa , Brombacher Frank 
Published: September 2017

SignificanceCutaneous leishmaniasis and schistosomiasis are neglected tropical diseases for which there are no effective vaccines and limited treatment strategies. To develop vaccine and therapeutic alternatives, a detailed understanding of host immunity is essential. We show a role for IL-4Rα–responsive B cells in host susceptibility toLeishmania majorand protection againstSchistosoma mansoniinfection through the production of early IL-4, which in turn regulates Th2 cell polarization and disease outcome in mice. These important findings highlight the significant impacts that B cell-specific IL-4Rα and IL-4 responsiveness have in the context of type 1 (L. major) and type 2 (S. mansoni) pathogens. Thus, vaccine and therapeutic development should aim to target both B and T cell immunity for optimal efficacy.
FMtree: a fast locating algorithm of FM-indexes for genomic data
Authors: Cheng Haoyu , Wu Ming , Xu Yun 
Published: September 2017

Abstract

Motivation
As a fundamental task in bioinformatics, searching for massive short patterns over a long text has been accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to classical indexes, e.g. suffix trees and suffix arrays, while requiring less space. For genomic data, a well-known family of compressed full-text indexes, called FM-indexes, presents unmatched performance in practice. One major drawback of FM-indexes is that their locating operations, which report all occurrence positions of patterns in a given text, are not efficient, especially for the patterns with many occurrences.

Results
In this paper, we introduce a novel locating algorithm, FMtree, to fast retrieve all occurrence positions of any pattern via FM-indexes. When searching for a pattern over a given text, FMtree organizes the search space of the locating operation into a conceptual multiway tree. As a result, multiple occurrence positions of this pattern can be retrieved simultaneously by traversing the multiway tree. Compared with existing locating algorithms, our tree-based algorithm reduces large numbers of redundant operations and presents better data locality. Experimental results show that FMtree is usually one order of magnitude faster than the state-of-the-art algorithms, and still memory-efficient.

Availability and implementation
FMtree is freely available at https://github.com/chhylp123/FMtree.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cyclotomic Discriminantal Arrangements and Diagram Automorphisms of Lie Algebras
Authors: Varchenko Alexander , Young Charles 
Published: September 2017

Abstract
We identify a class of affine hyperplane arrangements that we call cyclotomic discriminantal arrangements. We establish correspondences between the flag and Aomoto complexes of such arrangements and chain complexes for nilpotent subalgebras of Kac–Moody type Lie algebras with diagram automorphisms. As part of this construction, we find that flag complexes naturally give rise to a certain cocycle on the fixed-point subalgebras of such diagram automorphisms.
As a byproduct, we show that the Bethe vectors of cyclotomic Gaudin models associated to diagram automorphisms are nonzero. We also obtain the Poincare polynomial for the cyclotomic discriminantal arrangements.
Interpolating Sequences in Spaces with the Complete Pick Property
Authors: Aleman Alexandru , Hartz Michael , McCarthy John E , Richter Stefan 
Published: September 2017

Abstract
We characterize interpolating sequences for multiplier algebras of spaces with the complete Pick property. Specifically, we show that a sequence is interpolating if and only if it is separated and generates a Carleson measure. This generalizes results of Carleson for the Hardy space and of Bishop, Marshall, and Sundberg for the Dirichlet space. Furthermore, we investigate interpolating sequences for pairs of Hilbert function spaces.
Aerosol and boundary-layer interactions and impact on air quality
Authors: Li Zhanqing , Guo Jianping , Ding Aijun , Liao Hong , Liu Jianjun , Sun Yele , Wang Tijian , Xue Huiwen , Zhang Hongsheng , Zhu Bin 
Published: September 2017

Abstract
Air quality is concerned with pollutants in both the gas phase and solid or liquid phases. The latter are referred to as aerosols, which are multifaceted agents affecting air quality, weather and climate through many mechanisms. Unlike gas pollutants, aerosols interact strongly with meteorological variables with the strongest interactions taking place in the planetary boundary layer (PBL). The PBL hosting the bulk of aerosols in the lower atmosphere is affected by aerosol radiative effects. Both aerosol scattering and absorption reduce the amount of solar radiation reaching the ground and thus reduce the sensible heat fluxes that drive the diurnal evolution of the PBL. Moreover, aerosols can increase atmospheric stability by inducing a temperature inversion as a result of both scattering and absorption of solar radiation, which suppresses dispersion of pollutants and leads to further increases in aerosol concentration in the lower PBL. Such positive feedback is especially strong during severe pollution events. Knowledge of the PBL is thus crucial for understanding the interactions between air pollution and meteorology. A key question is how the diurnal evolution of the PBL interacts with aerosols, especially in vertical directions, and affects air quality. We review the major advances in aerosol measurements, PBL processes and their interactions with each other through complex feedback mechanisms, and highlight the priorities for future studies.
Understanding Risks: Practitioner’s Perceptions of the Lottery of Mental Healthcare Available for Detainees in Custody
Authors: Williams Emma , Norman Jenny , Sondhi Arun 
Published: September 2017

Abstract
The range and growing number of healthcare requirements being presented within custody environments has been widely debated (Rekrut-Lapa, T. and Lapa, A. (2014). ‘Health Needs of Detainees in Police Custody in England and Wales: Literature Review’. Journal of Forensic and Legal Medicine 69–75). Despite a number of reforms following the recommendations of the Bradley Review (Bradley (2009). Lord Bradley’s Review of People with Mental Health Problems or Learning Disabilities in the Criminal Justice System. Department of Health and Ministry of Justice) and the amendments made to the ACPO guidance on safe detention in 2012, research continues to highlight a lack of consistency to services available to effectively identify the needs of individuals in these arenas. This article is based on part of a wider research project conducted in the Metropolitan Police Service and portrays the voice of the police practitioners working in custody suites. The research found that various notions of risk are central within this setting and that current practices are not sufficient for ensuring the safety of both detainees and officers. The research concludes by offering a proposal for capturing good practice and learning in order to create a more reflective and learning environment in custody suites.
Evaluation of Metrics for Benchmarking Antimicrobial Use in the United Kingdom Dairy Industry
Authors: Mills Harriet L. , Turner Andrea , Morgans Lisa , Massey Jonathan , Schubert Hannah , Rees Gwen , Broadfoot Fraser , Barrett David , Dowsey Andrew , Reyher Kristen K. 
Published: September 2017

AbstractThe issue of antimicrobial resistance is of global concern across human and animal health. In 2016 the UK government committed to new targets for reducing antimicrobial use (AMU) in livestock. However, though a number of metrics for quantifying AMU are defined in the literature, all give slightly different interpretations.This paper reviews a selection of metrics for AMU in the dairy industry: total mg, total mg/kg, daily dose and daily course metrics. Although the focus is on their application to the dairy industry, the metrics and issues discussed are relevant across livestock sectors.In order to be used widely, a metric should be understandable and relevant to the veterinarians and farmers who are prescribing and using antimicrobials. This means that clear methods, assumptions (and possible biases), standardised values and exceptions should be published for all metrics. Particularly relevant are assumptions around the number and weight of cattle at risk of treatment and definitions of dose rates and course lengths; incorrect assumptions can mean metrics over- or under-represent AMU.The authors recommend that the UK dairy industry work towards UK-specific metrics using UK-specific medicine dose and course regimens as well as cattle weights in order to monitor trends nationally.
Ceasing the use of the highest priority critically important antimicrobials does not adversely affect production, health or welfare parameters in dairy cows
Authors: Turner Andrea , Tisdall David , Barrett David C. , Wood Sarah , Dowsey Andrew , Reyher Kristen K. 
Published: September 2017

AbstractDue to scientific, public and political concern regarding antimicrobial resistance (AMR), several EU countries have already taken steps to reduce antimicrobial (AM) usage in production animal medicine, particularly that of the highest priority critically important AMs (HP-CIAs). While veterinarians are aware of issues surrounding AMR, barriers to change such as concerns of reduced animal health, welfare or production may inhibit AM prescribing changes.Farmers from seven dairy farms in South West England engaged in changing AM use through an active process of education and herd health planning meetings. Prescribing data was collected from veterinary sales records; production and health data were accessed via milk recording and farm-recorded data.This study demonstrates that cattle health and welfare - as measured by production parameters, fertility, udder health, mobility data and culling rates - can be maintained and even improved alongside a complete cessation in the use of HP-CIAs as well as an overall reduction of AM use on dairy farms.This study also identified a need to consider different metrics when analysing AM use data, including dose-based metrics as well as those of total quantities to allow better representation of the direction and magnitude of changes in AM use.
Optimization-based synthesis of stochastic biocircuits with statistical specifications
Authors: Sakurai Yuta , Hori Yutaka 
Published: September 2017

AbstractModel-guided design has become a standard approach to engineering biomolecular circuits in current synthetic biology. However, the stochastic nature of biomolecular reactions is often overlooked in the design process. As a result, cell-cell heterogeneity causes unexpected deviation of biocircuit behaviors from model predictions and requires additional iterations of design-build-test cycles. To enhance the design process of stochastic biocircuits, this paper presents a computational framework to systematically specify the level of intrinsic noise using well-defined metrics of statistics and design highly heterogeneous biocircuits based on the specifications. Specifically, we use descriptive statistics of population distributions as an intuitive specification language of stochastic biocircuits and develop an optimization based computational tool that explores parameter configurations satisfying design requirements. Sensitivity analysis methods are also developed to ensure the robustness of a biocircuit design. These design tools are formulated using convex optimization programs to enable efficient and rigorous quantification of the statistics without approximation, and thus, they are amenable to the synthesis of stochastic biocircuits that require high reliability. We demonstrate these features by designing a stochastic negative feedback biocircuit that satisfies multiple statistical constraints. In particular, we use a rigorously quantified parameter map of feasible design space to perform in-depth study of noise propagation and regulation in negative feedback pathways.