bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silymarin attenuates cigarette smoke extract-induced inflammation via simultaneous inhibition of autophagy and ERK/p38 MAPK pathway in human bronchial epithelial cells
Authors: Li Diandian , Hu Jun , Wang Tao , Zhang Xue , Liu Lian , Wang Hao , Wu Yanqiu , Xu Dan , Wen Fuqiang 
Published: November 2016

AbstractCigarette smoke (CS) is a major risk of chronic obstructive pulmonary disease (COPD), contributing to airway inflammation. Our previous study revealed that silymarin had an anti-inflammatory effect in CS-exposed mice. In this study, we attempt to further elucidate the molecular mechanisms of silymarin in CS extract (CSE)-induced inflammation using human bronchial epithelial cells. Silymarin significantly suppressed autophagy activation and the activity of ERK/p38 mitogen-activated protein kinase (MAPK) pathway in Beas-2B cells. We also observed that inhibiting the activity of ERK with specific inhibitor U0126 led to reduced autophagic level, while knockdown of autophagic gene Beclin-1 and Atg5 decreased the levels of ERK and p38 phosphorylation. Moreover, silymarin attenuated CSE-induced upregulation of inflammatory cytokines TNF-α, IL-6 and IL-8 which could also be dampened by ERK/p38 MAPK inhibitors and siRNAs for Beclin-1 and Atg5. Finally, we validated decreased levels of both autophagy and inflammatory cytokines (TNF-α and KC) in CS-exposed mice after silymarin treatment. The present research has demonstrated that CSE-induced autophagy in bronchial epithelia, in synergism with ERK MAPK pathway, may initiate and exaggerate airway inflammation. Silymarin could attenuate inflammatory responses through intervening in the crosstalk between autophagy and ERK MAPK pathway, and might be an ideal agent treating inflammatory pulmonary diseases.
The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding
Authors: Vallebueno-Estrada Miguel , Rodríguez-Arévalo Isaac , Rougon-Cardoso Alejandra , Martínez González Javier , García Cook Angel , Montiel Rafael , Vielle-Calzada Jean-Philippe 
Published: November 2016

Significance
The valley of Tehuacán in Mexico is an important center of early Mesoamerican agriculture. To characterize the genetic constitution of the earliest phase of maize cultivation, we reexamined San Marcos cave in Tehuacán and sequenced DNA from three newly discovered maize samples dating at a similar age of 5,000 y B.P. The genomes of these samples reveal unforeseen levels of genetic diversity as compared with modern maize, indicating that the effects of domestication were not yet complete. We find that their genetic constitution was similar and influenced by inbreeding, suggesting that the corresponding plants come from a reduced population of isolated and perhaps self-pollinated individuals.
Nonlinear fishbone dynamics in spherical tokamaks
Authors: Wang Feng , Fu G.Y. , Shen Wei 
Published: November 2016

Abstract
Linear and nonlinear kinetic-MHD hybrid simulations have been carried out to investigate linear stability and nonlinear dynamics of beam-driven fishbone instability in spherical tokamak plasmas. Realistic NSTX parameters with finite toroidal rotation were used. The results show that the fishbone is driven by both trapped and passing particles. The instability drive of passing particles is comparable to that of trapped particles in the linear regime. The effects of rotation are destabilizing and a new region of instability appears at higher q
min (>1.5) values, q
min being the minimum of safety factor profile. In the nonlinear regime, the mode saturates due to flattening of beam ion distribution, and this persists after initial saturation while mode frequency chirps down in such a way that the resonant trapped particles move out radially and keep in resonance with the mode. Correspondingly, the flattening region of beam ion distribution expands radially outward. A substantial fraction of initially non-resonant trapped particles become resonant around the time of mode saturation and keep in resonance with the mode as frequency chirps down. On the other hand, the fraction of resonant passing particles is significantly smaller than that of trapped particles. Our analysis shows that trapped particles provide the main drive to the mode in the nonlinear regime.
SarConfoCal: simultaneous sarcomere length and cytoplasmic calcium measurements for laser scanning confocal microscopy images
Authors: Pasqualin Côme , Gannier François , Yu Angèle , Malécot Claire O , Bredeloux Pierre , Maupoil Véronique 
Published: November 2016

Abstract

Summary
Simultaneous recordings of myocytes contractility and their cytoplasmic calcium concentration allow powerful studies, particularly on heart failure and other cardiac dysfunctions. Such studies require dedicated and expensive experimental devices that are difficult to use. Thus we propose SarConfoCal, the first and only software to simultaneously analyse both cytoplasmic calcium variations (from fluorescence signal) and myocytes contractility (from sarcomere length measurement) on laser scanning confocal microscopy images. SarConfoCal is easy to set up and use, especially by people without programming skills.

Availability and implementation
The software is freely distributed under the GNU General Public License. Download and setup instructions are available at http://pccv.univ-tours.fr/ImageJ/SarConfoCal. It is provided as a toolset for ImageJ (the open-source program for image analysis provided by the National Institutes of Health). SarConfoCal has been tested under Windows, Mac and Linux operating systems.

Supplementary information
Supplementary data are available at Bioinformatics online.
Statistical inference of protein structural alignments using information and compression
Authors: Collier James H , Allison Lloyd , Lesk Arthur M , Stuckey Peter J , Garcia de la Banda Maria , Konagurthu Arun S 
Published: November 2016

Abstract

Motivation
Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power—the amount of lossless compression achieved to explain the protein coordinates using that alignment.

Results
We have implemented this approach in MMLigner, the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner’s alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes.

Availability and Implementation
Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner.

Supplementary information
Supplementary data are available at Bioinformatics online.
Balearic Islands boat seine fisheries: the transparent goby fishery an example of co-management
Authors: Morales-Nin Beatriz , Grau Antoni María , Aguilar Juan Salvador , Gil María del Mar , Pastor Elena 
Published: November 2016

Abstract
An economically important, small-scale fishery operates during the winter months in Mallorca. Using a special surrounding net that is hauled over the sand and gravel bottoms of bays at depths reaching 30 m, it primarily targets Aphia minuta and Pseudaphya ferreri, but other goby species and juveniles of the Pagellus spp are also caught. Similar fisheries are operated on the Spanish coast and in Italy. This fishery is run with specific licenses, equipment controls, and closed seasons (based on species availability). In cooperation with local fishermen, the administration has in recent years established a daily quota for sustaining the sales prices 22of the species caught. A management plan was set up in 2013 in accordance with European Union rules to ensure the sustainability of the fishery. Its sustainable quotas have been set at 30 kg/day/boat for A. minuta and 50 kg/day/boat for P. ferreri, and the by-catch cannot exceed 10% of the total catch. Landings are permitted in 11 fixed ports and only 35 boats can fish with the regulated nets from December 15 to April 30. A co-management committee was created with the participation of the public administration, fishermen’s associations, researchers, and certain non-governmental organizations. The co-management process was revised and fishermen’s opinions were obtained in a successful enquiry that was answered by the majority of the operating fleet, and their views on the management rules will be considered in future regulations. The co-management of the small-scale boat seine fishery in the Balearic Islands is thus an ongoing collaborative and communicative process in a local community that continues to evolve over time. Although the fishermen are represented by their port guilds, communication efforts are necessary in the near future to ensure the success of the co-management process.
Rhinitis: adherence to treatment and new technologies
Authors: Braido Fulvio , Baiardini Ilaria , Puggioni Francesca , Garuti Silvia , Pawankar Ruby , Walter Canonica G. 
Published: November 2016

Purpose of review
Nonadherence to treatment is a major issue in approximately 50% of patients suffering from chronic diseases. The availability of new technologies could represent a possible way to improve patients’ engagement and adherence in a real-life setting. Research and technology tools made available or in process of being made available to patients with allergic diseases and their physicians could potentially improve the management of these disease in daily life by improving adherence. In this review, we sought to outline many of the recent advances in these technological approaches.

Recent findings
Short Message Service (SMS) reminder, social networks, wearable devices, mobile applications (Apps), monitoring systems of inhaled device use, often presented as ‘serious game’ are changing the way of approaching to chronic disease, such as rhinitis, management.

Summary
Studies of the role played by various technologies in improving adherence to treatment in rhinitis are still limited as compared with other diseases such as asthma, but the results are encouraging. Further studies in this area may lead to the discovery of novel management approaches that is easy to be integrated in patients’ daily life.
A biomechanical comparison of conventional versus cable pin fixation for transverse patellar fractures
Authors: Schrayer Aaron , Morris Randal P. , Patton Andrew G. , Buford William L. , Lindsey Ronald W. 
Published: November 2016

Background:
Transverse patellar fractures require fixation that anatomically restores continuity of the knee extensor complex and resiliency to the loads of early postoperative knee mobilization. The objective of this study was to evaluate the biomechanical fixation strength of three patellar osteosynthesis techniques.

Methods:
Transverse osteotomies were created in 24 custom fourth-generation composite left patellae, randomized into three equal groups for osteosynthesis fixation: group I, modified anterior tension wiring; group II, cannulated lag screws with anterior tension wiring; group III, cable pin fixation system. All patellae were loaded in simulated 60-degree knee flexion at 15 mm/min until complete failure.

Results:
Mean load to failure for group I (415.14±150.10 N) was significantly less than the load for group II (814.37±281.98 N), P=0.023 and group III (1103.64±358.70 N), P<0.0001. Mean stiffness for group II and group III were 51.60±5.01 N/mm and 46.53±3.09 N/mm, respectively, and statistically higher (P<0.0001) than group I (23.86±7.02 N/mm). Mean medial gapping in group III (10.33±6.50 mm) was statistically higher (P=0.041) than that in group II (4.59±3.19 mm).

Conclusions:
Greater compression across the fracture site was likely in the more robust constructs of cannulated lag screws with anterior tension wiring (group II) and cable pin fixation (group III), which may allow more timely and aggressive postoperative mobilization.
The Role of Dedicated Musculoskeletal Urgent Care Centers in Reducing Cost and Improving Access to Orthopaedic Care
Authors: Anderson Travis J. , Althausen Peter L. 
Published: November 2016

Objectives:
Over the past few years, the United States has seen the rapid growth of dedicated musculoskeletal urgent care centers owned and operated by individual orthopaedic practices. In June of 2014, our practice opened the first dedicated orthopaedic urgent care in the region staffed by physician assistants and supervised by orthopaedic surgeons. Our hypothesis is that such centers can safely improve orthopaedic care for ambulatory orthopaedic injuries, decrease volume for overburdened emergency departments (EDs), reduce wait times and significantly decrease the cost of care while improving access to orthopaedic specialists.

Design:
Retrospective review.

Setting:
Level 2 trauma center and physician-owned orthopaedic urgent care.

Patients:
Consecutive series of patients seen in the hospital ED (n = 87,629) and orthopaedic urgent care (n = 12,722).

Intervention:
None.

Outcomes:
ED wait time, total visit time, time until being seen by provider, time until consultation with orthopaedic surgeon, total visit charges, and effect on orthopaedic practice revenue.

Results:
During the 12 months of study, 12,722 patients were treated in our urgent care. The average urgent care wait time until being seen by a provider was 17 minutes compared with 45 minutes in hospital ED. Total visit time was 43 minutes in the urgent care and 156 minutes in the hospital ED. Time to being seen by an orthopaedic specialist was 1.2 days for urgent care patients compared with 3.4 days for ED patients. The average charge for an urgent care visit was $461 compared with $8150 in hospital ED. During the course of study, urgent care treatment reduced charges to health care system by $97,819,458. Hospital ED orthopaedic volume did decrease as expected but total ED patient volume remained the same. There was no measureable effect on hospital ED wait times. Hospital surgical case volume did not change over the period of study and the orthopaedic census remained stable. Urgent care construction, marketing, administration, imaging, and labor costs totaled $1,664,445. Urgent care revenue from evaluation and management, imaging, durable medical equipment, and casting totaled $2,577,707. Practice revenue from follow-up care of patients who entered practice through the urgent care totaled $7,657,998.

Conclusion:
Dedicated musculoskeletal urgent care clinics operated by orthopaedic surgery practices can be extremely beneficial to patients, physicians, and the health care system. They clearly improve access to care, whereas significantly decreasing overall health care costs for patients with ambulatory orthopaedic conditions and injuries. In addition, they can be financially beneficial to both patients and orthopaedic surgeons alike without cannibalizing local hospital surgical volumes.

Level of Evidence:
Therapeutic Level III.
Operating Room Supply Costs in Orthopaedic Trauma: Cost Containment Opportunities
Authors: Gurnea Taylor P. , Frye Wesley P. , Althausen Peter L. 
Published: November 2016

Summary:
In the current health care environment, cost containment is more important than ever. Most physicians currently are unaware of the cost of operating room supplies. A large amount of waste occurs secondary to lack of knowledge and absence of physician incentives for cost saving. Many of the decisions for supply use can be based on good scientific evidence, which supports specific cost saving measures. Careful attention to blood utilization and use of tranexamic acid has the potential to save millions in the hip fracture treatment and arthroplasty treatments. Standardization of surgical preparation and draping can decrease costs and prevent costly surgical site infections. Following protocols and guidelines for bone graft and orthobiologics is critical. The clinical and legal repercussions of retained instruments and costs associated with dropped implants is a huge source of wasted health care dollars. Reprocessing programs for external fixators and tourniquets have been extremely successful. A myriad of opportunities for intraoperative cost savings exist that could be applied to nearly every orthopaedic surgery performed in the United States. It is incumbent on all surgeons to put aside the choices made out of habit and take part in reducing operating room waste for the benefit of hospitals, patients, and the health care system. When applied to the 5.3 million orthopaedic surgeries performed annually in the United States, billions of dollars could easily be saved with no adverse effect on patient care.
Cutaneous Sebaceous Lesions in a Patient With MUTYH-Associated Polyposis Mimicking Muir-Torre Syndrome
Authors: Kacerovska Denisa , Drlik Lubomir , Slezakova Lenka , Michal Michal , Stehlik Jan , Sedivcova Monika , Hadravsky Ladislav , Kazakov Dmitry V. 
Published: November 2016

Abstract:
A 76-year-old white male with a history of adenocarcinoma of the rectosigmoideum and multiple colonic polyps removed at the age of 38 and 39 years by an abdominoperitoneal amputation and total colectomy, respectively, presented with multiple whitish and yellowish papules on the face and a verrucous lesion on the trunk. The lesions were surgically removed during the next 3 years and a total of 13 lesions were investigated histologically. The diagnoses included 11 sebaceous adenomas, 1 low-grade sebaceous carcinoma, and 1 squamous cell carcinoma. In some sebaceous lesions, squamous metaplasia, intratumoral heterogeneity, mucinous changes, and peritumoral lymphocytes as sometimes seen in sebaceous lesions in Muir–Torre syndrome were noted. Mutation analysis of the peripheral blood revealed a germline mutation c.692G>A,p.(Arg231His) in exon 9 and c.1145G>A, p.(Gly382Asp) in exon 13 of the MUTYH gene. A KRAS mutation G12C (c.34G>T, p.Gly12Cys) was detected in 1 sebaceous adenoma and a NRAS mutation Q61K (c.181C>A, p.Gln61Lys) was found in 2 other sebaceous adenomas. No germline mutations in MLH1, MSH2, MSH6 and PMS2 genes, no microsatellite instability, no aberrant methylation of MLH1 promoter, and no somatic mutations in MSH2 and MSH6 were found. An identical MUTYH germline mutation was found in the patient's daughter. Despite striking clinicopathological similarities with Muir–Torre syndrome, the molecular biologic testing confirmed the final diagnosis of MUTYH-associated polyposis.
Aggressive Digital Papillary Adenocarcinoma With Multiple Organ Metastases: A Case Report and Review of the Literature
Authors: Kobayashi Tadahiro , Hiura Azusa , Oishi Kyosuke , Maeda Shintaro , Le Pavoux Andres James , Ohara Kuniaki , Uruga Hironori 
Published: November 2016

Abstract:
Aggressive digital papillary adenocarcinoma (ADPA) is a rare sweat gland neoplasm with a high recurrence rate and metastatic potential. In this study, the authors describe a case that originally appeared to benign spiradenoma, but took an ominous course eventually resulting in the diagnosis of ADPA. A 73-year-old woman developed a gradually growing nodule on the second toe of her left foot, which she had first noticed 4 years previously. An excisional biopsy was performed followed by histological examination. The authors initially considered the tumor to be a benign spiradenoma and did not perform reexcision. However, she experienced local recurrence 24 months later, and multiple pulmonary metastasis 31 months later. On histological examination, both the primary and locally recurrent tumors were found to be composed of discrete and well-circumscribed solid nodules, lacking cystic space. All tumors (the primary tumor, locally recurrent tumor, and lung metastases) presented with a pattern of fused back-to-back tubular structures and myoepithelial differentiation confirmed by immunohistochemical examination. On the basis of these findings, the authors finally diagnosed ADPA with multiple pulmonary metastases. The patient underwent chemotherapy, but died of disease 49 months later. This case highlights the importance of high clinical suspicion of ADPA when digital lesions present.
Targeting β3-Adrenergic Receptors in the Heart: Selective Agonism and β-Blockade
Authors: Cannavo Alessandro , Koch Walter J. 
Published: November 2016

Abstract:
Cardiac diseases, such as heart failure, remain leading causes of morbidity and mortality worldwide, with myocardial infarction as the most common etiology. HF is characterized by β-adrenergic receptor (βAR) dysregulation that is primarily due to the upregulation of G protein–coupled receptor kinases that leads to overdesensitization of β1 and β2ARs, and this clinically manifests as a loss of inotropic reserve. Interestingly, the “minor” βAR isoform, the β3AR, found in the heart, lacks G protein–coupled receptor kinases recognition sites, and is not subject to desensitization, and as a consequence of this, in human failing myocardium, the levels of this receptor remain unchanged or are even increased. In different preclinical studies, it has been shown that β3ARs can activate different signaling pathways that can protect the heart. The clinical relevance of this is also supported by the effects of β-blockers which are well known for their proangiogenic and cardioprotective effects, and data are emerging showing that these are mediated, at least in part, by enhancement of β3AR activity. In this regard, targeting of β3ARs could represent a novel potential strategy to improve cardiac metabolism, function, and remodeling.
Reconstruction of the Ptotic Breast Using Wise Pattern Skin Deepithelialization
Authors: Newman Michael K. 
Published: November 2016

Summary:
Reconstruction of ptotic or large breasts is challenging due to skin redundancy after skin-sparing mastectomy. Skin reduction can be performed with a long horizontal ellipse, but this often flattens the breast and leaves conspicuous scars medially on the chest. Wise pattern skin reduction is an effective technique for shaping, but excision of skin within the Wise pattern can lead to high rates of skin necrosis and implant exposure or infection. This study describes a technique where the Wise pattern skin is preserved, but deepithelialized, allowing apparent reduction of the skin with preservation of the subdermal plexus. This study reviews data for case series of 26 breasts in 15 patients who have undergone this technique with simultaneous prosthetic reconstruction using an expander.