bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep‐learning contact‐map guided protein structure prediction in CASP13
Authors: Zheng Wei , Li Yang , Zhang Chengxin , Pearce Robin , Mortuza S. M. , Zhang Yang 
Published: July 2019

AbstractWe report the results of two fully automated structure prediction pipelines, “Zhang‐Server” and “QUARK”, in CASP13. The pipelines were built upon the C‐I‐TASSER and C‐QUARK programs, which in turn are based on I‐TASSER and QUARK but with three new modules: (a) a novel multiple sequence alignment (MSA) generation protocol to construct deep sequence‐profiles for contact prediction; (b) an improved meta‐method, NeBcon, which combines multiple contact predictors, including ResPRE that predicts contact‐maps by coupling precision‐matrices with deep residual convolutional neural‐networks; and (c) an optimized contact potential to guide structure assembly simulations. For 50 CASP13 FM domains that lacked homologous templates, average TM‐scores of the first models produced by C‐I‐TASSER and C‐QUARK were 28% and 56% higher than those constructed by I‐TASSER and QUARK, respectively. For the first time, contact‐map predictions demonstrated usefulness on TBM domains with close homologous templates, where TM‐scores of C‐I‐TASSER models were significantly higher than those of I‐TASSER models with a P‐value <.05. Detailed data analyses showed that the success of C‐I‐TASSER and C‐QUARK was mainly due to the increased accuracy of deep‐learning‐based contact‐maps, as well as the careful balance between sequence‐based contact restraints, threading templates, and generic knowledge‐based potentials. Nevertheless, challenges still remain for predicting quaternary structure of multi‐domain proteins, due to the difficulties in domain partitioning and domain reassembly. In addition, contact prediction in terminal regions was often unsatisfactory due to the sparsity of MSAs. Development of new contact‐based domain partitioning and assembly methods and training contact models on sparse MSAs may help address these issues.
Evaluation of model refinement in CASP13
Authors: Read Randy J. , Sammito Massimo D. , Kryshtafovych Andriy , Croll Tristan I. 
Published: July 2019

AbstractPerformance in the model refinement category of the 13th round of Critical Assessment of Structure Prediction (CASP13) is assessed, showing that some groups consistently improve most starting models whereas the majority of participants continue to degrade the starting model on average. Using the ranking formula developed for CASP12, it is shown that only 7 of 32 groups perform better than a “naïve predictor” who just submits the starting model. Common features in their approaches include a dependence on physics‐based force fields to judge alternative conformations and the use of molecular dynamics to relax models to local minima, usually with some restraints to prevent excessively large movements. In addition to the traditional CASP metrics that focus largely on the quality of the overall fold, alternative metrics are evaluated, including comparisons of the main‐chain and side‐chain torsion angles, and the utility of the models for solving crystal structures by the molecular replacement method. It is proposed that the introduction of these metrics, as well as consideration of the accuracy of coordinate error estimates, would improve the discrimination between good and very good models.
Effect and mechanism of verbascoside on hypoxic memory injury in plateau
Authors: Li Maoxing , Zhu Yuting , Li Jing , Chen Liping , Tao Wendi , Li Xiaoling , Qiu Yan 
Published: July 2019

Verbascoside is a water‐soluble natural phenylethanoid glycoside and distributes widely in plants. It has been proved with antioxidant, neuroprotective, anti‐inflammatory, antibacterial, and immunomodulatory bioactivities. In this experiment, the effect and mechanism of verbascoside on hypoxic memory injury were studied in a low‐pressure and low‐oxygen chamber. Verbascoside (50, 150, and 300 mg/kg) was intragastrically administered once a day for 7 days. On the fourth day, rats were placed in the chamber to simulate a 7,500 m high‐altitude environment The eight‐arm maze was used to test the memory ability. The levels of MDA, GSH, and T‐SOD in plasma, brain‐NH, and hippocampus were detected. The mRNA expression of mTOR, P70S6K, and 4E‐BP1 in the hippocampus tissue was determined by PCR. The protein expression of P‐mTOR, P‐P70S6K, P‐4E‐BP1, and Cleaved Caspase‐3 in the hippocampus tissue was determined by western blot. The results indicated that administration with verbascoside could obviously reduce the working memory error, reference memory error, total errors, and total time; relieve the neuron damage in CA1 region of the hippocampus; and decrease the oxidative stress correlation enzyme activity in plasma, brain, and hippocampus. The amelioration of verbascoside on high altitude–induced memory impairment may be associated with the adjustment of oxidative stress and mTOR signaling pathway.
Reshaping demand landscapes: How firms change customer preferences to better fit their products
Authors: Vinokurova Natalya 
Published: July 2019

AbstractResearch SummaryWhat strategies do firms use to change their customers' preferences? This paper addresses this question by developing a conceptual model that combines the representation of customer preferences as a demand landscape with research on marketing and psychology. I suggest that in addition to changing their products to accommodate customer preferences, firms also change the distribution of customer preferences to accommodate the firms' products. Specifically, I argue that firms alter customer preferences by adding, removing, and transforming the dimensions of the demand landscape. I illustrate the model with an historical case study of the U.S. market for mortgage‐backed securities (MBS) between 1968 and 1987, a period during which MBS issuers succeeded in reshaping the bond demand landscape to promote the acceptance of MBS as bonds.Managerial SummaryManagers often assume that customer tastes are fixed and that the only way to improve a product's appeal to customers is to change the product's attributes to better accommodate the customers' preferences. In this paper, I consider two approaches firms can take to changing customer preferences to better accommodate their products. One approach is to convince the customers that the combination of attributes offered by the firm's product is more valuable than that in a product a customer is used to buying. An alternative approach is to manipulate the customer's perception of similarity between a product she is used to and the firm's product.
Experimental study on the performance of the UHPC longitudinal joint between existing bridge decks and lateral extensions
Authors: Chao Liu , Yuhao Huang , Yuanchun Lu 
Published: July 2019

AbstractAn experiment on high‐strain hardening ultra‐high‐performance concrete (UHPC) stitching joints was conducted based on the bridge‐stitching project of Jiyang viaduct, Shanghai. In this experiment, asymmetrical loading was used to simulate the bridge differential settlement caused by soil settlement. The experimental results showed that the entire process could be divided into three stages: elastic stage, cracks developing stage, and failure stage. During these stages, cracks appeared at the bottom of the UHPC slab. Then, many microcracks appeared at the side of the UHPC slab. These microcracks appeared in the form of microcrack clusters, and the width of these cracks increased slowly. It indicated that UHPC had good crack‐control ability. Finally, the main crack appeared at the bottom of the UHPC slab, and the transverse reinforcements yielded. It indicated that the reinforcement layout met the requirements of the failure mode of the specimen. For further analysis, the finite‐element model (FEM) was established. And the results showed that the bending resistance of the joints could be effectively enhanced by increasing the free length of the joint or reducing the thickness of the joint. Based on this experiment and analysis, a nonconnected joint form between slabs and girders was put forward. And the detailed reinforcement scheme of this nonconnected joint form was given. This reinforcement scheme could serve as a reference for similar projects.
Influences of design parameters on the properties of self‐compacting concrete produced with structurally different polycarboxylates
Authors: Erzengin Siddika G. , Öcal Cenk 
Published: July 2019

AbstractNew mixes were prepared according to the EFNARC self‐compacting concrete criteria with synthesized polycarboxylate‐type superplasticizers. For this purpose, superplasticizers possessing different side‐chain lengths and cross‐linkages were produced to overcome the workability and workability‐retention problems in self‐compacting concrete (SCC) by time. Not only the fresh properties but also hardened properties of SCCs were improved. With this study it was determined that, cross‐linked polycarboxylate‐type superplasticizer shows better performance in SCC compared to its counterparts and commercial polycarboxylate. It provides better self‐compaction by discharging its bubbles during molding. Besides, the effects of water‐powder ratio and superplasticizer dosage were also examined and discussed in this study.
Experimental study of lateral load behavior of H‐shaped precast reinforced concrete shear walls with bolted steel connections
Authors: Sun Jian , Qiu Hongxing , Lu Yong , Jiang Hongbo 
Published: July 2019

SummaryThis paper presents an experimental study of H‐shaped precast reinforced concrete shear walls involving vertical connections under combined vertical and lateral loading. The H‐wall is composed of two prefabricated flange wall panels: one prefabricated web wall panel and vertical bolted steel connections between the flange and web panels. The assembling of the H‐wall is completely dry without any in situ casting. Three H‐wall specimens were constructed and tested to investigate the mechanical behavior and seismic performance of them. The lateral load‐bearing capacity, ductility, energy dissipation, lateral stiffness, strain in the connecting steel frame, and sliding within the bolted steel connections are presented and discussed to evaluate the effectiveness of the vertical connections. The ultimate shear‐resistance mechanism of the precast H‐wall assembly is also analyzed. The H‐wall assemblies generally possess high load‐bearing capacity, favorable ductility, and good energy‐dissipating capacity. The thickness of the steel plates in the connecting steel frame affects the lateral stiffness and the ultimate load‐bearing capacity of the H‐walls. Furthermore, the encasing steel plates for the web wall panel not only helps transfer the stress in the wall steel bars but also confines the concrete resulting in improved ductility.
Surgical Notes: To Play or Not to Play
Authors: Mitta Nivedita , Jayakumar Vivekanandan , Dhanpal Nikhil , Raj Jeffrey Pradeep , Prabhakaran Roshini Antony , Kannan Karthikeyan , Venugopal Anirudh , Subramanyam S. G. 
Published: July 2019

AbstractIntroductionMusic is any sound that is perceived as pleasingly harmonious. The link between music and healthcare can be traced long back in the history of mankind. Thus, our study aimed at assessing the impact of different genre of music on the cognition functioning, memory and attention levels of the surgeons.Materials and methodsIt was a single‐arm interventional trial assessing 45 surgeons from different specialities. Each participant was expected to do 5 sets of tasks, one set each for the 5 music tracks played. Each task set further contained 5 different types of tasks, namely trail marking, jigsaw puzzle, backward counting, comprehension and memory game using cards. The 5 music tracks included ambient OR noise, music of personal preference, western classical, heavy metal and pop music. Scores were assigned for each task and compared.ResultsThe total score for music of personal choice was much less (19.68) when compared to the other genre and that for pop was the highest (25.03). Memory card tests and backward counting (tests of short‐term memory) were comparatively better with music of personal choice. However, trail marking (test of speed) and jigsaw puzzle and comprehension tests (tests of complex neurological functions) were least performed when music of personal choice was played.ConclusionMusic of choice may help in short‐term memory recall, but an over‐familiarity with the music played can serve as a distractor thus affecting the speed and accuracy.
Drop formation in microfluidic cross-junction: jetting to dripping to jetting transition
Authors: Kovalchuk Nina M. , Sagisaka Masanobu , Steponavicius Kasparas , Vigolo Daniele , Simmons Mark J. H. 
Published: July 2019

AbstractThe regimes of drop generation were studied in a Dolomite microfluidic device which combined both hydrodynamic and geometrical flow focusing over a broad range of flow rates. A series of aqueous dispersed phases were used with a viscosity ratio between continuous and dispersed phases of close to unity. Surfactants were added to alter the interfacial tension. It was shown that the transition from dripping to jetting is well described by the capillary numbers of both the dispersed and continuous phases. Only the jetting regime was observed if the capillary number of the dispersed phase was above a critical value, whereas at smaller values of this parameter a jetting → dripping → jetting transition was observed by increasing the capillary number of the continuous phase. The analysis performed has shown that the conditions for a dripping to jetting transition at moderate and large values of the capillary number of the continuous phase can be predicted theoretically by comparison of the characteristic time scales for drop pinch-off and jet growth, whereas the transition at small values cannot. It is suggested that this transition is geometry mediated and is a result of the interplay of jet confinement in the focusing part and a decrease of confinement following entry into the main channel. The flow fields inside the jet of the dispersed phase were qualitatively different for small and large values of the capillary number of the continuous phase revealing the relative contribution of the dispersed phase flow in jet formation. The volume of the drops formed in the jetting regime increased as a power law function of the flow rate ratio of the dispersed to continuous phase, independent of the interfacial tension.
Influence of surrounding land-use on mussel growth and glycogen levels in the St. Croix and Minnesota River Basins
Authors: Hornbach Daniel J. , Stutzman Hayley N. , Hove Mark C. , Kozarek Jessica L. , MacGregor Kelly R. , Newton Teresa J. , Ries Patricia R. 
Published: July 2019

AbstractFreshwater mussels face threats from climate change and changing land use that are dramatically altering their habitat. The health of mussel populations and the state of current and past environmental conditions can be monitored by measuring mussel growth and glycogen levels. In this study, we measured growth and glycogen levels in mussels from two small river basins impacted by different land uses. The Snake River in the St. Croix Basin, Minnesota, had low levels of suspended sediments and was surrounded mostly by forest and some developed land. The Chippewa, Cottonwood, and Le Sueur rivers in the Minnesota River Basin had significantly higher annual suspended sediment loads and highly agricultural basins. Mussel growth was highest in the Le Sueur and Cottonwood rivers followed by the Chippewa and the Snake rivers. Mussels in the Minnesota Basin rivers all had higher mussel foot glycogen concentrations than the Snake River. These patterns were similar for two mussel species, suggesting that environmental conditions are likely determining levels of growth. Although agriculture had a negative effect on mussel population abundance and diversity, it had a positive effect on growth and glycogen levels.
Sharing De-identified Medical Images Electronically for Research: A Survey of Patients' Opinion regarding Data Management
Authors: Mahmoud Rasha , Moody Alan R. , Foster Moran , Girdharry Natasha , Sinn Loreta , Zhang Bowen , Afshin Mariam , Vivekanandan Thayalasuthan , Santoro Samantha , Tyrrell Pascal N. 
Published: July 2019

Purpose Secondary usage of patient data has recently become of increasing interest for the development and application of computer analytic techniques. Strict oversight of these data is required and the individual patients themselves are integral to providing guidance. We sought to understand patients' attitudes to sharing their imaging data for research purposes. These images could provide a great wealth of information for researchers. Methods Patients from the Greater Toronto Area attending Sunnybrook Health Sciences Centre for imaging (magnetic resonance imagining, computed tomography, or ultrasound) examination areas were invited to participate in an electronic survey. Results Of the 1083 patients who were approached (computed tomography 609, ultrasound 314, and magnetic resonance imaging 160), 798 (74%) agreed to take the survey. Overall median age was 60 (interquartile range = 18, Q1 = 52, Q3 = 70), 52% were women, 42% had a university degree, and 7% had no high school diploma. In terms of willingness to share de-identified medical images for research, 76% were willing (agreed and strongly agreed), while 7% refused. Most participants gave their family physicians (73%) and other physicians (57%) unconditional data access. Participants chose hospitals/research institutions to regulate electronic images databases (70%), 89% wanted safeguards against unauthorized access to their data, and over 70% wanted control over who will be permitted, for how long, and the ability to revoke that permission. Conclusions Our study found that people are willing to share their clinically acquired de-identified medical images for research studies provided that they have control over permissions and duration of access.
Outcomes after Percutaneous Angioplasty of Arteriovenous Fistulas and Grafts in African American Patients
Authors: Kochanek Malgorzata A. , McGill Rita L. , Navuluri Rakesh , Shah Vipuj , Hammes Mary 
Published: July 2019

Purpose Arteriovenous fistulas and grafts, necessary for hemodialysis, may develop stenoses due to neointimal hyperplasia, which often require percutaneous transluminal angioplasty. Patient and lesion characteristics were evaluated prior to angioplasty and were correlated with 1- and 6-month outcomes. Materials and Methods This was an observational study of African American hemodialysis patients who presented for angioplasty of a dysfunctional fistula or graft. Clinical outcomes were ascertained from dialysis facilities 1 month and 6 months after angioplasty. One-month clinical success was defined as dialyzer blood flows of 450 mL/min without complications or interval shunt thrombosis, interventions, or loss of access, which was rarely achieved at 6 months. Logistic regression models were used to evaluate associations of clinical variables with outcomes. Results There were 150 stenoses treated during 99 procedures performed on 82 patients. The clinical success rate at one month was 67% with no complications as a result of the percutaneous transluminal angioplasty. Success at 1 month was positively associated with use of aspirin ( P = .005) and with referral for high venous pressures ( P = .004). Six-month data were available for 81 procedures, with 45.7% requiring repeat angioplasty and 12.3% suffering major complications (thrombectomy, revision surgery, or access abandonment). Major complications were seen predominantly in patients who were not receiving aspirin. Conclusions Aspirin use and high venous pressure were associated with 1-month clinical success and fewer major complications at 6 months. Future work should investigate biologic mechanisms of action of aspirin and long-term effects of use to maintain vascular access.
Building and strengthening relationships between academic departments/divisions of emergency medicine and rural and regional emergency departments
Authors: Johnston Aaron , Booth Kylie , Christenson Jim , Fu David , Lee Shirley , Mawji Yasmine , Myhre Doug , van der Linde Etienne , Lang Eddy 
Published: July 2019

ABSTRACTObjectivesMake recommendations on approaches to building and strengthening relationships between academic departments or divisions of Emergency Medicine and rural and regional emergency departments.MethodsA panel of leaders from both rural and urban/academic practice environments met over 8 months. Draft recommendations were developed from panel expertise as well as survey data and presented at the 2018 Canadian Association of Emergency Physicians (CAEP) Academic Symposium. Symposium feedback was incorporated into final recommendations.ResultsSeven recommendations emerged and are summarized below:
1)CAEP should ensure engagement with other rural stakeholder organizations such as the College of Family Physicians of Canada and the Society of Rural Physicians of Canada.2)Engagement efforts require adequate financial and manpower resources.3)Training opportunities should be promoted.4)The current operational interface between the academic department of Emergency Medicine and the emergency departments in the catchment area must be examined and gaps addressed as part of building and strengthening relationships.5)Initial engagement efforts should be around projects with common value.6)Academic Departments should partner with and support rural scholars.7)Academic departments seeking to build or strengthen relationships should consider successful examples from elsewhere in the country as well as considering local culture and challenges.ConclusionThese recommendations serve as guidance for building and strengthening mutually beneficial relationships between academic departments or divisions of Emergency Medicine and rural and regional emergency departments.
Impact of decolonization on methicillin-resistant Staphylococcus aureus transmission and infection in a neonatal intensive care unit
Authors: Bozzella Michael J. , Soghier Lamia , Harris Tracie , Zell Lisa , Short Billie Lou , Song Xiaoyan 
Published: July 2019

AbstractBackground:The value of decolonization as a strategy for preventing methicillin-resistantStaphylococcus aureus (MRSA) in the neonatal intensive care unit (NICU) remains to be determined.Objective:After adding decolonization to further reduce MRSA transmission in our NICU, we conducted this retrospective review to evaluate its effectiveness.Method:The review included patients who were admitted to our NICU between April 2015 and June 2018 and were eligible for decolonization including twice daily intranasal mupirocin and daily chlorhexidine gluconate bathing over 5 consecutive days. Patients were considered successfully decolonized if 3 subsequent MRSA screenings conducted at 1-week intervals were negative. The MRSA acquisition rate (AR) was calculated as hospital-acquired (HA) MRSA per 1,000 patient days (PD) and was used to measure the effectiveness of the decolonization.Results:Of the 151 MRSA patients being reviewed, 78 (51.6%) were HA-MRSA, resulting in an overall AR of 1.27 per 1,000 PD. Between April 2015 and February 2016, when only the decolonization was added, the AR was 2.38 per 1,000 PD. Between March 2016 and June 2018 after unit added a technician dedicated to the cleaning of reusable equipment, the AR decreased significantly to 0.92 per 1,000 PD (P < .05). Of the 78 patients who were started on the decolonization, 49 (62.8%) completed the protocol, 11 (14.1%) remained colonized, and 13 (16.7%) were recolonized prior to NICU discharge.Conclusion:In a NICU with comprehensive MRSA prevention measures in place, enhancing the cleaning of reusable equipment, not decolonization, led to significant reduction of MRSA transmission.