bluuebunny/crossref_metadata_2025_split huggingface dataset:
PDID: database of molecular-level putative protein–drug interactions in the structural human proteome
Authors: Wang Chen , Hu Gang , Wang Kui , Brylinski Michal , Xie Lei , Kurgan Lukasz 
Published: October 2015

Abstract
Motivation: Many drugs interact with numerous proteins besides their intended therapeutic targets and a substantial portion of these interactions is yet to be elucidated. Protein–Drug Interaction Database (PDID) addresses incompleteness of these data by providing access to putative protein–drug interactions that cover the entire structural human proteome.
Results: PDID covers 9652 structures from 3746 proteins and houses 16 800 putative interactions generated from close to 1.1 million accurate, all-atom structure-based predictions for several dozens of popular drugs. The predictions were generated with three modern methods: ILbind, SMAP and eFindSite. They are accompanied by propensity scores that quantify likelihood of interactions and coordinates of the putative location of the binding drugs in the corresponding protein structures. PDID complements the current databases that focus on the curated interactions and the BioDrugScreen database that relies on docking to find putative interactions. Moreover, we also include experimentally curated interactions which are linked to their sources: DrugBank, BindingDB and Protein Data Bank. Our database can be used to facilitate studies related to polypharmacology of drugs including repurposing and explaining side effects of drugs.
Availability and implementation: PDID database is freely available at http://biomine.ece.ualberta.ca/PDID/.
Contact: lkurgan@vcu.edu
Low Concordance With Guidelines for Treatment of Acute Cystitis in Primary Care
Authors: Grigoryan Larissa , Zoorob Roger , Wang Haijun , Trautner Barbara W. 
Published: October 2015

Abstract
Background.  The updated 2010 Infectious Diseases Society of America guidelines recommended 3 first-line therapies for uncomplicated cystitis: nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), and fosfomycin, while fluoroquinolones (FQs) remained as second-line agents. We assessed guideline concordance for antibiotic choice and treatment duration after introduction of the updated guidelines and studied patient characteristics associated with prescribing of specific antibiotics and with treatment duration.
Methods.  We used the Epic Clarity database (electronic medical record system) to identify all female patients aged ≥18 years with uncomplicated cystitis in 2 private family medicine clinics in the period of 2011–2014. For each eligible visit, we extracted type of antibiotic prescribed, duration of treatment, and patient and visit characteristics.
Results.  We included 1546 visits. Fluoroquinolones were the most common antibiotic class prescribed (51.6%), followed by nitrofurantoin (33.5%), TMP-SMX (12.0%), and other antibiotics (3.2%). A significant trend occurred toward increasing TMP-SMX and toward decreasing nitrofurantoin use. The duration of most prescriptions for TMP-SMX, nitrofurantoin, and FQs was longer than guidelines recommendations (longer durations were prescribed for these agents in 82%, 73%, and 71% of the prescriptions, respectively). No patient or visit characteristic was associated with use of specific antibiotics. Older age and presence of diabetes were independently associated with longer treatment duration.
Conclusions.  We found low concordance with the updated guidelines for both the choice of drug and duration of therapy for uncomplicated cystitis in primary care. Identifying barriers to guideline adherence and designing interventions to decrease overuse of FQs may help preserve the antimicrobial efficacy of these important antimicrobials.
Maxillary Ameloblastoma with Orbital Involvement: An Institutional Experience and Literature Review
Authors: Milman Tatyana , Lee Vivian , LiVolsi Virginia 
Published: October 2015

Purpose:
To describe 8 patients with orbital involvement by ameloblastoma and to review the literature on this topic.

Methods:
The electronic medical records and pathology databases of the Hospital of the University of Pennsylvania were searched to identify all patients with histopathologically confirmed ameloblastoma diagnosed between 1990 and 2015. PubMed database was searched for all well-documented cases of maxillary ameloblastoma and ameloblastic carcinoma ex-ameloblastoma with orbital involvement published in the English literature. The information collected on the compiled 23 patients included age, sex, clinical presentation, imaging findings, management, tumor histopathologic features, and follow up.

Results:
Review of medical records identified 8 patients with orbital involvement by ameloblastoma. Literature search yielded 15 patients with well-documented orbital involvement by ameloblastoma. Most tumors occurred in men (19 of 23, M:F = 4–5:1) with an average age of 56 years. The overall rates of recurrence, visual compromise, death, and confirmed disease-related mortality were 70% (16/23), 26% (6/23), 39% (9/23), and 22% (5/23), respectively. The initial surgical approach correlated with prognosis. The rates of recurrence, orbital exenteration, and mortality in the cohort managed with conservative surgery or partial maxillectomy were 57% (8/14), 29% (4/14), and 50% (7/14), respectively. In contrast, the patients initially managed with a radical resection had substantially lower frequencies of tumor recurrence (2/7, 29%), exenteration (1/7, 14%), and death (1/7, 14%). Malignant transformation to ameloblastic carcinoma occurred in the setting of recurrent disease in 3 patients and in 1 patient with prolonged duration of symptoms, suggestive of a long-standing tumor.

Conclusions:
Maxillary ameloblastoma can rarely involve the orbit, leading to significant ocular morbidity and occasional mortality. Prompt radical resection of the tumor has the potential to decrease the likelihood of recurrence and visual compromise, and can improve survival.
Extreme Eyelid Lymphedema Associated With Rosacea (Morbihan Disease): Case Series, Literature Review, and Therapeutic Considerations
Authors: Carruth Bryant P. , Meyer Dale R. , Wladis Edward J. , Bradley Elizabeth A. , Al-Rohil Rami , Jones David M. , Bartley George B. 
Published: October 2015

Purpose:
To describe severe lymphedema of the eyelids, known as Morbihan disease, a previously characterized but infrequently reported and poorly understood entity related to rosacea that features solid mid-facial and eyelid lymphedema.

Methods:
Retrospective chart review, histopathologic and immunohistochemical analysis, and pertinent literature consideration.

Results:
Five cases of Morbihan disease were identified. Histopathologic examination revealed pleomorphic perivascular and perilymphatic inflammation with profound lymphangiectasis and lymph stasis, thus suggesting elements of both rosacea and localized, chronic lymphedema. Multiple therapeutic interventions were performed including systemic anti-inflammatory therapy, surgical debulking, and corticosteroid injection.

Conclusions:
Extreme eyelid edema associated with characteristic skin changes and histopathologic findings represents an entity known as Morbihan disease which is rare and difficult to treat. While multiple modalities have been employed with variable results, future therapeutic considerations may include the use of targeted biologic agents.
Apoptosis in snowflake yeast: novel trait, or side effect of toxic waste?
Authors: Pentz Jennifer T. , Taylor Bradford P. , Ratcliff William C. 
Published: October 2015

AbstractRecent experiments evolving de novo multicellularity in yeast have found that large-cluster forming genotypes also exhibit higher rates of programmed cell death (apoptosis). This was previously interpreted as the evolution of a simple form of cellular division of labor: apoptosis results in the scission of cell-cell connections, allowing snowflake yeast to produce proportionally smaller, faster-growing propagules. Through spatial simulations, Duran-Nebreda and Solé (2015) develop the novel null hypothesis that apoptosis is not an adaptation, per se, but is instead caused by the accumulation of toxic metabolites in large clusters. Here we test this hypothesis by synthetically creating unicellular derivatives of snowflake yeast through functional complementation with the ancestral ACE2 allele. We find that multicellular snowflake yeast with elevated apoptosis exhibit a similar rate of apoptosis when cultured as single cells. We also show that larger snowflake yeast clusters tend to contain a greater fraction of older, senescent cells, which may explain why larger clusters of a given genotype are more apoptotic. Our results show that apoptosis is not caused by side effects of spatial structure, such as starvation or waste product accumulation, and are consistent with the hypothesis that elevated apoptosis is a trait which co-evolves with large cluster size.
Recycler: an algorithm for detecting plasmids fromde novoassembly graphs
Authors: Rozov Roye , Kav Aya Brown , Bogumil David , Shterzer Naama , Halperin Eran , Mizrahi Itzhak , Shamir Ron 
Published: October 2015

AbstractPlasmids are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new plasmid-specific assembly algorithm, leveraging assembly graphs provided by a conventionalde novoassembler and alignments of paired- end reads to assembled graph nodes. We introduce the first tool for this task, called Recycler, and demonstrate its merits in comparison with extant approaches. We show that Recycler greatly increases the number of true plasmids recovered while remaining highly accurate. On simulated plasmidomes, Recycler recovered 5-14% more true plasmids compared to the best extant method with overall precision of about 90%. We validated these resultsin silicoon real data, as well asin vitroby PCR validation performed on a subset of Recycler’s predictions on different data types. All 12 of Recycler’s outputs on isolate samples matched known plasmids or phages, and had alignments having at least 97% identity over at least 99% of the reported reference sequence lengths. For the two E. Coli strains examined, most known plasmid sequences were recovered, while in both cases additional plasmids only known to be present in different hosts were found. Recycler also generated plasmids in high agreement with known annotation on real plasmidome data. Moreover, in PCR validations performed on 77 sequences, Recycler showed mean accuracy of 89% across all data types – isolate, microbiome, and plasmidome. Recycler is available athttp://github.com/Shamir-Lab/Recycler
Torque production improvement of a five phase fractional-slot PM machine under faulty operation
Authors: Rebai Hajer , Abdennadher Imen , Masmoudi Ahmed 
Published: October 2015

Purpose
– The purpose of this paper is to deal with several approach to recover the torque production capability of a five phase double-layer fractional-slot PM machine under faulty operation. The considered fault is an open-circuit coil in a given phase.

Design/methodology/approach
– In a first step, the mean futures, such as the phase back-EMFs and the electromagnetic torque, are computed by finite element analysis under healthy operation, and are taken as references. Then, they are investigated, under a faulty coil, for different approaches to recover the torque production capability.

Findings
– A comparison of the potentialities of the torque recovery approaches has clearly highlight the superiority of the approach consisting in the re-adjustment of the current initial phases, in an attempt to equilibrate the resulting air gap MMF.

Research limitations/implications
– This work should be extended by an experimental validation of the predicted results regarding the back-EMFs and the electromagnetic torque.

Practical implications
– The investigation of the considered five phase fractional-slot PM machine under faulty operation should be extended to several faulty scenarios in order to fulfill the requirements of many applications such as the propulsion systems.

Originality/value
– The paper proposes different approaches to recover the torque production capability of a five phase fractional-slot PM machine under faulty operation.
Improvement of output current waveforms using SVM technique and fuzzy logic controller for matrix converter
Authors: Boukadoum Aziz , Bahi Tahar , Soufi Youcef , Bouguerne Abla , Oudina Sofiane 
Published: October 2015

Purpose
– The use of power electronic equipment such as conventional AC-DC-AC converters cause several problems in electrical networks and its components. They generate harmonic currents and disturb the electrical power sources; so, it is necessary to research alternative topologies of power electronic converters based on advanced intelligent controllers, which reduce or even eliminate harmonics to achieve energy-saving and environmental protection. The use of matrix converter (MC) is, considered as an attractive solution to maintain pure sinusoidal input and output current waveforms. The paper aims to discuss this issue.

Design/methodology/approach
– The studied system is composed of a three phase matrix converter (TMC) feeding a linear R, L load and a trees phase rectifier considered as a non-linear load; the proposed control strategy is based on a fuzzy logic controller (FLC) associated to the (space vector modulation) SVM modulation technique, this choice is motivated by the advantages that represent the combination of FLC and SVM in term of power quality enhancement in both input and output sides of MC.

Findings
– The model is validated based on simulation results that illustrate the effectiveness of the proposed system in term of power quality amelioration. The high performance of the proposed FLC is illustrated in all study cases especially in the case of perturbed input voltage, it is not only able to keep the whole system stable, but also it reduces harmonic distortion THD to respect international standards recommendation.

Originality/value
– In this paper, an associated linear (RL), non-linear loads and TMC is studied. From the mathematical point of view, the MC is modeled and analyzed. From the technique point of view, the MC allows sinusoidal current absorbance from the network with good qualities in term of harmonic distortion compensation, and high reliability under various loads and disturbed input voltage.
Novel linear switched-flux PM machine with 9/10 primary/secondary pole number combination
Authors: Lu Qinfen , Li Yanxin , Ye Yunyue , Chen J.T. , Zhu Z.Q. 
Published: October 2015

Purpose
– Due to linear structure, linear switched flux permanent magnet machines (LSFPMMs) also may have odd pole primary, such as 9, 15, 21, etc., without unbalanced magnetic force in equivalent rotary machines. The paper aims to discuss these issues.

Design/methodology/approach
– In order to increase the thrust force density, the influence of some major design parameters, including split ratio, PM thickness, primary slot width and secondary pole width, are investigated by finite element analysis. For reducing the thrust force ripple under on-load condition, the end auxiliary teeth are adopted and their positions are also optimized.

Findings
– This novel 9/10 primary/secondary poles LSFPMM has high average thrust force and low thrust force ripple by optimization. The results demonstrate that the odd pole primary may be a good candidate for long-stroke linear direct drive application.

Originality/value
– A novel 9/10 primary/secondary poles linear switched flux permanent magnet machine is developed in this paper. The similar conclusions could be obtained for other LSFPMMs with odd pole primary.
Quantitative analysis of the cities’ innovation capacity based on grey variable weight clustering
Authors: Guan Yeqing , Liu Hua , Zhu Ying 
Published: October 2015

Purpose
– The purpose of this paper is to find the reason which the results of grey variable weight clustering method do not correspond with the reality. It proposes reconstructing the whitenization weight function, outlining why and how inconsistency is avoided. The study aims to improve the model of grey clustering method based on the whitenization weight function and list the steps of the new clustering model so that analysis and application of innovation capacity in a broader range is normally found.

Design/methodology/approach
– First the reason for the problem that the clustering results of grey variable weight clustering do not correspond with the reality is analyzed in two existing literature. And then a new whitenization weight function is reconstructed, two properties of the whitenization weight function are proved. The solution of the new grey variable weight clustering based on the whitenization weight function is built by following six steps.

Findings
– The paper provides a new whitenization weight function which satisfies the normative and non-triplecrossing. It suggests that successful clustering results of innovation capacity act on two levels: integrating the elements of innovation capacity indexes, and following steps of grey variable weight clustering.

Originality/value
– This paper improves the existing method of grey variable weight clustering and fulfills an identified need to study how cities’ innovation capacity can be clustered.
Optimisation of building shape and orientation for better energy efficient architecture
Authors: Fallahtafti Reza , Mahdavinejad Mohammadjavad 
Published: October 2015

Purpose
– This paper aims to optimise building orientation in Tehran, as well as determining the impact of its shape, relative compactness (RC) and glazing percentage on its optimised orientation.

Design/methodology/approach
– A cubic module was used and a set of 8 of the same module with 16 different formations were analysed for their orientation (360°), the RC (four groups) and the amount of glazing percentage (25, 50 and 75 per cent).

Findings
– The results show that the optimised orientation of a building in Tehran strongly depends on its passive solar heat gain elements, their orientation and their position in building; furthermore, glazing percentage amount, amongst the studied factors, plays the most important role in determining a building’s orientation.

Practical implications
– The application of the findings of this study in Tehran city planning and also technical details of buildings will lead to a great energy saving in construction sector. Furthermore, the deployment of the proposed design guidelines in construction has explicitly been proven to save a prodigious amount of energy.

Originality/value
– The main research question is taken directly from authors’ initiative when working as university professor and research associate. The case study buildings, their morphological configurations and sustainable features have not been presented before in an academic journal.
Accrual accounting in Italian universities: a technical perspective
Authors: Agasisti Tommaso , Catalano Giuseppe , Di Carlo Ferdinando , Erbacci Angelo 
Published: October 2015

Purpose– The purpose of this paper is to examine the impact of full accrual accounting on the Italian public universities and, in this context, how some technical-accounting problems typical of public sector (recognition and valuation issues) have been addressed. An additional purpose investigated in this paper is the role of International Public Sector Accounting Standards (IPSASs) in helping to overcome these technical-accounting issues, for the case under examination.Design/methodology/approach– The paper involves studying whether, and to what degree, some of the accounting choices made by the universities complied with the principles of full accrual accounting for several specific accounting registrations characterised by the presence of recognition and valuation issues. During this investigation, the paper also analyses whether the universities followed the accounting rules set out by the IPSAS Board.Findings– The findings highlight that, in general, there is a low degree of compliance with full accrual accounting principles and they also revealed that IPSASs do not provide any detailed guidelines that can help universities in overcoming the recognition and valuation problems typical of the public sector.Originality/value– The analysis presented in the paper confirms the findings of previous literature identifying a low level of compliance to full accrual accounting principles. This research shed light also on the longstanding debate about the role of IPSASs in promoting full accrual accounting in the public sector, revealing the scarce contribution of IPSASs to this process.
Building a resilient local council: evidence from flood disasters in Italy
Authors: Sciulli Nick , D'Onza Giuseppe , Greco Giulio 
Published: October 2015

Purpose
– The purpose of this paper is to investigate resilience to extreme weather events (EWE) in a sample of Italian local councils (LCs), impacted by flood disasters. Whether resilience as a concept is adopted by the affected councils and factors that promote or inhibit LC resilience are explored.

Design/methodology/approach
– Using semi-structured interviews, the authors investigate seven Italian LCs that were severely impacted by the flood event. An interview protocol was developed and background information collected. A number of themes were drawn from the interview transcripts and relationships with the relevant literature were examined.

Findings
– The findings highlight that the adoption of the concept of resilience is at an early stage in the LCs decision and policy making. The authors find that the financial resources and the external relations management with other public entities, NGOs and local communities, promote the LCs resilience during and after an EWE. By contrast, bureaucratic constraints and poor urban planning restrain resilience. The findings suggest that LCs resilience needs to be distinguished from local community resilience.

Originality/value
– The paper contributes to the literature on public sector management and investigates the under-researched area of resilience within the context of the public sector, vis-à-vis, local government. In particular the realization that EWE are not the realm only of emergency personnel, but that local government managers have an integral role placed upon them during and especially after the EWE.