bluuebunny/crossref_metadata_2025_split huggingface dataset:
MEPSA: minimum energy pathway analysis for energy landscapes
Authors: Marcos-Alcalde Iñigo , Setoain Javier , Mendieta-Moreno Jesús I. , Mendieta Jesús , Gómez-Puertas Paulino 
Published: August 2015

Abstract
Summary: From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA’s output such as the generation of molecular dynamics restraints from a calculated path.
Availability and implementation: MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/
Contact: pagomez@cbm.csic.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Climbing back up what slippery slope? Dynamics of the European eel stock and its management in historical perspective
Authors: Dekker Willem , Beaulaton Laurent 
Published: August 2015

Abstract
Few fish stocks are as influenced by (intentional and inadvertent) human impacts as the European eel, all across the continent. The dynamics of this stock, however, are poorly understood—neither the causes of the historically low abundance, nor minimal protection levels, are beyond discussion. Rather than analysing contemporary processes, this article turns back in time—two centuries or more—unravelling historical abundances and distribution patterns; reviewing historical actions and objectives; and discussing technical developments and scientific advice—picturing the slippery slope the eel stock has come down from. The first claim, that the continental stock was in decline, dates from the early 1800s; stock-enhancement actions were initiated shortly after. Diffuse objectives, technical innovations, eternal optimism, and—above all—no quantification impede the exact evaluation of historical reports. After 1950, when quantification improved, a slow but consistent decline was observed, but it is only two decades after the crash in glass eel recruitment (in 1980), that protection plans addressed the bad status of the stock. A slippery slope, full of pitfalls—yet, we now observe several years of increasing recruitment.
Normalizing clinical terms using learned edit distance patterns
Authors: Kate Rohit J 
Published: August 2015

Abstract
Background Variations of clinical terms are very commonly encountered in clinical texts. Normalization methods that use similarity measures or hand-coded approximation rules for matching clinical terms to standard terminologies have limited accuracy and coverage.
Materials and Methods In this paper, a novel method is presented that automatically learns patterns of variations of clinical terms from known variations from a resource such as the Unified Medical Language System (UMLS). The patterns are first learned by computing edit distances between the known variations, which are then appropriately generalized for normalizing previously unseen terms. The method was applied and evaluated on the disease and disorder mention normalization task using the dataset of SemEval 2014 and compared with the normalization ability of the MetaMap system and a method based on cosine similarity.
Results Excluding the mentions that already exactly match in UMLS and the training dataset, the proposed method obtained 64.7% accuracy on the rest of the test dataset. The accuracy was calculated as the number of mentions that correctly matched the gold-standard concept unique identifiers (CUIs) or correctly matched to be without a CUI. In comparison, MetaMap’s accuracy was 41.9% and cosine similarity’s accuracy was 44.6%. When only the output CUIs were evaluated, the proposed method obtained 54.4% best F -measure (at 92.1% precision and 38.6% recall) while MetaMap obtained 19.4% best F -measure (at 38.0% precision and 13.0% recall) and cosine similarity obtained 38.1% best F -measure (at 70.3% precision and 26.1% recall).
Conclusions The novel method was found to perform much better than the MetaMap system and the cosine similarity based method in normalizing disease mentions in clinical text that did not exactly match in UMLS. The method is also general and can be used for normalizing clinical terms of other semantic types as well.
Wrong to be Right
Authors: Kang Jung J. , Reiter Robert E. , Kummer Nicolas , DeKernion Jean , Steinberg Michael L. , King Christopher R. 
Published: August 2015

Objectives:
To examine the impact of positive surgical margin (PSM) laterality on failure after radical prostatectomy (RP). A PSM can influence local recurrence and outcomes after salvage radiation. Unlike intrinsic risk factors, a PSM is caused by intervention and thus iatrogenic failures may be elucidated by analyzing margin laterality as surgical approach is itself lateralized.

Patients and Methods:
We reviewed 226 RP patients between 1991 and 2013 with PSM. Data includes operation type, pre/postoperative PSA, surgical pathology, and margin type (location, focality, laterality). The median follow-up was 47 months. Biochemical recurrence after RP was defined as PSA≥0.1 ng/mL or 2 consecutive rises above nadir. Ninety-two patients received salvage radiation therapy (SRT). Failure after SRT was defined as any PSA≥0.2 ng/mL or greater than presalvage. Kaplan-Meier and Cox multivariate analyses compared relapse rates.

Results:
The majority of PSM were iatrogenic (58%). Laterality was associated with differences in median relapse: right 20 versus left 51 versus bilateral 14 months (P<0.01). Preoperative PSA, T-stage, Gleason grade, and laterality were associated with biochemical progression on univariate and multivariate analyses. Right-sided margins were more likely to progress than left (hazard ratio, 1.67; P=0.04). More right-sided margins were referred for SRT (55% right vs. 23% left vs. 22% bilateral), but were equally salvaged. Only T-stage and pre-SRT PSA independently influenced SRT success.

Conclusions:
Most PSM are iatrogenic, with right-sided more likely to progress (and sooner) than left sided. Margin laterality is a heretofore unrecognized independent predictor of biochemical relapse and hints at the need to modify the traditional unilateral surgical technique.
Predicting the Surgical Margin of Resection in Periocular Cutaneous Neoplasms and the Significance of Reconstruction Following Mohs Micrographic Surgery
Authors: Sines Daniel T. , Polomsky Matej , Dutton Jonathan J. 
Published: August 2015

Purpose:
To evaluate the features of periocular cutaneous malignancies that may contribute to larger surgical defects or require more complex reconstructive procedures.

Methods:
A retrospective review of 181 patients with biopsy proven periocular cutaneous malignancies seen between April 2005 and September 2010, and undergoing Mohs micrographic surgery was performed. The longest horizontal and vertical diameters of the tumor and the post-Mohs surgical defect were measured in each patient. These measurements were used to calculate the relative margin of resection (MOR) required for tumor eradication as well as the size of the surgical defect. The date of surgery, histologic diagnosis and location of the tumor, type of reconstruction, and the presence of recurrence were also recorded.

Results:
The average MOR for all tumor subtypes taken together was 3.4 mm horizontally and 2.6 mm vertically for basal cell carcinomas (BCCA). The post-Mohs defect area was 3.2 times greater than the preoperative tumor area for all BCCA subtypes, and 3.9 times greater for morphea type (p = 0.8083). The average MOR for squamous cell carcinomas (SCCA) was 5.1 mm horizontally and 3.7 mm vertically. The post-Mohs defect area was 3.8 times greater than the preoperative tumor area for SCCAs. When comparing the preoperative horizontal tumor diameter to the horizontal MOR of BCCAs and SCCAs, the correlation was 0.23 (p < 0.0001) and 0.31 (p < 0.0001), respectively. While the average MOR was within standard limits, a significant number of tumors required a greater MOR. On review of the data, 30.6% of patients with BCCA required a MOR greater than 3 mm, 17.3% of patients with BCCA required a MOR greater than 4 mm, and 29.1% of patients with SCCA required a MOR of greater than 5 mm. Tumors located at the lateral canthus required the largest MOR (p < 0.01), while those on the lower eyelid were associated with the smallest MOR in BCCAs. As expected from anatomical considerations, tumors at the medial canthus required significantly more complex reconstruction procedures (p < 0.01). An ordered logistic regression model demonstrated that BCCA preoperative clinical tumor surface area was a significant indicator for the degree of reconstruction required (p < 0.01).

Conclusions:
Standard 3 mm to 4 mm MOR for BCCAs, and 5 mm MOR for SCCAs could result in an unacceptable risk of tumor recurrence if the surgical margins are not examined histologically. With increasing preoperative tumor size, there is an increase in the MOR required for BCCA and SCCA, supporting that large tumors require a greater MOR.
Prostaglandin Eyedrops Are Associated With Decreased Thicknesses of Eyelid Dermis and Orbicularis Oculi Muscle: Ultrasonographic Findings
Authors: Goh Alice S. , Nassiri Nariman , Kohn Jocelyne C. , Rootman Daniel B. , Giaconi JoAnn , Law Simon K. , Coleman Anne L. , Caprioli Joseph , Goldberg Robert A. 
Published: August 2015

Purpose:
To investigate the effect of prostaglandin analog eyedrops on the periorbital soft tissue using high-resolution ultrasonography.

Methods:
In this cross-sectional study, the authors included patients with bilateral glaucoma on unilateral prostaglandin therapy for the past 12 or more contiguous months. High-resolution ultrasonography was performed bilaterally on the upper and lower eyelids of each subject to measure thicknesses of dermis, orbicularis oculi muscle, and skin to arcus marginalis distance. Comparisons were made between eyes on prostaglandin eyedrops versus those not on prostaglandin analogs.

Results:
Twenty patients (16 females, 4 males) with a mean age of 67.2 ± 6.4 years were recruited. The mean duration of prostaglandin analog therapy was 5.4 ± 3.9 years. The authors found that eyes on prostaglandin analog therapy had statistically significantly reduced thicknesses of dermis, orbicularis oculi muscle, and skin to arcus marginalis distance in the upper and lower eyelids compared with the fellow eyes (p < 0.05 for all). In univariate regression analysis, the amount of changes in thicknesses of dermis, orbicularis oculi muscle, and skin to arcus marginalis distance among eyes on prostaglandin analog therapy and the fellow eyes was not statistically significantly associated with different variables including age, gender, years of being on prostaglandin analog therapy, type of prostaglandin analog, history of glaucoma and/or cataract surgeries, intraocular pressure, and number of glaucoma medications.

Conclusions:
The findings indicate that eyes on prostaglandin analog therapy have reduced thicknesses of dermis, orbicularis oculi muscle, and skin to arcus marginalis distance compared with the fellow eyes.
A Review of Eyelid Margin Malpositions: A Unique Spectrum in a South-East Asian Tertiary Hospital
Authors: Tan Benjamin Boon Chuan , Mansurali Vanessa Naseem , Sundar Gangadhara , Amrith Shantha 
Published: August 2015

Purpose:
Due to the anatomical differences between the Asian and non-Asian eyelid, the authors hypothesize a different spectrum of eyelid margin malposition conditions seen in Singapore as compared with a predominant Caucasian population. The purpose of the study is to describe the spectrum of eyelid margin malpositions that were operated in a South-East Asian Tertiary Hospital.

Methods:
Retrospective study involving all patients who required surgery for eyelid margin malpositions over a 2-year period. The etiology and ethnic spread of patients were analyzed for each eyelid margin malposition.

Results:
A total of 249 eyelids (144 patients) were analyzed. There were 127 Chinese (88.2%), 8 Malays (5.6%), 6 Indians (4.2%), 2 Indonesians (1.4%), and 1 Korean (0.7%). Epiblepharon (53.4%) was the commonest surgery performed, followed by entropion (25.7%) and ectropion (20.9%). Among patients with epiblepharon and entropion, Chinese patients formed the overwhelming majority (>95%). There were no Eurasians or Indians who presented with epiblepharon or entropion. Among patients with ectropion, there was a higher representation of Indian patients (16.7%).

Conclusions:
This study shows that the spectrum of eyelid margin malpositions in Singapore is unique and that developmental epiblepharon remains the commonest eyelid margin malposition requiring surgery. In terms of involutional eyelid margin malpositions, entropion is more common than ectropion, especially among the Chinese. The similarity in terms of eyelid involvement and ethnic distribution of both epiblepharon and involutional entropion suggests that there is a common factor in both these conditions, which the authors infer is due to the unique anatomy of the Asian eyelid.
Ambulance patients with nondocumented sepsis have a high mortality risk: a retrospective study
Authors: Roest Asselina A. , Stoffers Judith , Pijpers Evelien , Jansen Jochen , Stassen Patricia M. 
Published: August 2015

Objective
Sepsis is a serious disease leading to high mortality. Early recognition is important because treatment is most effective when started quickly.
The primary aim of this retrospective cohort study was to assess how many sepsis patients are documented as septic by ambulance staff. The secondary aims were to investigate how many sepsis patients are transported by ambulance, to compare them with patients transported otherwise, to investigate which factors influence documentation of sepsis and to assess whether documentation influences mortality.

Methods
We retrieved all data from ambulance and emergency department charts of patients who visited the internist in the emergency department from March 2011 to July 2012.

Results
In total, 47.4% (n=363) sepsis patients were transported by ambulance. These patients were older (71.5 vs. 55.7 years, P<0.0001), admitted more frequently (97.2 vs. 85.4%, P<0.001), significantly more frequently had severe sepsis (47.4 vs. 25.8%, P<0.0001) or septic shock (12.4 vs. 4.0%, P<0.0001), and died more frequently within 28 days (17.9 vs. 7.2%, P<0.0001) than those who were transported otherwise.
In 41.9% of ambulance patients, sepsis was not documented by ambulance staff. Measurement of temperature was important for documentation of sepsis (odds ratio 11.2, 95% confidence interval 5.2–24.4). In 32.1% of ambulance patients, sepsis could have been identified by assessing vital signs. Mortality in these nondocumented patients was higher than that in documented patients (25.7 vs. 12.9%, P=0.003).

Conclusion
Ambulance patients are seriously ill, but sepsis is often not documented by ambulance staff. Nondocumentation is associated with high mortality and could be resolved by assessing vital signs, particularly the temperature.
A Nursing Survey on Nutritional Care Practices in French‐Speaking Pediatric Intensive Care Units
Authors: Valla Frédéric V. , Gaillard‐Le Roux Bénédicte , Ford‐Chessel Carole , De Monte Malorie , Tume Lyvonne , Letois Flavie , Mura Thibault , Choueiry Elie , Rooze Shancy , Moullet Clémence , Jotterand‐Chaparro Corinne , Jacquot Aurélien 
Published: August 2015

ABSTRACTObjectives:Malnutrition in critically ill children contributes to morbidity and mortality. The French‐speaking pediatric intensive care nutrition group (NutriSIP) aims to promote optimal nutrition through education and research.Methods:The NutriSIP‐designed NutriRéa‐Ped study included a cross‐sectional survey. This 62‐item survey was sent to the nursing teams of all of the French‐speaking pediatric intensive care units (PICUs) to evaluate nurses’ nutrition knowledge and practices. One nurse per PICU was asked to answer and describe the practices of their team.Results:Of 44 PICUs, 40 responded in Algeria, Belgium, Canada, France, Lebanon, Luxemburg, and Switzerland. The majority considered nutrition as a priority care but only 12 of the 40 (30%) had a nutrition support team, 26 of the 40 (65%) had written nutrition protocols, and 19 of 39 (49%) nursing teams felt confident with the nutrition goals. Nursing staff generally did not know how to determine nutritional requirements or to interpret malnutrition indices. They were also unaware of reduced preoperative fasting times and fast‐track concepts. In 17 of 35 (49%) PICUs, the target start time for enteral feeding was within the first 24 hours; however, frequent interruptions occurred because of neuromuscular blockade, fasting for extubation or surgery, and high gastric residual volumes. Combined pediatric neonatal intensive care units were less likely to perform systematic nutritional assessment and to start enteral nutrition rapidly.Conclusions:We found a large variation in nursing practices around nutrition, exacerbated by the lack of nutritional guidelines but also because of the inadequate nursing knowledge around nutritional factors. These findings encourage the NutriSIP to improve nutrition through focused education programs and research.
Nutritional/Growth Status in a Large Cohort of Medically Fragile Children Receiving Long‐Term Enteral Nutrition Support
Authors: Khan Zahra , Marinschek Sabine , Pahsini Karoline , Scheer Peter , Morris Nicholas , Urlesberger Berndt , Dunitz‐Scheer Marguerite 
Published: August 2015

ABSTRACTObjective:The aim of the present study was to assess the nutritional status and growth of medically fragile children receiving long‐term enteral nutritional support (ENS).Methods:A retrospective cross‐sectional survey was conducted at a tertiary‐level pediatric hospital. Growth features and nutritional intake of children (n = 287) receiving ENS were evaluated. During a period of 5 years (2009–2013), study patients in the age group of 1 to 36 months had been referred for the explicit reason of tube weaning. Data were documented with the help of ARCHIMED (version 46.2) and analyzed using SPSS for Windows version 21. Nutritional/growth status was determined by using World Health Organization growth standard tables.Results:Anthropometric parameters of children were compared with World Health Organization standards, and the prevalence of underweight, wasting, and stunting was very high despite being exclusively or predominantly on ENS. Results revealed that the age of a child, inadequate amount of caloric supply/day, the diagnosis of small‐for‐gestational age, and the type of tube (nasogastric tube) were significantly associated with growth/nutritional status (P < 0.05). Duration of ENS in the percentage of the cohort's lifetime and the main diagnosis were not associated with nutritional/growth outcomes.Conclusions:In medically fragile children, ENS does not ensure adequate growth per se. ENS requires highly specialized and individually tailored management and in many cases regular adjustments. Long‐term tube feeding plans often seem unable to ensure the required amount of nutritional support, which surely compromise the individual efficacy of ENS.
Bibliometric Analysis of Medication Errors and Adverse Drug Events Studies
Authors: Huang Hung-Chi , Wang Cheng-Hua , Chen Pi-Ching , Lee Yen-Der 
Published: August 2015

Objectives
Medication errors and adverse drug events are a key concern of the health-care industry. The objectives of this study were to map the intellectual structure of the studies of medication errors and adverse drug events and to investigate the developing path of this literature and interrelationships among the main topics.

Methods
The Web of Science database was searched for documentation of medication errors and adverse drug events from 1961 to 2013. The most cited articles and references were profiled and analyzed using HistCite software to draw a historiograph and Ucinet software to draw a sociogram.

Results
The database search revealed 3343 medication errors and 3342 adverse drug event documents. The most cited articles on medication errors focused on 3 key themes from 1961 to 2013, namely, medication errors in adult inpatients, computerized physician order entry in medication error studies, and medication errors in pediatric inpatients. The developing path for the most cited articles about adverse drug events from 1987 to 2013 was as follows: detection, analysis, effect, and prevention from adult inpatient to pediatric inpatient settings and from hospitalized care to ambulatory care. In addition, social network analysis based on the most cited references revealed a close relationship between medication errors and adverse drug events.

Conclusions
The mapping results provide a valuable tool for researchers to access the literature in this field and can be used to help identify the direction of medication errors and adverse drug events research.
Stabilizing the dynamics of laboratory populations ofDrosophila melanogasterthrough upper and lower limiter controls
Authors: Tung Sudipta , Mishra Abhishek , Dey Sutirth 
Published: August 2015

AbstractAlthough a large number of methods exist to control the dynamics of populations to a desired state, few of them have been empirically validated. This limits the scope of using these methods in real-life scenarios. To address this issue, we tested the efficacy of two well-known control methods in enhancing different kinds of stability in highly fluctuating, extinction-prone populations ofDrosophila melanogaster. The Upper Limiter Control (ULC) method was able to reduce the fluctuations in population sizes as well as the extinction probability of the populations. On the negative side, it had no effect on the effective population size and required a large amount of effort. On the other hand, Lower Limiter Control (LLC) enhanced effective population size and reduced extinction probability at a relatively low amount of effort. However, its effects on population fluctuations were equivocal. We examined the population size distributions with and without the control methods, to derive biologically intuitive explanations for how these control methods work. We also show that biologically-realistic simulations, using a very general population dynamics model, are able to capture most of the trends of our data. This suggests that our results are likely to be generalizable to a wide range of scenarios.