bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
Authors: Bietz Stefan , Urbaczek Sascha , Schulz Benjamin , Rarey Matthias 
Published: April 2014

Abstract

Abstract
The calculation of hydrogen positions is a common preprocessing step when working with crystal structures of protein-ligand complexes. An explicit description of hydrogen atoms is generally needed in order to analyze the binding mode of particular ligands or to calculate the associated binding energies. Due to the large number of degrees of freedom resulting from different chemical moieties and the high degree of mutual dependence this problem is anything but trivial. In addition to an efficient algorithm to take care of the complexity resulting from complicated hydrogen bonding networks, a robust chemical model is needed to describe effects such as tautomerism and ionization consistently. We present a novel method for the placement of hydrogen coordinates in protein-ligand complexes which takes tautomers and protonation states of both protein and ligand into account. Our method generates the most probable hydrogen positions on the basis of an optimal hydrogen bonding network using an empirical scoring function. The high quality of our results could be verified by comparison to the manually adjusted Astex diverse set and a remarkably low rate of undesirable hydrogen contacts compared to other tools.
Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development
Authors: Frantzi Maria , Bhat Akshay , Latosinska Agnieszka 
Published: March 2014

AbstractBiomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic–based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well‐defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
Catalytic Efficacy of Copper(II)– and Cobalt(III)–Schiff Base Complexes in Alkene Epoxidation
Authors: Maiti Monami , Sadhukhan Dipali , Thakurta Santarupa , Zangrando Ennio , Pilet Guillaume , Signorella Sandra , Bellú Sebastián , Mitra Samiran 
Published: April 2014

Abstract
A potentially hexadentate N2O4 donor Schiff base ligand N,N′-bis(5-bromo-3-methoxysalicylideneimino)-1,3-diaminopropane (H2L1) has been used to synthesize two mononuclear coordination complexes [Cu(L1)]·H2O (1) and [Co(L1)(HL2)]ClO4·CH3CN (2). The cobalt complex is a unique mixed-ligand species comprising both the di- and mono-condensed ligands; the latter (HL2) resulted from in situ hydrolytic cleavage of H2L1. Ligand L1 assumes a planar arrangement in 1 and a folded β-cis configuration in 2, induced in this case by the chelating HL2 ligand. The complexes are characterized by elemental analyses, FT-IR, and UV–vis spectral methods, and their structures are established by single-crystal X-ray diffraction study. Both the complexes are proven to be efficient catalysts for the epoxidation of alkenes by H2O2 or PhIO. The efficiency of alkene epoxidation is however somewhat superior with PhIO, and in each case, 2 appears to be a slightly better catalyst than 1.
Business Analytics for Flexible Resource Allocation Under Random Emergencies
Authors: Angalakudati Mallik , Balwani Siddharth , Calzada Jorge , Chatterjee Bikram , Perakis Georgia , Raad Nicolas , Uichanco Joline 
Published: April 2014

In this paper, we describe both applied and analytical work in collaboration with a large multistate gas utility. The project addressed a major operational resource allocation challenge that is typical to the industry. We study the resource allocation problem in which some of the tasks are scheduled and known in advance, and some are unpredictable and have to be addressed as they appear. The utility has maintenance crews that perform both standard jobs (each must be done before a specified deadline) as well as respond to emergency gas leaks (that occur randomly throughout the day and could disrupt the schedule and lead to significant overtime). The goal is to perform all the standard jobs by their respective deadlines, to address all emergency jobs in a timely manner, and to minimize maintenance crew overtime. We employ a novel decomposition approach that solves the problem in two phases. The first is a job scheduling phase, where standard jobs are scheduled over a time horizon. The second is a crew assignment phase, which solves a stochastic mixed integer program to assign jobs to maintenance crews under a stochastic number of future emergencies. For the first phase, we propose a heuristic based on the rounding of a linear programming relaxation formulation and prove an analytical worst-case performance guarantee. For the second phase, we propose an algorithm for assigning crews that is motivated by the structure of an optimal solution. We used our models and heuristics to develop a decision support tool that is being piloted in one of the utility's sites. Using the utility's data, we project that the tool will result in a 55% reduction in overtime hours. This paper was accepted by Noah Gans, special issue on business analytics.
Axillary lymph node clearance in patients with positive sentinel lymph node biopsy
Authors: Hussain T , Kneeshaw PJ 
Published: March 2014

Introduction The use of adjuvant radiotherapy is standard practice following breast conserving surgery and mastectomy in selected patients. Prospective clinical trials are currently being designed to assess the effect of omitting axillary lymph node clearance (ALNC) in selected patients. The aim of this study was to identify the percentage of patients understaged and not considered for postmastectomy radiotherapy (PMRT) and/or supraclavicular fossa radiotherapy (SCFRT) with positive sentinel lymph node (SLN) macrometastasis if the proposed prospective trial inclusion/exclusion protocols are followed. Methods A total of 38 women who were found negative for axillary metastases preoperatively but positive at SLN biopsy and who had ALNC were analysed. PMRT or SCFRT was offered to patients if ≥4 positive lymph nodes (including sentinel nodes) were positive for macrometastasis and/or a tumour size of ≥5cm was detected. Fisher’s exact test was used to determine the statistical significance of omitting ALNC. Results The mean age of the 38 patients was 55 years. A fifth (21.1%) of patients had T1, 76.3% had T2 and 2.6% had T3 disease. The percentage of positive SLNs was 52.6% (1 node), 34.2% (2 nodes) and 13.1% (3 nodes). The number of positive nodes at clearance was 0–3. If the inclusion criteria for trials that consider omitting ALNC are followed (eg POSNOC trial), 23.7% of patients (p=0.0001) with ≥4 positive nodes (including SLNs) would not be offered SCFRT and PMRT. Similarly, if multicentric disease were to be excluded from the trial criteria, the proportion of undertreated patients would reduce by 15.7%. Conclusions Our study has shown a significant risk of missing patients for PMRT or SCFRT if no ALNC is offered in the presence of SLN macrometastasis. Tumour multicentricity is an important factor in predicting high axillary nodal involvement. Consequently, exclusion of T2 tumours with multicentric involvement in trials considering omitting ALNC may be more appropriate.
The aetiology and current management of prepubertal epididymitis
Authors: Gkentzis A , Lee L 
Published: March 2014

Introduction The aim of this study was to review the published evidence on the pathogenesis and management of acute epididymitis (AE) in prepubertal boys after the authors encountered an unexpectedly large number of such cases in their institution. Methods Using MEDLINE®, a literature search was performed for articles in English with the words “pre-pubertal” OR “boys” OR “p(a)ediatric” OR “children” AND “epididymitis” OR “epididymo-orchitis”. Results The literature suggests that it is rare to find a bacterial infection or anatomical anomaly as a cause for AE in this population. A postviral infectious phenomenon is the most likely explanation. The management should be supportive and antibiotics reserved for those with pyuria or positive cultures. Urodynamic studies and renal tract ultrasonography have been advocated for those with recurrent epididymitis. Conclusions AE in prepubertal boys is more common than believed previously. A careful history for recent viral illnesses should be included. Antibiotics, urinary tract imaging and functional studies should be used in selected cases.
Patient outcomes after treatment with percutaneous cholecystostomy for biliary sepsis
Authors: Flexer SM , Peter MB , Durham-Hall AC , Ausobsky JR 
Published: March 2014

Introduction Acute cholecystitis is among the most common general surgical presentations. There is a cohort of patients who develop systemic sepsis and complications of acute cholecystitis. These patients are often elderly and co-morbid. Conservative management with percutaneous cholecystostomy has been shown to be a safe and effective management option in the acute setting. However, there is currently no consensus for the further management of these patients. In particular, there is a paucity of data on readmission rates and subsequent operative or non-operative management. Methods A retrospective study was carried out of patients treated with a percutaneous cholecystostomy for biliary sepsis over a three-year period in a UK teaching hospital. Outcome measures were subsequent operative or conservative management, conversion rates, operative complications and readmission rates. Results Twenty-five patients had a percutaneous cholecystostomy for the treatment of acute biliary sepsis. The median follow-up duration was 35 months. Thirteen patients (52%) had operative treatment. In the operative group, 6/13 had a laparoscopic cholecystectomy, 2/13 had a planned open cholecystectomy, 2/13 had abandoned procedures and 3/13 had a converted procedure. Complications in the operative group included: postoperative mortality (1/13), common bile duct injury requiring drainage and endoscopic stenting (1/13) and one patient required readmission with recurrent pain. In the non-operative group, 5/12 patients were readmitted with biliary sepsis, 5/12 had no readmissions, 1/12 died in the community and 1/12 was readmitted with biliary colic. Conclusions Percutaneous cholecystostomy is a recognised treatment modality for elderly, co-morbid patients with biliary sepsis. Nevertheless, the readmission rate in this group is relatively high at 5/12 (42%). Patients who undergo subsequent operative management have a conversion rate of 3/13 (23%) and a significant complication rate of 2/13 (15%). The further management of patients having undergone percutaneous cholecystostomy requires careful consideration on an individual case basis. The P-POSSUM (Portsmouth Physiological and Operative Severity Score for the enUmeration of Mortality and morbidity) may aid decision making.
Media Ecology Education
Authors: Postman Neil 
Published: March 2014

Abstract
In a keynote address delivered to the Speech Communication Association in 1973, Neil Postman discussed the new graduate program in media ecology that he established in New York University's School of Education. Media ecology is presented as a field of inquiry based on the metaphor that all communication is an environment, and utilizing a methodology called context analysis. Discussing communication environments as systems with boundaries, in relation to suprasystems and subsystems, Postman also considered the question of how technology affects human perception, feeling, and value.
Neil Postman and the Evangelicals
Authors: Hunt, III Arthur W. 
Published: March 2014

Abstract
American evangelicalism finds its roots in the Great Awakening of the 18th century, a movement that has proven to be both multifaceted and populist. The early half of the 20th century saw evangelicalism marginalized from cultural powerbrokers, only to resurface again in the later 20th century as a political force. Nevertheless, evangelicals today as a whole still mirror the same entrepreneurial, individualistic, and pragmatic values that have been part and parcel of American enterprise, a bustle now gone hyperconsumer. Not all evangelicals are oblivious to the reshaping of Old World Protestant sensibilities by mass culture forces. Confessionalists, as named in this article, are fully aware of how media forms can shape cultural institutions like the Church. Neil Postman’s ideas have been useful to evangelicals who understand that the Christian faith, like the Jewish faith, is logocentric. Although Postman’s Enlightenment values sometimes clash with the values of those who lay claim to the Protestant Reformation, both have much in common.
Neil Postman‘s Rules of Public Speaking
Authors: Sternberg Janet 
Published: March 2014

Abstract
Best known as a prolific writer of social criticism, Neil Postman was also a master of public speaking, an art he considered worthy of special attention and too often neglected. So dear was public speaking to him that Postman developed a set of ten rules for giving a good speech. Postman never published these guidelines, instead passing them on to his students in classroom lectures. The following is a reconstruction of Postman’s rules of public speaking, based on his own personal notes complemented by notes taken during his lectures. The author originally delivered this reconstruction in June 2005, at the Sixth Annual Convention of the Media Ecology Association.
The antiplaque effect of herbal mouthwash in comparison to chlorhexidine in human gingival disease: a randomized placebo controlled clinical trial
Authors: Bhat Nagesh , Mitra Ruchi , Oza Swapnil , Mantu Vinayak Kumar , Bishnoi Sharda , Gohil Mandeepsinh , Gupta Rupam 
Published: April 2014

Abstract

Background: The aim of this study was to compare the efficacy, safety, antiplaque and antigingivitis properties of a herbal mouthwash with chlorhexidine mouthwash.

Methods: A double-blinded randomized clinical trial was conducted among 72 undergraduate students with age group 18–24 years. They were randomly divided into three mouthwash group with 24 participants in each group. Group A (herbal), Group B (chlorhexidine) and Group C (normal saline).The Turesky et al. 1970 plaque index and Loe and Silness 1963 gingival index was recorded. Student’s t-test and one-way ANOVA were used to test the significance.

Results: A statistically highly significant difference was obtained between mouthwash B and C (p=0.00) and a significant difference between mouthwash A and C (p=0.004), showing that chlorhexidine was superior to herbal mouthwash and saline. However, there was a nonsignificant difference between mouthwash A and B (p=0.435) showing that herbal and chlorhexidine mouthwash was equally effective in reducing plaque and gingivitis.

Conclusions: The efficacy of herbal mouthwash was equally effective in reducing plaque and gingivitis as compared to chlorhexidine mouthwash and may be considered as a good alternative. The chlorhexidine mouthwash was reported with many side effects which limits its acceptability and long-term use, whereas the presently tested herbal mouthwash had no side effects apart from mild burning sensation.
Mercury exposure in pregnancy: a review
Authors: Solan Tom Daniel , Lindow Stephen W. 
Published: April 2014

Abstract
Mercury exposure in pregnancy has been associated with both pregnancy complications and developmental problems in infants. Apart from industrial accidents and contaminated food, mercury exposure is likely to arise from predatory fish consumption, environmental contamination and dental amalgam restorations placed before or during pregnancy. It would be prudent to recommend that pregnant women avoid these potential problems and minimize any risk. The available literature indicates a linear relationship with mercury levels and IQ deficit, and therefore a safe limit of mercury cannot be calculated.
Protection of spores from ultraviolet-C irradiation by auto-fluorescent substances in the spore mass of the cellular slime mold Dictyostelium discoideum
Authors: Uchiyama Saburo , Hatakeyama Ikuo 
Published: April 2014

Abstract
In this study, native spores surrounded by fluorescent substances in the spore mass of Dictyostelium discoideum were found to be resistant to relatively strong ultraviolet-C (UV-C) irradiation (2880 J/m2). The remaining emergency activity of the native mass of spores was over 80% even after exposure to strong UV-C irradiation (2880 J/m2). In contrast, the washed spores were very sensitive to weak UV-C irradiation (144 J/m2). The mass of spores in the fruiting body formed by amoebae with a low concentration of fluorescent substances was less resistant to UV-C than that in the fruiting body formed by normally grown amoebae. Based on the remaining emergency activity of washed spores with appropriate lumazine solution, the concentration of fluorescent substances in the native mass of spores was estimated to be equivalent to approximately 5 mmol/L of lumazine.
Mobilization Against the Left? Partisan Consequences of Voter Turnout in the Post-Communist Context
Authors: Nový Michal 
Published: April 2014

AbstractDoes higher turnout support left-wing parties, as many previous studies assume? Theoretical discussions thus far have been relatively inconclusive. This study proposes three different explanatory mechanisms for examining an aggregate-level relationship between turnout and electoral support for political parties in the post-communist milieu. The conventional hypothesis, based on the assumptions of a successful re-stratification of society and the relevance of class voting, states that higher turnout benefits the left. The second hypothesis is derived from the Michigan model of party identification. In this case, political parties with less loyal electorates would be expected to profit from higher rates of electoral participation. However, this article makes the case for a third possible explanation, termed simply “mobilization against the left,” which reverses the conventional hypothesis. The idea is that the more people come to the polls, the stronger the post-communist right-wing parties will be. This analysis includes two Czech regions that can be said to be farthest away from each other in terms of their socioeconomic and political characteristics. Having analyzed the 2010 Czech parliamentary election results across 1444 electoral districts in two regions, Central Bohemia and Moravia-Silesia, we conclude that there is certain empirical evidence that supports the proposed explanatory mechanism regarding the relationship between voter turnout and share of votes for political parties.
A Novel Running-In Specification with Strengthening Effects in Fatigue
Authors: Lu Xi 
Published: April 2014

Abstract
Using two types of automobile transmission assemblies, a novel running-in specification with strengthening effects is proposed and investigated by the strengthening of low-amplitude forces below the fatigue limit. The phenomenon is also referred to as understressing or coaxing. In this novel running-in specification, the fatigue life will be prolonged and the assembly cost is unchanged. The average fatigue life of one transmission assembly was increased ∼40 % when the original running-in force was replaced by the optimal strengthening force in the new running-in specification. The average fatigue life of the other type of transmission assembly was improved ∼26 % when the estimated optimal strengthening force was applied in another new running-in specification with the strengthening effects.
Remaining Life Assessment of Low-Pressure Turbine Rotor Using Monte Carlo Simulation
Authors: Young Lih-jier , Yeh Bo-Han , Young Phansia Rose 
Published: April 2014

Abstract
This paper presents the development of a fracture-mechanics-based probability analysis that can be used to estimate the remaining life of a low-pressure turbine with an unstable fracture in the rotor disk keyway. The analysis focuses on the stability of crack growth of a semi-elliptical flaw in the rotor disk keyway. The crack stability is judged on the basis of linear elastic fracture mechanics. Then the Monte Carlo technique is introduced to deal with several random variables. Based on the evaluation results, the probability of failure of observed crack indications can be determined. The inspection interval could be justified.
Interlaminar Shear and Electrical Resistance Responses of Woven-Carbon-Fiber-Reinforced-Polymer Composite Laminates at Cryogenic Temperatures From Cyclic Short Beam Shear Tests
Authors: Shindo Yasuhide , Takeda Tomo , Narita Fumio , Fukuzaki Tatsuya 
Published: April 2014

Abstract
This paper studies the interlaminar shear and electrical resistance responses of woven-carbon-fiber-reinforced-polymer (CFRP) composite laminates subjected to fatigue loading at cryogenic temperatures. Fatigue tests were conducted on the composite specimens at room temperature and liquid-hydrogen temperature (20 K) using the short beam shear method, and measurements of the specimen electrical resistance were made during the tests. Also, the tested specimens were examined by microscopy to observe the damage and the failure mode. In addition, a finite-element analysis was performed to examine the stress distributions in the short beam shear specimens. The dependence of the interlaminar shear fatigue performance of the woven-CFRP laminates on the temperature was discussed, and the applicability of the electrical resistance method for assessing the fatigue failure was demonstrated.