bluuebunny/crossref_metadata_2025_split huggingface dataset:
An iterative self‐refining and self‐evaluating approach for protein model quality estimation
Authors: Wang Zheng , Cheng Jianlin 
Published: November 2011

AbstractEvaluating or predicting the quality of protein models (i.e., predicted protein tertiary structures) without knowing their native structures is important for selecting and appropriately using protein models. We describe an iterative approach that improves the performances of protein Model Quality Assurance Programs (MQAPs). Given the initial quality scores of a list of models assigned by a MQAP, the method iteratively refines the scores until the ranking of the models does not change. We applied the method to the model quality assessment data generated by 30 MQAPs during the Eighth Critical Assessment of Techniques for Protein Structure Prediction. To various degrees, our method increased the average correlation between predicted and real quality scores of 25 out of 30 MQAPs and reduced the average loss (i.e., the difference between the top ranked model and the best model) for 28 MQAPs. Particularly, for MQAPs with low average correlations (<0.4), the correlation can be increased by several times. Similar experiments conducted on the CASP9 MQAPs also demonstrated the effectiveness of the method. Our method is a hybrid method that combines the original method of a MQAP and the pair‐wise comparison clustering method. It can achieve a high accuracy similar to a full pair‐wise clustering method, but with much less computation time when evaluating hundreds of models. Furthermore, without knowing native structures, the iterative refining method can evaluate the performance of a MQAP by analyzing its model quality predictions.
TREATING FLOODPLAIN LAKES OF LARGE RIVERS AS STUDY UNITS FOR VARIABLES THAT VARY WITHIN LAKES; AN EVALUATION USING CHLOROPHYLL A AND INORGANIC SUSPENDED SOLIDS DATA FROM FLOODPLAIN LAKES OF THE UPPER MISSISSIPPI RIVER
Authors: Gray B. R. , Rogala J. R. , Houser J. N. 
Published: November 2011

ABSTRACTContiguous floodplain lakes (‘lakes’) have historically been used as study units for comparative studies of limnological variables that vary within lakes. The hierarchical nature of these studies implies that study variables may be correlated within lakes and that covariate associations may differ not only among lakes but also by spatial scale. We evaluated the utility of treating lakes as study units for limnological variables that vary within lakes based on the criteria of important levels of among‐lake variation in study variables and the observation of covariate associations that vary among lakes. These concerns were selected, respectively, to ensure that lake signatures were distinguishable from within‐lake variation and that lake‐scale effects on covariate associations might provide inferences not available by ignoring those effects. Study data represented chlorophyll a (CHL) and inorganic suspended solids (ISS) data from lakes within three reaches of the Upper Mississippi River. Sampling occurred in summer from 1993 through 2005 (except 2003); numbers of lakes per reach varied from 7 to 19, and median lake area varied from 53 to 101 ha. CHL and ISS levels were modelled linearly, with lake, year and lake × year effects treated as random. For all reaches, the proportions of variation in CHL and ISS attributable to differences among lakes (including lake and lake × year effects) were substantial (range: 18%–73%). Finally, among‐lake variation in CHL and ISS was strongly associated with covariates and covariate effects that varied by lakes or lake‐years (including with vegetation levels and, for CHL, log(ISS)). These findings demonstrate the utility of treating floodplain lakes as study units for the study of limnological variables and the importance of addressing hierarchy within study designs when making inferences from data collected within floodplain lakes. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.
Incidence of Malignancy in Thyroid Nodules Determined to be Follicular Lesions of Undetermined Significance on Fine‐Needle Aspiration
Authors: Teixeira Gilberto V. , Chikota Horacio , Teixeira Thiago , Manfro Gabriel , Pai Sara I. , Tufano Ralph P. 
Published: November 2011

AbstractBackgroundFine‐needle aspiration (FNA) for thyroid nodules is the most important method for determining a diagnosis. The system for reporting results is based on a cytopathologic classification that stratifies the risk of malignancy.MethodsWe retrospectively studied 197 patients who underwent FNA for diagnostic evaluation of a thyroid nodule and had their results reported as a follicular lesion of undetermined significance (FLUS) using the Bethesda classification system. The objective of the study was to analyze the incidence and histopathologic types of malignancy in these cases.ResultsThe final histopathologic breakdown is as follows: 65 cases (32.9%) of follicular adenoma, 81 cases (41.1%) of microfollicular adenomatoid nodule, 19 cases (9.6%) of microfollicular adenomatoid nodule on the background of thyroiditis, 17 cases (8.6%) of follicular carcinoma, 9 cases (4.6%) of follicular variant papillary carcinoma, and 6 cases (3.1%) of classic papillary carcinoma, for a 16.2% incidence of malignancy. Beyond these diagnoses in the FNA‐biopsied nodules, we observed 29 cases (14.7%) of incidental ipsilateral papillary thyroid microcarcinoma (PTM) and 13 cases (6.6%) of incidental contralateral thyroid lobe PTM.ConclusionsThis study observed a 16.2% incidence of thyroid cancer in the nodule designated FLUS compared to the 5 to 15% rate reported by the Bethesda FNA classification. The overall incidence of incidental PTM in the thyroid gland was 21.3%. These data support considering surgical intervention for at least diagnostic purposes in a patient with the FNAB diagnosis of FLUS.
The closer the sportier? Children’s sports activity and their distance to sports facilities
Authors: Steinmayr Andreas , Felfe Christina , Lechner Michael 
Published: November 2011

AbstractWe investigate whether the distance between the next sports facilities and children’s homes matter for their sports activities inside and outside of sports clubs. Our analysis is based on a large and informative cross-section of individual data on children and their families, the so-called German Health Interview and Examination Survey for Children and Adolescents data. We use a semiparametric econometric method to investigate this relationship empirically. Our results suggest that while the distance does not matter in larger towns and cities, it does matter in smaller towns and in particular on the countryside.
Changing Radiation Dose from Diagnostic Computed Tomography Examinations in Saskatchewan
Authors: Dumaine Chance S. , Leswick David A. , Fladeland Derek A. , Lim Hyun J. , Toews Lori J. 
Published: November 2011

Purpose Follow-up study to observe if provincial mean effective radiation dose for head, chest, and abdomen-pelvis (AP) computed tomographies (CTs) remained stable or changed since the initial 2006 survey. Methods Data were collected in July 2008 from Saskatchewan's 13 diagnostic CT scanners of 3358 CT examinations. These data included the number of scan phases and projected dose length product (DLP). Technologists compared projected DLP with 2006 reference data before scanning. Projected DLP was converted to effective dose (ED) for each head, chest, and AP CT. The total dose that the patients received with scans of multiple body parts at the same visit also was determined. Results The mean (± SD) provincial ED was 3.4 ± 1.6 mSv for 1023 head scans (2.7 ± 1.6 mSv in 2006), 9.6 ± 4.8 mSv for 588 chest scans (11.3 ± 8.9 mSv in 2006), and 16.1 ± 9.9 mSv for 983 AP scans (15.5 ± 10.0 mSv in 2006). Single-phase multidetector row CT ED decreased by 31% for chest scans (9.5 ± 3.9 mSv vs 13.7 ± 9.7 mSv in 2006) and 17% for AP scans (13.9 ± 6.0 mSv vs 16.8 ± 10.6 mSv in 2006) and increased by 19% for head scans (3.2 ± 1.2 mSv vs 2.7 ± 1.5 mSv in 2006). The total patient dose was highest (33.8 ± 10.1 mSv) for the 20 patients who received head, neck, chest, and AP scans during a single visit. Because of increased utilisation and the increased CT head dose, Saskatchewan per capital radiation dose from CT increased by 21% between 2006 and 2008 (1.14 vs 1.38 mSv/person per year). Conclusion Significant dose and variation reduction was seen for single-phase CT chest and AP examinations between 2006 and 2008, whereas CT head dose increased over the same interval. These changes, combined with increased utilisation, resulted in per capita increase in radiation dose from CT between the 2 studies.
The Minister and His People
Authors: Brooks Phillips 
Published: November 2011

The Faculty of the Harvard Divinity School provided for their students in 1883 six lectures by oflBcers of the University representing other departments of government and instruction, as follows:The Minister and the People: Phillips Brooks, D.D., of the Board of Overseers.The Evolution of a Christian Minister: J. F. Clarke, D.D., of the Board of Overseers.One Word more about Free-Will: William James, M.D., Assistant Professor of Philosophy.Plato's Idea of Immortality: W. W. Goodwin, LL.D., Professor of Greek.The Natural History of Altruism: N. S. Shaler, S.D., Professor of Palaeontology.Vivisection: H. P. Bowditch, M.D., Professor of Physiology, and Dean of the Medical Faculty.
Religion and Socialism
Authors: Scudder Vida D. 
Published: November 2011

That a coöperative commonwealth is on the way, it would be rash to assert; but that forces tending in such a direction are gathering strength is even more evident in England and on the continent of Europe than with us. While discussions of socialist theory on economic and political lines increase and multiply another line of thought suggests itself to people preëminently interested in the spiritual rather than in the economic conditions of the race. Supposing a socialist organization of society realized, what would be the reaction on the ethical and religious consciousness,—on creed, on worship, on conduct?It is the purpose of this paper to suggest a few points on the second of these themes,—the probable future of religion under socialism. The subject is less remote from present interests than appears: hypothetical though it be, the attitude of many people toward socialism itself will depend on their conclusions on this point.
Some Recent Books on Theology
Authors: Fenn W. W. 
Published: November 2011

Illingworth, J. R., The Doctrine of the Trinity.Hall, F. J., Introduction to Dogmatic Theology.Ritchie, W. B., Revelation and Religious Certitude.Bowne, B. P., Personalism.Rogers, A. K., The Religious Conception of the World.Lloyd, A. H., The Will to Doubt.Drummond, James, Studies in Christian Doctrine.Peile, J. H. F., The Reproach of the Gospel.Nash, H. S., The Atoning Life.The Christ that is to Be.Worcester, McComb, Coriat, Religion and Medicine.Powell, L. P., Christian Science, its Faith and its Founder.Campbell, J. M., Paul the Mystic.Scott, W. M., Aspects of Christian Mysticism.Inge, W. R., Personal Idealism and Mysticism.
God in All and over All
Authors: Archibald Warren Seymour 
Published: November 2011

Each generation and each century seems to have its own peculiar danger and its own peculiar genius. The Christian church, for example, was confronted in the early centuries with the dangerous and subtle opposition of Greek thought; and the genius of the church victoriously faced this opposition with that spiritual interpretation of the life and teachings of Jesus which we find in the Fourth Gospel. Later, in the sixteenth century, the danger appeared in a materialistic church, and the genius of the Reformation was unmistakably present in the religion of the spirit and the liberty of the individual. In the eighteenth century the peril was seen in dogma, or irreligion, or a tepid morality; and the opposition developed Pietism in Germany, Methodism in England, and the Great Awakening in New England. Every century appears to be led into the wilderness to be tempted by the devil in some new guise, and is compelled to find the apt, victorious text in Scripture.And yet, whatever be the temptation and whatever be the triumphant reply, the issues are always the same,—sin and salvation. In the Greek myth of Proteus, when that old man of the sea was grappled with, he assumed most horrible and terrifying forms. Now he was a fire, now a wild stag, now a screaming seabird, now a three-headed dog, now a serpent. Sin is always protean, and presents to the wrestling centuries new and terrible aspects. What, then, we ask, seem to be the principalities and protean powers against which we are compelled to wrestle? I venture to think they may be suggested in one word, Materialism.
The New Criticism of the Gospels
Authors: Scott E. F. 
Published: November 2011

Twenty years ago it was possible to regard the Synoptic Problem as virtually solved. There might still be difference of opinion on a number of details, but the main conclusions seemed to be unassailable. The sources of the three gospels, like those of the Nile, had been hidden in mystery, and the discovery of them was justly hailed as the chief triumph of nineteenth-century scholarship.For some time it has been apparent that the rejoicings were premature. Those matters of detail which had yet to be settled have turned out to be serious, and we are now realizing, with something of a shock, that the Synoptic Problem is still with us. Instead of reaching a solution we have only come in sight of the real difficulties. If the confidence of twenty years ago is ever regained it will only be after another long spell of patient labor.We certainly owe much to the great scholars of the last century, though their claim to discovery has been found wanting. They gave us the clues which we have still to follow. The materials they collected and the observations they made will always be valuable. Their theory itself, although it calls for drastic revision, will continue, in some essential points, to stand. It will remain certain that Mark is the earliest of our gospels and has been used by the other evangelists. It seems equally impossible to doubt that along with Mark there was another source, now lost, on which Matthew and Luke must have drawn for their record of Jesus' teaching. These results, however they may be qualified, must always form the starting-point for critical investigation. But we now recognize that the older scholars conceived of their task too narrowly. The problem before them was far more intricate than they supposed, and has to be solved not merely by comparing the editorial methods of the several evangelists but by a deeper analysis, affecting the substance as well as the formal structure of the gospels.
John Robinson and the Beginnings of the Pilgrim Movement
Authors: Powicke Frederick James 
Published: November 2011

The scope of this article is strictly limited. It takes no account of the great issues, social, national, and international, which, in the course of time, flowed from the few simple folk “in the north parts” of England about Scrooby and Gainsborough who obeyed what they believed to be a divine impulse.Others far more competent for the purpose have already dealt with, or will deal with, these. Nor does it do more than touch the details of the life into which the exiles passed at Amsterdam and Leyden. For on these, Dr. Dexter and his son — to mention but two of the workers in this fieldx — may almost be said to have spoken the last word. Nor does it follow the Pilgrims into the new world where they struck root with such heroic fortitude, except so far as is required to correct one or two somewhat inveterate mistakes. It is, in fact, limited to the man who, beyond any one else, was the chief spiritual influence in those earliest pioneers whose character and ideals imparted a permanent direction to the development of New England. At the same time, while relating the substance of what is known of Robinson, I have tried to state the truth with regard to the circumstances in which the Pilgrim movement took its start; and if, in so doing, it has seemed necessary to criticize adversely the conclusions of one writer in particular, my excuse must be that his narrative has been accepted, in some high quarters, as that of an authority on the subject whose word is final. It is not by any means final, as the sequel, I think, will show.
Christian Experience the Key to Christian History
Authors: Walker Henry H. 
Published: November 2011

No field of theological study surpasses in interest or in importance the history of the Christian Church. Here is a great complex of institutions and beliefs. Where have these come from? What was it that gave them birth? What is the secret of their persistence and power? What are they worth to mankind? Is there to be found beneath the variant, shifting forms of institution and life, of organization and creed, as they appear in Christian history, any underlying, unifying principle, which can account for their rise and explain their right to be? These questions must be answered. They involve the fundamental problems of the unity of Christian history and of the rationality and worth of institutions and confessions and rituals, which, unless they can thus justify themselves, cannot permanently survive.It is the purpose of this article to show that there is such a unifying principle of interpretation, and that this principle is to be found in the reality of the Christian experience itself. Behind every movement in the history of the church, behind every institution which she has developed for the expression and perpetuation of her life, behind every doctrine and creed, there stands a human soul which has met God, and in the great silence, unbroken save by the cry of penitence or the exultant note of spiritual conquest, has found the path to peace.
A Rejoinder by Rabbi Klausner
Authors: Moore George F. 
Published: November 2011

In the January number of the Harvard Theological Review for this year I published a review of the recent “Life of Jesus of Nazareth,” by Rabbi Joseph Klausner and of a criticism of the volume by Doctor Kaminka of Vienna.In a letter from Doctor Klausner he replies to some points in my criticism and restates his own position. It is proper, therefore, that this part of his letter should be put before the readers of the Review and Professor Wolfson has been kind enough to translate it for that purpose.
Biofilm accumulation on endotracheal tubes following prolonged intubation
Authors: Lee J M , Hashmi N , Bloom J D , Tamashiro E , Doghramji L , Sarani B , Palmer J N , Cohen N A , Mirza N 
Published: November 2011

AbstractObjective:To demonstrate that patients who have been intubated for prolonged periods of time will have an increased likelihood of developing bacterial biofilm on their endotracheal tubes.Methods:We collected endotracheal tubes from patients at the time of extubation, and analysed representative sections with scanning electron microscopy for morphologic evidence of biofilms.Results:From September 2007 to September 2008, 32 endotracheal tubes were analysed with electron microscopy. Patients who had been intubated for 6 days or longer had a significantly higher percentage of endotracheal tubes that exhibited bacterial biofilms, compared with patients intubated for less than 6 days (88.9 versus 57.1 per cent,p = 0.0439).Conclusions:Longer duration of intubation is associated with a higher incidence of bacterial biofilm. Further research is needed to link the presence of bacterial biofilms to acquired laryngotracheal damage.
THE REFORMATION OF THE GENERATIONS: YOUTH, AGE AND RELIGIOUS CHANGE IN ENGLAND,c. 1500–1700
Authors: Walsham Alexandra 
Published: November 2011

ABSTRACTThis exploratory essay adopts the life-cycle as a tool with which to investigate religious change in the sixteenth and seventeenth centuries. It examines how inherited tropes about youth and age were deployed and the ways in which the notion of generational strife was invoked at various stages of England's long Reformation. These provide insight into how contemporaries understood and experienced the theological and cultural upheavals of the era and the process by which Protestantism ‘aged’ as it progressed beyond its unruly protest phase and became institutionalised as the official faith.
Geodesics in Margulis spacetimes
Authors: GOLDMAN WILLIAM M. , LABOURIE FRANÇOIS 
Published: November 2011

AbstractLet M3 be a Margulis spacetime whose associated complete hyperbolic surface Σ2 has a compact convex core. Generalizing the correspondence between closed geodesics on M3 and closed geodesics on Σ2, we establish an orbit equivalence between recurrent spacelike geodesics on M3 and recurrent geodesics on Σ2. In contrast, no timelike geodesic recurs in either forward or backward time.
Salmonellosis and charter tourism: epidemiology and trends of imported human cases to Norway from the Canary Islands and Thailand, 1994–2008
Authors: EMBERLAND K. E. , NYGÅRD K. , AAVITSLAND P. 
Published: November 2011

SUMMARYMore than 70% of reported human Salmonella infections in Norway are infected abroad. The Canary Islands and Thailand are two of the most popular charter tourist destinations for Norwegians. Using surveillance data for the years 1994–2008, and denominator data on travel to the Canary Islands 2000–2008 and to Thailand 1997–2008, we present the epidemiology and trends of Salmonella infections in Norwegian tourists to these destinations. We found a declining trend in risk of salmonellosis in tourists returning from the Canary Islands, and a change in serovar distribution in travellers to Thailand with more S. Enteritidis infections, similar to that observed in Western European countries. The use of denominator data is important when studying risk of travel-related disease, as surveillance data tend to reflect travel activity more than the risk. Infections among tourists do not always affect the local residents and therefore may not be detected by local public health authorities. Sharing knowledge on the epidemiology of infections in tourists could be useful for observation of changes in trends in the countries visited, and in future outbreak investigations.
The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001–2007
Authors: SPENCER S. E. F. , MARSHALL J. , PIRIE R. , CAMPBELL D. , BAKER M. G. , FRENCH N. P. 
Published: November 2011

SUMMARYDespite recent improvements, New Zealand still has one of the highest per-capita incidence rates of campylobacteriosis in the world. To reduce the incidence, a thorough understanding of the epidemiology of infection is needed. This retrospective analysis of 36 000 notified human cases during a high-risk period between 2001 and 2007 explored the spatial and temporal determinants of Campylobacter notifications at a fine spatial scale in order to improve understanding of the complex epidemiology. Social deprivation was associated with a decreased risk of notification, whereas urban residence was associated with an increased risk. However, for young children rural residence was a risk factor. High dairy cattle density was associated with an increased risk of notification in two of the three regions investigated. Campylobacter notification patterns exhibit large temporal variations; however, few factors were associated with periods of increased risk, in particular temperature did not appear to drive the seasonality in campylobacteriosis.
Diagnostic challenges of Marfan syndrome in an XYY young man
Authors: Lebreiro Ana , Martins Elisabete , Machado José Carlos , Abreu-Lima Cassiano 
Published: November 2011

AbstractTall stature is a common feature of both Marfan syndrome and XYY syndrome. Differential diagnosis between these entities has important prognostic implications. We report the case of a 21-year-old young man with a previously known diagnosis of XYY syndrome, in whom the identification of a fibrilin-1 mutation was determinant to establish an appropriate diagnosis, medical follow-up, and genetic counselling.