bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementing an X-ray validation pipeline for the Protein Data Bank
Authors: Gore Swanand , Velankar Sameer , Kleywegt Gerard J. 
Published: March 2012

There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.
Use of noncrystallographic symmetry for automated model building at medium to low resolution
Authors: Wiegels Tim , Lamzin Victor S. 
Published: March 2012

A novel method is presented for the automatic detection of noncrystallographic symmetry (NCS) in macromolecular crystal structure determination which does not require the derivation of molecular masks or the segmentation of density. It was found that throughout structure determination the NCS-related parts may be differently pronounced in the electron density. This often results in the modelling of molecular fragments of variable length and accuracy, especially during automated model-building procedures. These fragments were used to identify NCS relations in order to aid automated model building and refinement. In a number of test cases higher completeness and greater accuracy of the obtained structures were achieved, specifically at a crystallographic resolution of 2.3 Å or poorer. In the best case, the method allowed the building of up to 15% more residues automatically and a tripling of the average length of the built fragments.
Ingestion by an endemic frugivore enhances seed germination of endemic plant species but decreases seedling survival of exotics
Authors: Zuël Nicolas , Griffiths Christine J. , Hector Andy , Hansen Dennis M. , Jones Carl G. , Albrecht Matthias 
Published: March 2012

AbstractAim  To test whether ingestion by endemic frugivores differentially affects the seed germination time, germination percentage and seedling survival of endemic, native and exotic fleshy fruited plant species, and to identify the principal processes and attributes driving such effects.Location  Round Island, Mauritius.Methods  We conducted a germination and seedling survival experiment for 3 months to test whether ingestion (gut passage and deposition in faeces) by the endemic Telfair’s skink (Leiolopisma telfairii) had a differential effect on the germination time, germination percentage and seedling survival of two endemic, four native and two exotic fleshy fruited plant species. To assess the importance of factors involved in the ingestion process, we used a factorial design with gut passage (gut‐passed vs. not gut‐passed), depulping (whole fruit vs. manually depulped seed) and the presence of faecal material (faeces vs. without faeces). In addition, the roles of species‐specific traits, seed size and deposition density (average number of seeds per faeces) were examined.Results  Exotic species had a higher germination percentage than indigenous (native and endemic) species when not ingested. Following skink ingestion, there was no longer a difference, as ingestion enhanced germination percentage most in endemic species. The exotic species still germinated faster overall than the indigenous species, despite ingestion accelerating the germination time of endemics. However, ingestion strongly reduced seedling survival of the exotic species, while having no negative effect on the survival of indigenous seedlings. Overall, ingested indigenous seeds were more likely to germinate and the seedlings more likely to survive than ingested exotic seeds and seedlings. Seed size, deposition density and the removal of fruit pulp by either manual depulping or gut passage were important predictors of germination time, germination percentage and seedling survival.Main conclusions  These endemic frugivores can enhance the competitiveness of endemic compared with exotic fleshy fruited plants at the critical germination and seedling establishment stage. Consequently, conservation and restoration of mutualistic endemic plant–animal interactions may be vital to mitigating the degradation of habitats invaded by exotic plants, which is of particular relevance for island ecosystems in which large numbers of endemics are threatened by exotic invaders.
Stem cells in asexual reproduction of Enchytraeus japonensis (Oligochaeta, Annelid): Proliferation and migration of neoblasts
Authors: Sugio Mutsumi , Yoshida‐Noro Chikako , Ozawa Kaname , Tochinai Shin 
Published: March 2012

Enchytraeus japonensis is a small oligochaete that reproduces mainly asexually by fragmentation (autotomy) and regeneration. As sexual reproduction can also be induced, it is a good animal model for the study of both somatic and germline stem cells. To clarify the features of stem cells in regeneration, we investigated the proliferation and lineage of stem cells in E. japonensis. Neoblasts, which have the morphological characteristics of undifferentiated cells, were found to firmly adhere to the posterior surface of septa in each trunk segment. Also, smaller neoblast‐like cells, which are designated as N‐cells in this study, were located dorsal to the neoblasts on the septa. By conducting 5‐bromo‐2′‐deoxyuridine (BrdU)‐labeling‐experiments, we have shown that neoblasts are slow‐cycling (or quiescent) in intact growing worms, but proliferate rapidly in response to fragmentation. N‐cells proliferate more actively than do neoblasts in intact worms. The results of pulse‐chase experiments indicated that neoblast and N‐cell lineage mesodermal cells that incorporated BrdU early in regeneration migrated toward the autotomized site to form the mesodermal region of the blastema, while the epidermal and intestinal cells also contributed to the blastema locally near the autotomized site. We have also shown that neoblasts have stem cell characteristics by expressing Ej‐vlg2 and by the activity of telomerase during regeneration. Telomerase activity was high in the early stage of regeneration and correlated with the proliferation activity in the neoblast lineage of mesodermal stem cells. Taken together, our results indicate that neoblasts are mesodermal stem cells involved in the regeneration of E. japonensis.
Unusual cause of neonatal rectal bleeding: Colonic intramural haematoma
Authors: Shankarnaryanan Srinivas , Hardikar Winita 
Published: March 2012

AbstractBright rectal bleeding in a neonate is most commonly due to necrotising enterocolitis, gastrointestinal infection or cows milk protein intolerance. We present here an infant who developed PR bleeding after cardiac surgery. Bleeding persisted despite presumptive treatment for the most common causes. A colonic intramural haematoma was identified on colonoscopy most likely related to anticoagulation in the setting of cardiac surgery.
High‐dose aprotinin, blood product transfusions, and short‐term outcome in neonates and infants: a pediatric cardiac surgery center experience
Authors: Bojan Mirela , Boulat Claire , Peperstraete Harlinde , Pouard Philippe 
Published: March 2012

SummaryBackground:  The efficacy of aprotinin, the most popular antifibrinolytic agent in congenital cardiac surgery, was still uncertain in small infants when its prophylactic use was suspended for safety reasons. The aim of this study is to describe associations between the prophylactic use of high‐dose aprotinin, the need for blood product transfusions, and short‐term outcome in neonates and infants with cardiac surgery.Methods/materials:  This retrospective study included all patients younger than 1 year undergoing surgery with cardiopulmonary bypass through 42 months, before and after withdrawal of aprotinin. Each patient who received aprotinin was matched with a control with similar baseline and surgical characteristics, who have not received any antifibrinolytic agent. Associations between the use of aprotinin and the exposure to red blood cells, fresh frozen plasma, and platelet transfusions were estimated from a logistic regression model, and the exposure to additional transfusions from a polytomous regression model.Results:  Matching resulted in two groups of 283 patients each, well balanced except for the priming volume and the ultrafiltration rate, larger in the aprotinin group. After adjustment for the priming volume and ultrafiltration rate, there was no significant association between the use of aprotinin, the exposure to any blood product transfusion, or the exposure to additional transfusions, the rate of re‐exploration for bleeding, and short‐term outcome. Two patients in the control group required re‐exploration for bleeding.Conclusions:  No association was found between the prophylactic use of aprotinin, blood product transfusions, and short‐term outcome in this population of neonates and infants.
The functional genomics of an eco‐evolutionary feedback loop: linking gene expression, trait evolution, and community dynamics
Authors: Becks Lutz , Ellner Stephen P. , Jones Laura E. , Hairston Nelson G. 
Published: March 2012

Ecology Letters (2012) 15: 492–501AbstractFeedbacks between ecological and evolutionary change may play important roles in community and ecosystem functioning, but a complete eco‐evolutionary feedback loop has not been demonstrated at the community level, and we know little about molecular mechanisms underlying this kind of eco‐evolutionary dynamics. In predator–prey (rotifer‐alga) microcosms, cyclical changes in predator abundance generated fluctuating selection for a heritable prey defence trait, cell clumping. Predator population growth was affected more by prey evolution than by changes in prey abundance, and changes in predator abundance drove further prey evolution, completing the feedback loop. Within a predator–prey cycle, genes up‐regulated as clumping declined were down‐regulated as clumping increased, and vice‐versa. Genes changing most in expression tended to be associated with defence or its cost. Expression patterns of individual genes differed greatly between consecutive cycles (often reversing direction), suggesting that a particular phenotype may be produced by several (perhaps many) different gene transcription pathways.
When serial prostate biopsy is recommended: most cancers detected are clinically insignificant
Authors: Zaytoun Osama M. , Stephenson Andrew J. , Fareed Khaled , El‐Shafei Ahmed , Gao Tianming , Levy David , Jones J. Stephen 
Published: March 2012

Study Type – Disagnostic (exploratory cohort)Level of Evidence 2bWhat's known on the subject? and What does the study add?Many patients undergo serial biopsy with a low rate of detection of prostate cancer, and the rate of detection declines as more biopsies are pursued. Furthermore, the clinical significance of detected cancer appears to decline as well. It is important to follow all possible methods to detect cancer; however, there should be a parallel consideration for the clinical value for detection of these tumours with low malignant potential.The present study investigated in detail the total rate of cancer detection in serial biopsy and how many of these were deemed clinically insignificant. Moreover, it addressed the impact of detecting premalignant lesions on further detection of cancer in serial biopsy.OBJECTIVE
Many patients pursue serial prostate biopsies after two consecutive negative biopsy sessions. The objective of this study is to determine the indications of serial prostate biopsy and to compare outcomes, including the risk of detecting clinically insignificant cancer using different biopsy protocols in this highly selected population.
PATIENTS AND METHODS
Most cases of prostate cancer are detected on initial or one repeat biopsy, but persistent suspicion of prostate cancer occasionally leads to serial biopsy, which we define as more than two biopsy sessions. We recently showed that transrectal saturation biopsy (sPBx) significantly increases cancer detection when compared with extended schemes (ePBx) in the initial repeat biopsy (second overall biopsy) population, and that most cases identified are clinically significant.
In the past decade, 479 men underwent 749 repeat prostate biopsies after two prior negative biopsy sessions.
The ePBx group included 347 biopsies with 10–14 cores.
The sPBx group included 402 biopsies with >20 cores.
We analysed overall cancer detection and risk of detecting clinically significant vs insignificant tumours.
RESULTS
Prostate cancer was detected in 15.9% of 749 serial biopsies, representing a cumulative prostate cancer detection rate of 24.8% (119/479 patients).
The sPBx group had a significantly higher detection rate per biopsy session (18.6% vs 12.7%, P= 0.026).
Nevertheless, most positive biopsies 75/119 (63%) revealed clinically insignificant cancer, including 74.6% of cancers detected by sPBx.
CONCLUSION
In men with two prior negative prostate biopsies, prostate cancer detection remains low regardless of clinical indication or transrectal biopsy protocol; most cancers identified are clinically insignificant, suggesting the threshold to repeat biopsy after more than one negative session should be very high.
Obesity: a disease or a biological adaptation? An update
Authors: Chaput J.‐P. , Doucet É. , Tremblay A. 
Published: March 2012

SummaryObesity is characterized by the accumulation of excess body fat and can be conceptualized as the physical manifestation of chronic energy excess. An important challenge of today's world is that our so‐called obesogenic environment is conducive to the consumption of energy and unfavourable to the expenditure of energy. The modern, computer‐dependent, sleep‐deprived, physically inactive humans live chronically stressed in a society of food abundance. From a physiological standpoint, the excess weight gain observed in prone individuals is perceived as a normal consequence to a changed environment rather than a pathological process. In other words, weight gain is a sign of our contemporary way of living or a ‘collateral damage’ in the physiological struggle against modernity. Additionally, substantial body fat loss can complicate appetite control, decrease energy expenditure to a greater extent than predicted, increase the proneness to hypoglycaemia and its related risk towards depressive symptoms, increase the plasma and tissue levels of persistent organic pollutants that promote hormone disruption and metabolic complications, all of which are adaptations that can increase the risk of weight regain. In contrast, body fat gain generally provides the opposite adaptations, emphasizing that obesity may realistically be perceived as an a priori biological adaptation for most individuals. Accordingly, prevention and treatment strategies for obesity should ideally target the main drivers or root causes of body fat gain in order to be able to improve the health of the population.
Successful Wage Concertation: The Economic Effects of Wage Pacts and Their Alternatives
Authors: Brandl Bernd 
Published: March 2012

AbstractRecent debates on pacts have focused on the prerequisites for their emergence, whereas questions of their efficacy have receded into the background. In particular, systematic analyses of the effectiveness of pacts in terms of their capacity to enhance economic performance are missing. The aim of this article is therefore to assess the economic impact of pacts. As the majority of pacts concern wages, the assessment will concentrate on a comparison of the performance of pacts with alternative governance mechanisms for wage policies, that is, alternative pay‐setting modes. The findings show that when wage pacts are endowed with the ability to govern lower‐level pay determination, they are better at enhancing economic performance than other forms of coordination.
Indeterminacy and the Regulation of Task Allocation: The Shape of Support Roles in Healthcare
Authors: Kessler Ian , Heron Paul , Dopson Sue 
Published: March 2012

AbstractDrawing upon Marsden's typology of employment systems, this article explores how the indeterminacy of the employment relationship is enacted and resolved in relation to the healthcare assistant (HCA), a key work role in the delivery of nursing care in a hospital setting. It suggests that the regulation of task allocation within nursing assumes a hybrid form, requiring further analysis of the influences shaping the HCA role. Based on multi‐method hospital case studies, the article distinguishes different types of HCA, explaining their emergence by reference to the interaction between organizational structure and personal agency. The article illustrates the value of Marsden's framework, and by addressing its limits in a healthcare setting seeks to develop a deeper understanding of task allocation in different workplace employment systems.
The phenomenon of ‘chronic Lyme’; an observational study
Authors: Ljøstad U. , Mygland Å. 
Published: March 2012

Purposes:  To chart clinical, laboratory, and psychometric profiles in patients who attribute their complaints to chronic Lyme disease.Methods:  We assessed the patients by clinical examination, laboratory tests, and questionnaires measuring fatigue, depression, anxiety, health‐related quality of life, hypochondriasis, and illness perceptions.Results:  We found no evidence of ongoing Borrelia burgdorferi (Bb) infection in any of the 29 included patients using current diagnostic guidelines and an extended array of tests. Eight (28%) had other well‐defined illnesses. Twenty‐one (72%) had symptoms of unknown cause, of those six met the suggested criteria for post‐Lyme disease syndrome. Fourteen (48%) had presence of anti‐Bb antibodies. The patients had more fatigue and poorer health‐related quality of life as compared to normative data, but were not more depressed, anxious, or hypochondriacal. Their beliefs about the illness were characterized by negative expectations.Conclusion:  Our patients, who all attributed their symptoms to chronic Lyme disease, were heterogeneous. None had evidences of persistent Bb infection, but whether current diagnostic criteria are functional in patients with longstanding complaints is controversial. Other well‐defined illnesses or sequelae from earlier Lyme disease were probable as main explanatory factor in some cases. The patients were not more depressed, anxious, or hypochondriacal than the normal population, but they had poorer health‐related quality of life, more fatigue, and negative expectations about their illness.
Foreigners and Outsiders: Exclusionist Attitudes towards Labour Migrants in Israel
Authors: Raijman Rebeca 
Published: March 2012

AbstractThis paper examines theoretical propositions regarding the social mechanisms that produce hostility and discriminatory attitudes towards out‐group populations. Specifically, we compare the effect of perceptions of socio‐economic and national threats, social contact and prejudice on social distance expressed towards labour migrants. To do so, we examine exclusionary views held by majority and minority groups (Jews and Arabs) towards non‐Jewish labour migrants in Israel. Data analysis is based on a survey of the adult Israeli population based on a stratified sample of 1,342 respondents, conducted in Israel in 2007. Altogether, our results show that Israelis (both Jews and Arabs) are resistant to accepting and integrating foreigners into Israeli society. Among Jews, this is because the incorporation of non‐Jews challenges the definition of Israel as a Jewish state and poses a threat to the homogeneity of the nation. Among Arabs, this is probably due to threat and competition over resources. The meanings of the findings are discussed within the unique ethno‐national context of Israeli society and in light of sociological theories on ethnic exclusionism.
The magnitude of hydraulic redistribution by plant roots: a review and synthesis of empirical and modeling studies
Authors: Neumann Rebecca B. , Cardon Zoe G. 
Published: March 2012

SummaryHydraulic redistribution (HR) – the movement of water from moist to dry soil through plant roots – occurs worldwide within a range of different ecosystems and plant species. The proposed ecological and hydrologic impacts of HR include increasing dry‐season transpiration and photosynthetic rates, prolonging the life span of fine roots and maintaining root–soil contact in dry soils, and moving rainwater down into deeper soil layers where it does not evaporate. In this review, we compile estimates of the magnitude of HR from ecosystems around the world, using representative empirical and modeling studies from which we could extract amounts of water redistributed by plant root systems. The reported average magnitude of HR varies by nearly two orders of magnitude across ecosystems, from 0.04 to 1.3 mm H2O d−1in the empirical literature, and from 0.1 to 3.23 mm H2O d−1in the modeling literature. Using these synthesized data, along with other published studies, we examine this variation in the magnitude of upward and downward HR, considering effects of plant, soil and ecosystem characteristics, as well as effects of methodological details (in both empirical and modeling studies) on estimates of HR. We take both ecological and hydrologic perspectives.ContentsSummary337I.Introduction337II.Synthesis of the magnitudes of HR across ecosystems338III.Hydraulic redistribution models339IV.Methodological considerations affecting the magnitude of HR344V.Site characteristics affecting the magnitude of HR346VI.Plant characteristics affecting the magnitude of HR347VII.Conclusions349Acknowledgements350References350
Recurrent delusional ideas due to left caudate head infarction, without dementia
Authors: MEGURO Kenichi , MEGURO Mitsue , AKANUMA Kyoko 
Published: March 2012

AbstractHerein we report the case of a 77‐year‐old, right‐handed man, without dementia, who had a cerebral infarction in the left caudate head that manifested recurrent delusional ideas. He experienced three episodes of delusional ideas; the first two occurred after loss of consciousness and the third after delirium at night. MRI findings of left caudate head infarction were the same for all three episodes. An unstable cerebral perfusion may have caused problems in the cerebral network between the caudate head and cerebral cortex. Decreased cerebral blood flow in the frontal lobe was noted particularly in the second and third episodes, supporting the neurological background of disinhibition of emotional behaviour. Antipsychotic drugs and a small dose of risperidone were effective in controlling the patient's delusional ideas.