bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Genome Characterization and Genotyping of Global WU Polyomavirus Strains
Authors: Bialasiewicz Seweryn , Rockett Rebecca , Whiley David W. , Abed Yacine , Allander Tobias , Binks Michael , Boivin Guy , Cheng Allen C. , Chung Ju-Young , Ferguson Patricia E. , Gilroy Nicole M. , Leach Amanda J. , Lindau Cecilia , Rossen John W. , Sorrell Tania C. , Nissen Michael D. , Sloots Theo P. 
Published: April 2010

ABSTRACT
Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.
Contrasting fluid events giving rise to apparently similar diagenetic products; late-stage dolomite cements from the Southern Alps and central Apennines, Italy
Authors: Ronchi P. , Giulio A. Di , Ceriani A. , Scotti P. 
Published: April 2010

Abstract
Precipitation of dolomite cements in Jurassic carbonate platform sediments and slope breccias has been studied from well cores and outcrops of the central Southern Alps and central Apennines in Italy.
In both areas, an initial, massive dolomite replacement was followed by multiphase precipitation of dolomite cements. The replacement occurred during burial, in a passive margin regime, in response to compaction-driven flow of formational fluids. This interpretation is based on results from fluid inclusion and stable isotope analyses which have been related to the thermal history. The dolomite cements precipitated when both areas were involved in collisional tectonics. In spite of the similar diagenetic evolution, the fluids causing dolomite cementation in each case were compositionally different. In the Alps a decrease in salinity was recorded from sea water to brackish fluids, whereas in the Apennines an increase in salinity from sea water up to >10% NaCl equivalent was recorded. The remarkable salinity differences in diagenetic fluids are considered to be related to the different sub-aerial relief of the two belts during dolomite precipitation. In the Alps, the dilution of fluids is related to the infiltration of meteoric waters from the mountain chain, that was widely emergent. In the Apennines, dolomite cements precipitated whilst the structural units were still widely submerged, preventing meteoric dilution of cementing fluids and promoting an increase in salinity through mixing with fluids rising from older evaporate-bearing layers. In both Alpine and Apennine cases, the same diagenetic trend is observed in thrust-fold belt and foreland basin units; in both structural systems the diagenetic events start precipitating dolomite cements in the inner part of the collision zone and then the diagenetic processes migrate towards the foreland basin along with the structural evolution of the area.
Sedimentary evolution of an Upper Jurassic epeiric carbonate ramp, Iberian Basin, NE Spain
Authors: Aurell M. , Bádenas B. , Ipas J. , Ramajo J. 
Published: April 2010

Abstract
A synthesis of the sedimentary evolution of the Upper Jurassic carbonate epeiric ramps that developed in the northern part of the Iberian Basin (NE Spain) is presented. The facies distributions reconstructed from the analysis of a 200 km-long transect, show a transition from shallow to relatively deep sedimentation sites. The studied carbonate ramps record major long-term transgression, from mid-Oxfordian to mid-Kimmeridgian followed by progressive basinwards coastal shift until the major regressive event around the mid-Berriasian. Subsidence was relatively homogeneous across the northern Iberian Basin during most of the studied interval. Major episodes of differential subsidence occurred around the Oxfordian–Kimmeridgian transition and onwards from the mid-Tithonian.
The sedimentary evolution and particular facies types of the successive Iberian carbonate ramps is described, considering five depositional sequences that have a long-term transgressive-regressive evolution. The Oxfordian sequence shows a sharp transition from shallow to deep ramp areas: from mixed siliciclastic-carbonate (ooidal, skeletal, peloidal) facies to condensed (i.e. spongiolithic, peloidal, glauconitic) facies in the open platform domain. In the two Kimmeridgian sequences (Kim1 and Kim2), the transition between shallow and deep areas is more gradual and thickness distribution across the ramp is more homogeneous. Coral-microbial reefs and oolitic-peloidal-skeletal shoals characterized the shallow areas. Towards the offshore domain, these facies grade rapidly to a tempestite-dominated lithofacies and then into thick lime mudstone successions (i.e. rhythmic marls-mudstone alternations). Shallow oncolitic-peloidal and skeletal facies covered wide areas of the carbonate ramp during the early Tithonian (Ti1 sequence) and graded basinwards to thick successions of well-bedded micrites. The middle Tithonian to lower Berriasian platform (Ti2 sequence) is only partly exposed and formed during a stage of more heterogeneous subsidence. It is characterized by a thick succession with metre-scale shallowing-upward sequences with local development of peritidal, algal-laminated caps. The factors that controlled the sedimentary evolution and major facies changes across the successive epeiric carbonate ramps are discussed by comparison to other Upper Jurassic platforms developed in the western Tethyan realm.
Obtaining optimal
k
-cardinality trees fast
Authors: Chimani Markus , Kandyba Maria , Ljubić Ivana , Mutzel Petra 
Published: April 2010

Given an undirected graph
G
= (
V
,
E
) with edge weights and a positive integer number
k
, the
k
-cardinality tree problem consists of finding a subtree
T
of
G
with exactly
k
edges and the minimum possible weight. Many algorithms have been proposed to solve this NP-hard problem, resulting in mainly heuristic and metaheuristic approaches.

In this article, we present an exact ILP-based algorithm using directed cuts. We mathematically compare the strength of our formulation to the previously known ILP formulations of this problem, and show the advantages of our approach. Afterwards, we give an extensive study on the algorithm's practical performance compared to the state-of-the-art metaheuristics.
In contrast to the widespread assumption that such a problem cannot be efficiently tackled by exact algorithms for medium and large graphs (between 200 and 5,000 nodes), our results show that our algorithm not only has the advantage of proving the optimality of the computed solution, but also often outperforms the metaheuristic approaches in terms of running time.
Cache-, hash-, and space-efficient bloom filters
Authors: Putze Felix , Sanders Peter , Singler Johannes 
Published: April 2010

A Bloom filter is a very compact data structure that supports approximate membership queries on a set, allowing false positives.
We propose several new variants of Bloom filters and replacements with similar functionality. All of them have a better cache-efficiency and need less hash bits than regular Bloom filters. Some use SIMD functionality, while the others provide an even better space efficiency. As a consequence, we get a more flexible trade-off between false-positive rate, space-efficiency, cache-efficiency, hash-efficiency, and computational effort. We analyze the efficiency of Bloom filters and the proposed replacements in detail, in terms of the false-positive rate, the number of expected cache-misses, and the number of required hash bits. We also describe and experimentally evaluate the performance of highly tuned implementations. For many settings, our alternatives perform better than the methods proposed so far.
Feasibility of semiring-based timing constraints
Authors: Yu Yue , Ren Shangping , Frieder Ophir 
Published: April 2010

Real-time and embedded applications often involve different types of timing constraints, such as precedence constraints and real-time constraints. As real-time and embedded applications further advance, new timing constraint types are emerging as well. Recent research on interval-based timing constraints is an example. Thus, it is important to have a uniformed timing constraint representation so that a generalized approach can be developed to analyze the variant constraint types.
A semiring-based timing constraint model is introduced to generalize the representations of different constraint types. Under this model, we develop an algorithm to check the satisfaction feasibility for a given set of semiring-based timing constraints. This algorithm provides better performance in the average case as compared to applying the Bellman-Ford algorithm directly on the constraint set.
In addition, for a set of feasible semiring-based timing constraints, event occurrence points that satisfy the constraint set form a (hyperdimension) feasible region. For the given two sets of timing constraints, we develop a necessary and sufficient condition to testify whether the two constraint sets' feasible regions have an inclusion relation. If one feasible region is included in the other, we know that the real-time event occurrences that satisfy the included constraint set will necessarily satisfy the including set.
Pharmacodynamic Trial of Nimotuzumab in Unresectable Squamous Cell Carcinoma of the Head and Neck: A SENDO Foundation Study
Authors: Rojo Federico , Gracias Elías , Villena Nadia , Cruz Teresa , Corominas Josep Maria , Corradino Irene , Cedeño Mercedes , Campas Clara , Osorio Marta , Iznaga Normando , Bellosillo Beatriz , Rovira Ana , Marsoni Silvia , Gascon Pere , Serrano Sergio , Sessa Cristiana , Crombet Tania , Albanell Joan 
Published: April 2010

Abstract
Purpose: To assess the pharmacodynamic effects of nimotuzumab, an anti–epidermal growth factor receptor (EGFR) monoclonal antibody with intermediate affinity for the receptor, in skin and tumor tissues from head and neck cancer patients.
Experimental design: Pharmacodynamic study in patients with advanced squamous cell carcinoma of the head and neck, unsuitable for chemoradiotherapy, enrolled in a single-center trial. Patients received 8 weekly infusions of nimotuzumab. The first nimotuzumab infusion was administered 1 week before starting radiation, whereas the remaining doses were administered concomitantly with irradiation. Paired biopsies were taken from skin and primary tumors, before (pretherapy) and 1 week (on single-agent therapy) after first infusion. Immunohistochemistry was conducted to assay the effects of nimotuzumab on total and phosphorylated EGFR, phosphorylated extracellular signal-regulated kinase 1/2 (p-ERK1/2), p-AKT, and proliferation (Ki-67).
Results: Nimotuzumab was well tolerated and there was no evidence of skin rash. Objective response was achieved in 9 of 10 patients. The pharmacodynamic assays showed inhibition of p-EGFR in both skin and tumor (P = 0.042 in skin and P = 0.034 in tumor). No significant changes in p-ERK1/2, p-AKT, or Ki-67 were detected in skin. In addition, lymphocytic infiltrates, folliculitis, or perifolliculitis were not observed. In tumor samples, there was an upregulation of p-AKT (P = 0.043), a reduction in proliferation index (P = 0.012), and a nonsignificant trend toward a decrease of p-ERK1/2 (P = 0.091).
Conclusions: The pharmacodynamic data confirmed the ability of nimotuzumab to decrease EGFR phosphorylation. Downstream effects were observed in tumor cells but not in skin, a finding that may help to explain the lack of skin rash in patients treated with nimotuzumab. Clin Cancer Res; 16(8); 2474–82. ©2010 AACR.
Survival of Patients with Newly Diagnosed Glioblastoma Treated with Radiation and Temozolomide in Research Studies in the United States
Authors: Grossman Stuart A. , Ye Xiaobu , Piantadosi Steven , Desideri Serena , Nabors Louis B. , Rosenfeld Myrna , Fisher Joy ,   for the NABTT CNS Consortium
Published: April 2010

Abstract
Purpose: Novel agents are currently combined with radiation and temozolomide (RT + TMZ) in newly diagnosed glioblastoma using overall survival as the primary end point. Results of these phase II studies are typically compared with the phase III European Organization for Research and Treatment of Cancer (EORTC) survival data that resulted in RT + TMZ becoming standard therapy.
Experimental Design: The New Approaches to Brain Tumor Therapy (NABTT) Consortium assigned 365 patients with glioblastoma to four single-cohort studies with similar eligibility criteria. Patients received RT + TMZ with talampanel (n = 72), poly-ICLC (n = 97), or cilengitide (n = 112) or RT + TMZ alone with monitoring of CD4 counts (n = 84). Overall survival of those ages 18 to 70 years with glioblastoma was compared with published EORTC data.
Results: NABTT and EORTC patients had comparable performance status and debulking surgery. Median, 12-month, and 24-month survival rates for the EORTC patients (n = 287) and the comparable NABTT patients receiving RT + TMZ and novel agents (n = 244) are 14.6 versus 19.6 months, 61% versus 81%, and 27% versus 37%, respectively. This represents a 37% reduction in odds of death (P &lt; 0.0001) through 2 years of follow-up. NABTT and EORTC patients receiving only RT + TMZ had similar survival.
Conclusions: Newly diagnosed glioblastoma treated recently with RT + TMZ and talampanel, poly-ICLC, or cilengitide had significantly longer survival than similar patients treated with only RT + TMZ accrued internationally from 2000 to 2002. These differences could result from the novel agents or changing patterns of care. Until the reasons for these different survival rates are clarified, comparisons of outcomes from phase II studies with published RT + TMZ survival data should be interpreted with caution. Clin Cancer Res; 16(8); 2443–9. ©2010 AACR.
A Molecularly Targeted Theranostic Probe for Ovarian Cancer
Authors: Chen Wenxue , Bardhan Rizia , Bartels Marc , Perez-Torres Carlos , Pautler Robia G. , Halas Naomi J. , Joshi Amit 
Published: April 2010

Abstract
Overexpression of the human epidermal growth factor receptor (HER) family has been implicated in ovarian cancer because of its participation in signaling pathway regulating cellular proliferation, differentiation, motility, and survival. Currently, effective diagnostic and therapeutic schemes are lacking for treating ovarian cancer, and consequently ovarian cancer has a high mortality rate. Although HER2 receptor expression does not usually affect the survival rates of ovarian cancer to the same extent as in breast cancer, it can be used as a docking site for directed nanotherapies in cases with de novo or acquired chemotherapy resistance. In this study, we have exploited a novel gold nanoshell–based complex (nanocomplex) for targeting, dual modal imaging, and photothermal therapy of HER2-overexpressing and drug-resistant ovarian cancer OVCAR3 cells in vitro. The nanocomplexes are engineered to simultaneously provide contrast as fluorescence optical imaging probe and a magnetic resonance imaging agent. Immunofluorescence staining and magnetic resonance imaging successfully show that nanocomplex–anti-HER2 conjugates specifically bind to OVCAR3 cells as opposed to the control, MDA-MB-231 cells, which have low HER2 expression. In addition, nanocomplexes targeted to OVCAR3 cells, when irradiated with near-IR laser, result in selective destruction of cancer cells through photothermal ablation. We also show that near-IR light therapy and the nanocomplexes by themselves are noncytotoxic in vitro. To the best of our knowledge, this is the first successful integration of dual modal bioimaging with photothermal cancer therapy for treatment of ovarian cancer. Based on their efficacy in vitro, these nanocomplexes are highly promising for image-guided photothermal therapy of ovarian cancer, as well as other HER2-overexpressing cancers. Mol Cancer Ther; 9(4); 1028–38. ©2010 AACR.
Ming Princes and Daoist Ritual
Authors: Wang Richard 
Published: April 2010

AbstractThis essay explores the relationship between the patronage of Ming princes and local Daoism, focusing on ritual. While the role of Ming princes in local religion is an under-appreciated subject, this essay demonstrates that their support is crucial to our understanding of Daoism during that period. The efforts of princes made local Daoist ritual visible. In fact, they occupied an important role in propagating Daoism as an element of cultural and religious identity. Moreover, by different approaches to Daoist ritual, the Ming princes represented the various religious and social needs of lay patrons in the local community. Cet article explore la relation entre le patronage des princes Ming et le taoïsme local, en s'attachant plus particulièrement au rituel. Alors qu'on tend à sous-estimer le rôle des princes Ming dans le domaine des religions locales, l'article montre que prendre en compte leur soutien est décisif pour notre compréhension du taoïsme pendant cette période. Les efforts des princes ont rendu visible les rituels taoïstes au niveau local. Ils ont en fait joué un rôle important dans la propagation du taoïsme comme élément d'identité culturelle et religieuse. En outre, par leurs approches différentes du rituel taoïste les princes Ming étaient représentatifs de la variété des demandes religieuses et sociales des laïques au sein de la communauté locale.
Writing Emotions: Ritual Innovation as Emotional Expression
Authors: Epstein Maram 
Published: April 2010

AbstractThis article examines the chronological biographies of the Qing ritualists Yan Yuan (1635-1704) and Li Gong (1659-1733) to witness how they negotiated and wrote about the ritual and emotional priorities in their relationships with various family members. It argues that rather than being just a form of ritual duty, filial piety was a core emotion at the center of many people's affective and spiritual lives. Although the conservative nature of nianpu (chronological biography) as a genre meant that some of the most intimate relationships in these two men's lives would get passed over in silence, the recording of their manipulation of ritual forms allowed them an indirect means of expressing their affective bonds.
Which Method of Rotator Cuff Repair Leads to the Highest Rate of Structural Healing?
Authors: Duquin Thomas R. , Buyea Cathy , Bisson Leslie J. 
Published: April 2010

Background The purpose of rotator cuff repair is to diminish pain and restore function, and this most predictably occurs when the tendon is demonstrated to heal. Recent improvements in repair methods have led to improved biomechanical performance, but this has not yet been demonstrated to result in higher healing rates. The purpose of our study was to determine whether different repair methods resulted in different rates of recurrent tearing after surgery. Hypotheses We hypothesized that (1) the rotator cuff repair method will not affect retear rate, and (2) the surgical approach will not affect the retear rate for a given repair method. Study Design Systematic review of the literature. Methods The literature was systematically searched to find articles reporting imaging study assessment of structural healing rates after rotator cuff repair, with data stratified according to tear size. Retear rates were compared for transosseous (TO), single-row suture anchor (SA), double-row suture anchor (DA), and suture bridge (SB) repair methods, as well as for open (O), miniopen (MO), and arthroscopic (A) approaches. Results Retear rates were available for 1252 repairs collected from 23 studies. Retear rates were significantly lower for double-row repairs when compared with TO or SA for all tears greater than 1 cm and ranged from 7% for tears less than 1 cm to 41% for tears greater than 5 cm, in comparison with retear rates for single-row techniques (TO and SA) of 17% to 69% for tears less than 1 cm and greater than 5 cm, respectively. There was no significant difference in retear rates between TO and SA repair methods or between arthroscopic and nonarthroscopic approaches for any tear size. Conclusion Double-row repair methods lead to significantly lower retear rates when compared with single-row methods for tears greater than 1 cm. Surgical approach has no significant effect on retear rate.
Biomechanical Analysis of an Ovine Rotator Cuff Repair via Porous Patch Augmentation in a Chronic Rupture Model
Authors: Santoni Brandon G. , McGilvray Kirk C. , Lyons Amy S. , Bansal Manjula , Turner A. Simon , MacGillivray John D. , Coleman Struan H. , Puttlitz Christian M. 
Published: April 2010

Background Rotator cuff repair is a commonly performed procedure, but many of these repairs fail in the postoperative term. Despite advances in surgical methods to optimize the repair, failure rates still persist clinically, thereby suggesting the need for novel mechanical or biological augmentation strategies. Nonresorbable implants provide an appealing approach because patch materials may confer acute mechanical stability and act as a conductive scaffold for tissue ingrowth at the site of the tendon insertion. Hypothesis The polyurethane scaffold mesh will confer greater biomechanical function relative to a nonaugmented repair after 12 weeks in vivo using a chronic ovine model of rotator cuff repair. Study Design Controlled laboratory study. Methods After development of the chronic rupture model, the tensile failure properties of the nonresorbable mesh-augmented repair (n, 9) were compared with those of a surgical control in an ovine model (n, 8). Results Rotator cuff repair with the scaffold mesh in the chronic model resulted in a significant 74.2% increase in force at failure relative to the nonaugmented surgical control (P = .021). Apparent increases in stiffness (55.4%) and global displacement at failure (21.4%) in the mesh-augmented group relative to nonaugmented controls were not significant (P = .126 and P = .123, respectively). At the study endpoint, the augmented shoulders recovered 37.8% and 40.7% of the force at failure and stiffness, respectively, of intact, nonoperated controls. Conclusion Using the previously described chronic rupture model, this study demonstrated that repair of a chronic tendon tear with the polyurethane scaffold mesh provides greater mechanical strength in the critical healing period than that of traditional suture anchor repair. Clinical Relevance This device could be used to enhance the surgical repair of the rotator cuff and consequently improve long-term clinical outcome.