bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fungal diversity in activated sludge from membrane bioreactors in Berlin
Authors: Awad Mohamed F. , Kraume M. 
Published: August 2011

The objective of this study was to evaluate the occurrence of fungi in aerobic and anoxic activated sludge from membrane bioreactors. Thirty-six samples from each aerobic and anoxic activated sludge were taken from two membrane bioreactors treating domestic wastewater. Over a period of 9 months, four samples from each plant were taken per month. The samples were prepared for count and identification of fungi. Sixty species belonging to 30 genera were collected from activated sludge samples under aerobic and anoxic conditions. In terms of fungal identification, under aerobic conditions Geotrichum candidum was found at 94.4% followed by Penicillium species at 80.6%, yeasts at 75.0%, and Trichoderma species at 50.0%; under anoxic conditions G. candidum at 86.1%, yeasts at 66.6%, and Penicillium species at 61.1% were the most prevalent. The results indicate that activated sludge is a habitat for growth and sporulation of different groups of fungi, both saprophytic and pathogenic.
TRAWLING TRAFFIC UNDER ATTACK OVERCOMING DDoS ATTACKS BY TARGET-CONTROLLED TRAFFIC FILTERING
Authors: DOLEV SHLOMI , ELOVICI YUVAL , KESSELMAN ALEX , ZILBERMAN POLINA 
Published: August 2011

As more and more services are provided by servers via the Internet, Denial-of-Service (DoS) attacks pose an increasing threat to the Internet community. A DoS attack overloads the target server with a large volume of adverse requests, thereby rendering the server unavailable to "well-behaved" users. In this paper, we propose two algorithms that allow attack targets to dynamically filter their incoming traffic based on a distributed policy. The proposed algorithms defend the target against DoS and distributed DoS (DDoS) attacks and simultaneously ensure that it continues to serve "well-behaved" users. In a nutshell, a target can define a filtering policy which consists of a set of traffic classification rules and the corresponding amounts of traffic for each rule. A filtering algorithm is enforced by the ISP's routers when a target is being overloaded with traffic. The goal is to maximize the amount of filtered traffic forwarded to the target, according to the filtering policy, from the ISP. The first proposed algorithm is a collaborative algorithm which computes and delivers to the target the best possible traffic mix in polynomial time. The second algorithm is a distributed non-collaborative algorithm for which we prove a lower bound on the worst-case performance.
Rounding coefficients and artificially underflowing terms in non-numeric expressions
Authors: Corless Robert , Postma Erik , Stoutemyer David R. 
Published: August 2011

This article takes an analytical viewpoint to address the following questions:
1. How can we justifiably beautify an input or result sum of non-numeric terms that has some approximate coefficients by deleting some terms and/or rounding some coefficients to simpler floating-point or rational numbers?
2. When we add two expressions, how can we justifiably delete more non-zero result terms and/or round some result coefficients to even simpler floating-point, rational or irrational numbers?
The methods considered in this paper provide a justifiable scale-invariant way to attack these problems for subexpressions that are multivariate sums of monomials with real exponents.
Overcoming Antiangiogenic Resistance
Authors: Yao James C. , Phan Alexandria 
Published: August 2011

Abstract
The success of drugs targeting angiogenesis is tempered by the transient duration of disease control and modest survival improvement. The very hypoxic stress produced by successful therapy may lead to upregulation of multiple pathways that promote angiogenesis and invasive behavior. Overcoming this evasive resistance may further improve outcome. Clin Cancer Res; 17(16); 5217–9. ©2011 AACR.
Curcumin Treatment Suppresses IKKβ Kinase Activity of Salivary Cells of Patients with Head and Neck Cancer: A Pilot Study
Authors: Kim Suejung G. , Veena Mysore S. , Basak Saroj K. , Han Eugene , Tajima Tracey , Gjertson David W. , Starr Joshua , Eidelman Ofer , Pollard Harvey B. , Srivastava Meera , Srivatsan Eri S. , Wang Marilene B. 
Published: August 2011

Abstract
Purpose: To determine whether curcumin would inhibit IκB kinase β (IKKβ) kinase activity and suppress expression of proinflammatory cytokines in head and neck squamous cell carcinoma cancer (HNSCC) patients.
Experimental Design: Saliva was collected before and after subjects chewed curcumin tablets. Protein was extracted and IKKβ kinase activity measured. Interleukin (IL)-6 and IL-8 levels in the salivary supernatants were measured by ELISA. IL-6, IL-8, and other interleukin were also measured independently with ELISA to confirm the inhibitory effect of curcumin on expression and secretion of salivary cytokines.
Results: Curcumin treatment led to a reduction in IKKβ kinase activity in the salivary cells of HNSCC patients (P &lt; 0.05). Treatment of UM-SCC1 cells with curcumin as well as with post-curcumin salivary supernatant showed a reduction of IKKβ kinase activity. Significant reduction of IL-8 levels (P &lt; 0.05) was seen in post-curcumin samples from patients with dental caries. Although there was reduced IL-8 expression in 8 of 21 post-curcumin samples of HNSCC patients, the data did not reach statistical significance. Saliva samples from HNSCC patients were also analyzed in a blinded fashion for expression of cytokines. IL-10, IFN-γ, IL-12p70, and IL-2 clustered together, and granulocyte macrophage colony stimulating factor and TNF-α clustered together. Log10 ratio analysis showed decrease in expression of all nine cytokines in both the salivary supernatant and salivary cells of curcumin-treated samples.
Conclusions: Curcumin inhibited IKKβ kinase activity in the saliva of HNSCC patients, and this inhibition correlated with reduced expression of a number of cytokines. IKKβ kinase could be a useful biomarker for detecting the effect of curcumin in head and neck cancer. Clin Cancer Res; 17(18); 5953–61. ©2011 AACR.
Prevalence and associated risk factors for postpartum depression in women attending a tertiary hospital, Delhi, India
Authors: Dubey Chandan , Gupta Neha , Bhasin Sangeeta , Muthal Rathore Asmita , Arora Raksha 
Published: August 2011

Background: Maternal mental health is a largely ignored issue in the Indian population. Considering the high prevalence of postpartum depression, mental health assessment and screening of high-risk cases should be a part of routine antenatal care. Aim: To study the prevalence of women at risk for peripartum depression using Edinburgh Postnatal Depression Scale (EPDS) score in a tertiary teaching hospital in New Delhi, and to study the associated risk factors in the Indian population. Method: Five hundred and six (506) peripartum women were interviewed using a structured questionnaire, which included sociodemographic details like socioeconomic status, family structure, relationship with husband and mother-in-law, past obstetric history and gender of children, any history of previous psychiatric illness and outcome of current pregnancy in terms of mode of delivery, gender of newborn and neonatal complications. EPDS scoring was done using a Hindi translated version. Data were analysed using Epi Info version 3.32. Results: Thirty one (6%) out of 506 women scored ≥ 10 on the EPDS. Birth of female child, nuclear family structure and poor marital relationship were found to have a statistically significant correlation with peripartum depression. Conclusion: The 6% prevalence of women at risk of peripartum depression in our study, which is similar to other such studies, is significant and hence maternal mental health assessment should be made a part of routine antenatal and postnatal care.
Airfoil Structural Morphing Based on S.M.A. Actuator Series: Numerical and Experimental Studies
Authors: Barbarino S. , Pecora R. , Lecce L. , Concilio A. , Ameduri S. , De Rosa L. 
Published: August 2011

Multiple flight regimes during typical aircraft missions mean that a single unique optimized configuration, that maximizes aerodynamic efficiency and maneuverability, cannot be defined. Discrete components such as ailerons and flaps provide some adaptability, although they are far from optimal. Wing morphing can significantly improve the performance of future aircraft, by adapting the wing shape to the specific flight regime requirements, but also represents a challenging problem: the structure has to be stiff to maintain its shape under loads, and yet be flexible to deform without collapse. One solution is to adopt structural elements made of smart materials; Shape Memory Alloys (SMAs) have demonstrated their suitability for many static applications due to their high structural integration potential and remarkable actuation capabilities. In this work, the airfoil camber at the wing trailing edge on a full scale wing of a civil regional transportation aircraft is controlled by substituting a traditional split flap with a hingeless, smooth morphed flap. Firstly, the development and testing of an actuator device based on a SMA ribbon, capable of a net rotation of 5 deg, is presented. Then, a flap bay is designed and experimentally tested in presence of static loads, based on a compliant rib built as a series repetition of the proposed actuator. An aero-thermo-mechanical simulation within a FE approach was adopted to estimate the behavior and performance of the compliant rib, integrating both aerodynamic loads, by means of a Vortex Lattice Method (VLM) code, and SMA phenomenology, implementing Liang and Rogers’ constitutive model. The prototype showed good actuation performance even in presence of external loads. Very good numerical-experimental correlation is found for the unloaded case, while some fatigue issues emerged in presence of static loads.
Interleukin-10 Predicts Preterm Birth in Acculturated Hispanics
Authors: Wommack Joel C. , Ruiz R. Jeanne , Marti C. Nathan , Stowe Raymond P. , Brown Charles E. L. , Murphey Christina 
Published: August 2011

Objective: Among Hispanics living in the United States, acculturation is associated with an increased risk for preterm birth. Inflammatory pathways are also associated with preterm birth. As such, the current study sought to investigate the potential relationships among preterm birth, acculturation of Hispanic women, and inflammatory markers. Study Design: The authors performed an observational study on pregnant Hispanic women in Texas at 22–24 weeks' gestation ( n = 470). The authors obtained demographic data prenatally as well as birth outcome data from the medical chart after delivery. The authors obtained venous blood and used plasma to assay interleukin-1 receptor antagonist (IL-1RA), interleukin-6 (IL-6), and interleukin-10 (IL-10). The authors used logistic regression to understand whether the presence or the absence of IL-10 levels was related to acculturation and the risk of preterm birth. Results: The authors observed interactions between undetectable IL-10 levels and years in the United States and undetectable IL-10 levels and being born in the United States in models predicting preterm birth. Follow-up probes of these interactions suggested that when IL-10 was undetectable, preterm birth became more likely as time living in the United States increased, χ2 = 5.15 (1, 416), p = .020, odds ratio (OR) = 3.17, and was more likely in participants born in the United States than in those born elsewhere, χ2 = 5.35 (1, 462), p = .020, OR = 16.78. The authors observed no interactions among acculturation, preterm birth, and IL-1RA and IL-6 levels. Conclusion: Acculturated Hispanics who lack the protective effects of IL-10 experience a markedly higher risk of preterm birth than nonacculturated Hispanics.
Dominant-negative C/ebpα and polycomb group protein Bmi1 extend short-lived hematopoietic stem/progenitor cell life span and induce lethal dyserythropoiesis
Authors: Zhou Ting , Wang Lei , Zhu Kang-Yong , Dong Mei , Xu Peng-Fei , Chen Yi , Chen Sai-Juan , Chen Zhu , Deng Min , Liu Ting Xi 
Published: August 2011

AbstractThe primitive hematopoietic stem/progenitor cells (HSPCs) during embryonic hematopoiesis are thought to be short-lived (SL) with limited self-renewal potential. The fate and consequence of these short-lived HSPCs, once reprogrammed into “long-lived” in a living animal body, remain unknown. Here we show that targeted expression of a dominant-negative C/ebpα (C/ebpαDN) in the primitive SL-HSPCs during zebrafish embryogenesis extends their life span, allowing them to survive to later developmental stage to colonize the definitive hematopoietic sites, where they undergo a proliferative expansion followed by erythropoietic dysplasia and embryonic lethality because of circulation congestion. Mechanistically, C/ebpαDN binds to a conserved C/EBP-binding motif in the promoter region of bmi1 gene, associated with a specific induction of bmi1 transcription in the transgenic embryos expressing C/ebpαDN. Targeted expression of Bmi1 in the SL-HSPCs recapitulates nearly all aberrant phenotypes induced by C/ebpαDN, whereas knockdown of bmi1 largely rescues these abnormalities. The results indicate that Bmi1 acts immediately downstream of C/ebpαDN to regulate the survival and self-renewal of HSPCs and contribute to the erythropoietic dysplasia.
Development of thymic NK cells from double negative 1 thymocyte precursors
Authors: Vargas Claudia L. , Poursine-Laurent Jennifer , Yang Liping , Yokoyama Wayne M. 
Published: August 2011

AbstractThe differentiation of natural killer (NK) cells and a subpopulation of NK cells which requires an intact thymus, that is, thymic NK cells, is poorly understood. Previous in vitro studies indicate that double negative (CD4−CD8−, DN) thymocytes can develop into cells with NK cell markers, but these cells have not been well characterized. Herein, we generated and characterized NK cells differentiating from thymic DN precursors. Sorted DN1 (CD44+CD25−) CD122−NK1.1− thymocytes from Rag1−/− mice were adoptively transferred into Rag1−/−Ly5.1 congenic mice. After intrathymic injection, donor-derived cells phenotypically resembling thymic NK cells were found. To further study their differentiation, we seeded sorted DN1 CD122−NK1.1− thymocytes on irradiated OP9 bone marrow stromal cells with IL-15, IL-7, Flt3L, and stem cell factor. NK1.1+ cells emerged after 7 days. In vitro differentiated NK cells acquired markers associated with immature bone marrow–derived NK cells, but also expressed CD127, which is typically found on thymic NK cells. Furthermore, we found that in vitro cells generated from thymic precursors secreted cytokines when stimulated and degranulated on target exposure. Together, these data indicate that functional thymic NK cells can develop from a DN1 progenitor cell population.
Domain architecture conservation in orthologs
Authors: Forslund Kristoffer , Pekkari Isabella , Sonnhammer Erik LL 
Published: August 2011

Abstract

Background
As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence.
To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs.

Results
The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation.
The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent.

Conclusions
On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the notion that orthologs are functionally more similar than other types of homologs at the same evolutionary distance.
Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection
Authors: Toofanny Rudesh D , Simms Andrew M , Beck David AC , Daggett Valerie 
Published: August 2011

Abstract

Background
Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008.

Results
Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes.

Conclusions
The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008.
Polymorphic variability in the 3' untranslated region (UTR) of IL12B is associated with susceptibility to severe anaemia in Kenyan children with acute Plasmodium falciparum malaria
Authors: Ong'echa John M , Raballah Evans O , Kempaiah Prakasha M , Anyona Samuel B , Were Tom , Davenport Gregory C , Konah Stephen , Vulule John M , Ouma Collins , Hittner James B , Perkins Douglas J 
Published: August 2011

AbstractBackgroundPlasmodium falciparummalaria remains a leading cause of morbidity and mortality among African children. Innate immunity provides the first line of defence againstP. falciparuminfections, particularly in young children that lack naturally-acquired malarial immunity, such as the population examined here. Consistent with the fact that elevated interleukin (IL)-12 is an important component of the innate immune response that provides protective immunity against malaria, we have previously shown that suppression of IL-12 in African children is associated with the development of severe malarial anaemia (SMA). Since the role ofIL12Bvariants in conditioning susceptibility to SMA remains largely unexplored, the association between a single nucleotide polymorphism (1188A→C, rs3212227), SMA (Hb<6.0g/dL), circulating IL-12p40/p70 levels, and longitudinal clinical outcomes in Kenyan children (n = 756) residing in a holoendemic falciparum malaria transmission area were investigated.ResultsMultivariate logistic regression analysis in children with acute malaria (n = 544) demonstrated that carriers of the C allele had increased susceptibility to SMA (CC: OR, 1.674; 95% CI, 1.006-2.673;P= 0.047, and AC: OR, 1.410; 95% CI, 0.953-2.087;P= 0.086) relative to wild type (AA). Although children with SMA had lower IL-12p40/p70 levels than the non-SMA group (P= 0.037), levels did not differ significantly according to genotype. Longitudinal analyses in the entire cohort (n = 756) failed to show any significant relationships between rs3212227 genotypes and either susceptibility to SMA or all-cause mortality throughout the three year follow-up.ConclusionThe rs3212227 is a marker of susceptibility to SMA in children with acute disease, but does not appear to mediate functional changes in IL-12 production or longitudinal outcomes during the acquisition of naturally-acquired malarial immunity.