bluuebunny/crossref_metadata_2025_split huggingface dataset:
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs
Authors: Sanders Marijn PA , Fleuren Wilco WM , Verhoeven Stefan , van den Beld Sven , Alkema Wynand , de Vlieg Jacob , Klomp Jan PG 
Published: August 2011

Abstract

Background
G-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM) domain. Because of their structural and sequence conservation, the TM domains are often used in bioinformatics approaches to first create a multiple sequence alignment (MSA) and subsequently identify ligand binding positions. So far methods have been developed to predict the common ligand binding residue positions for class A GPCRs.

Results
Here we present 1) ss-TEA, a method to identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information. 2) The largest MSA of class A non olfactory GPCRs in the public domain consisting of 13324 sequences covering most of the species homologues of the human set of GPCRs. A set of ligand binding residue positions extracted from literature of 10 different receptors shows that our method has the best ligand binding residue prediction for 9 of these 10 receptors compared to another state-of-the-art method.

Conclusions
The combination of the large multi species alignment and the newly introduced residue selection method ss-TEA can be used to rapidly identify subfamily specific ligand binding residues. This approach can aid the design of site directed mutagenesis experiments, explain receptor function and improve modelling. The method is also available online via GPCRDB at http://www.gpcr.org/7tm/.
SNP and gene networks construction and analysis from classification of copy number variations data
Authors: Liu Yang , Lee Yiu Fai , Ng Michael K 
Published: August 2011

Abstract

Background
Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. It is interesting to identify and represent relevant CNVs from a genome-wide data due to high data volume and the complexity of interactions.

Results
In this paper, we incorporate the DNA copy number variation data derived from SNP arrays into a computational shrunken model and formalize the detection of copy number variations as a case-control classification problem. More than 80% accuracy can be obtained using our classification model and by shrinkage, the number of relevant CNVs to disease can be determined. In order to understand relevant CNVs, we study their corresponding SNPs in the genome and a statistical software PLINK is employed to compute the pair-wise SNP-SNP interactions, and identify SNP networks based on their P-values. Our selected SNP networks are statistically significant compared with random SNP networks and play a role in the biological process. For the unique genes that those SNPs are located in, a gene-gene similarity value is computed using GOSemSim and gene pairs that have similarity values being greater than a threshold are selected to construct gene networks. A gene enrichment analysis show that our gene networks are functionally important.
Experimental results demonstrate that our selected SNP and gene networks based on the selected CNVs contain some functional relationships directly or indirectly to disease study.

Conclusions
Two datasets are given to demonstrate the effectiveness of the introduced method. Some statistical and biological analysis show that this shrunken classification model is effective in identifying CNVs from genome-wide data and our proposed framework has a potential to become a useful analysis tool for SNP data sets.
Molecular evolution of the LNX gene family
Authors: Flynn Michael , Saha Orthis , Young Paul 
Published: August 2011

AbstractBackgroundLNX (Ligand of Numb Protein-X) proteins typically contain an amino-terminal RING domain adjacent to either two or four PDZ domains - a domain architecture that is unique to the LNX family. LNX proteins function as E3 ubiquitin ligases and their domain organisation suggests that their ubiquitin ligase activity may be targeted to specific substrates or subcellular locations by PDZ domain-mediated interactions. Indeed, numerous interaction partners for LNX proteins have been identified, but thein vivofunctions of most family members remain largely unclear.ResultsTo gain insights into their function we examined the phylogenetic origins and evolution of theLNXgene family. We find that aLNX1/LNX2-like gene arose in an early metazoan lineage by gene duplication and fusion events that combined a RING domain with four PDZ domains. These PDZ domains are closely related to the four carboxy-terminal domains from multiple PDZ domain containing protein-1 (MUPP1). Duplication of theLNX1/LNX2-like gene and subsequent loss of PDZ domains appears to have generated a gene encoding a LNX3/LNX4-like protein, with just two PDZ domains. This protein has novel carboxy-terminal sequences that include a potential modular LNX3 homology domain. The two ancestralLNXgenes are present in some, but not all, invertebrate lineages. They were, however, maintained in the vertebrate lineage, with further duplication events giving rise to five LNX family members in most mammals. In addition, we identify novel interactions of LNX1 and LNX2 with three known MUPP1 ligands using yeast two-hybrid asssays. This demonstrates conservation of binding specificity between LNX and MUPP1 PDZ domains.ConclusionsTheLNXgene family has an early metazoan origin with a LNX1/LNX2-like protein likely giving rise to a LNX3/LNX4-like protein through the loss of PDZ domains. The absence of LNX orthologs in some lineages indicates that LNX proteins are not essential in invertebrates. In contrast, the maintenance of both ancestralLNXgenes in the vertebrate lineage suggests the acquisition of essential vertebrate specific functions. The revelation that the LNX PDZ domains are phylogenetically related to domains in MUPP1, and have common binding specificities, suggests that LNX and MUPP1 may have similarities in their cellular functions.
Synergistic use of plant-prokaryote comparative genomics for functional annotations
Authors: Gerdes Svetlana , El Yacoubi Basma , Bailly Marc , Blaby Ian K , Blaby-Haas Crysten E , Jeanguenin Linda , Lara-Núñez Aurora , Pribat Anne , Waller Jeffrey C , Wilke Andreas , Overbeek Ross , Hanson Andrew D , de Crécy-Lagard Valérie 
Published: August 2011

Abstract

Background
Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vaguely known function, and a large number are wrongly annotated. Many of these ‘unknown’ proteins are common to prokaryotes and plants. We set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction integrates comparative genomics based mainly on microbial genomes with functional genomic data from model microorganisms and post-genomic data from plants. This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations.

Results
Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) occur in prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology-independent characteristics associated in the SEED database with the prokaryotic members of each family. In-depth comparative genomic analysis was performed for 360 top candidate families. From this pool, 78 families were connected to general areas of metabolism and, of these families, specific functional predictions were made for 41. Twenty-one predicted functions have been experimentally tested or are currently under investigation by our group in at least one prokaryotic organism (nine of them have been validated, four invalidated, and eight are in progress). Ten additional predictions have been independently validated by other groups. Discovering the function of very widespread but hitherto enigmatic proteins such as the YrdC or YgfZ families illustrates the power of our approach.

Conclusions
Our approach correctly predicted functions for 19 uncharacterized protein families from plants and prokaryotes; none of these functions had previously been correctly predicted by computational methods. The resulting annotations could be propagated with confidence to over six thousand homologous proteins encoded in over 900 bacterial, archaeal, and eukaryotic genomes currently available in public databases.
Adjuvant gemcitabine versus NEOadjuvant gemcitabine/oxaliplatin plus adjuvant gemcitabine in resectable pancreatic cancer: a randomized multicenter phase III study (NEOPAC study)
Authors: Heinrich Stefan , Pestalozzi Bernhard , Lesurtel Mickael , Berrevoet Frederik , Laurent Stéphanie , Delpero Jean-Robert , Raoul Jean-Luc , Bachellier Phillippe , Dufour Patrick , Moehler Markus , Weber Achim , Lang Hauke , Rogiers Xavier , Clavien Pierre-Alain 
Published: August 2011

Abstract

Background
Despite major improvements in the perioperative outcome of pancreas surgery, the prognosis of pancreatic cancer after curative resection remains poor. Adjuvant chemotherapy increases disease-free and overall survival, but this treatment cannot be offered to a significant proportion of patients due to the surgical morbidity. In contrast, almost all patients can receive (neo)adjuvant chemotherapy before surgery. This treatment is safe and effective, and has resulted in a median survival of 26.5 months in a recent phase II trial. Moreover, neoadjuvant chemotherapy improves the nutritional status of patients with pancreatic cancer. This multicenter phase III trial (NEOPAC) has been designed to explore the efficacy of neoadjuvant chemotherapy.

Methods/Design
This is a prospective randomized phase III trial. Patients with resectable cytologically proven adenocarcinoma of the pancreatic head are eligible for this study. All patients must be at least 18 years old and must provide written informed consent. An infiltration of the superior mesenteric vein > 180° or major visceral arteries are considered exclusion criteria. Eligible patients will be randomized to surgery followed by adjuvant gemcitabine (1000 mg/m2) for 6 months or neoadjuvant chemotherapy (gemcitabine 1000 mg/m2, oxaliplatin 100 mg/m2) followed by surgery and the same adjuvant treatment. Neoadjuvant chemotherapy is given four times every two weeks. The staging as well as the restaging protocol after neoadjuvant chemotherapy include computed tomography of chest and abdomen and diagnostic laparoscopy. The primary study endpoint is progression-free survival. According to the sample size calculation, 155 patients need to be randomized to each treatment arm. Disease recurrence will be documented by scheduled computed tomography scans 9, 12, 15, 21 and thereafter every 6 months until disease progression. For quality control, circumferential resection margins are marked intraoperatively, and representative histological sections will be centrally reviewed by a dedicated pathologist.

Discussion
The NEOPAC study will determine the efficacy of neoadjuvant chemotherapy in pancreatic cancer for the first time and offers a unique potential for translational research. Furthermore, this trial will provide the unbiased overall survival of all patients undergoing surgery for resectable cancer of the pancreatic head.

Trial registration
clinicalTrials.gov NCT01314027
A trigger model of apoptosis induced by tumor necrosis factor signaling
Authors: Gu Chang , Zhang Junjie , Chen Yingyu , Lei Jinzhi 
Published: August 2011

Abstract

Background
The ability of living cells to respond appropriately to apoptosis signals is crucial for the proper development and homeostasis of multicellular organisms. For example, viable cells must be stable enough to appropriately respond to apoptosis signaling so that an irreversible death program is only induced when apoptosis signaling reaches a certain threshold. Previous studies have introduced bistability models in which signaling by caspase-3 activity represents a key regulator of cell fate in response to apoptosis stimuli.

Results
In this study, apoptosis induced by tumor necrosis factor (TNF) signaling is investigated, and a mathematical model without the requirement for bistability is proposed. In this model, rapid degradation of the active forms of caspases -8 and -3 are included, and TNF-signaling is found to induce a pulse of caspase-3 activation and trigger an irreversible death program. This result agrees with experimental observations. The ability of a cell to respond to, or resist, apoptosis stimuli is also discussed. Furthermore, the activation efficiencies of caspases -8 and -3 that are essential to a cell’s response to extracellular apoptosis stimuli are defined. Based on the simulations performed, it is observed that activation efficiencies must be sufficiently sensitive to appropriately compromise a cell’s resistance and effectiveness in response to apoptosis stimuli.

Conclusions
Our results suggest that bistability may not be a necessary condition for the induction of apoptosis by TNF signaling. Rather, a sharp increase in caspase-3 activity might be sufficient to trigger the induction of an irreversible death program. Accordingly, regulation of caspase activity and degradation of active caspases is essential for a cell’s response to apoptosis stimuli.
Health financing in Africa: overview of a dialogue among high level policy makers
Authors: Sambo Luis Gomes , Kirigia Joses Muthuri , Ki-Zerbo Georges 
Published: August 2011

Abstract

Background
Even though Africa has the highest disease burden compared with other regions, it has the lowest per capita spending on health. In 2007, 27 (51%) out the 53 countries spent less than US$50 per person on health. Almost 30% of the total health expenditure came from governments, 50% from private sources (of which 71% was from out-of-pocket payments by households) and 20% from donors. The purpose of this article is to reflect on the proceedings of the African Union Side Event on Health Financing in the African continent.

Methods
Methods employed in the session included presentations, panel discussion and open public discussion with ministers of health and finance from the African continent.

Discussion
The current unsatisfactory state of health financing was attributed to lack of clear vision and plan for health financing; lack of national health accounts and other evidence to guide development and implementation of national health financing policies and strategies; low investments in sectors that address social determinants of health; predominance of out-of-pocket spending; underdeveloped prepaid health financing mechanisms; large informal sectors vis-à-vis small formal sectors; and unpredictability and non-alignment of majority of donor funds with national health priorities.
Countries need to develop and adopt a comprehensive national health policy and a costed strategic plan; a comprehensive evidence-based health financing strategy; allocate at least 15% of the national budget to health development; use GFATM and PEPFAR funds for health systems strengthening; strengthen intersectoral collaboration to address health determinants; advocate among donors to implement the Paris Declaration on Aid Effectiveness and its Accra Agenda for Action; ensure universal access to health services for pregnant women, lactating mothers and children aged under five years; strengthen financial management capacities; and develop prepaid health financing systems, especially health insurance to complement tax funding.
In addition, countries need to institutionalize national health accounts; undertake feasibility studies of various health financing mechanisms; and document and share best practices in health financing.

Conclusion
There was consensus that every country ought to have an evidence-based comprehensive health financing strategy with a road map for attaining universal health service coverage vision; and increase physical and financial access by pregnant women, lactating mothers and by children under five years to quality health services.
Activation of protease activated receptor 1 increases the excitability of the dentate granule neurons of hippocampus
Authors: Han Kyung-Seok , Mannaioni Guido , Hamill Cecily E , Lee Jaekwang , Junge Candice E , Lee C Justin , Traynelis Stephen F 
Published: August 2011

Abstract
Protease activated receptor-1 (PAR1) is expressed in multiple cell types in the CNS, with the most prominent expression in glial cells. PAR1 activation enhances excitatory synaptic transmission secondary to the release of glutamate from astrocytes following activation of astrocytically-expressed PAR1. In addition, PAR1 activation exacerbates neuronal damage in multiple in vivo models of brain injury in a manner that is dependent on NMDA receptors. In the hippocampal formation, PAR1 mRNA appears to be expressed by a subset of neurons, including granule cells in the dentate gyrus. In this study we investigate the role of PAR activation in controlling neuronal excitability of dentate granule cells. We confirm that PAR1 protein is expressed in neurons of the dentate cell body layer as well as in astrocytes throughout the dentate. Activation of PAR1 receptors by the selective peptide agonist TFLLR increased the intracellular Ca2+ concentration in a subset of acutely dissociated dentate neurons as well as non-neuronal cells. Bath application of TFLLR in acute hippocampal slices depolarized the dentate gyrus, including the hilar region in wild type but not in the PAR1-/- mice. PAR1 activation increased the frequency of action potential generation in a subset of dentate granule neurons; cells in which PAR1 activation triggered action potentials showed a significant depolarization. The activation of PAR1 by thrombin increased the amplitude of NMDA receptor-mediated component of EPSPs. These data suggest that activation of PAR1 during normal function or pathological conditions, such as during ischemia or hemorrhage, can increase the excitability of dentate granule cells.
Hypothyroidism and mood disorders: integrating novel insights from brain imaging techniques
Authors: Pilhatsch Maximilian , Marxen Michael , Winter Christine , Smolka Michael N , Bauer Michael 
Published: August 2011

Abstract
Thyroid hormones play a critical role in brain development but also in the adult human brain by modulating metabolic activity. Hypothyroid states are associated with both functional and structural brain alterations also seen in patients with major depression. Recent animal experimental and preclinical data indicate subtle changes in myelination, microvascular density, local neurogenesis, and functional networks. The translational validity of such studies is obviously limited. Clinical evidence for neurobiological correlates of different stages and severities of hypothyroidism and effects of pharmacological intervention is lacking but may be achieved using advanced imaging techniques, e.g. functional and quantitative MRI techniques applied to patients with hypothyroidism before and after hormone replacement therapy.
O2 delivery and CO2 production during cardiopulmonary bypass as determinants of acute kidney injury: time for a goal-directed perfusion management?
Authors: de Somer Filip , Mulholland John W , Bryan Megan R , Aloisio Tommaso , Van Nooten Guido J , Ranucci Marco 
Published: August 2011

Abstract
Introduction
Acute kidney injury (AKI) is common after cardiac operations. There are different risk factors or determinants of AKI, and some are related to cardiopulmonary bypass (CPB). In this study, we explored the association between metabolic parameters (oxygen delivery (DO2) and carbon dioxide production (VCO2)) during CPB with postoperative AKI.

Methods
We conducted a retrospective analysis of prospectively collected data at two different institutions. The study population included 359 adult patients. The DO2 and VCO2 levels of each patient were monitored during CPB. Outcome variables were related to kidney function (peak postoperative serum creatinine increase and AKI stage 1 or 2). The experimental hypothesis was that nadir DO2 values and nadir DO2/VCO2 ratios during CPB would be independent predictors of AKI. Multivariable logistic regression models were built to detect the independent predictors of AKI and any kind of kidney function damage.

Results
A nadir DO2 level < 262 mL/minute/m2 and a nadir DO2/VCO2 ratio < 5.3 were independently associated with AKI within a model including EuroSCORE and CPB duration. Patients with nadir DO2 levels and nadir DO2/VCO2 ratios below the identified cutoff values during CPB had a significantly higher rate of AKI stage 2 (odds ratios 3.1 and 2.9, respectively). The negative predictive power of both variables exceeded 90%. The most accurate predictor of AKI stage 2 postoperative status was the nadir DO2 level.

Conclusions
The nadir DO2 level during CPB is independently associated with postoperative AKI. The measurement of VCO2-related variables does not add accuracy to the AKI prediction. Since DO2 during CPB is a modifiable factor (through pump flow adjustments), this study generates the hypothesis that goal-directed perfusion management aimed at maintaining the DO2 level above the identified critical value might limit the incidence of postoperative AKI.
Elastic deformation and energy loss of flapping fly wings
Authors: Lehmann Fritz-Olaf , Gorb Stanislav , Nasir Nazri , Schützner Peter 
Published: August 2011

SUMMARYDuring flight, the wings of many insects undergo considerable shape changes in spanwise and chordwise directions. We determined the origin of spanwise wing deformation by combining measurements on segmental wing stiffness of the blowfly Calliphora vicina in the ventral and dorsal directions with numerical modelling of instantaneous aerodynamic and inertial forces within the stroke cycle using a two-dimensional unsteady blade elementary approach. We completed this approach by an experimental study on the wing's rotational axis during stroke reversal. The wing's local flexural stiffness ranges from 30 to 40 nN m2 near the root, whereas the distal wing parts are highly compliant (0.6 to 2.2 nN m2). Local bending moments during wing flapping peak near the wing root at the beginning of each half stroke due to both aerodynamic and inertial forces, producing a maximum wing tip deflection of up to 46 deg. Blowfly wings store up to 2.30 μJ elastic potential energy that converts into a mean wing deformation power of 27.3 μW. This value equates to approximately 5.9 and 2.3% of the inertial and aerodynamic power requirements for flight in this animal, respectively. Wing elasticity measurements suggest that approximately 20% or 0.46 μJ of elastic potential energy cannot be recovered within each half stroke. Local strain energy increases from tip to root, matching the distribution of the wing's elastic protein resilin, whereas local strain energy density varies little in the spanwise direction. This study demonstrates a source of mechanical energy loss in fly flight owing to spanwise wing bending at the stroke reversals, even in cases in which aerodynamic power exceeds inertial power. Despite lower stiffness estimates, our findings are widely consistent with previous stiffness measurements on insect wings but highlight the relationship between local flexural stiffness, wing deformation power and energy expenditure in flapping insect wings.