bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peacekeepers under Fire: Prosecuting the RUF for Attacks against the UN Assistance Mission in Sierra Leone
Authors: Sloan James 
Published: October 2010

AbstractIn the “RUF case”, the Special Court for Sierra Leone considered charges brought against senior officials of the Revolutionary United Front (RUF) in relation, inter alia, to a series of notorious attacks against the UN Assistance Mission in Sierra Leone (UNAMSIL) in May 2000. In finding the accused guilty of certain of the crimes charged, the Trial Chamber relied heavily on single-source evidence, hearsay evidence and circumstantial evidence. The Trial Chamber addressed a number of difficult factual and legal issues relating to the definition of peacekeeping and the status of robust peacekeepers for the first time; however, not all such findings appear to have been accurately grounded in fact and law.
An Inquiry into the ICC Appeals Chamber’s Exercise of the Power of Remand
Authors: Waite Prince Neto D.C.B. 
Published: October 2010

AbstractThe ICC’s Appeals Chamber (AC) has the authority to review, on appeal, judgments, decisions, orders and the exercise of power by the Pre-Trial and Trial Chambers. The Rome Statute and the Rules of Procedure and Evidence expressly provide that the AC may confirm, reverse or amend matters on appeal, and has the power of remand in Article 81 and Article 83 appeals against decisions of acquittal, conviction or sentence. There is no express power to remand an issue in Article 82 (interlocutory) appeals. This article discusses whether the AC has the power, generally, to remand a matter to Chambers below, thereby not coming to a determination itself. The article concludes by suggesting that the AC has the power of remand, and that it springs from two sources: (1) for appeals generally, the Court’s inherent powers and (2) for Article 81 and Article 83 appeals, the Court’s Statutory powers in Article 83(2). Therefore, the AC, under its inherent jurisdiction, may exercise the power of remand for Article 82 (interlocutory) appeals.
Multilayer Cloud Detection with the MODIS Near-Infrared Water Vapor Absorption Band
Authors: Wind Galina , Platnick Steven , King Michael D. , Hubanks Paul A. , Pavolonis Michael J. , Heidinger Andrew K. , Yang Ping , Baum Bryan A. 
Published: October 2010

Abstract
Data Collection 5 processing for the Moderate Resolution Imaging Spectroradiometer (MODIS) on board the NASA Earth Observing System (EOS) Terra and Aqua spacecraft includes an algorithm for detecting multilayered clouds in daytime. The main objective of this algorithm is to detect multilayered cloud scenes, specifically optically thin ice cloud overlying a lower-level water cloud, that present difficulties for retrieving cloud effective radius using single-layer plane-parallel cloud models. The algorithm uses the MODIS 0.94-μm water vapor band along with CO2 bands to obtain two above-cloud precipitable water retrievals, the difference of which, in conjunction with additional tests, provides a map of where multilayered clouds might potentially exist. The presence of a multilayered cloud results in a large difference in retrievals of above-cloud properties between the CO2 and the 0.94-μm methods. In this paper the MODIS multilayered cloud algorithm is described, results of using the algorithm over example scenes are shown, and global statistics for multilayered clouds as observed by MODIS are discussed. A theoretical study of the algorithm behavior for simulated multilayered clouds is also given. Results are compared to two other comparable passive imager methods. A set of standard cloudy atmospheric profiles developed during the course of this investigation is also presented. The results lead to the conclusion that the MODIS multilayer cloud detection algorithm has some skill in identifying multilayered clouds with different thermodynamic phases.
The Effective Static Stability Experienced by Eddies in a Moist Atmosphere
Authors: O’Gorman Paul A. 
Published: October 2010

AbstractWater vapor directly affects the dynamics of atmospheric eddy circulations through the release of latent heat. But it is difficult to include latent heat release in dynamical theories because of the associated nonlinearity (precipitation generally occurs where there is upward motion). A new effective static stability is derived that fundamentally captures the effect of latent heat release on moist eddy circulations. It differs from the usual dry static stability by an additive term that depends on temperature and a parameter measuring the up–down asymmetry of vertical velocity statistics. Latent heat release reduces the effective static stability experienced by eddies but cannot reduce it to zero so long as there are nonprecipitating regions of the eddies. Evaluation based on reanalysis data indicates that the effective static stability in the lower troposphere ranges from ∼80% of the dry static stability at high latitudes to ∼25% in the tropics.The effective static stability provides a solution to the longstanding problem of how to adapt dry dynamical theories to the moist circulations in the atmosphere. Its utility for climate change problems is illustrated based on simulations with an idealized general circulation model. It is shown to help account for changes in the thermal stratification of the extratropical troposphere, the extent of the Hadley cells, the intensity of extratropical transient eddies, and the extratropical eddy length.
Modulation of Caribbean Precipitation by the Madden–Julian Oscillation
Authors: Martin Elinor R. , Schumacher Courtney 
Published: October 2010

Abstract
Based on 12 years of daily satellite precipitation data and reanalysis winds, intraseasonal (30–90 days) variability in Caribbean precipitation is linked to phases of the Madden–Julian oscillation (MJO). Intraseasonal variability is largest during September–November (SON), but some modulation of precipitation by the MJO appears throughout all seasons. Precipitation anomalies up to 50% above (below) the annual mean are observed in phases 1 and 2 (5 and 6) of the MJO. The changes in Caribbean precipitation associated with the MJO are shown to be related to changes in the low-level (925 hPa) winds. When precipitation anomalies are above (below) average in phases 1 and 2 (5 and 6), wind anomalies act to decrease (increase) the strength of the prevailing easterly trade winds. The changes in the low-level winds are most apparent in the region of the Caribbean low-level jet (CLLJ), and divergence anomalies associated with the entrance and exit regions of the CLLJ precede the precipitation anomalies. The CLLJ itself is also shown to be subject to intraseasonal variability, and its magnitude varies with the phase of the MJO. Again, intraseasonal variability in the CLLJ associated with the MJO is observed in all seasons and shows a significant coherence with intraseasonal variability in the precipitation. Extreme rainfall events over islands in the Caribbean show a strong relationship with the MJO phase, with extreme events being most common in phases 1 and 2 of an MJO event. This relationship between the MJO and extreme events has important implications for the predictability of precipitation extremes in the Caribbean.
Characteristics of Large-Scale Orographic Precipitation in a Linear Perspective
Authors: Kunz Michael 
Published: October 2010

Abstract
Simulations of orographic precipitation over the low mountain ranges of southwestern Germany and eastern France with two different physics-based linear precipitation models are presented. Both models are based on 3D airflow dynamics from linear theory and consider advection of condensed water and leeside drying. Sensitivity studies for idealized conditions and a real case study show that the amount and spatial distribution of orographic precipitation is strongly controlled by characteristic time scales for cloud and hydrometeor advection and background precipitation due to large-scale lifting. These parameters are estimated by adjusting the model results on a 2.5-km grid to observed precipitation patterns for a sample of 40 representative orography-dominated stratiform events (24 h) during a calibration period (1971–80). In general, the best results in terms of lowest rmse and bias are obtained for characteristic time scales of 1600 s and background precipitation of 0.4 mm h−1. Model simulations of a sample of 84 events during an application period (1981–2000) with fixed parameters demonstrate that both models are able to reproduce quantitatively precipitation patterns obtained from observations and reanalyses from a numerical model [Consortium for Small-scale Modeling (COSMO)]. Combining model results with observation data shows that heavy precipitations over mountains are restricted to situations with strong atmospheric forcings in terms of synoptic-scale lifting, horizontal wind speed, and moisture content.
Warm Season Afternoon Thunderstorm Characteristics under Weak Synoptic-Scale Forcing over Taiwan Island
Authors: Lin Pin-Fang , Chang Pao-Liang , Jou Ben Jong-Dao , Wilson James W. , Roberts Rita D. 
Published: October 2010

Abstract
The spatial and temporal characteristics and distributions of thunderstorms in Taiwan during the warm season (May–October) from 2005 to 2008 and under weak synoptic-scale forcing are documented using radar reflectivity, lightning, radiosonde, and surface data. Average hourly rainfall amounts peaked in midafternoon (1500–1600 local solar time, LST). The maximum frequency of rain was located in a narrow strip, parallel to the orientation of the mountains, along the lower slopes of the mountains. Significant diurnal variations were found in surface wind, temperature, and dewpoint temperature between days with and without afternoon thunderstorms (TSA and non-TSA days). Before thunderstorms occurred, on TSA days, the surface temperature was warmer (about 0.5°–1.5°C) and the surface dewpoint temperature was moister (about 0.5°–2°C) than on non-TSA days. Sounding observations from northern Taiwan also showed warmer and higher moisture conditions on TSA days relative to non-TSA days. The largest average difference was in the 750–550-hPa layer where the non-TSA days averaged 2.5°–3.5°C drier. These preconvective factors associated with the occurrences of afternoon thunderstorms could be integrated into nowcasting tools to enhance warning systems and decision-making capabilities in real-time operations.
Mantle cell lymphoma: biology, pathogenesis, and the molecular basis of treatment in the genomic era
Authors: Pérez-Galán Patricia , Dreyling Martin , Wiestner Adrian 
Published: October 2010

AbstractMantle cell lymphoma (MCL) is a B-cell non-Hodgkin lymphoma of which at least a subset arises from antigen-experienced B cells. However, what role antigen stimulation plays in its pathogenesis remains ill defined. The genetic hallmark is the chromosomal translocation t(11;14) resulting in aberrant expression of cyclin D1. Secondary genetic events increase the oncogenic potential of cyclin D1 and frequently inactivate DNA damage response pathways. In combination these changes drive cell-cycle progression and give rise to pronounced genetic instability. Several signaling pathways contribute to MCL pathogenesis, including the often constitutively activated PI3K/AKT/mTOR pathway, which promotes tumor proliferation and survival. WNT, Hedgehog, and NF-κB pathways also appear to be important. Although MCL typically responds to frontline chemotherapy, it remains incurable with standard approaches. Proteasome inhibitors (bortezomib), mTOR inhibitors (temsirolimus), and immunomodulatory drugs (lenalidomide) have recently been added to the treatment options in MCL. The molecular basis for the antitumor activity of these agents is an area of intense study that hopefully will lead to further improvements in the near future. Given its unique biology, relative rarity, and the difficulty in achieving long-lasting remissions with conventional approaches, patients with MCL should be encouraged to participate in clinical trials.
A tick salivary protein targets cathepsin G and chymase and inhibits host inflammation and platelet aggregation
Authors: Chmelar Jindrich , Oliveira Carlo J. , Rezacova Pavlina , Francischetti Ivo M. B. , Kovarova Zuzana , Pejler Gunnar , Kopacek Peter , Ribeiro José M. C. , Mares Michael , Kopecky Jan , Kotsyfakis Michail 
Published: October 2010

AbstractPlatelet aggregation and acute inflammation are key processes in vertebrate defense to a skin injury. Recent studies uncovered the mediation of 2 serine proteases, cathepsin G and chymase, in both mechanisms. Working with a mouse model of acute inflammation, we revealed that an exogenous salivary protein of Ixodes ricinus, the vector of Lyme disease pathogens in Europe, extensively inhibits edema formation and influx of neutrophils in the inflamed tissue. We named this tick salivary gland secreted effector as I ricinus serpin-2 (IRS-2), and we show that it primarily inhibits cathepsin G and chymase, while in higher molar excess, it affects thrombin activity as well. The inhibitory specificity was explained using the crystal structure, determined at a resolution of 1.8 Å. Moreover, we disclosed the ability of IRS-2 to inhibit cathepsin G-induced and thrombin-induced platelet aggregation. For the first time, an ectoparasite protein is shown to exhibit such pharmacological effects and target specificity. The stringent specificity and biological activities of IRS-2 combined with the knowledge of its structure can be the basis for the development of future pharmaceutical applications.
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology
Authors: Ning Kang , Ng Hoong Kee , Srihari Sriganesh , Leong Hon Wai , Nesvizhskii Alexey I 
Published: October 2010

Abstract

Background
In many protein-protein interaction (PPI) networks, densely connected hub proteins are more likely to be essential proteins. This is referred to as the "centrality-lethality rule", which indicates that the topological placement of a protein in PPI network is connected with its biological essentiality. Though such connections are observed in many PPI networks, the underlying topological properties for these connections are not yet clearly understood. Some suggested putative connections are the involvement of essential proteins in the maintenance of overall network connections, or that they play a role in essential protein clusters. In this work, we have attempted to examine the placement of essential proteins and the network topology from a different perspective by determining the correlation of protein essentiality and reverse nearest neighbor topology (RNN).

Results
The RNN topology is a weighted directed graph derived from PPI network, and it is a natural representation of the topological dependences between proteins within the PPI network. Similar to the original PPI network, we have observed that essential proteins tend to be hub proteins in RNN topology. Additionally, essential genes are enriched in clusters containing many hub proteins in RNN topology (RNN protein clusters). Based on these two properties of essential genes in RNN topology, we have proposed a new measure; the RNN cluster centrality. Results from a variety of PPI networks demonstrate that RNN cluster centrality outperforms other centrality measures with regard to the proportion of selected proteins that are essential proteins. We also investigated the biological importance of RNN clusters.

Conclusions
This study reveals that RNN cluster centrality provides the best correlation of protein essentiality and placement of proteins in PPI network. Additionally, merged RNN clusters were found to be topologically important in that essential proteins are significantly enriched in RNN clusters, and biologically important because they play an important role in many Gene Ontology (GO) processes.
Geoseq: a tool for dissecting deep-sequencing datasets
Authors: Gurtowski James , Cancio Anthony , Shah Hardik , Levovitz Chaya , George Ajish , Homann Robert , Sachidanandam Ravi 
Published: October 2010

Abstract

Background
Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest.

Results
Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment.

Conclusions
Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a) identify differential isoform expression in mRNA-seq datasets, b) identify miRNAs (microRNAs) in libraries, and identify mature and star sequences in miRNAS and c) to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.
The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications
Authors: Huang Shengfeng , Tian Haozheng , Chen Zelin , Yu Ting , Xu Anlong 
Published: October 2010

Abstract

Background
The vertebrate tetraspanin family has many features which make it suitable for preserving the imprint of ancient sequence evolution and amenable for phylogenomic analysis. So we believe that an in-depth analysis of the tetraspanin evolution not only provides more complete understanding of tetraspanin biology, but offers new insights into the influence of the two rounds of whole genome duplication (2R-WGD) at the origin of vertebrates.

Results
A detailed phylogeny of vertebrate tetraspanins was constructed by using multiple lines of information, including sequence-based phylogenetics, key structural features, intron configuration and genomic synteny. In particular, a total of 38 modern tetraspanin ortholog lineages in bony vertebrates have been identified and subsequently classified into 17 ancestral lineages existing before 2R-WGD. Based on this phylogeny, we found that the ohnolog retention rate of tetraspanins after 2R-WGD was three times as the average (a rate similar to those of transcription factors and protein kinases). This high rate didn't increase the tetrapanin family size, but changed the family composition, possibly by displacing vertebrate-specific gene lineages with the lineages conserved across deuterostomes. We also found that the period from 2R-WGD to recent time is controlled by gene losses. Meanwhile, positive selection has been detected on 80% of the branches right after 2R-WGDs, which declines significantly on both magnitude and extensity on the following speciation branches. Notably, the loss of mammalian RDS2 is accompanied by strong positive selection on mammalian ROM1, possibly due to gene loss-induced compensatory evolution.

Conclusions
First, different from transcription factors and kinases, high duplicate retention rate after 2R-WGD didn't increase the tetraspanin family size but just reshaped the family composition. Second, the evolution of tetraspanins right after 2R-WGD had been impacted by a massive wave of gene loss and positive selection on coding sequences. Third, the lingering effect of 2R-WGD on tetraspanin gene loss and positive selection might last for 300-400 million years.
Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence
Authors: Fonknechten Nuria , Chaussonnerie Sébastien , Tricot Sabine , Lajus Aurélie , Andreesen Jan R , Perchat Nadia , Pelletier Eric , Gouyvenoux Michel , Barbe Valérie , Salanoubat Marcel , Le Paslier Denis , Weissenbach Jean , Cohen Georges N , Kreimeyer Annett 
Published: October 2010

Abstract

Background

Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed.

Results

C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms.

Conclusions
Analysis of the C. sticklandii genome and additional experimental procedures have improved our understanding of anaerobic amino acid degradation. Several specific metabolic features have been detected, some of which are very unusual for anaerobic fermenting bacteria. Comparative genomics has provided the opportunity to study the lifestyle of pathogenic and non-pathogenic clostridial species as well as to elucidate the difference in metabolic features between clostridia and other anaerobes.