bluuebunny/crossref_metadata_2025_split huggingface dataset:
CDS: A Fold-Change Based Statistical Test for Concomitant Identification of Distinctness and Similarity in Gene Expression Analysis
Authors: Tchitchek Nicolas , Golib Dzib José Felipe , Targat Brice , Noth Sebastian , Benecke Arndt , Lesne Annick 
Published: June 2012

Abstract
The problem of identifying differential activity such as in gene expression is a major defeat in biostatistics and bioinformatics. Equally important, however much less frequently studied, is the question of similar activity from one biological condition to another. The fold-change, or ratio, is usually considered a relevant criterion for stating difference and similarity between measurements. Importantly, no statistical method for concomitant evaluation of similarity and distinctness currently exists for biological applications. Modern microarray, digital PCR (dPCR), and Next-Generation Sequencing (NGS) technologies frequently provide a means of coefficient of variation estimation for individual measurements. Using fold-change, and by making the assumption that measurements are normally distributed with known variances, we designed a novel statistical test that allows us to detect concomitantly, thus using the same formalism, differentially and similarly expressed genes (http://cds.ihes.fr). Given two sets of gene measurements in different biological conditions, the probabilities of making type I and type II errors in stating that a gene is differentially or similarly expressed from one condition to the other can be calculated. Furthermore, a confidence interval for the fold-change can be delineated. Finally, we demonstrate that the assumption of normality can be relaxed to consider arbitrary distributions numerically. The Concomitant evaluation of Distinctness and Similarity (CDS) statistical test correctly estimates similarities and differences between measurements of gene expression. The implementation, being time and memory efficient, allows the use of the CDS test in high-throughput data analysis such as microarray, dPCR, and NGS experiments. Importantly, the CDS test can be applied to the comparison of single measurements (N = 1) provided the variance (or coefficient of variation) of the signals is known, making CDS a valuable tool also in biomedical analysis where typically a single measurement per subject is available.
Interannual variability of H218O in precipitation over the Asian monsoon region
Authors: Ishizaki Yasuhiro , Yoshimura Kei , Kanae Shinjiro , Kimoto Masahide , Kurita Naoyuki , Oki Taikan 
Published: June 2012

The stable isotopic composition of water has been used as a paleoproxy to reconstruct past climates over the Asian monsoon region, but the main controls on the variability of isotopes of water in precipitation have not been characterized quantitatively in this region. Therefore, we used an atmospheric general circulation model incorporating stable water isotope physics to quantitatively estimate the relative contributions to isotope variability in precipitation falling in the Asian monsoon region. As in previous research, we identified two primary factors controlling the interannual variability of δ18Oprecip (defined as (Rsample/RVSMOW − 1) × 1000, where RVSMOW is the 18O ratio in Vienna Standard Mean Ocean Water) and its correlation with El Niño–Southern Oscillation (ENSO) events: the amount of precipitation at the observation site, and distillation during transport from source regions. Two sensitivity experiments revealed that distillation during transport from source regions was the dominant controlling factor; at Bangkok, Bombay, and Hong Kong, the amount of local precipitation contributed 27%, 33%, and 25% while distillation processes contributed 70%, 60%, and 70%, respectively. Similarly, distillation processes accounted for 80%, 82%, and 83% of observed differences in δ18Oprecip between El Niño and La Niña years at these three cities, respectively. Therefore, interannual variability of δ18Oprecipat the three stations primarily reflects distillation during transport from source regions, and it is also governed by the large‐scale tropical variability (ENSO).
Terrestrial VLF transmitter injection into the magnetosphere
Authors: Cohen M. B. , Inan U. S. 
Published: June 2012

Very Low Frequency (VLF, 3–30 kHz) radio waves emitted from ground sources (transmitters and lightning) strongly impact the radiation belts, driving electron precipitation via whistler‐electron gyroresonance, and contributing to the formation of the slot region. However, calculations of the global impacts of VLF waves are based on models of trans‐ionospheric propagation to calculate the VLF energy reaching the magnetosphere. Limited comparisons of these models to individual satellite passes have found that the models may significantly (by >20 dB) overestimate amplitudes of ground based VLF transmitters in the magnetosphere. To form a much more complete empirical picture of VLF transmitter energy reaching the magnetosphere, we present observations of the radiation pattern from a number of ground‐based VLF transmitters by averaging six years of data from the DEMETER satellite. We divide the slice at ∼700 km altitude above a transmitter into pixels and calculate the average field for all satellite passes through each pixel. There are enough data to see 25 km features in the radiation pattern, including the modal interference of the subionospheric signal mapped upwards. Using these data, we deduce the first empirical measure of the radiated power into the magnetosphere from these transmitters, for both daytime and nighttime, and at both the overhead and geomagnetically conjugate region. We find no detectable variation of signal intensity with geomagnetic conditions at low and mid latitudes (L < 2.6). We also present evidence of ionospheric heating by one VLF transmitter which modifies the trans‐ionospheric absorption of signals from other transmitters passing through the heated region.
Functional and ecological consequences of saprotrophic fungus–grazer interactions
Authors: Crowther Thomas W , Boddy Lynne , Hefin Jones T 
Published: June 2012

Abstract
Saprotrophic fungi are key regulators of nutrient cycling in terrestrial ecosystems. They are the primary agents of plant litter decomposition and their hyphal networks, which grow throughout the soil–litter interface, represent highly dynamic channels through which nutrients are readily distributed. By ingesting hyphae and dispersing spores, soil invertebrates, including Arthropoda, Oligochaetae and Nematoda, influence fungal-mediated nutrient distribution within soil. Fungal physiological responses to grazing include changes to hydrolytic enzyme production and respiration rates. These directly affect nutrient mineralisation and the flux of CO2 between terrestrial and atmospheric pools. Preferential grazing may also exert selective pressures on saprotrophic communities, driving shifts in fungal succession and community composition. These functional and ecological consequences of grazing are intrinsically linked, and influenced by invertebrate grazing intensity. High-intensity grazing often reduces fungal growth and activity, whereas low-intensity grazing can have stimulatory effects. Grazing intensity is directly related to invertebrate abundance, and varies dramatically between species and functional groups. Invertebrate diversity and community composition, therefore, represent key factors determining the functioning of saprotrophic fungal communities and the services they provide.
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
Authors: Mason Olivia U , Hazen Terry C , Borglin Sharon , Chain Patrick S G , Dubinsky Eric A , Fortney Julian L , Han James , Holman Hoi-Ying N , Hultman Jenni , Lamendella Regina , Mackelprang Rachel , Malfatti Stephanie , Tom Lauren M , Tringe Susannah G , Woyke Tanja , Zhou Jizhong , Rubin Edward M , Jansson Janet K 
Published: June 2012

Abstract
The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.
Erythrocyte storage increases rates of NO and nitrite scavenging: implications for transfusion-related toxicity
Authors: Stapley Ryan , Owusu Benjamin Y. , Brandon Angela , Cusick Marianne , Rodriguez Cilina , Marques Marisa B. , Kerby Jeffrey D. , Barnum Scott R. , Weinberg Jordan A. , Lancaster Jack R. , Patel Rakesh P. 
Published: June 2012

Storage of erythrocytes in blood banks is associated with biochemical and morphological changes to RBCs (red blood cells). It has been suggested that these changes have potential negative clinical effects characterized by inflammation and microcirculatory dysfunction which add to other transfusion-related toxicities. However, the mechanisms linking RBC storage and toxicity remain unclear. In the present study we tested the hypothesis that storage of leucodepleted RBCs results in cells that inhibit NO (nitric oxide) signalling more so than younger cells. Using competition kinetic analyses and protocols that minimized contributions from haemolysis or microparticles, our data indicate that the consumption rates of NO increased ~40-fold and NO-dependent vasodilation was inhibited 2–4-fold comparing 42-day-old with 0-day-old RBCs. These results are probably due to the formation of smaller RBCs with increased surface area: volume as a consequence of membrane loss during storage. The potential for older RBCs to affect NO formation via deoxygenated RBC-mediated nitrite reduction was also tested. RBC storage did not affect deoxygenated RBC-dependent stimulation of nitrite-induced vasodilation. However, stored RBCs did increase the rates of nitrite oxidation to nitrate in vitro. Significant loss of whole-blood nitrite was also observed in stable trauma patients after transfusion with 1 RBC unit, with the decrease in nitrite occurring after transfusion with RBCs stored for &gt;25 days, but not with younger RBCs. Collectively, these data suggest that increased rates of reactions between intact RBCs and NO and nitrite may contribute to mechanisms that lead to storage-lesion-related transfusion risk.
Combination renin–angiotensin system blockade and angiotensin-converting enzyme 2 in experimental myocardial infarction: implications for future therapeutic directions
Authors: Burchill Luke J. , Velkoska Elena , Dean Rachael G. , Griggs Karen , Patel Sheila K. , Burrell Louise M. 
Published: June 2012

The RAS (renin–angiotensin system) is activated after MI (myocardial infarction), and RAS blockade with ACEis [ACE (angiotensin-converting enzyme) inhibitors] or ARBs (angiotensin receptor blockers) slows but does not completely prevent progression to heart failure. Cardiac ACE is increased after MI and leads to the formation of the vasoconstrictor AngII (angiotensin II). The enzyme ACE2 is also activated after MI and degrades AngII to generate the vasodilator Ang-(1–7) [angiotensin-(1–7)]. Overexpression of ACE2 offers cardioprotective effects in experimental MI, but there is conflicting evidence as to whether the benefits of ACEis and ARBs are mediated through increasing ACE2 after MI. In the present study, we assessed the effect of an ACEi and ARB, alone and in combination, on cardiac ACE2 in a rat MI model. MI rats received vehicle, ACEi (ramipril; 1 mg/kg of body weight), ARB (valsartan; 10 mg/kg of body weight) or combination (ramipril at 1 mg/kg of body weight and valsartan at 10 mg/kg of body weight) orally for 28 days. Sham-operated rats were also studied and received vehicle alone. MI increased LV (left ventricular) mass (P&lt;0.0001), impaired cardiac contractility (P&lt;0.05) and activated cardiac ACE2 with increased gene (P&lt;0.05) and protein expression (viable myocardium, P&lt;0.05; border zone, P&lt;0.001; infarct, P&lt;0.05). Ramipril and valsartan improved remodelling (P&lt;0.05), with no additional effect of dual therapy. Although ramipril inhibited ACE, and valsartan blocked the angiotensin receptor, neither treatment alone nor in combination augmented cardiac ACE2 expression. These results suggest that the cardioprotective effects of ramipril and valsartan are not mediated through up-regulation of cardiac ACE2. Strategies that do augment ACE2 after MI may be a useful addition to standard RAS blockade after MI.
Endemicity analysis, parsimony and biotic elements: a formal comparison using hypothetical distributions
Authors: Casagranda M. Dolores , Taher Leila , Szumik Claudia A. 
Published: June 2012

AbstractThere is as yet no general agreement regarding the most appropriate solution to the problem of identifying areas of endemism, not even in particular cases. In this study, we compared Endemicity Analysis (EA), Parsimony Analysis of Endemicity (PAE), and Biotic Elements Analysis (BE) based on their ability to identify hypothetical predefined patterns that represent nested, overlapping, and disjoint areas of endemism supported by species with different degrees of sympatry. We found that PAE performs poorly when applied to patterns that either overlap with each other or are supported by species with imperfect sympatry. BE exhibits a counterintuitive sensitivity to the degree of congruence among the distributions of endemic species, being unable to recognize areas of endemism supported by perfectly sympatric species. In contrast, in all cases examined we found that EA results in a high proportion of correctly identified distributional patterns. In addition to highlighting the strengths and limitations of these approaches, our results show how different methods can lead to seemingly conflicting conclusions and caution about the possibility of identifying distributional patterns that are merely methodological artefacts.© The Willi Hennig Society 2012.
SYT‐SSX breakpoint peptide vaccines in patients with synovial sarcoma: A study from the Japanese Musculoskeletal Oncology Group
Authors: Kawaguchi Satoshi , Tsukahara Tomohide , Ida Kazunori , Kimura Shigeharu , Murase Masaki , Kano Masanobu , Emori Makoto , Nagoya Satoshi , Kaya Mitsunori , Torigoe Toshihiko , Ueda Emiri , Takahashi Akari , Ishii Takeshi , Tatezaki Shin‐ichiro , Toguchida Junya , Tsuchiya Hiroyuki , Osanai Toshihisa , Sugita Takashi , Sugiura Hideshi , Ieguchi Makoto , Ihara Koichiro , Hamada Ken‐ichiro , Kakizaki Hiroshi , Morii Takeshi , Yasuda Taketoshi , Tanizawa Taisuke , Ogose Akira , Yabe Hiroo , Yamashita Toshihiko , Sato Noriyuki , Wada Takuro 
Published: June 2012

In the present study, we evaluated the safety and effectiveness of SYT‐SSX‐derived peptide vaccines in patients with advanced synovial sarcoma. A 9‐mer peptide spanning the SYT‐SSX fusion region (B peptide) and its HLA‐A*2402 anchor substitute (K9I) were synthesized. In Protocols A1 and A2, vaccines with peptide alone were administered subcutaneously six times at 14‐day intervals. The B peptide was used in Protocol A1, whereas the K9I peptide was used in Protocol A2. In Protocols B1 and B2, the peptide was mixed with incomplete Freund's adjuvant and then administered subcutaneously six times at 14‐day intervals. In addition, interferon‐α was injected subcutaneously on the same day and again 3 days after the vaccination. The B peptide and K9I peptide were used in Protocols B1 and B2, respectively. In total, 21 patients (12 men, nine women; mean age 43.6 years) were enrolled in the present study. Each patient had multiple metastatic lesions of the lung. Thirteen patients completed the six‐injection vaccination schedule. One patient developed intracerebral hemorrhage after the second vaccination. Delayed‐type hypersensitivity skin tests were negative in all patients. Nine patients showed a greater than twofold increase in the frequency of CTLs in tetramer analysis. Recognized disease progression occurred in all but one of the nine patients in Protocols A1 and A2. In contrast, half the 12 patients had stable disease during the vaccination period in Protocols B1 and B2. Of note, one patient showed transient shrinkage of a metastatic lesion. The response of the patients to the B protocols is encouraging and warrants further investigation.
Eutrophication, recovery and temperature in Lake Mjøsa: detecting trends with monitoring data and sediment records
Authors: HOBÆK ANDERS , LØVIK JARL EIVIND , ROHRLACK THOMAS , MOE S. JANNICKE , GRUNG MERETE , BENNION HELEN , CLARKE GINA , PILIPOSYAN GAYANE T. 
Published: June 2012

Summary1. How climate warming may interact with other pressures on aquatic ecosystems is an important issue for research and management. We combined lake monitoring data with a palaeolimnological study to explore the combined effects of eutrophication and subsequent oligotrophication with a long‐term temperature increase in epilimnetic waters. Our goals were (i) to evaluate how well sediment‐based reconstructions reflect the instrumental observations, (ii) to use the palaeo‐record to characterise a reference state for the lake and (iii) to explore whether data from the sediment record can aid in separating the effects of nutrient load and temperature in a large and deep lake.2. Lake Mjøsa is a large and deep lake in south‐eastern Norway. Eutrophication symptoms peaked in the 1970s, which led to extensive measures to reduce the phosphorus load. A monitoring programme has run continuously from 1972. Monitoring has documented a marked decrease in phosphorus load and algal biomass and also revealed an increase in epilimnetic temperature and extended summer stratification.3. Records of algal pigments and diatoms were extracted from sediment cores taken from 236 m depth. The pigment record documented dramatic changes in lake production consistent with the monitoring record. The diatom record reflected well the eutrophication history of the lake and also demonstrated that the assemblage of the recent recovery stage differs from that of the pre‐eutrophication period.4. Ordination of diatom assemblages over time constrained by proxies for nutrient load and temperature indicated that the diatom assemblage correlated with both factors, which together accounted for 60% of the variation in diatom composition. No interaction was detected between these factors. The results suggest that the diatom assemblage has responded to varying nutrient loads as well as to changes in temperature and/or factors that correlate with temperature.5. Reconstructions of algal biomass and total phosphorus content mirrored known changes through the monitoring period, although the absolute phosphorus estimates were too high relative to the instrumental record. The sediment record from Lake Mjøsa provides a baseline for lake production in terms of algal pigments and organic contents, and for the diatom assemblage composition in a pristine stage.
Reproductive implications of herkogamy in homostylous primroses: variation during anthesis and reproductive assurance in alpine environments
Authors: de Vos Jurriaan M. , Keller Barbara , Isham Samuel T. , Kelso Sylvia , Conti Elena 
Published: June 2012

Summary1.Unreliable pollinator service is thought to promote the evolution of self‐compatible plant breeding systems, because selfing may provide reproductive assurance when outcrossing opportunity is limited. The recurrent evolution of self‐compatible homostyly from obligately outcrossing heterostylous species has been regarded as a classic example of evolutionary response to lack of pollinators or mates, as homostyly frequently occurs in pollinator‐limited or marginal environments. However, male and female sexual organs of homostylous species may display spatial separation (herkogamy), an arrangement presumed to promote outcrossing. It is largely unknown to what extent variation in herkogamy affects opportunities for autonomous selfing and reproductive assurance in self‐compatible, homostylous species.2.Using the homostylousPrimula halleri, restricted to alpine environments, we investigated whether herkogamy occurs and varies during anthesis, among individuals, and populations, and compared the effects of herkogamy on seed set among three experimental treatments, to elucidate how herkogamy affects reproductive strategies in a homostylous species.3.Herkogamy decreases during anthesis, but the ultimate expression of herkogamy in mature flowers differs among individuals and populations. Caging caging experiments indicate that herkogamy reduces a plant's potential for autonomous selfing, and emasculation and open‐pollination treatments demonstrate that herkogamy markedly decreases total seed set and the potential for reproductive assurance.4.Herkogamy early in anthesis may enhance outcrossing potential, while its decrease later could enable reproductive assurance via delayed autonomous selfing in some, but not all plants. Conversely, pronounced herkogamy in older flowers comes at the cost of reduced total reproductive output and imposes pollinator dependence for reproduction, but may promote the genetic diversity of populations.5.Our study suggests that even small amounts of herkogamy can have large effects on the reproductive strategy of homostylous species, by enabling more outcrossing than generally thought to be typical of homostyly.