bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes
Authors: Cohen David , Bogeat-Triboulot Marie-Béatrice , Tisserant Emilie , Balzergue Sandrine , Martin-Magniette Marie-Laure , Lelandais Gaëlle , Ningre Nathalie , Renou Jean-Pierre , Tamby Jean-Philippe , Le Thiec Didier , Hummel Irène 
Published: November 2010

AbstractBackgroundComparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from otherPopulusspecies.ResultsUsing a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought.ConclusionsIn poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.
Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry
Authors: Ayyadurai Saravanan , Flaudrops Christophe , Raoult Didier , Drancourt Michel 
Published: November 2010

Abstract

Background
Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species.

Results
When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes.

Conclusion
These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates.
The cross-sectional GRAS sample: A comprehensive phenotypical data collection of schizophrenic patients
Authors: Ribbe Katja , Friedrichs Heidi , Begemann Martin , Grube Sabrina , Papiol Sergi , Kästner Anne , Gerchen Martin F , Ackermann Verena , Tarami Asieh , Treitz Annika , Flögel Marlene , Adler Lothar , Aldenhoff Josef B , Becker-Emner Marianne , Becker Thomas , Czernik Adelheid , Dose Matthias , Folkerts Here , Freese Roland , Günther Rolf , Herpertz Sabine , Hesse Dirk , Kruse Gunther , Kunze Heinrich , Franz Michael , Löhrer Frank , Maier Wolfgang , Mielke Andreas , Müller-Isberner Rüdiger , Oestereich Cornelia , Pajonk Frank-Gerald , Pollmächer Thomas , Schneider Udo , Schwarz Hans-Joachim , Kröner-Herwig Birgit , Havemann-Reinecke Ursula , Frahm Jens , Stühmer Walter , Falkai Peter , Brose Nils , Nave Klaus-Armin , Ehrenreich Hannelore 
Published: November 2010

Abstract

Background
Schizophrenia is the collective term for an exclusively clinically diagnosed, heterogeneous group of mental disorders with still obscure biological roots. Based on the assumption that valuable information about relevant genetic and environmental disease mechanisms can be obtained by association studies on patient cohorts of ≥ 1000 patients, if performed on detailed clinical datasets and quantifiable biological readouts, we generated a new schizophrenia data base, the GRAS (Göttingen Research Association for Schizophrenia) data collection. GRAS is the necessary ground to study genetic causes of the schizophrenic phenotype in a 'phenotype-based genetic association study' (PGAS). This approach is different from and complementary to the genome-wide association studies (GWAS) on schizophrenia.

Methods
For this purpose, 1085 patients were recruited between 2005 and 2010 by an invariable team of traveling investigators in a cross-sectional field study that comprised 23 German psychiatric hospitals. Additionally, chart records and discharge letters of all patients were collected.

Results
The corresponding dataset extracted and presented in form of an overview here, comprises biographic information, disease history, medication including side effects, and results of comprehensive cross-sectional psychopathological, neuropsychological, and neurological examinations. With >3000 data points per schizophrenic subject, this data base of living patients, who are also accessible for follow-up studies, provides a wide-ranging and standardized phenotype characterization of as yet unprecedented detail.

Conclusions
The GRAS data base will serve as prerequisite for PGAS, a novel approach to better understanding 'the schizophrenias' through exploring the contribution of genetic variation to the schizophrenic phenotypes.
Simultaneous identification of the Anopheles funestus group and Anopheles longipalpis type C by PCR-RFLP
Authors: Choi Kwang Shik , Coetzee Maureen , Koekemoer Lizette L 
Published: November 2010

Abstract

Background

Anopheles longipalpis is morphologically similar to the major African malaria vector Anopheles funestus at the adult stage although it is very different at the larval stage. Despite the development of the species-specific multiplex PCR assay for the An. funestus group, the genomic DNA of Anopheles longipalpis type C specimens can be amplified with the Anopheles vaneedeni and Anopheles parensis primers from this assay. The standard, species-specific An. funestus group PCR, results in the amplification of two fragments when An. longipalpis type C specimens are included in the analysis. This result can easily be misinterpreted as being a hybrid between An. vaneedeni and An. parensis. Anopheles longipalpis type C can be identified using a species-specific PCR assay but this assay is not reliable if other members of the An. funestus group, such as An. funestus, An. funestus-like and An. parensis, are included. The present study provides a multiplex assay that will identify An. longipalpis along with other common members of the African An. funestus group, including Anopheles leesoni.

Methods
A total of 70 specimens from six species (An. funestus, An. funestus-like, An. parensis, Anopheles rivulorum, An. vaneedeni and An. leesoni) in the An. funestus group and An. longipalpis type C from Malawi, Mozambique, South Africa and Zambia were used for the study. A restriction fragment length polymorphism (RFLP) assay was designed based on the DNA sequence information in the GenBank database.

Results
The enzyme, EcoRI digested only An. longipalpis type C and An. funestus-like after the species-specific An. funestus group PCR assay. The An. longipalpis and An. funestus-like digestion profiles were characterized by three fragments, 376 bp, 252 bp and 211 bp for An. longipalpis type C and two fragments, 375 bp and 15 bp for An. funestus-like.

Conclusions
An RFLP method for the group was developed that is more accurate and efficient than those used before. Hence, this assay would be useful for field-collected adult specimens to be identified routinely in malaria vector research and control studies.
Pim-selective inhibitor DHPCC-9 reveals Pim kinases as potent stimulators of cancer cell migration and invasion
Authors: Santio Niina M , Vahakoski Riitta L , Rainio Eeva-Marja , Sandholm Jouko A , Virtanen Sanna S , Prudhomme Michelle , Anizon Fabrice , Moreau Pascale , Koskinen Päivi J 
Published: November 2010

Abstract

Background
Pim family kinases are small constitutively active serine/threonine-specific kinases, elevated levels of which have been detected in human hematopoietic malignancies as well as in solid tumours. While we and others have previously shown that the oncogenic Pim kinases stimulate survival of hematopoietic cells, we now examined their putative role in regulating motility of adherent cancer cells. For this purpose, we inhibited Pim kinase activity using a small molecule compound, 1,10-dihydropyrrolo[2,3-a]carbazole-3-carbaldehyde (DHPCC-9), which we had recently identified as a potent and selective inhibitor for all Pim family members.

Results
We now demonstrate that the Pim kinase inhibitor DHPCC-9 is very effective also in cell-based assays. DHPCC-9 impairs the anti-apoptotic effects of Pim-1 in cytokine-deprived myeloid cells and inhibits intracellular phosphorylation of Pim substrates such as Bad. Moreover, DHPCC-9 slows down migration and invasion of cancer cells derived from either prostate cancer or squamocellular carcinoma patients. Silencing of Pim expression reduces cell motility, while Pim overexpression enhances it, strongly suggesting that the observed effects of DHPCC-9 are dependent on Pim kinase activity. Interestingly, DHPCC-9 also abrogates NFATc-dependent migration of cancer cells, implying that NFATc factors mediate at least part of the pro-migratory effects of Pim kinases.

Conclusions
Altogether, our data indicate that DHPCC-9 is not only a powerful tool to investigate physiological effects of the oncogenic Pim family kinases, but also an attractive molecule for drug development to inhibit invasiveness of Pim-overexpressing cancer cells.
Measurement properties of the benign prostatic hyperplasia impact index in tadalafil studies
Authors: Angalakuditi Mallik , Seifert Rita F , Hayes Risa P , O'Leary Michael P , Viktrup Lars 
Published: November 2010

Abstract

Background
To assess the measurement properties of the Benign Prostatic Hyperplasia Impact Index (BII) for use in men with Lower Urinary Tract Symptoms (LUTS) secondary to Benign Prostatic Hyperplasia (BPH) treated with tadalafil.

Methods
Data from a dose-titration (Study 1) and a dose-finding placebo-controlled (Study 2) tadalafil studies of men 45 years of age or older with moderate to severe LUTS (N = 281; N = 1053) were included in this post-hoc analysis. Measures included the BII, International Prostate Symptom Score (IPSS), IPSS Quality of Life Index (IPSS-QoL), LUTS Global Assessment Question, uroflowmetry measure peak flow rate (Qmax) and postvoid residual volume (PVR). Spearman rank and Pearson correlation coefficients were computed between the BII score and the other measures at each visit. Wilcoxin two-sample tests, t-tests and general linear modeling compared BII scores of subjects with global ratings of improvement versus no improvement, and subjects taking tadalafil versus placebo. Effect size, standardized response mean and Guyatt's responsiveness statistic were calculated for BII and IPSS change scores.

Results
There were high correlations between BII and IPSS & IPSS-QoL and low correlations between BII and Qmax & PVR at each visit. There were significant differences in BII at the End-of-Study Visit between subjects reporting improvement versus subjects reporting no improvement (Studies 1 and 2, P < .0001) and subjects taking tadalafil versus subjects taking placebo (Study 1, P = .0045; Study 2, P = .0064). The BII and IPSS were both responsive to change.

Conclusions
Results show that the BII is reliable, shows responsiveness to change in patients with BPH-LUTS, and demonstrates construct validity.
Modeling CICR in rat ventricular myocytes: voltage clamp studies
Authors: Krishna Abhilash , Sun Liang , Valderrábano Miguel , Palade Philip T , Clark John W 
Published: November 2010

AbstractBackgroundThe past thirty-five years have seen an intense search for the molecular mechanisms underlying calcium-induced calcium-release (CICR) in cardiac myocytes, with voltage clamp (VC) studies being the leading tool employed. Several VC protocols including lowering of extracellular calcium to affectCa2+loading of the sarcoplasmic reticulum (SR), and administration of blockers caffeine and thapsigargin have been utilized to probe the phenomena surrounding SRCa2+release. Here, we develop a deterministic mathematical model of a rat ventricular myocyte under VC conditions, to better understand mechanisms underlying the response of an isolated cell to calcium perturbation. Motivation for the study was to pinpoint key control variables influencing CICR and examine the role of CICR in the context of a physiological control system regulating cytosolicCa2+concentration ([Ca2+]myo).MethodsThe cell model consists of an electrical-equivalent model for the cell membrane and a fluid-compartment model describing the flux of ionic species between the extracellular and several intracellular compartments (cell cytosol, SR and the dyadic coupling unit (DCU), in which resides the mechanistic basis of CICR). The DCU is described as a controller-actuator mechanism, internally stabilized by negative feedback control of the unit's two diametrically-opposedCa2+channels (trigger-channel and release-channel). It releasesCa2+flux into the cyto-plasm and is in turn enclosed within a negative feedback loop involving the SERCA pump, regulating[Ca2+]myo.ResultsOur model reproduces measured VC data published by several laboratories, and generates gradedCa2+release at highCa2+gain in a homeostatically-controlled environment where [Ca2+]myois precisely regulated. We elucidate the importance of the DCU elements in this process, particularly the role of the ryanodine receptor in controlling SRCa2+release, its activation by triggerCa2+, and its refractory characteristics mediated by the luminal SRCa2+sensor. Proper functioning of the DCU, sodium-calcium exchangers and SERCA pump are important in achieving negative feedback control and henceCa2+homeostasis.ConclusionsWe examine the role of the aboveCa2+regulating mechanisms in handling various types of induced disturbances inCa2+levels by quantifying cellularCa2+balance. Our model provides biophysically-based explanations of phenomena associated with CICR generating useful and testable hypotheses.
Fulminant necrotizing fasciitis following the use of herbal concoction: a case report
Authors: Adigun Ismaila A , Nasir Abdulrasheed A , Aderibigbe Adebiyi B 
Published: November 2010

Abstract

Introduction
Necrotizing fasciitis is a rare and life-threatening rapidly progressive soft tissue infection. A fulminant case could involve muscle and bone. Necrotizing fasciitis after corticosteroid therapy and intramuscular injection of non-steroidal anti-inflammatory drugs has been reported. We present a case of fulminant necrotizing fasciitis occurring in a patient who used a herbal concoction to treat a chronic leg ulcer.

Case presentation
A 20-year-old Ibo woman from Nigeria presented with a three-year history of recurrent chronic ulcer of the right leg. She started applying a herbal concoction to dress the wound two weeks prior to presentation. This resulted in rapidly progressive soft tissue necrosis that spread from the soft tissue to the bone, despite aggressive emergency debridement. As a result she underwent above-knee amputation.

Conclusion
The herbal concoction used is toxic, and can initiate and exacerbate necrotizing fasciitis. Its use for wound dressing should be discouraged.
Lower respiratory tract infection and rapid expansion of an abdominal aortic aneurysm: a case report
Authors: Naylor Steven , Gamie Zakareya , Vohra Ravinder S , Puppala Sapna , Kent Patrick J , Scott D Julian A 
Published: November 2010

Abstract

Introduction
The rate of abdominal aortic aneurysm expansion is related to multiple factors. There is some evidence that inflammation can accelerate aneurysm expansion. However, the association between pulmonary sepsis and rapid abdominal aortic aneurysm expansion is rarely reported.

Case presentation
Here we present a case of a rapidly expanding abdominal aortic aneurysm in a 68-year-old Caucasian man with a concomitant lower respiratory tract infection and systemic sepsis requiring intensive monitoring and urgent endovascular intervention. Our patient had an uncomplicated post-operative recovery and a follow-up computed tomography scan at one month demonstrated no evidence of an endoleak.

Conclusion
This case highlights the potential association between pulmonary sepsis and rapid abdominal aortic aneurysm expansion. In such cases, a policy of frequent monitoring should be adopted to identify those patients requiring definitive management.
Relationship between muscle forces, joint loading and utilization of elastic strain energy in equine locomotion
Authors: Harrison Simon M. , Whitton R. Chris , Kawcak Chris E. , Stover Susan M. , Pandy Marcus G. 
Published: November 2010

SUMMARYStorage and utilization of strain energy in the elastic tissues of the distal forelimb of the horse is thought to contribute to the excellent locomotory efficiency of the animal. However, the structures that facilitate elastic energy storage may also be exposed to dangerously high forces, especially at the fastest galloping speeds. In the present study, experimental gait data were combined with a musculoskeletal model of the distal forelimb of the horse to determine muscle and joint contact loading and muscle–tendon work during the stance phase of walking, trotting and galloping. The flexor tendons spanning the metacarpophalangeal (MCP) joint – specifically, the superficial digital flexor (SDF), interosseus muscle (IM) and deep digital flexor (DDF) – experienced the highest forces. Peak forces normalized to body mass for the SDF were 7.3±2.1, 14.0±2.5 and 16.7±1.1 N kg–1 in walking, trotting and galloping, respectively. The contact forces transmitted by the MCP joint were higher than those acting at any other joint in the distal forelimb, reaching 20.6±2.8, 40.6±5.6 and 45.9±0.9 N kg–1 in walking, trotting and galloping, respectively. The tendons of the distal forelimb (primarily SDF and IM) contributed between 69 and 90% of the total work done by the muscles and tendons, depending on the type of gait. The tendons and joints that facilitate storage of elastic strain energy in the distal forelimb also experienced the highest loads, which may explain the high frequency of injuries observed at these sites.
The mass-specific energy cost of human walking is set by stature
Authors: Weyand Peter G. , Smith Bethany R. , Puyau Maurice R. , Butte Nancy F. 
Published: November 2010

SUMMARYThe metabolic and mechanical requirements of walking are considered to be of fundamental importance to the health, physiological function and even the evolution of modern humans. Although walking energy expenditure and gait mechanics are clearly linked, a direct quantitative relationship has not emerged in more than a century of formal investigation. Here, on the basis of previous observations that children and smaller adult walkers expend more energy on a per kilogram basis than larger ones do, and the theory of dynamic similarity, we hypothesized that body length (or stature, Lb) explains the apparent body-size dependency of human walking economy. We measured metabolic rates and gait mechanics at six speeds from 0.4 to 1.9 m s–1 in 48 human subjects who varied by a factor of 1.5 in stature and approximately six in both age and body mass. In accordance with theoretical expectation, we found the most economical walking speeds measured (J kg–1 m–1) to be dynamically equivalent (i.e. similar U, where U=velocity2/gravity · leg length) among smaller and larger individuals. At these speeds, stride lengths were directly proportional to stature whereas the metabolic cost per stride was largely invariant (2.74±0.12 J kg–1 stride–1). The tight coupling of stature, gait mechanics and metabolic energy expenditure resulted in an inverse relationship between mass-specific transport costs and stature (Etrans/Mb∝Lb–0.95, J kg–1 m–1). We conclude that humans spanning a broad range of ages, statures and masses incur the same mass-specific metabolic cost to walk a horizontal distance equal to their stature.
Behaviour and buoyancy regulation in the deepest-diving reptile: the leatherback turtle
Authors: Fossette Sabrina , Gleiss Adrian C. , Myers Andy E. , Garner Steve , Liebsch Nikolai , Whitney Nicholas M. , Hays Graeme C. , Wilson Rory P. , Lutcavage Molly E. 
Published: November 2010

SUMMARYIn the face of the physical and physiological challenges of performing breath-hold deep dives, marine vertebrates have evolved different strategies. Although behavioural strategies in marine mammals and seabirds have been investigated in detail, little is known about the deepest-diving reptile – the leatherback turtle (Dermochelys coriacea). Here, we deployed tri-axial accelerometers on female leatherbacks nesting on St Croix, US Virgin Islands, to explore their diving strategy. Our results show a consistent behavioural pattern within dives among individuals, with an initial period of active swimming at relatively steep descent angles (∼–40 deg), with a stroke frequency of 0.32 Hz, followed by a gliding phase. The depth at which the gliding phase began increased with the maximum depth of the dives. In addition, descent body angles and vertical velocities were higher during deeper dives. Leatherbacks might thus regulate their inspired air-volume according to the intended dive depth, similar to hard-shelled turtles and penguins. During the ascent, turtles actively swam with a stroke frequency of 0.30 Hz but with a low vertical velocity (∼0.40 ms–1) and a low pitch angle (∼+26 deg). Turtles might avoid succumbing to decompression sickness (‘the bends’) by ascending slowly to the surface. In addition, we suggest that the low body temperature of this marine ectotherm compared with that of endotherms might help reduce the risk of bubble formation by increasing the solubility of nitrogen in the blood. This physiological advantage, coupled with several behavioural and physical adaptations, might explain the particular ecological niche the leatherback turtle occupies among marine reptiles.