bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of Drought Indices for Ecological, Agricultural, and Hydrological Applications
Authors: Vicente-Serrano Sergio M. , Beguería Santiago , Lorenzo-Lacruz Jorge , Camarero Jesús Julio , López-Moreno Juan I. , Azorin-Molina Cesar , Revuelto Jesús , Morán-Tejeda Enrique , Sanchez-Lorenzo Arturo 
Published: June 2012

Abstract
In this study, the authors provide a global assessment of the performance of different drought indices for monitoring drought impacts on several hydrological, agricultural, and ecological response variables. For this purpose, they compare the performance of several drought indices [the standardized precipitation index (SPI); four versions of the Palmer drought severity index (PDSI); and the standardized precipitation evapotranspiration index (SPEI)] to predict changes in streamflow, soil moisture, forest growth, and crop yield. The authors found a superior capability of the SPEI and the SPI drought indices, which are calculated on different time scales than the Palmer indices to capture the drought impacts on the aforementioned hydrological, agricultural, and ecological variables. They detected small differences in the comparative performance of the SPI and the SPEI indices, but the SPEI was the drought index that best captured the responses of the assessed variables to drought in summer, the season in which more drought-related impacts are recorded and in which drought monitoring is critical. Hence, the SPEI shows improved capability to identify drought impacts as compared with the SPI. In conclusion, it seems reasonable to recommend the use of the SPEI if the responses of the variables of interest to drought are not known a priori.
Veno-right ventricular cannulation reduces recirculation in extracorporeal membrane oxygenation
Authors: Lindstrom SJ , Mennen MT , Rosenfeldt FL , Salmonsen RF 
Published: June 2012

Background: Veno-venous extracorporeal membrane oxygenation has several advantages over veno-arterial support for patients with severe reversible respiratory failure. However, recirculation can limit oxygen delivery as pump flow increases. This could be ameliorated by placing the return catheter in the right ventricle instead of the central veins. We compared recirculation in veno-right ventricular support with that in conventional veno-venous support and its relationship with pump flow. Methods: Five greyhound dogs were sequentially cannulated percutaneously for both veno-venous and veno-right ventricular support. Recirculation was measured by comparing oxygen levels in the circuit drainage and return lines before and immediately after a sudden increase in circuit oxygenation at pump flows between 0.5 L/min and 4 L/min for both modalities. Results: Recirculation was reduced in veno-right ventricular support compared with conventional veno-venous support at 4 L/min pump flow (8.4% versus 37.9%, p=0.0076) and increased less with increases in pump flow (2.9% per 1 L/min vs. 11.1% per 1 L/min, p<0.0001). Conclusions: Recirculation can be dramatically reduced by returning blood into the right ventricle, which improves oxygen delivery to the lungs and the systemic circulation. The design of specialized catheters may facilitate percutaneous ventricular cannulation, improve safety and further reduce recirculation.
Orientation and mobility training for adults with low vision: a new standardized approach
Authors: Zijlstra GA Rixt , Ballemans Judith , Kempen Gertrudis IJM 
Published: June 2012

Background: Orientation and mobility training aims to facilitate independent functioning and participation in the community of people with low vision. Objective: (1) To gain insight into current practice regarding orientation and mobility training, and (2) to develop a theory-driven standardized version of this training to teach people with low vision how to orientate and be safe in terms of mobility. Study of current practice: Insight into current practice and its strengths and weaknesses was obtained via reviewing the literature, observing orientation and mobility training sessions ( n = 5) and interviewing Dutch mobility trainers ( n = 18). Current practice was mainly characterized by an individual, face-to-face orientation and mobility training session concerning three components: crystallizing client’s needs, providing information and training skills. A weakness was the lack of a (structured) protocol based on evidence or theory. New theory-driven training: A new training protocol comprising two face-to-face sessions and one telephone follow-up was developed. Its content is partly based on the components of current practice, yet techniques from theoretical frameworks (e.g. social-cognitive theory and self-management) are incorporated. Discussion: A standardized, tailor-made orientation and mobility training for using the identification cane is available. The new theory-driven standardized training is generally applicable for teaching the use of every low-vision device. Its acceptability and effectiveness are currently being evaluated in a randomized controlled trial.
Natural, innate improvements in multiple sclerosis disability
Authors: Tremlett Helen , Zhu Feng , Petkau John , Oger Joel , Zhao Yinshan ,   and the BC MS Clinic Neurologists
Published: June 2012

Background: Improvements in multiple sclerosis (MS) disability have recently been reported in immunomodulatory drug (IMD) clinical trials and observational studies. However, improvements have rarely been examined in natural history or IMD naive patients. We investigated annual and biennial improvements in Expanded Disability Status Scale (EDSS) scores in British Columbia, Canada. Methods: The British Columbian MS database was accessed for definite MS patients (1980–2009). Consecutive IMD-free EDSS scores one and two years apart (± 3 months) were examined; improvements (≥0.5,≥1,≥2 EDSS points) and sustained improvements (confirmed at one year) were described. The influence of patient characteristics on improvements was examined using logistic regression. Results: From 16,132 EDSS scores, 7653 yearly and 5845 biennial EDSS intervals were available for 2961 and 2382 patients respectively. Of the yearly intervals, 14.9% showed an improvement (≥0.5 points), 8.3% ≥1 point and 2.2% ≥2 point improvement, with nearly half being sustained. Corresponding worsenings were observed in 32.9%, 20.5% and 7.9% respectively, with stability in just over half (53%). Biennial findings were similar. Characteristics generally associated with improvements included: female sex, younger age, shorter disease duration, relapsing-onset and presence of moderate disability (compared with mild or advanced) and a previous episode of worsening (disassociated from a relapse). However, improvements were also observed after periods of stability and in primary-progressive MS. Conclusion: Improvements in MS disability over one or two years are not unusual. We suggest the term ‘innate improvements’. Our findings have implication for the design of clinical trials and observational studies in MS targeting improvements on the EDSS.
Treatment-influenced associations of PML-RARα mutations, FLT3 mutations, and additional chromosome abnormalities in relapsed acute promyelocytic leukemia
Authors: Gallagher Robert E. , Moser Barry K. , Racevskis Janis , Poiré Xavier , Bloomfield Clara D. , Carroll Andrew J. , Ketterling Rhett P. , Roulston Diane , Schachter-Tokarz Esther , Zhou Da-cheng , Chen I-Ming L. , Harvey Richard , Koval Greg , Sher Dorie A. , Feusner James H. , Tallman Martin S. , Larson Richard A. , Powell Bayard L. , Appelbaum Frederick R. , Paietta Elisabeth , Willman Cheryl L. , Stock Wendy 
Published: June 2012

AbstractMutations in the all-trans retinoic acid (ATRA)–targeted ligand binding domain of PML-RARα (PRα/LBD+) have been implicated in the passive selection of ATRA-resistant acute promyelocytic leukemia clones leading to disease relapse. Among 45 relapse patients from the ATRA/chemotherapy arm of intergroup protocol C9710, 18 patients harbored PRα/LBD+ (40%), 7 of whom (39%) relapsed Off-ATRA selection pressure, suggesting a possible active role of PRα/LBD+. Of 41 relapse patients coanalyzed, 15 (37%) had FMS-related tyrosine kinase 3 internal tandem duplication mutations (FLT3-ITD+), which were differentially associated with PRα/LBD+ depending on ATRA treatment status at relapse: positively, On-ATRA; negatively, Off-ATRA. Thirteen of 21 patients (62%) had additional chromosome abnormalities (ACAs); all coanalyzed PRα/LBD mutant patients who relapsed off-ATRA (n = 5) had associated ACA. After relapse Off-ATRA, ACA and FLT3-ITD+ were negatively associated and were oppositely associated with presenting white blood count and PML-RARα type: ACA, low, L-isoform; FLT3-ITD+, high, S-isoform. These exploratory results suggest that differing PRα/LBD+ activities may interact with FLT3-ITD+ or ACA, that FLT3-ITD+ and ACA are associated with different intrinsic disease progression pathways manifest at relapse Off-ATRA, and that these different pathways may be short-circuited by ATRA-selectable defects at relapse On-ATRA. ACA and certain PRα/LBD+ were also associated with reduced postrelapse survival.
Ancient DNA studies: new perspectives on old samples
Authors: Rizzi Ermanno , Lari Martina , Gigli Elena , De Bellis Gianluca , Caramelli David 
Published: June 2012

AbstractIn spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
A previously uncharacterized gene stm0551 plays a repressive role in the regulation of type 1 fimbriae in Salmonella enterica serotype Typhimurium
Authors: Wang Ke-Chuan , Hsu Yuan-Hsun , Huang Yi-Ning , Yeh Kuang-Sheng 
Published: June 2012

Abstract

Background

Salmonella enterica serotype Typhimurium produces surface-associated fimbriae that facilitate adherence of the bacteria to a variety of cells and tissues. Type 1 fimbriae with binding specificity to mannose residues are the most commonly found fimbrial type. In vitro, static-broth culture favors the growth of S. Typhimurium with type 1 fimbriae, whereas non-type 1 fimbriate bacteria are obtained by culture on solid-agar media. Previous studies demonstrated that the phenotypic expression of type 1 fimbriae is the result of the interaction and cooperation of the regulatory genes fimZ, fimY, fimW, and fimU within the fim gene cluster. Genome sequencing revealed a novel gene, stm0551, located between fimY and fimW that encodes an 11.4-kDa putative phosphodiesterase specific for the bacterial second messenger cyclic-diguanylate monophosphate (c-di-GMP). The role of stm0551 in the regulation of type 1 fimbriae in S. Typhimurium remains unclear.

Results
A stm0551-deleted stain constructed by allelic exchange constitutively produced type 1 fimbriae in both static-broth and solid-agar medium conditions. Quantative RT-PCR revealed that expression of the fimbrial major subunit gene, fimA, and one of the regulatory genes, fimZ, were comparably increased in the stm0551-deleted strain compared with those of the parental strain when grown on the solid-agar medium, a condition that normally inhibits expression of type 1 fimbriae. Following transformation with a plasmid possessing the coding sequence of stm0551, expression of fimA and fimZ decreased in the stm0551 mutant strain in both culture conditions, whereas transformation with the control vector pACYC184 relieved this repression. A purified STM0551 protein exhibited a phosphodiesterase activity in vitro while a point mutation in the putative EAL domain, substituting glutamic acid (E) with alanine (A), of STM0551 or a FimY protein abolished this activity.

Conclusions
The finding that the stm0551 gene plays a negative regulatory role in the regulation of type 1 fimbriae in S. Typhimurium has not been reported previously. The possibility that degradation of c-di-GMP is a key step in the regulation of type 1 fimbriae warrants further investigation.
Analysis of the P1promoter in response to UV-B radiation in allelic variants of high-altitude maize
Authors: Rius Sebastián Pablo , Grotewold Erich , Casati Paula 
Published: June 2012

Abstract

Background
Plants living at high altitudes are typically exposed to elevated UV-B radiation, and harbor mechanisms to prevent the induced damage, such as the accumulation of UV-absorbing compounds. The maize R2R3-MYB transcription factor P1 controls the accumulation of several UV-B absorbing phenolics by activating a subset of flavonoid biosynthetic genes in leaves of maize landraces adapted to high altitudes.

Results
Here, we studied the UV-B regulation of P1 in maize leaves of high altitude landraces, and we investigated how UV-B regulates P1binding to the CHS promoter in both low and high altitude lines. In addition, we analyzed whether the expansion in the P1 expression domain between these maize landraces and inbred lines is associated to changes in the molecular structure of the proximal promoter, distal enhancer and first intron of P1. Finally, using transient expression experiments in protoplasts from various maize genotypes, we investigated whether the different expression patterns of P1 in the high altitude landraces could be attributed to trans- or cis-acting elements.

Conclusions
Together, our results demonstrate that, although differences in cis-acting elements exist between the different lines under study, the different patterns of P1 expression are largely a consequence of effects in trans.
PeanutDB: an integrated bioinformatics web portal for Arachis hypogaea transcriptomics
Authors: Duan Xiaohong , Schmidt Emily , Li Pei , Lenox Douglas , Liu Lin , Shu Changlong , Zhang Jie , Liang Chun 
Published: June 2012

Abstract

Background
The peanut (Arachis hypogaea) is an important crop cultivated worldwide for oil production and food sources. Its complex genetic architecture (e.g., the large and tetraploid genome possibly due to unique cross of wild diploid relatives and subsequent chromosome duplication: 2n = 4x = 40, AABB, 2800 Mb) presents a major challenge for its genome sequencing and makes it a less-studied crop. Without a doubt, transcriptome sequencing is the most effective way to harness the genome structure and gene expression dynamics of this non-model species that has a limited genomic resource.

Description
With the development of next generation sequencing technologies such as 454 pyro-sequencing and Illumina sequencing by synthesis, the transcriptomics data of peanut is rapidly accumulated in both the public databases and private sectors. Integrating 187,636 Sanger reads (103,685,419 bases), 1,165,168 Roche 454 reads (333,862,593 bases) and 57,135,995 Illumina reads (4,073,740,115 bases), we generated the first release of our peanut transcriptome assembly that contains 32,619 contigs. We provided EC, KEGG and GO functional annotations to these contigs and detected SSRs, SNPs and other genetic polymorphisms for each contig. Based on both open-source and our in-house tools, PeanutDB presents many seamlessly integrated web interfaces that allow users to search, filter, navigate and visualize easily the whole transcript assembly, its annotations and detected polymorphisms and simple sequence repeats. For each contig, sequence alignment is presented in both bird’s-eye view and nucleotide level resolution, with colorfully highlighted regions of mismatches, indels and repeats that facilitate close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors.

Conclusion
As a public genomic database that integrates peanut transcriptome data from different sources, PeanutDB (http://bioinfolab.muohio.edu/txid3818v1) provides the Peanut research community with an easy-to-use web portal that will definitely facilitate genomics research and molecular breeding in this less-studied crop.
Immunophenotyping invasive breast cancer: paving the road for molecular imaging
Authors: Vermeulen Jeroen F , van Brussel Aram SA , van der Groep Petra , Morsink Folkert HM , Bult Peter , van der Wall Elsken , van Diest Paul J 
Published: June 2012

Abstract

Background
Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers might increase specificity and sensitivity of detection. Because development of new tracers is labor-intensive and costly, we searched for the smallest panel of tumor membrane markers that would allow detection of the wide spectrum of invasive breast cancers.

Methods
Tissue microarrays containing 483 invasive breast cancers were stained by immunohistochemistry for a selected set of membrane proteins known to be expressed in breast cancer.

Results
The combination of highly tumor-specific markers glucose transporter 1 (GLUT1), epidermal growth factor receptor (EGFR), insulin-like growth factor-1 receptor (IGF1-R), human epidermal growth factor receptor 2 (HER2), hepatocyte growth factor receptor (MET), and carbonic anhydrase 9 (CAIX) 'detected' 45.5% of tumors, especially basal/triple negative and HER2-driven ductal cancers. Addition of markers with a 2-fold tumor-to-normal ratio increased the detection rate to 98%. Including only markers with >3 fold tumor-to-normal ratio (CD44v6) resulted in an 80% detection rate. The detection rate of the panel containing both tumor-specific and less tumor-specific markers was not dependent on age, tumor grade, tumor size, or lymph node status.

Conclusions
In search of the minimal panel of targeted probes needed for the highest possible detection rate, we showed that 80% of all breast cancers express at least one of a panel of membrane markers (CD44v6, GLUT1, EGFR, HER2, and IGF1-R) that may therefore be suitable for molecular imaging strategies. This study thereby serves as a starting point for further development of a set of antibody-based optical tracers with a high breast cancer detection rate.
Increased expression of MMP-9 and IL-8 are correlated with poor prognosis of Bladder Cancer
Authors: Reis Sabrina Thalita , Leite Katia Ramos M , Piovesan Luís Felipe , Pontes-Junior José , Viana Nayara Izabel , Abe Daniel Kanda , Crippa Alexandre , Moura Caio Martins , Adonias Sanarelly Pires , Srougi Miguel , Dall’Oglio Marcos Francisco 
Published: June 2012

Abstract

Background
Extracellular matrix homeostasis is strictly maintained by a coordinated balance between the expression of metalloproteinases (MMPs) and their inhibitors. The purpose of this study was to investigate whether the expression of MMP-9, MMP-2 and its specific inhibitors, are expressed in a reproducible, specific pattern and if the profiles are related to prognosis in Bladder Cancer (BC).

Methods
MMP-9, MMP-2 and its specific inhibitors expression levels were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) in fresh-frozen malignant tissue collected from 40 patients with BC submitted to transurethral resection of bladder. The control group consisted of normal bladder tissue from five patients who had undergone retropubic prostatectomy to treat benign prostatic hyperplasia.

Results
MMP-9 was overexpressed in 59.0 % of patients, and MMP-2, TIMP-1, TIMP-2, MMP-14, RECK and IL-8 was underexpressed in most of the patients. Regarding prognostic parameters we observed that high-grade tumors exhibited significantly higher levels of MMP-9 and IL-8 (p = 0.012, p = 0.003). Invasive tumors (pT1-pT2) had higher expression levels of MMP-9 than superficial tumors (pTa) (p = 0.026). The same was noted for IL-8 that was more expressed by invasive tumors (p = 0.015, p = 0.048). Most importantly tumor recurrence was related with higher levels of both MMP-9 (p = 0.003) and IL-8 (p = 0.005).

Conclusion
We have demonstrated that the overexpression of MMP-9 and higher expression of IL-8 are related to unfavorable prognostic factors of urothelial bladder cancer and tumor recurrence and may be useful in the follow up of the patients.
Identification of immunogenic proteins and generation of antibodies against SalmonellaTyphimurium using phage display
Authors: Meyer Torsten , Schirrmann Thomas , Frenzel André , Miethe Sebastian , Stratmann-Selke Janin , Gerlach Gerald F , Strutzberg-Minder Katrin , Dübel Stefan , Hust Michael 
Published: June 2012

Abstract

Background
Solely in Europoe, Salmonella Typhimurium causes more than 100,000 infections per year. Improved detection of livestock colonised with S. Typhimurium is necessary to prevent foodborne diseases. Currently, commercially available ELISA assays are based on a mixture of O-antigens (LPS) or total cell lysate of Salmonella and are hampered by cross-reaction. The identification of novel immunogenic proteins would be useful to develop ELISA based diagnostic assays with a higher specificity.

Results
A phage display library of the entire Salmonella Typhimurium genome was constructed and 47 immunogenic oligopeptides were identified using a pool of convalescent sera from pigs infected with Salmonella Typhimurium. The corresponding complete genes of seven of the identified oligopeptids were cloned. Five of them were produced in E. coli. The immunogenic character of these antigens was validated with sera from pigs infeced with S. Tyhimurium and control sera from non-infected animals. Finally, human antibody fragments (scFv) against these five antigens were selected using antibody phage display and characterised.

Conclusion
In this work, we identified novel immunogenic proteins of Salmonella Typhimurium and generated antibody fragments against these antigens completely based on phage display. Five immunogenic proteins were validated using a panel of positive and negative sera for prospective applications in diagnostics of Salmonela Typhimurium.