bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climatic Controls on the Snowmelt Hydrology of the Northern Rocky Mountains
Authors: Pederson Gregory T. , Gray Stephen T. , Ault Toby , Marsh Wendy , Fagre Daniel B. , Bunn Andrew G. , Woodhouse Connie A. , Graumlich Lisa J. 
Published: December 2010

AbstractThe northern Rocky Mountains (NRMs) are a critical headwaters region with the majority of water resources originating from mountain snowpack. Observations showing declines in western U.S. snowpack have implications for water resources and biophysical processes in high-mountain environments. This study investigates oceanic and atmospheric controls underlying changes in timing, variability, and trends documented across the entire hydroclimatic-monitoring system within critical NRM watersheds. Analyses were conducted using records from 25 snow telemetry (SNOTEL) stations, 148 1 April snow course records, stream gauge records from 14 relatively unimpaired rivers, and 37 valley meteorological stations. Over the past four decades, midelevation SNOTEL records show a tendency toward decreased snowpack with peak snow water equivalent (SWE) arriving and melting out earlier. Temperature records show significant seasonal and annual decreases in the number of frost days (days ≤0°C) and changes in spring minimum temperatures that correspond with atmospheric circulation changes and surface–albedo feedbacks in March and April. Warmer spring temperatures coupled with increases in mean and variance of spring precipitation correspond strongly to earlier snowmeltout, an increased number of snow-free days, and observed changes in streamflow timing and discharge. The majority of the variability in peak and total annual snowpack and streamflow, however, is explained by season-dependent interannual-to-interdecadal changes in atmospheric circulation associated with Pacific Ocean sea surface temperatures. Over recent decades, increased spring precipitation appears to be buffering NRM total annual streamflow from what would otherwise be greater snow-related declines in hydrologic yield. Results have important implications for ecosystems, water resources, and long-lead-forecasting capabilities.
Characteristics of 3–4- and 6–8-Day Period Disturbances Observed over the Tropical Indian Ocean
Authors: Yasunaga Kazuaki , Yoneyama Kunio , Moteki Qoosaku , Fujita Mikiko , Takayabu Yukari N. , Suzuki Junko , Ushiyama Tomoki , Mapes Brian 
Published: December 2010

Abstract
A field observational campaign [i.e., the Mirai Indian Ocean cruise for the Study of the MJO-convection Onset (MISMO)] was conducted over the central equatorial Indian Ocean in October–December 2006. During MISMO, large-scale organized convection associated with a weak Madden–Julian oscillation (MJO) broke out, and some other notable variations were observed.
Water vapor and precipitation data show a prominent 3–4-day-period cycle associated with meridional wind υ variations. Filtered υ anomalies at midlevels in reanalysis data [i.e., the Japan Meteorological Agency (JMA) Climate Data Assimilation System (JCDAS)] show westward phase velocities, and the structure is consistent with mixed Rossby–gravity waves. Estimated equivalent depths are a few tens of meters, typical of convectively coupled waves. In the more rainy part of MISMO (16–26 November), the 3–4-day waves were coherent through the lower and midtroposphere, while in the less active early November period midlevel υ fluctuations appear less connected to those at the surface.
SST diurnal variations were enhanced in light-wind and clear conditions. These coincided with westerly anomalies in prominent 6–8-day zonal wind variations with a deep nearly barotropic structure through the troposphere. Westward propagation and structure of time-filtered winds suggest n = 1 equatorial Rossby waves, but with estimated equivalent depth greater than is common for convectively coupled waves, although sheared background flow complicates the estimation somewhat.
An ensemble reanalysis [i.e., the AGCM for the Earth Simulator (AFES) Local Ensemble Transform Kalman Filter (LETKF) Experimental Reanalysis (ALERA)] shows enhanced spread among the ensemble members in the zonal confluence phase of these deep Rossby waves, suggesting that assimilating them excites rapidly growing differences among ensemble members.
Intratympanic Gentamicin Treatment for Meniere's Disease
Authors: Mcfeely William J. , Singleton George T. , Rodriguez Francisco J. , Antonelli Patrick J. 
Published: December 2010

OBJECTIVESThe purpose of this study was to evaluate the safety and efficacy of a modified intratympanic gentamicin technique in patients with intractable unilateral or bilateral Meniere's disease.METHODSA retrospective review of 25 consecutive patients who underwent gentamicin treatment for Meniere's disease was conducted between 1992 and 1996. Two separate delivery systems were used during this study, with the last 13 subjects undergoing placement of the new system (flanged polyethylene tubing).RESULTSFollow‐up averaged 23 months. Absence of vertigo spells was reported in 88%, and substantial control was achieved in 12%. Four of five patients with bilateral disease achieved complete control. Results for the two delivery systems were not significantly different. Absence of ice‐water caloric response was seen in 75% (15 of 20) patients. Clinically significant sensorineural hearing loss occurred in 5 (20%) of 25 ears. Nonserviceable hearing developed in only two (8%) patients.CONCLUSIONSOur results support the previously reported efficacy and relative safety of gentamicin infusion therapy for intractable Meniere's disease. Polyethylene tubing may be more advantageous than T‐tube delivery because of anatomic concerns in certain patients. (Otolaryngol Head Neck Surg 1998;118:589–96.)
Heat Shock Protein and p53 Expression in Head and Neck Squamous Cell Carcinoma
Authors: Gandour‐Edwards Regina , Trock Bruce J. , Gumerlock Paul , Donald Paul J. 
Published: December 2010

BACKGROUNDHeat shock proteins have been associated with the mutant form of the tumor suppressor gene, TP53, and with resistance to cancer chemotherapy.METHODSArchival tissues from 50 patients with head and neck squamous cell carcinoma who received primary surgical resection were examined for p53, HSP27, and HSP70 by immunohistochemistry and correlated with tumor stage, grade, and 5‐year survival (alive or deceased).RESULTSBoth heat shock proteins were strongly expressed in normal mucosa and in small (T1 and T2) tumors. Thirty (60%) of tumors were positive for p53, 43 (86%) for HSP27, and 34 (68%) for HSP70, with no association between p53 and heat shock protein expression. Twenty‐five patients were alive (4 with disease), and 25 patients were deceased (9 from other causes). p53 Protein overexpression correlated with low‐grade tumors. Only primary tumor site (i.e., oral cavity > larynx > oropharynx/base of tongue) and N stage were significantly associated with survival.CONCLUSIONSHeat shock proteins are expressed in normal upper respiratory tract squamous mucosa, and their role in carcinoma remains unclear. None of the markers, p53, HSP27, or HSP70, demonstrated prognostic significance for 5‐year survival. We confirm the recognized association of cervical lymph node metastases with decreased survival. (Otolaryngol Head Neck Surg 1998;118:610–5.)
Skin-Derived Tenocyte-like Cells for the Treatment of Patellar Tendinopathy
Authors: Clarke Andrew W. , Alyas Faisal , Morris Tim , Robertson Claire J. , Bell Jonathan , Connell David A. 
Published: December 2010

Background: Recent research of lateral elbow tendinopathy has led to the use of laboratory-amplified tenocyte-like cells. Hypothesis: Ultrasound-guided injection of autologous skin-derived tendon-like cells are effective compared with other injectable therapies for the treatment of refractory patellar tendinosis. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: From 60 patellar tendons in 46 patients with refractory patellar tendinopathy, a 4-mm skin biopsy was sampled to grow tenocyte-like collagen-producing cells. Patients were allocated into 2 groups: (1) injection with laboratory-prepared, amplified collagen-producing cells derived from dermal fibroblasts and suspended in autologous plasma from centrifuged autologous whole blood or (2) injection with autologous plasma alone. Injections were made into the sites of hypoechogenicity, intrasubstance tears, and fibrillar discontinuity within the patellar tendon. The Victorian Institute of Sport Assessment (VISA) score was used to assess pain, severity, and functional disability. Ultrasound was performed to assess structural and blood flow changes, evaluating 4 criteria: tendon thickness, hypoechogenicity, intrasubstance tears, and neovascularity. Results: In the cell group, mean VISA scores improved from 44 ± 15 before treatment to 75 ± 17 at 6 months; in the plasma group, from 50 ± 18 to 70 ± 14. Estimated average difference between groups was 8.1, a significantly higher score in the cell group. Patients treated with collagen-producing cells also had significantly faster improvement and a highly significant effect of treatment, with the difference between groups estimated as 2.5 per unit increase in [Formula: see text]. One patient treated with cell therapy had a late rupture and progressed to surgery; histopathology showed normal tendon structure. Conclusion: Ultrasound-guided injection of autologous skin-derived tendon-like cells can be safely used in the short term to treat patellar tendinopathy, with faster response of treatment and significantly greater improvement in pain and function than with plasma alone.
Limited clinical relevance of imaging techniques in the follow-up of patients with advanced chronic lymphocytic leukemia: results of a meta-analysis
Authors: Eichhorst Barbara F. , Fischer Kirsten , Fink Anna-Maria , Elter Thomas , Wendtner Clemens M. , Goede Valentin , Bergmann Manuela , Stilgenbauer Stephan , Hopfinger Georg , Ritgen Matthias , Bahlo Jasmin , Busch Raymonde , Hallek Michael ,   for the German CLL Study Group (GCLLSG)
Published: December 2010

AbstractThe clinical value of imaging is well established for the follow-up of many lymphoid malignancies but not for chronic lymphocytic leukemia (CLL). A meta-analysis was performed with the dataset of 3 German CLL Study Group phase 3 trials (CLL4, CLL5, and CLL8) that included 1372 patients receiving first-line therapy for CLL. Response as well as progression during follow-up was reassessed according to the National Cancer Institute Working Group1996 criteria. A total of 481 events were counted as progressive disease during treatment or follow-up. Of these, 372 progressions (77%) were detected by clinical symptoms or blood counts. Computed tomography (CT) scans or ultrasound were relevant in 44 and 29 cases (9% and 6%), respectively. The decision for relapse treatment was determined by CT scan or ultrasound results in only 2 of 176 patients (1%). CT scan results had an impact on the prognosis of patients in complete remission only after the administration of conventional chemotherapy but not after chemoimmunotherapy. In conclusion, physical examination and blood count remain the methods of choice for staging and clinical follow-up of patients with CLL as recommended by the International Workshop on Chronic Lymphocytic Leukemia 2008 guidelines. These trials are registered at http://www.isrctn.org as ISRCTN 75653261 and ISRCTN 36294212 and at http://www.clinicaltrials.gov as NCT00281918.
GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells
Authors: Yu Shuyang , Cui Kairong , Jothi Raja , Zhao Dong-Mei , Jing Xuefang , Zhao Keji , Xue Hai-Hui 
Published: December 2010

Abstract
Maintaining a steady pool of self-renewing hematopoietic stem cells (HSCs) is critical for sustained production of multiple blood lineages. Many transcription factors and molecules involved in chromatin and epigenetic modifications have been found to be critical for HSC self-renewal and differentiation; however, their interplay is less understood. The transcription factor GA binding protein (GABP), consisting of DNA-binding subunit GABPα and transactivating subunit GABPβ, is essential for lymphopoiesis as shown in our previous studies. Here we demonstrate cell-intrinsic, absolute dependence on GABPα for maintenance and differentiation of hematopoietic stem/progenitor cells. Through genome-wide mapping of GABPα binding and transcriptomic analysis of GABPα-deficient HSCs, we identified Zfx and Etv6 transcription factors and prosurvival Bcl-2 family members including Bcl-2, Bcl-XL, and Mcl-1 as direct GABP target genes, underlying its pivotal role in HSC survival. GABP also directly regulates Foxo3 and Pten and hence sustains HSC quiescence. Furthermore, GABP activates transcription of DNA methyltransferases and histone acetylases including p300, contributing to regulation of HSC self-renewal and differentiation. These systematic analyses revealed a GABP-controlled gene regulatory module that programs multiple aspects of HSC biology. Our studies thus constitute a critical first step in decoding how transcription factors are orchestrated to regulate maintenance and multipotency of HSCs.
Evidence for the cure of HIV infection by CCR5Δ32/Δ32 stem cell transplantation
Authors: Allers Kristina , Hütter Gero , Hofmann Jörg , Loddenkemper Christoph , Rieger Kathrin , Thiel Eckhard , Schneider Thomas 
Published: December 2010

Abstract
HIV entry into CD4+ cells requires interaction with a cellular receptor, generally either CCR5 or CXCR4. We have previously reported the case of an HIV-infected patient in whom viral replication remained absent despite discontinuation of antiretroviral therapy after transplantation with CCR5Δ32/Δ32 stem cells. However, it was expected that the long-lived viral reservoir would lead to HIV rebound and disease progression during the process of immune reconstitution. In the present study, we demonstrate successful reconstitution of CD4+ T cells at the systemic level as well as in the gut mucosal immune system after CCR5Δ32/Δ32 stem cell transplantation, while the patient remains without any sign of HIV infection. This was observed although recovered CD4+ T cells contain a high proportion of activated memory CD4+ T cells, ie, the preferential targets of HIV, and are susceptible to productive infection with CXCR4-tropic HIV. Furthermore, during the process of immune reconstitution, we found evidence for the replacement of long-lived host tissue cells with donor-derived cells, indicating that the size of the viral reservoir has been reduced over time. In conclusion, our results strongly suggest that cure of HIV has been achieved in this patient.
Ribonucleotide reduction - horizontal transfer of a required function spans all three domains
Authors: Lundin Daniel , Gribaldo Simonetta , Torrents Eduard , Sjöberg Britt-Marie , Poole Anthony M 
Published: December 2010

Abstract

Background
Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comprised of three classes. Each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class I RNRs have been identified in archaeal genomes, and classes II and III likewise appear rare across eukaryotes. In this study, we examine whether this distribution is best explained by presence of all three classes in the Last Universal Common Ancestor (LUCA), or by horizontal gene transfer (HGT) of RNR genes. We also examine to what extent environmental factors may have impacted the distribution of RNR classes.

Results
Our phylogenies show that the Last Eukaryotic Common Ancestor (LECA) possessed a class I RNR, but that the eukaryotic class I enzymes are not directly descended from class I RNRs in Archaea. Instead, our results indicate that archaeal class I RNR genes have been independently transferred from bacteria on two occasions. While LECA possessed a class I RNR, our trees indicate that this is ultimately bacterial in origin. We also find convincing evidence that eukaryotic class I RNR has been transferred to the Bacteroidetes, providing a stunning example of HGT from eukaryotes back to Bacteria. Based on our phylogenies and available genetic and genomic evidence, class II and III RNRs in eukaryotes also appear to have been transferred from Bacteria, with subsequent within-domain transfer between distantly-related eukaryotes. Under the three-domains hypothesis the RNR present in the last common ancestor of Archaea and eukaryotes appears, through a process of elimination, to have been a dimeric class II RNR, though limited sampling of eukaryotes precludes a firm conclusion as the data may be equally well accounted for by HGT.

Conclusions
Horizontal gene transfer has clearly played an important role in the evolution of the RNR repertoire of organisms from all three domains of life. Our results clearly show that class I RNRs have spread to Archaea and eukaryotes via transfers from the bacterial domain, indicating that class I likely evolved in the Bacteria. However, against the backdrop of ongoing transfers, it is harder to establish whether class II or III RNRs were present in the LUCA, despite the fact that ribonucleotide reduction is an essential cellular reaction and was pivotal to the transition from RNA to DNA genomes. Instead, a general pattern of ongoing horizontal transmission emerges wherein environmental and enzyme operational constraints, especially the presence or absence of oxygen, are likely to be major determinants of the RNR repertoire of genomes.
Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered european eel
Authors: Coppe Alessandro , Pujolar Jose Martin , Maes Gregory E , Larsen Peter F , Hansen Michael M , Bernatchez Louis , Zane Lorenzo , Bortoluzzi Stefania 
Published: December 2010

Abstract

Background
Once highly abundant, the European eel (Anguilla anguilla L.; Anguillidae; Teleostei) is considered to be critically endangered and on the verge of extinction, as the stock has declined by 90-99% since the 1980s. Yet, the species is poorly characterized at molecular level with little sequence information available in public databases.

Results
The first European eel transcriptome was obtained by 454 FLX Titanium sequencing of a normalized cDNA library, produced from a pool of 18 glass eels (juveniles) from the French Atlantic coast and two sites in the Mediterranean coast. Over 310,000 reads were assembled in a total of 19,631 transcribed contigs, with an average length of 531 nucleotides. Overall 36% of the contigs were annotated to known protein/nucleotide sequences and 35 putative miRNA identified.

Conclusions
This study represents the first transcriptome analysis for a critically endangered species. EeelBase, a dedicated database of annotated transcriptome sequences of the European eel is freely available at http://compgen.bio.unipd.it/eeelbase. Considering the multiple factors potentially involved in the decline of the European eel, including anthropogenic factors such as pollution and human-introduced diseases, our results will provide a rich source of data to discover and identify new genes, characterize gene expression, as well as for identification of genetic markers scattered across the genome to be used in various applications.
Brazilian Plasmodium falciparum isolates: investigation of candidate polymorphisms for artemisinin resistance before introduction of artemisinin-based combination therapy
Authors: Gama Bianca E , de Oliveira Natália K Almeida , de Souza José M , Santos Fátima , de Carvalho Leonardo JM , Melo Yonne FC , Rosenthal Philip J , Daniel-Ribeiro Cláudio T , Ferreira-da-Cruz Maria de Fátima 
Published: December 2010

Abstract

Background
This study was performed to better understand the genetic diversity of known polymorphisms in pfatpase6 and pfmdr1 genes before the introduction of ACT in Brazil, in order to get a genotypic snapshot of Plasmodium falciparum parasites that may be used as baseline reference for future studies.

Methods
Parasites from P. falciparum samples collected in 2002, 2004 and 2006-2007 were genotyped using PCR and DNA sequencing at codons 86, 130, 184, 1034, 1042, 1109 and 1246 for pfmdr1 gene, and 243, 263, 402, 431, 623, 630, 639, 683, 716, 776, 769 and 771 for pfatpase6 gene.

Results
A pfmdr1 haplotype NEF/CDVY was found in 97% of the samples. In the case of pfatpase6, four haplotypes, wild-type (37%), 630 S (35%), 402 V (5%) and double-mutant 630 S + 402 V (23%), were detected.

Conclusion
Although some polymorphism in pfmdr1 and pfatpase6 were verified, no reported haplotypes in both genes that may mediate altered response to ACT was detected before the introduction of this therapy in Brazil. Thus, the haplotypes herein described can be very useful as a baseline reference of P. falciparum populations without ACT drug pressure.
Kalman estimator- and general linear model-based on-line brain activation mapping by near-infrared spectroscopy
Authors: Hu Xiao-Su , Hong Keum-Shik , Ge Shuzhi S , Jeong Myung-Yung 
Published: December 2010

AbstractBackgroundNear-infrared spectroscopy (NIRS) is a non-invasive neuroimaging technique that recently has been developed to measure the changes of cerebral blood oxygenation associated with brain activities. To date, for functional brain mapping applications, there is no standard on-line method for analysing NIRS data.MethodsIn this paper, a novel on-line NIRS data analysis framework taking advantages of both the general linear model (GLM) and the Kalman estimator is devised. The Kalman estimator is used to update the GLM coefficients recursively, and one critical coefficient regarding brain activities is then passed to at-statistical test. Thet-statistical test result is used to update a topographic brain activation map. Meanwhile, a set of high-pass filters is plugged into the GLM to prevent very low-frequency noises, and an autoregressive (AR) model is used to prevent the temporal correlation caused by physiological noises in NIRS time series. A set of data recorded in finger tapping experiments is studied using the proposed framework.ResultsThe obtained results suggest that the method can effectively track the task related brain activation areas, and prevent the noise distortion in the estimation while the experiment is running. Thereby, the potential of the proposed method for real-time NIRS-based brain imaging was demonstrated.ConclusionsThis paper presents a novel on-line approach for analysing NIRS data for functional brain mapping applications. This approach demonstrates the potential of a real-time-updating topographic brain activation map.