bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic review and meta-analysis of mortality in crop protection product manufacturing workers
Authors: Jones D R , Sutton A J , Abrams K R , Fenty J , Warren F , Rushton L 
Published: December 2008

Objectives:The potential health effects of the manufacture and use of crop protection chemicals were investigated through systematic review and meta-analysis of studies of cohorts of workers in the crop protection product manufacturing industry.Methods:Several computerised literature databases were searched from inception until December 2003, with references listed in identified articles checked for further relevant articles. Random effects meta-analyses of log standardised mortality ratios (SMRs) were carried out. Heterogeneity was explored through subgroup analyses and meta-regression; sensitivity analyses of different approaches for zero events were performed.Results:21 references reporting information on 37 separate cohorts for mortality were identified. The meta-SMR for all cause mortality was 0.94 (95% CI 0.88 to 1.00) (37 cohorts). Significantly raised mortality was found for cancers of the buccal cavity and pharynx, oesophagus, rectum, larynx, lung, and lymphatic and haematopoietic system with little heterogeneity being observed. Excluding studies with zero events identified additional excesses.Conclusions:Evidence of multiple excesses, particularly in subgroups exposed to phenoxy herbicides contaminated with dioxins, substantiates previous findings. The importance of careful treatment of zero cases was highlighted. Future systematic reviews and meta-analyses would benefit from availability of results for a standard list of causes of disease.
Heterogeneity in enterohemorrhagicEscherichia coliO157:H7 fecal shedding in cattle is related toEscherichia coliO157:H7 colonization of the small and large intestine
Authors: Baines Danica , Lee Byron , McAllister Tim 
Published: December 2008

In the last decade, Escherichia coli O157:H7 have emerged as important pathogens of the gastrointestinal tract of humans. Healthy cattle have been identified as the primary reservoir, however, the factors affecting heterogeneous E. coli O157:H7 fecal shedding are not fully understood. The aim of this study was to investigate the contribution of E. coli O157:H7 colonization of small and large intestinal sites to the heterogeneity of fecal shedding in cattle. There was a dose-dependant E. coli O157:H7 E318N colonization of duodenum, jejunum, ileum, cecum, ascending colon, spiral colon, descending colon, and the rectoanal junction in vitro with no difference in E. coli O157:H7 colonization of the rectoanal junction and other intestinal sites. There were 10–100 times greater E. coli O157:H7 colonization of intestinal sites from persistent shedding cattle compared with nonpersistent shedding cattle. Novel pathologies were associated with E. coli O157:H7 colonization sites in the small and large intestine. The first pathology, focal petechiae, was present throughout the intestinal tract of cattle that ceased shedding E. coli O157:H7 for 5–12 weeks or in the jejunum, ileum, cecum, and ascending colon of cattle shedding E. coli O157:H7 for 4–5 months. The second pathology, mucosal hemorrhages, was present in the same sites as the focal petechiae in cattle shedding for 5 months and these hemorrhages were in the final stages of repair. Several features of these hemorrhages support this conclusion including the brown appearance, low amount of classic E. coli O157:H7 induced A/E lesions, flattened epithelium, and blunted villi. Although mucosal hemorrhages were present in the jejunum, ileum, cecum, and ascending colon in cattle shedding for 4 months, many other pathologies were also present that were indicative of hemorrhagic enteritis as evidenced by the blood red appearance of hemorrhages, severe edema, and dark red erythema. Escherichia coli O157:H7 were associated with both pathologies suggesting it is the causative agent. The current study supports a relationship between the amount of E. coli O157:H7 colonization in intestinal sites and heterogeneous fecal shedding by cattle.
Drainage and agriculture impacts on fire frequency in a southern Illinois forested bottomland
Authors: Nelson John L. , Ruffner Charles M. , Groninger John W. , Souter Ray A. 
Published: December 2008

Postsettlement (1909–2003) fire history of a forested bottomland in the Mississippi Embayment of southern Illinois, USA, was determined using fire-scar analysis. The study area is a forested bottomland hardwood site, with remnant pockets of the dominant presettlement bald cypress – tupelo (Taxodium–Nyssa) vegetation. Ditch drainage was installed in 1919, with agricultural clearing and abandonment varying throughout the early and mid-twentieth century. Commercial agricultural activities ceased after the site became part of a conservation area ca. 1950. The hydrology of the site was further modified in 1957 when it was inundated for waterfowl management. Both drainage and land clearing for agriculture were associated with increased fire frequency. Although drainage was a necessary precursor to agriculture across much of this landscape, land improvement played the stronger role in determining fire frequency. The mean fire interval for the study period (1895–1965) was 1.73 years, with a minimum of 1 year and a maximum of 15 years. This frequency contrasts with the complete fire exclusion that has prevailed in the area since 1965. These results have important implications for the maintenance and restoration of forested wetland ecosystems where the present fire regime differs dramatically from that under which the now-dominant forest vegetation developed.
Impacts of Climate Change on the Subduction of Mode and Intermediate Water Masses in the Southern Ocean
Authors: Downes Stephanie M. , Bindoff Nathaniel L. , Rintoul Stephen R. 
Published: December 2008

Abstract
Changes in the temperature, salinity, and subduction of Subantarctic Mode Water (SAMW) and Antarctic Intermediate Water (AAIW) between the 1950s and 2090s are diagnosed using the CSIRO Mark version 3.5 (Mk3.5) climate system model Caps under a CO2 forcing that reaches 860 ppm by the year 2100. These Southern Ocean upper-limb water masses ventilate the ocean interior, and changes in their properties have been related to climate change in numerous studies. Over time, the authors follow the low potential vorticity and salinity minimum layers describing SAMW and AAIW and find that the water column in the 2090s shifts to lighter densities by approximately 0.2 kg m−3. The model projects a reduction in the SAMW and AAIW annual mean subduction rates as a result of a combination of a shallower mixed layer, increased potential vorticity at the base of the mixed layer, and a net buoyancy gain. There is little change in the projected total volume of SAMW transported into the ocean interior via the subduction process; however, the authors find a significant decrease in the subduction of AAIW. The authors find overall that increases in the air–sea surface heat and freshwater fluxes mainly control the reduction in the mean loss of the SAMW and AAIW surface buoyancy flux when compared with the effect of changes supplied by Ekman transport because of increased zonal wind stress. In the A2 scenario, there are cooling and freshening on neutral density surfaces less than 27.3 kg m−3 in response to the warming and freshening observed at the ocean’s surface. The model projects deepening of density surfaces due to southward shifts in the outcrop regions and the downward displacement of these surfaces north of 45°S. The volume transport across 32°S is predicted to decrease in all three basins, with southward transport of SAMW and AAIW decreasing by up to 1.2 and 2.0 Sv (1 Sv ≡ 106 m3 s−1), respectively, in the Indian Ocean. These projected reductions in the subduction and transport of mode and intermediate water masses in the CSIRO Mk3.5 model could potentially decrease the absorption and storage of CO2 in the Southern Ocean.
Changes in Interannual Variability and Decadal Potential Predictability under Global Warming
Authors: Boer G. J. 
Published: December 2008

Abstract
Global warming will result in changes in mean temperature and precipitation distributions and is also expected to affect interannual and longer time-scale internally generated variability as a consequence of changes in climate processes and feedbacks. Multimodel estimates of changes in the variability of annual mean temperature and precipitation and in the variability of decadal potential predictability are investigated based on the collection of coupled climate model simulations in the Coupled Model Intercomparison Project phase 3 (CMIP3) data archive. Pooled, multimodel standard deviations of annual mean temperature and precipitation for the unforced preindustrial control climates of the models show good resemblance to observation-based estimates. The internally generated variability of the unforced climate is compared with that of the warmer conditions for simulations with the B1 and A1B climate change scenarios with forcing stabilized at year 2100 values. The standard deviation of annual mean temperature generally decreases with global warming at extratropical latitudes, with the largest percentage decreases over the oceans and largest percentage increases in the tropics and subtropics, although the magnitudes of these increases are smaller. The standard deviation of annual mean precipitation increases almost everywhere, with larger increases in the tropics. Changes are generally larger for the more strongly forced, warmer A1B scenario than for the B1 scenario. The characterization of decadal variability changes in terms of potential predictability stems from the growing interest in producing forecasts for the next decade or several decades. The potential predictability identifies that fraction of the long time-scale variability that is, at least potentially and with enough information, predictable on decadal time scales. There is a general decrease in the internally generated decadal variability of temperature and its potential predictability in the warmer world. The decrease tends to be largest where the decadal potential predictability of the unforced control climate is largest over the high-latitude oceans. The potential predictability of precipitation is small to begin with and generally decreases further. Therefore, there is a potential decrease in the decadal potential predictability of the internally generated component in a warmer world.
Evaluation of Long-Term Cloud-Resolving Model Simulations Using Satellite Radiance Observations and Multifrequency Satellite Simulators
Authors: Matsui Toshihisa , Zeng Xiping , Tao Wei-Kuo , Masunaga Hirohiko , Olson William S. , Lang Stephen 
Published: December 2008

Abstract
This paper proposes a methodology known as the Tropical Rainfall Measuring Mission (TRMM) Triple-Sensor Three-Step Evaluation Framework (T3EF) for the systematic evaluation of precipitating cloud types and microphysics in a cloud-resolving model (CRM). T3EF utilizes multisensor satellite simulators and novel statistics of multisensor radiance and backscattering signals observed from the TRMM satellite. Specifically, T3EF compares CRM and satellite observations in the form of combined probability distributions of precipitation radar (PR) reflectivity, polarization-corrected microwave brightness temperature (Tb), and infrared Tb to evaluate the candidate CRM.
T3EF is used to evaluate the Goddard Cumulus Ensemble (GCE) model for cases involving the South China Sea Monsoon Experiment (SCSMEX) and the Kwajalein Experiment (KWAJEX). This evaluation reveals that the GCE properly captures the satellite-measured frequencies of different precipitating cloud types in the SCSMEX case but overestimates the frequencies of cumulus congestus in the KWAJEX case. Moreover, the GCE tends to simulate excessively large and abundant frozen condensates in deep precipitating clouds as inferred from the overestimated GCE-simulated radar reflectivities and microwave Tb depressions. Unveiling the detailed errors in the GCE’s performance provides the better direction for model improvements.
Caught in the ACT: The Timing of Aspiration and Voicing in East Bengali
Authors: Mikuteit Simone , Reetz Henning 
Published: December 2008

East Bengali is a language that displays a four-way contrast of voiced/voiceless and aspirated/unaspirated oral stops and affricates in all word positions. Additionally, in intervocalic position there is a quantity contrast between long and short obstruents. In this production study we investigate medial palato-alveolar affricates and stops at the labial, dental, retroflex, and velar places of articulation and address the problems of VOT measurements. We introduce a different approach of measuring lag times, henceforth called after closure time (ACT). The results show that this approach can do away with the extra notion of breathy voice to distinguish between the voiced aspirates and unaspirates. Moreover, as a result of analyzing the aspirated stops and affricates, an additional term (superimposed aspiration—SA) had to be introduced. The results of combining the notions of ACT and SA show that aspiration, measured from the point of release, is timed equally for voiced and voiceless stops. However, the difference in voice emerges in a trade-off relationship between ACT and SA. The factors used for analysis were voice, aspiration, quantity, and place of articulation in correlation to closure duration, the length of the preceding vowel, ACT, and SA.
Specific activation of microRNA106b enables the p73 apoptotic response in chronic lymphocytic leukemia by targeting the ubiquitin ligase Itch for degradation
Authors: Sampath Deepa , Calin George A. , Puduvalli Vinay K. , Gopisetty Gopal , Taccioli Cristian , Liu Chang-Gong , Ewald Brett , Liu Chaomei , Keating Michael J. , Plunkett William 
Published: December 2008

Abstract
Chronic lymphocytic leukemia (CLL) is characterized by cells that exhibit dysfunctional apoptosis. Here, we show that deacetylase inhibition led to the E2F1- and myc-mediated transcriptional activation of the microRNA miR106b in primary CLL cells. Induction of miR106b was associated with a down-regulation in the levels of the E3-ubiquitin ligase Itch. Decreases in Itch protein levels were associated with a reciprocal accumulation of its proapoptotic substrate, TAp73 (p73), and induction of p53 up-regulated modulator of apoptosis (PUMA) mRNA and protein. This event was accompanied by mitochondrial dysfunction, processing of caspase-9, and apoptosis of CLL cells. Ectopic expression of miR106b in CLL cells demonstrated that Itch was a direct target of miR106b such that miR106b-induced decreases in Itch resulted in an accumulation of p73. Thus, our results identify a novel regulatory mechanism wherein microRNA regulate cell survival by mediating the posttranscriptional down-regulation of an ubiquitin ligase, leading to the induction of a proapoptotic regulator in malignant cells. Silencing of miRNA expression in CLL may selectively suppress proapoptotic pathways, providing such tumors with a survival advantage. Consequently, chemotherapeutic drugs that activate miR106b could initiate a p53-independent mechanism that targets CLL cells.
Prediction of regulatory elements in mammalian genomes using chromatin signatures
Authors: Won Kyoung-Jae , Chepelev Iouri , Ren Bing , Wang Wei 
Published: December 2008

Abstract

Background
Recent genomic scale survey of epigenetic states in the mammalian genomes has shown that promoters and enhancers are correlated with distinct chromatin signatures, providing a pragmatic way for systematic mapping of these regulatory elements in the genome. With rapid accumulation of chromatin modification profiles in the genome of various organisms and cell types, this chromatin based approach promises to uncover many new regulatory elements, but computational methods to effectively extract information from these datasets are still limited.

Results
We present here a supervised learning method to predict promoters and enhancers based on their unique chromatin modification signatures. We trained Hidden Markov models (HMMs) on the histone modification data for known promoters and enhancers, and then used the trained HMMs to identify promoter or enhancer like sequences in the human genome. Using a simulated annealing (SA) procedure, we searched for the most informative combination and the optimal window size of histone marks.

Conclusion
Compared with the previous methods, the HMM method can capture the complex patterns of histone modifications particularly from the weak signals. Cross validation and scanning the ENCODE regions showed that our method outperforms the previous profile-based method in mapping promoters and enhancers. We also showed that including more histone marks can further boost the performance of our method. This observation suggests that the HMM is robust and is capable of integrating information from multiple histone marks. To further demonstrate the usefulness of our method, we applied it to analyzing genome wide ChIP-Seq data in three mouse cell lines and correctly predicted active and inactive promoters with positive predictive values of more than 80%. The software is available at http://http:/nash.ucsd.edu/chromatin.tar.gz.
Genomic organization and phylogenetic utility of deer mouse (Peromyscus maniculatus) lymphotoxin-alpha and lymphotoxin-beta
Authors: Richens Tiffany , Palmer Aparna D~N , Prescott Joseph , Schountz Tony 
Published: December 2008

AbstractBackgroundDeer mice (Peromyscus maniculatus) are among the most common mammals in North America and are important reservoirs of several human pathogens, including Sin Nombre hantavirus (SNV). SNV can establish a life-long apathogenic infection in deer mice, which can shed virus in excrement for transmission to humans. Patients that die from hantavirus cardiopulmonary syndrome (HCPS) have been found to express several proinflammatory cytokines, including lymphotoxin (LT), in the lungs. It is thought that these cytokines contribute to the pathogenesis of HCPS. LT is not expressed by virus-specific CD4+T cells from infected deer mice, suggesting a limited role for this pathway in reservoir responses to hantaviruses.ResultsWe have cloned the genes encoding deer mouse LTα and LTβ and have found them to be highly similar to orthologous rodent sequences but with some differences in promoters elements. The phylogenetic analyses performed on the LTα, LTβ, and combined data sets yielded a strongly-supported sister-group relationship between the two murines (the house mouse and the rat). The deer mouse, a sigmodontine, appeared as the sister group to the murine clade in all of the analyses. High bootstrap values characterized the grouping of murids.ConclusionNo conspicuous differences compared to other species are present in the predicted amino acid sequences of LTα or LTβ; however, some promoter differences were noted in LTβ. Although more extensive taxonomic sampling is required to confirm the results of our analyses, the preliminary findings indicate that both genes (analyzed both separately and in combination) hold potential for resolving relationships among rodents and other mammals at the subfamily level.
Gemcitabine-based versusfluoropyrimidine-based chemotherapy with or without platinum in unresectable biliary tract cancer: a retrospective study
Authors: Kim Mi-Jung , Oh Do-Youn , Lee Se-Hoon , Kim Dong-Wan , Im Seock-Ah , Kim Tae-You , Heo Dae Seog , Bang Yung-Jue 
Published: December 2008

Abstract

Background
There is no standard palliative chemotherapy regimen in biliary tract cancers (BTC). Fluoropyrimidine or gemcitabine, with or without platinum, are most frequently used. We conducted this study to clarify the efficacy of palliative chemotherapy in BTC.

Methods
Patients with unresectable BTC treated with palliative chemotherapy between Oct 2001 and Aug 2006 at Seoul National University Hospital were reviewed retrospectively. Histologically confirmed cases of intrahepatic cholangiocarcinoma, gallbladder cancer, extrahepatic bile duct cancer, and ampulla of Vater carcinoma were enrolled. We analyzed the efficacy of regimens: gemcitabine (G) versus fluoropyrimidine (F) and with or without platinum (P).

Results
A total of 243 patients were enrolled. 159 patients (65%) were male and the median age of the patients was 60 years (range 26–81). Intrahepatic cholangiocarcinoma, gallbladder cancer, extrahepatic bile duct cancer, and ampulla of Vater carcinoma were 92, 72, 58, and 21 cases, respectively. The median progression free survival (PFS) was 4.3 months (95% CI, 3.7–4.9) and median overall survival (OS) was 8.7 months (95% CI, 7.4–10.0). Ninety-nine patients received G-based chemotherapy (94 GP, 5 G alone), and 144 patients received F-based chemotherapy (83 FP, 61 F alone). The response rate (RR), disease control rate (DCR), PFS and OS of G-based chemotherapy versus F-based chemotherapy were 16.7% vs. 19.5% (P = 0.591), 52.8% vs. 58.9% (P = 0.372), 4.0 months vs. 4.3 months (P = 0.816), and 7.8 months vs. 9.1 months (P = 0.848), respectively. Sixty-six patients received F or G without P, and 177 patients received F or G with P. The RR, DCR, PFS and OS of chemotherapy without P versus chemotherapy including P were 12.7% vs. 20.6% (P = 0.169), 46.0% vs. 60.6% (P = 0.049), 3.3 months vs. 4.4 months (P = 0.887), and 10.6 months vs. 8.1 months (P = 0.257), respectively.

Conclusion
In unresectable BTC, F-based and G-based chemotherapy showed similar efficacy in terms of RR, DCR, PFS and OS. The benefit of adding P to F or G was not significant except for DCR. Further prospective studies which define the efficacy of various chemotherapeutic regimens in BTC are warranted.