bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Catabolite Control Protein CcpA Binds to P
mga
and Influences Expression of the Virulence Regulator Mga in the Group A Streptococcus
Authors: Almengor Audry C. , Kinkel Traci L. , Day Stephanie J. , McIver Kevin S. 
Published: September 2007

ABSTRACT

Carbon catabolite repression (CCR) allows bacteria to alter metabolism in response to the availability of specific sugar sources, and increasing evidence suggests that CCR is involved in regulating virulence gene expression in many pathogens. A scan of the M1 SF370 group A streptococcus (GAS) genome using a
Bacillus subtilis
consensus identified a number of potential catabolite-responsive elements (
cre
) important for binding by the catabolite control protein A (CcpA), a mediator of CCR in gram-positive bacteria. Intriguingly, a putative
cre
was identified in the promoter region of
mga
upstream of its distal P1 start of transcription. Electrophoretic mobility shift assays showed that a His-CcpA fusion protein was capable of binding specifically to the
cre
in P
mga
in vitro. Deletion analysis of P
mga
using single-copy P
mga
-
gusA
reporter strains found that P
mga
P1 and its upstream
cre
were not required for normal autoregulated
mga
expression from P
mga
P2 as long as Mga was produced from its native locus. In fact, the P
mga
P1 region appeared to show a negative influence on P
mga
P2 in these studies. However, deletion of the
cre
at the native P
mga
resulted in a reduction of total
mga
transcripts as determined by real-time reverse transcription-PCR, supporting a role for CcpA in initial expression. Furthermore, normal transcriptional initiation from the P
mga
P1 start site alone was dependent on the presence of the
cre
. Importantly, inactivation of
ccpA
in the M6 GAS strain JRS4 resulted in a reduction in P
mga
expression and Mga protein levels in late-logarithmic-phase cell growth. These data support a role for CcpA in the early activation of the
mga
promoter and establish a link between CCR and Mga regulation in the GAS.
Identification of Promoters Recognized by RNA Polymerase-σ
E
Holoenzyme from
Thermus thermophilus
HB8
Authors: Shinkai Akeo , Ohbayashi Naomi , Terada Takaho , Shirouzu Mikako , Kuramitsu Seiki , Yokoyama Shigeyuki 
Published: September 2007

ABSTRACT

Thermus thermophilus
σ
E
, an extracytoplasmic function σ factor from the extremely thermophilic bacterium
Thermus thermophilus
HB8, bound to the RNA polymerase core enzyme and showed transcriptional activity. With the combination of in vitro transcription assay and GeneChip technology, we identified three promoters recognized by σ
E
. The predicted consensus promoter sequence for σ
E
is 5′-CA(A/T)(A/C)C(A/C)-N
15
-CCGTA-3′.
Site-Directed Disulfide Cross-Linking Shows that Cleft Flexibility in the Periplasmic Domain Is Needed for the Multidrug Efflux Pump AcrB of
Escherichia coli
Authors: Takatsuka Yumiko , Nikaido Hiroshi 
Published: September 2007

ABSTRACT

Escherichia coli
AcrB is a multidrug efflux transporter that recognizes multiple toxic chemicals having diverse structures. Recent crystallographic studies of the asymmetric trimer of AcrB suggest that each protomer in the trimeric assembly goes through a cycle of conformational changes during drug export. However, biochemical evidence for these conformational changes has not been provided previously. In this study, we took advantage of the observation that the external large cleft in the periplasmic domain of AcrB appears to become closed in the crystal structure of one of the three protomers, and we carried out in vivo cross-linking between cysteine residues introduced by site-directed mutagenesis on both sides of the cleft, as well as at the interface between the periplasmic domains of the AcrB trimer. Double-cysteine mutants with mutations in the cleft or the interface were inactive. The possibility that this was due to the formation of disulfide bonds was suggested by the restoration of transport activity of the cleft mutants in a
dsbA
strain, which had diminished activity to form disulfide bonds in the periplasm. Furthermore, rapidly reacting, sulfhydryl-specific chemical cross-linkers, methanethiosulfonates, inactivated the AcrB transporter with double-cysteine residues in the cleft expressed in
dsbA
cells, and this inactivation could be observed within a few seconds after the addition of a cross-linker in real time by increased ethidium influx into the cells. These observations indicate that conformational changes, including the closure of the external cleft in the periplasmic domain, are required for drug transport by AcrB.
Resistance to Bacitracin in
Bacillus subtilis
: Unexpected Requirement of the BceAB ABC Transporter in the Control of Expression of Its Own Structural Genes
Authors: Bernard Remi , Guiseppi Annick , Chippaux Marc , Foglino Maryline , Denizot François 
Published: September 2007

ABSTRACT

The
Bacillus subtilis
BceAB ABC transporter involved in a defense mechanism against bacitracin is composed of a membrane-spanning domain and a nucleotide-binding domain. Induction of the structural
bceAB
genes requires the BceR response regulator and the BceS histidine kinase of a signal transduction system. However, despite the presence of such a transduction system and of bacitracin, no transcription from an unaltered
bceA
promoter is observed in cells lacking the BceAB transporter. Expression in
trans
of the BceAB transporter in these
bceAB
cells restores the transcription from the
bceA
promoter. Cells possessing a mutated nucleotide-binding domain of the transporter are also no longer able to trigger transcription from the
bceA
promoter in the presence of bacitracin, although the mutated ABC transporter is still bound to the membrane. In these cells, expression of the
bceA
promoter can no longer be detected, indicating that the ABC transporter not only must be present in the cell membrane, but also must be expressed in a native form for the induction of the
bceAB
genes. Several hypotheses are discussed to explain the simultaneous need for bacitracin, a native signal transduction system, and an active BceAB ABC transporter to trigger transcription from the
bceA
promoter.
Hydroclimatic Trends in the Mississippi River Basin from 1948 to 2004
Authors: Qian Taotao , Dai Aiguo , Trenberth Kevin E. 
Published: October 2007

AbstractThe trends of the surface water and energy budget components in the Mississippi River basin from 1948 to 2004 are investigated using a combination of hydrometeorological observations and observation-constrained simulations of the land surface conditions using the latest version of the Community Land Model version 3 (CLM3). The atmospheric forcing data for the CLM3 were constructed by adding the intramonthly variations from the 6-hourly National Centers for Environmental Prediction–National Center for Atmospheric Research (NCEP–NCAR) reanalysis to observation-based analyses of monthly precipitation, surface air temperature, and cloud cover. The model-based analysis suggests that, for the surface water budget, the observed increase in basin-averaged precipitation is compensated by increases in both runoff and evapotranspiration. For the surface energy budget, the decrease of net shortwave radiation associated with observed increases in cloudiness is compensated by decreases in both net longwave radiation and sensible heat flux, while the latent heat flux increases in association with wetter soil conditions. Both the simulated surface water and energy budgets support the view that evapotranspiration has increased in the Mississippi River basin from 1948 to 2004. Sensitivity experiments show that the precipitation change dominates the evapotranspiration trend, while the temperature and solar radiation changes have only small effects. Large spatial variations within the Mississippi River basin and the contiguous United States are also found. However, the increased evapotranspiration is ubiquitous despite spatial variations in hydrometeorology.
Mechanisms of Summertime Subtropical Southern Indian Ocean Sea Surface Temperature Variability: On the Importance of Humidity Anomalies and the Meridional Advection of Water Vapor*
Authors: Chiodi A. M. , Harrison D. E. 
Published: October 2007

Abstract
It is well known that some austral summertime subtropical Indian Ocean sea surface temperature (SST) variability correlates with rainfall over certain regions of Africa that depend on rainfall for their economic well-being. Recent studies have determined that this SST variability is at least partially driven by latent heat flux variability, but the mechanism has not been fully described. Here, the mechanism that drives this SST variability is reexamined using analyses of operational air–sea fluxes, ocean mixed layer modeling, and simple atmospheric boundary layer physics. The SST variability of interest is confirmed to be mainly driven by latent heat flux variability, which is shown, for the first time, to be mainly caused by near-surface humidity variability. This humidity variability is then shown to be fundamentally driven by the anomalous meridional advection of water vapor. The meridional wind anomalies of interest are subsequently found to occur when the subtropical atmospheric anticyclone is preferentially located toward one of the sides (east/west) of the basin.
Residence and fractionation of rare earth elements during kaolinization of alkaline peraluminous granites in NW Spain
Authors: Galán E. , Fernández-Caliani J. C. , Miras A. , Aparicio P. , Márquez M. G. 
Published: October 2007

AbstractA geochemical and mineralogical study has allowed us to address the factors controlling distribution pattern, residence and behaviour of rare earth elements (REE) during kaolinization of Variscan granitoids in NW Spain. Mineral composition of the deeply weathered samples is dominated by kaolinite, with minor amounts of quartz, muscovite-illite, alkaline feldspar and traces of resistant minerals (rutile, ilmenite, zircon and monazite). Variable amounts of Si, Na, Ca, K, Rb, Cs, Ba, U and P were lost from the weathering profile, as a result of feldspars, mica and apatite breakdown, whereas Al, Fe, Ti, Zr, Th, Hf and REE were concentrated in the residual kaolin. Chondrite-normalized REE patterns of the kaolins show an overall enrichment of light REE (LaN/SmN = 1.22–2.53), heavy REE depletion (GdN/YbN = 2.42–15.10) and a strong negative Eu anomaly (Eu/Eu* = 0.11–0.25), probably inherited from the parent granite. Nevertheless, the normalization to the parent granite reveals some REE fractionation and increasing positive Eu anomalies with advancing weathering, in response to the breakdown of feldspars. Different grain-size fractions show similar REE distribution patterns, but differ in concentration levels. Although the fine fractions are the most important REE reservoir, there is no positive correlation with clay mineralogy. The correlative behaviour among P2O5, Th and REE in the <2 mm fraction suggests that monazite plays a dominant role controlling the REE budget in the weathering profile.
Validation of ICD-9-CM/ICD-10 coding algorithms for the identification of patients with acetaminophen overdose and hepatotoxicity using administrative data
Authors: Myers Robert P , Leung Yvette , Shaheen Abdel Aziz M , Li Bing 
Published: October 2007

Abstract
Background
Acetaminophen overdose is the most common cause of acute liver failure (ALF). Our objective was to develop coding algorithms using administrative data for identifying patients with acetaminophen overdose and hepatic complications.

Methods
Patients hospitalized for acetaminophen overdose were identified using population-based administrative data (1995–2004). Coding algorithms for acetaminophen overdose, hepatotoxicity (alanine aminotransferase >1,000 U/L) and ALF (encephalopathy and international normalized ratio >1.5) were derived using chart abstraction data as the reference and logistic regression analyses.

Results
Of 1,776 potential acetaminophen overdose cases, the charts of 181 patients were reviewed; 139 (77%) had confirmed acetaminophen overdose. An algorithm including codes 965.4 (ICD-9-CM) and T39.1 (ICD-10) was highly accurate (sensitivity 90% [95% confidence interval 84–94%], specificity 83% [69–93%], positive predictive value 95% [89–98%], negative predictive value 71% [57–83%], c-statistic 0.87 [0.80–0.93]). Algorithms for hepatotoxicity (including codes for hepatic necrosis, toxic hepatitis and encephalopathy) and ALF (hepatic necrosis and encephalopathy) were also highly predictive (c-statistics = 0.88). The accuracy of the algorithms was not affected by age, gender, or ICD coding system, but the acetaminophen overdose algorithm varied between hospitals (c-statistics 0.84–0.98; P = 0.003).

Conclusion
Administrative databases can be used to identify patients with acetaminophen overdose and hepatic complications. If externally validated, these algorithms will facilitate investigations of the epidemiology and outcomes of acetaminophen overdose.
Angiotensin II receptor blockers decreased blood glucose levels: a longitudinal survey using data from electronic medical records
Authors: Kitamura Noboru , Takahashi Yasuo , Yamadate Shuukoh , Asai Satoshi 
Published: September 2007

Abstract

Background
A beneficial effect on glucose metabolism is reported with angiotensin receptor blocker (ARB) treatment of hypertension. The effect on blood glucose level during the course of treatment with ARBs in clinical cases is uncertain. Our objectives were to survey the changes in glucose and HbA1c levels in patients with hypertension over a one-year period, and to study the correlations between these values and the time after the start of ARB therapy.

Methods
We conducted a retrospective longitudinal survey of blood glucose and HbA1c measurements in Japanese patients aged ≥20 years with newly diagnosed hypertension but without diabetes, who had received ARB monotherapy with candesartan cilexetil, losartan potassium, olmesartan medoxomil, telmisartan, or valsartan during the period from December 2004 to November 2005. Data including 2465 measurements of non-fasting blood glucose in 485 patients and 457 measurements of HbA1c in 155 patients were obtained from electronic medical records of Nihon University School of Medicine. Linear mixed effects models were used to analyze the relationship between these longitudinal data of blood examinations and covariates of patient age, sex, medication, and duration of ARB therapy.

Results
Casual blood glucose level was associated with the duration of treatment (P < 0.0001), but not with age, sex, or medication. Blood glucose level was significantly decreased during the periods of 0~3 months (P < 0.0001) and 3~6 months (P = 0.0081) compared with baseline, but was not significantly different between 6~12 months and baseline. There was no association between HbA1c level and covariates of sex, age, medication and duration of treatment.

Conclusion
Our findings provide new clinical evidence that the effects of ARBs on glucose metabolism may change during the course of treatment, suggesting a blood glucose-lowering effect in the short-term after the start of treatment.
A pharmacodynamic analysis of resistance trends in pathogens from patients with infection in intensive care units in the United States between 1993 and 2004
Authors: Eagye Kathryn J , Nicolau David P , Lockhart Shawn R , Quinn John P , Doern Gary V , Gallagher Gale , Abramson Murray A 
Published: October 2007

Abstract

Background
Increasing nosocomial pathogen resistance to available antimicrobial agents is of growing concern. While higher MICs can diminish antimicrobial effectiveness, dose adjustments often mitigate this effect. This study's objective was to ascertain whether MICs among major pathogens in the ICU to several commonly used agents have increased enough to significantly impact their ability to achieve bactericidal effect.

Methods
Cefepime, ceftriaxone, imipenem and piperacillin-tazobactam MICs were determined with 74,394 Gram-negative bacilli obtained from ICU patients with various infections in the US between 1993 and 2004. Results were grouped into four 3-year periods. The predicted cumulative fraction of response (CFR) was estimated based on patient-derived pharmacokinetic values and Monte Carlo simulation. Trends in CFR over the four study periods were assessed using the Cochran-Armitage test. The primary analysis included all organisms combined; Pseudomonas aeruginosa and Acinetobacter species were also evaluated individually.

Results
In the primary analysis, imipenem 500 mg q6h showed CFRs from 87% to 90% across all four study periods, with a trend toward slightly improved bactericidal target attainment (p < 0.01). CFRs for cefepime 2 g q12h and piperacillin-tazobactam 4.5 g q6h both declined by 2% (p < 0.01 and p < 0.05, respectively), reflecting upward shifts in the underlying MIC distributions. Ceftriaxone had <52% CFR for all regimens in all periods, with no significant trend. Against P. aeruginosa, significant declines in CFR were seen for (range, p-value): imipenem 1 g q8h (82%–79%, p < 0.01), cefepime 1 g q12h (70%–67%, p < 0.01), cefepime 2 g q12h (84%–82%, p < 0.05), piperacillin-tazobactam 3.375 g q6h (76%–73%, p < 0.01), piperacillin-tazobactam 4.5 g q8h (71%–68%, p < 0.01), and piperacillin-tazobactam 4.5 g q6h (80%–77%, p < .01). Against Acinetobacter spp., all regimens of imipenem, cefepime and piperacillin-tazobactam showed significant declines in CFR over time (p < 0.01).

Conclusion
Our observations suggest that as a result of increasing antimicrobial resistance among ICU pathogens in the US, drug effectiveness, assessed as a function of individual agents' ability to attain pharmacodynamic targets, has declined, especially with P. aeruginosa and Acinetobacter spp. Cefepime 2 g q8h and imipenem were the most potent agents against these species, respectively. More aggressive dosing of all of the agents characterized could preserve their clinical utility, but this must be balanced with safety and tolerability issues by the physician.
Activities contributing to energy expenditure among Guatemalan adults
Authors: Gregory Cria O , Ramirez-Zea Manuel , Martorell Reynaldo , Stein Aryeh D 
Published: October 2007

Abstract

Background
Guatemala has experienced a substantial increase in overweight and obesity in recent years, yet physical activity patterns and consequent energy expenditure are largely unexplored in this population.

Methods
To describe overall physical activity levels (PAL) and activities contributing to daily energy expenditure, we analyzed time spent in daily activities as reported by 985 women and 819 men, living in rural and urban areas of Guatemala in 2002–04.

Results
Physical activity levels recommended to prevent obesity (PAL ≥ 1.70) differed by residence/occupation among men (agricultural-rural: 77%; nonagricultural-rural: 36%; urban: 24%; P < 0.01), but not women (rural: 2%; urban: 3%; P = 0.5). Median energy expenditure was higher among agricultural-rural men (44 MET*h/d; MET = metabolic equivalent) compared to nonagricultural-rural (37 MET*h/d) and urban men (35 MET*h/d; P < 0.01); energy expenditure was slightly lower among rural compared to urban women (34 MET*h/d vs. 35 MET*h/d; P < 0.01). Occupation was the largest contributor to energy expenditure (19–24 MET*h/d); among women and nonagricultural-rural and urban men this was primarily of a light intensity. Energy expenditure in sedentary activities ranged from 2 MET*h/d among rural women to 6 MET*h/d among agricultural-rural men. Any sports/exercise time was reported by 35% and 5% of men and women, respectively. Nevertheless, the majority of participants believed they were significantly active to stay healthy.

Conclusion
Overall, energy expenditure was low in the population not dedicated to agricultural occupations; an increased focus on active leisure-time behaviors may be needed to counterbalance reductions in energy expenditure consequent to sedentarization of primary occupations.
Changing population characteristics, effect-measure modification, and cancer risk factor identification
Authors: Slattery Martha L , Murtaugh Maureen A , Quesenberry Charles , Caan Bette J , Edwards Sandra , Sweeney Carol 
Published: October 2007

AbstractEpidemiologic studies have identified a number of lifestyle factors, e.g. diet, obesity, and use of certain medications, which affect risk of colon cancer. However, the magnitude and significance of risk factor-disease associations differ among studies. We propose that population trends of changing prevalence of risk factors explains some of the variability between studies when factors that change prevalence also modify the effect of other risk factors. We used data collected from population-based control who were selected as study participants for two time periods, 1991–1994 and 1997–2000, along with data from the literature, to examine changes in the population prevalence of aspirin and non-steroidal anti-inflammatory medication (NSAID) use, obesity, and hormone replacement therapy (HRT) over time. Data from a population-based colon cancer case-control study were used to estimate effect-measurement modification among these factors. Sizeable changes in aspirin use, HRT use, and the proportion of the population that is obese were observed between the 1980s and 2000. Use of NSAIDs interacted with BMI and HRT; HRT use interacted with body mass index (BMI). We estimate that as the prevalence of NSAIDs use changed from 10% to almost 50%, the colon cancer relative risk associated with BMI >30 would change from 1.3 to 1.9 because of the modifying effect of NSAIDs. Similarly, the relative risk estimated for BMI would increase as the prevalence of use of HRT among post-menopausal women increased. In conclusion, as population characteristics change over time, these changes may have an influence on relative risk estimates for colon cancer for other exposures because of effect-measure modification. The impact of population changes on comparability between epidemiologic studies can be kept to a minimum if investigators assess exposure-disease associations within strata of other exposures, and present results in a manner that allows comparisons across studies. Effect-measure modification is an important component of data analysis that should be evaluated to obtain a complete understanding of disease etiology.
Management of small bowel volvulus in a patient with simultaneous pancreas-kidney transplantation (SPKT): a case report
Authors: Aydin Unal , Yazici Pinar , Toz Huseyin , Hoscoskun Cuneyt , Coker Ahmet 
Published: September 2007

Abstract
There are several surgical complications which can occur following simultaneous pancreas-kidney transplantation (SPKT). Although intestinal obstruction is known to be a common complication after any type of abdominal surgery, the occurrence of small bowel volvulus, which is one of the rare causes of intestinal obstruction, following SPKT has not been published before. A 24-year-old woman suffering from type I diabetes mellitus with complications of nephropathy resulting in end stage renal disease (ESRD), neuropathy and retinopathy underwent SPKT. On the postoperative month 5, she was brought to the emergency service due to abdominal distention with mild abdominal pain. After laboratory research and diagnostic radiological tests had been carried out, she underwent exploratory laparotomy to determine the pathology for acute abdominal symptoms. Intra-operative observation revealed the presence of an almost totally ischemic small bowel which had occurred due to clockwise rotation of the mesentery. Initially, simple derotation was performed to avoid intestinal resection because of her risky condition, particularly for short bowel syndrome, and subsequent intestinal response was favorable. Thus, surgical treatment was successfully employed to solve the problem without any resection procedure. The patient's postoperative follow-up was uneventful and she was discharged from hospital on postoperative day 7. According to our clinical viewpoint, this study emphasizes that if there is even just a suspicion of acute abdominal problem in a patient with SPKT, surgical intervention should be promptly performed to avoid any irreversible result and to achieve a positive outcome.