bluuebunny/crossref_metadata_2025_split huggingface dataset:
The management of large perforations of duodenal ulcers
Authors: Gupta Sanjay , Kaushik Robin , Sharma Rajeev , Attri Ashok 
Published: June 2005

Abstract
Background
Duodenal ulcer perforations are a common surgical emergency, but literature is silent on the exact definition, incidence, management and complications of large perforations of duodenal ulcers.

Methods
The case files of 162 patients who underwent emergency laparotomy for duodenal ulcer perforations over a period of three years (2001 – 2003) were retrospectively reviewed and sorted into groups based on the size of the perforations – one group was defined as 'small 'perforations (less than 1 cm in diameter), another 'large' (when the perforation was more than 1 cm but less than 3 cms), and the third, 'giant'(when the perforation exceeded 3 cm). These groups of patients were then compared with each other in regard to the patient particulars, duration of symptoms, surgery performed and the outcome.

Results
A total of 40 patients were identified to have duodenal ulcer perforations more than 1 cm in size, thus accounting for nearly 25 % of all duodenal ulcer perforations operated during this period. These patients had a significantly higher incidence of leak, morbidity and mortality when compared to those with smaller perforations.

Conclusion
There are three distinct types of perforations of duodenal ulcers that are encountered in clinical practice. The first, are the 'small' perforations that are easy to manage and have low morbidity and mortality. The second are the 'large' perforations, that are also not uncommon, and omental patch closure gives the best results even in this subset of patients. The word 'giant' should be reserved for perforations that exceed 3 cms in diameter, and these are extremely uncommon.
Pruritus in hemodialysis patients
Authors: Akhyani Maryam , Ganji Mohammad-Reza , Samadi Nasrin , Khamesan Behnaz , Daneshpazhooh Maryam 
Published: June 2005

Abstract
Background
Pruritus is one of the most bothersome symptoms in patients on maintenance hemodialysis (HD), however little progress is seen in our understanding of its pathogenesis. The aim of this study was to evaluate the frequency of pruritus in HD patients in Tehran, Iran, and to correlate its presence and intensity with relevant clinical and laboratory parameters.

Methods
One hundred sixty-seven patients on maintenance HD at three out-patient HD units were enrolled in the study. Itch intensity was scored as mild, moderate and severe. Some relevant clinical and laboratory parameters (age, sex, xerosis, presence of neuropathy, duration of dialysis, history of atopy and laboratory findings including hematocrit, creatinine, urea, calcium, phosphorus, parathyroid hormone [PTH] and alkaline phosphatase) were evaluated.

Results
Pruritus was found in 41.9% of patients. The intensity of itching was mild, moderate and severe, in 51.4%, 11.4% and 37.7% of patients, respectively. In 22 patients (31.4%) pruritus intensified during and after dialysis. There was no significant difference in the serum levels of creatinine, blood urea nitrogen, calcium, phosphorus, alkaline phosphatase, PTH and hematocrit between patients with and without pruritus. Age, sex, xerosis, underlying renal disease, history of atopy and duration of haemodialysis were not significantly different between the two groups. However, neuropathy was significantly more common in the pruritic group (63.8% versus 42.1%) (pv = 0.006).

Conclusion
Clinical neuropathy was the only significant finding in the pruritic group in our study. This finding justifies further research on nerve function and neurotransmitters in hemodialysis patients and the introduction of new drugs targeting neuropathy.
Do medical outpatients want 'out of hours' clinics?
Authors: Feeney Claire L , Roberts Nicola J , Partridge Martyn R 
Published: June 2005

Abstract

Background
Patient choice is a major theme in current healthcare delivery. Little is known about patients' wishes regarding the timing of medical outpatient clinics.

Methods
A questionnaire survey of 300 sequential patients attending cardiac and respiratory clinics to determine patients preferences for out of hours and weekend outpatient clinics. (Out of hours defined as a clinic after 5 pm on Mon – Fri)

Results
Two hundred and 64 patients completed the survey of which 165 (62.5%) wanted either an out of hours clinics or a weekend clinic. Sixty four (38.8%) specifically stated that this was because of work commitments but for many others, the reasons given were easy to justify.

Conclusion
Current provision for outpatient consultation may not be convenient for many patients with heart and lung disease. A fuller evaluation of the cost and benefits of more flexible clinic hours is now needed.
Clustered local transmission and asymptomatic Plasmodium falciparum and Plasmodium vivax malaria infections in a recently emerged, hypoendemic Peruvian Amazon community
Authors: Branch OraLee , Casapia W Martin , Gamboa Dionicia V , Hernandez Jean N , Alava Freddy F , Roncal Norma , Alvarez Eugenia , Perez Enrique J , Gotuzzo Eduardo 
Published: June 2005

Abstract

Background
There is a low incidence of malaria in Iquitos, Peru, suburbs detected by passive case-detection. This low incidence might be attributable to infections clustered in some households/regions and/or undetected asymptomatic infections.

Methods
Passive case-detection (PCD) during the malaria season (February-July) and an active case-detection (ACD) community-wide survey (March) surveyed 1,907 persons. Each month, April-July, 100-metre at-risk zones were defined by location of Plasmodium falciparum infections in the previous month. Longitudinal ACD and PCD (ACP+PCD) occurred within at-risk zones, where 137 houses (573 persons) were randomly selected as sentinels, each with one month of weekly active sampling. Entomological captures were conducted in the sentinel houses.

Results
The PCD incidence was 0.03 P. falciparum and 0.22 Plasmodium vivax infections/person/malaria-season. However, the ACD+PCD prevalence was 0.13 and 0.39, respectively. One explanation for this 4.33 and 1.77-fold increase, respectively, was infection clustering within at-risk zones and contiguous households. Clustering makes PCD, generalized to the entire population, artificially low. Another attributable-factor was that only 41% and 24% of the P. falciparum and P. vivax infections were associated with fever and 80% of the asymptomatic infections had low-density or absent parasitaemias the following week. After accounting for asymptomatic infections, a 2.6-fold increase in ACD+PCD versus PCD was attributable to clustered transmission in at-risk zones.

Conclusion
Even in low transmission, there are frequent highly-clustered asymptomatic infections, making PCD an inadequate measure of incidence. These findings support a strategy of concentrating ACD and insecticide campaigns in houses adjacent to houses were malaria was detected one month prior.
Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach
Authors: Boulesteix Anne-Laure , Strimmer Korbinian 
Published: June 2005

Abstract

Background
The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard microarray experiments it is not possible to measure the transcription factor activities (TFAs) directly, as their own transcription levels are subject to post-translational modifications.

Results
Here we propose a statistical approach based on partial least squares (PLS) regression to infer the true TFAs from a combination of mRNA expression and DNA-protein binding measurements. This method is also statistically sound for small samples and allows the detection of functional interactions among the transcription factors via the notion of "meta"-transcription factors. In addition, it enables false positives to be identified in ChIP data and activation and suppression activities to be distinguished.

Conclusion
The proposed method performs very well both for simulated data and for real expression and ChIP data from yeast and E. Coli experiments. It overcomes the limitations of previously used approaches to estimating TFAs. The estimated profiles may also serve as input for further studies, such as tests of periodicity or differential regulation. An R package "plsgenomics" implementing the proposed methods is available for download from the CRAN archive.
Binding of Estrogen Receptor β to Estrogen Response Element in Situ Is Independent of Estradiol and Impaired by Its Amino Terminus
Authors: Huang Jing , Li Xiaodong , Maguire Casey A. , Hilf Russell , Bambara Robert A. , Muyan Mesut 
Published: June 2005

Abstract
The functions of 17β-estradiol (E2) are mediated by estrogen receptor (ER) α and β. ERs display similar DNA- and ligand-binding properties in vitro. However, ERβ shows lower transcriptional activity than ERα from the estrogen response element (ERE)-dependent signaling. We predicted that distinct amino termini contribute to differences in transcription efficacies of ERs by affecting in situ ER-ERE interactions. We used chromatin immunoprecipitation and a novel in situ ERE competition assay, which is based on the ability of ER to compete for ERE binding with a designer activator that constitutively induces transcription from an ERE-driven reporter construct. Interference of activator-mediated transcription by unliganded or liganded ERs was taken as an indication of ER-ERE interaction. Results revealed that ERs interacted with ERE similarly in the absence of E2. However, E2 enhanced the ERE binding of ERα but not that of ERβ. The removal of the amino terminus increased the ERβ-ERE interaction independent of E2. The ERβ amino terminus also prevented E2-mediated enhancement of the chimeric ERα-ERE interaction. Thus, the amino terminus of ERβ impairs the binding of ERβ to ERE. The abrogation of ligand-dependent activation function 2 of the amino-terminally truncated ERβ resulted in the manifestation of E2 effect on ERβ-ERE interaction. This implies that E2-mediated enhancement of ERβ-ERE interaction is masked by the activation function 2, whereas the intact amino terminus is a dominant region that decreases the binding of ERβ to ERE. Thus, ERβ-ERE interaction is independent of E2 and is impaired by its amino terminus. These findings provide an additional explanation for differences between ERα and ERβ functions that could differentially affect the physiology and pathophysiology of E2 signaling.
Molecular Analysis of a Congenital Iodide Transport Defect: G543E Impairs Maturation and Trafficking of the Na+/I− Symporter
Authors: De la Vieja Antonio , Ginter Christopher S. , Carrasco Nancy 
Published: June 2005

Abstract
The Na+/I− symporter (NIS) is a key membrane glycoprotein that mediates active I− transport in the thyroid and other tissues. Upon isolation of the cDNA encoding NIS, 10 NIS mutations that cause congenital iodide transport defect have been identified. Three of these mutations (T354P, G395R, and Q267E) have been thoroughly characterized at the molecular level. All three NIS mutant proteins are correctly targeted to the plasma membrane; however, whereas Q267E displays minimal activity, T354P and G395R are inactive. Here, we show that in contrast to these mutants, G543E NIS matures only partially and is retained intracellularly; thus, it is not targeted properly to the cell surface, apparently because of faulty folding. These findings indicate that the G543 residue plays significant roles in NIS maturation and trafficking. Remarkably, NIS activity was rescued by small neutral amino acid substitutions (volume &lt; 129 Å3) at this position, suggesting that G543 is in a tightly packed region of NIS.
Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS
Authors: Liang Yunfei , Wan Ying , Qiu Li-wen , Zhou Jingran , Ni Bing , Guo Bo , Zou Qiang , Zou Liyun , Zhou Wei , Jia Zhengcai , Che Xiao-yan , Wu Yuzhang 
Published: June 2005

Abstract
Background: The epidemic outbreak of severe acute respiratory syndrome (SARS) posed a worldwide threat to public health and economic stability. Although the pandemic has been contained, concerns over its recurrence remain. It is essential to identify specific diagnostic agents and antiviral vaccine candidates to fight this highly contagious disease.
Methods: We generated 14 monoclonal antibodies (mAbs) specific to the SARS coronavirus (SARS-CoV) nucleocapsid (N) protein and used these to thoroughly map the N protein antigenic determinants. We identified the immunodominant antigenic sites responsible for the antibodies in sera from SARS patients and antisera from small animals and differentiated the linear from the conformational antibody-combining sites comprising the natural epitopes by use of yeast surface display.
Results: We identified 5 conformational and 3 linear epitopes within the entire N protein; 3 conformational and 3 linear epitopes were immunodominant. The antibody responses to the N protein fragments in mammalian sera revealed that 3 regions of the N protein are strong antigenic domains. We expanded the specificity of the N protein epitope and identified 4 novel conformational epitopes (amino acids 1–69, 68–213, 212–341, and 337–422).
Conclusion: The antigenic structures identified for the SARS-CoV N protein, the epitope-specific mAbs, and the serum antibody profile in SARS patients have potential use in the clinical diagnosis and understanding of the protective immunity to SARS-CoV.
Genetic Interaction of Lobe With Its Modifiers in Dorsoventral Patterning and Growth of the Drosophila Eye
Authors: Singh Amit , Chan Jeeder , Chern Joshua J , Choi Kwang-Wook 
Published: June 2005

Abstract
Dorsoventral (DV) patterning is essential for growth of the Drosophila eye. Recent studies suggest that ventral is the default state of the early eye, which depends on Lobe (L) function, and that the dorsal fate is established later by the expression of the dorsal selector gene pannier (pnr). However, the mechanisms of regulatory interactions between L and dorsal genes are not well understood. For studying the mechanisms of DV patterning in the early eye disc, we performed a dominant modifier screen to identify additional genes that interact with L. The criterion of the dominant interaction was either enhancement or suppression of the L ventral eye loss phenotype. We identified 48 modifiers that correspond to 16 genes, which include fringe (fng), a gene involved in ventral eye patterning, and members of both Hedgehog (Hh) and Decapentaplegic (Dpp) signaling pathways, which promote L function in the ventral eye. Interestingly, 29% of the modifiers (6 enhancers and 9 suppressors) identified either are known to interact genetically with pnr or are members of the Wingless (Wg) pathway, which acts downstream from pnr. The detailed analysis of genetic interactions revealed that pnr and L mutually antagonize each other during second instar of larval development to restrict their functional domains in the eye. This time window coincides with the emergence of pnr expression in the eye. Our results suggest that L function is regulated by multiple signaling pathways and that the mutual antagonism between L and dorsal genes is crucial for balanced eye growth.
Maximum Sustainable Yield and Bycatch Minimization “to the Extent Practicable”
Authors: Powers Joseph E. 
Published: June 2005

Abstract
Two goals of marine fisheries management in the USA are (1) to achieve maximum sustainable yield (MSY) and (2) to minimize bycatch “to the extent practicable.” However, the determination of MSY is contingent on the selectivity of the various fisheries involved and the mix of these fisheries that managers desire. I compare several methods of computing MSY and associated parameters that involve alternative assumptions about the balance between target and bycatch fisheries. These methods were evaluated using a deterministic population simulation model. Additionally, biological risk was evaluated by computing relative spawning levels in the presence and absence of bycatch. While the choice of the method will largely be driven by socioeconomic factors, some implications for management are discussed. Before analysts can calculate MSY and associated parameters, managers must determine their desired mix of fishing and the definition of “to the extent practicable.”
Seasonal Movement Patterns of Stream‐Dwelling Rainbow Trout in North‐Central British Columbia, Canada
Authors: Mellina Eric , Hinch Scott G. , MacKenzie Kirsten D. , Pearson Greg 
Published: June 2005

AbstractMovement forms an important part of salmonid life histories, and although previous studies have largely concluded that the majority of stream‐dwelling salmonids are sedentary, the paradigm of restricted movement has been questioned by recent findings. We conducted a 3‐year study to examine the seasonal movement patterns of rainbow trout Oncorhynchus mykiss in three small, lake‐headed streams situated in north‐central British Columbia and to determine whether movement was related to environmental conditions. Two of the three streams were subjected to streamside clear‐cut logging during the second year. The trout in our study streams generally remained sedentary during the summer, autumn, and winter seasons for a period of approximately 1–2 years before undertaking long‐range (>372–607‐m) movements during springtime. These springtime long‐range movements were most closely linked to stream discharge, as they generally ceased with the onset of summer low flows (<10–20 L/s), but they did not resume in the autumn despite increasing flows. Links between movement patterns and stream temperature were less clear, as long‐range movements occurred over a wide range (0–30°C) of temperatures. The predominant direction of long‐range movements was lakeward. All three streams supported relatively large populations of resident trout during the summer and autumn months; densities of 0.4–1.0 trout/m2 were primarily associated with age‐0 to age‐2 fish. Our data provide insights into how the movement patterns and life history strategies of stream‐dwelling rainbow trout are intertwined, as well as how the timing of sampling efforts may be an important factor when assessing whether stream‐dwelling fish are sedentary or mobile.
Ecological Consequences of Swim Bladder Noninflation for Larval Yellow Perch
Authors: Czesny Sergiusz J. , Graeb Brian D. S. , Dettmers John M. 
Published: June 2005

AbstractSwim bladder inflation is a fundamental developmental step during the larval stage of many fishes. Although the physiological mechanisms of swim bladder inflation are well documented, the ecological costs of noninflation are poorly understood. If high proportions of newly hatched fish larvae fail to inflate their swim bladders and swim bladder noninflation negatively affects individual survival probability, the population‐level effects could be dramatic. To determine whether fish larvae without inflated swim bladders perform differently than their conspecifics with inflated swim bladders, we compared growth rate, feeding selectivity and efficiency, susceptibility to predation, oxygen consumption, and starvation mortality of two size‐classes of larval yellow perch Perca flavescens with and without inflated swim bladders in a series of experiments. In the laboratory, growth rates of yellow perch with uninflated swim bladders were less than those for fish with inflated swim bladders, and fish with inflated swim bladders fed more efficiently than those with uninflated swim bladders. In addition, predation risk, metabolic demands, and vulnerability to starvation mortality were higher in fish lacking an inflated swim bladder than in fish with an inflated swim bladder. In the field, individuals with uninflated swim bladders were smaller than their conspecifics with inflated swim bladders. The relative occurrence of yellow perch larvae without inflated swim bladders declined as the sampling season progressed until only fish with inflated swim bladders were collected. Our results demonstrate that a larval yellow perch's failure to inflate its swim bladder results in a higher probability of dying. Thus, on the population scale, the factors affecting swim bladder inflation among larval fishes may have a profound effect on recruitment dynamics.
Influences of Spawning Habitat Characteristics and Interstitial Predators on Lake Trout Egg Deposition and Mortality
Authors: Claramunt Randall M. , Jonas Jory L. , Fitzsimons John D. , Marsden J. Ellen 
Published: June 2005

AbstractTo understand the factors affecting natural recruitment of lake trout Salvelinus namaycush, we evaluated natural egg deposition, the rate of egg loss of seeded eggs, and the relationship of interstitial predators to egg mortality at a protected nearshore lake trout spawning area in Lake Michigan. Egg mortality and predator densities were evaluated with collection bags that were buried above the drop‐off on spawning substrate at 1‐, 3‐, and 9‐m depths. Habitat selection by spawning lake trout was probably related to the coverage by periphyton and zebra mussels Dreissena polymorpha given that abiotic characteristics of the spawning habitat such as slope (55– 65°), interstitial depth (30–50 cm), and substrate type did not differ across depths. The results of seeding eggs during spawning and recovering them throughout the incubation period (2–177 d) indicated that egg mortality was extremely high early in the spawning period: Over 40% of seeded eggs were lost by 2 d and over 80% of the eggs were lost after only 2 weeks. The rate of egg loss declined significantly after the spawning period, possibly as a result of declining water temperature, which caused reduced predator activity, and ice cover, which reduced the impact of physical disturbance. The greatest proportions of seeded eggs were recovered at the shallowest depths (12.5 ± 1.2% [mean ± SE] at 1 m and 9.0 ± 1.5% at 3 m), where predator densities averaged 11.4 ± 1.8/m2; a significantly smaller proportion was recovered at 9 m (3.9 ± 1.2), where predator densities were highest (22.3 ± 2.0/m2). Because lake trout preferred the shallowest depth for spawning and predation was lowest at this depth, we conclude that this strategy improved the probability of egg survival.
Catch Rates Relative to Angler Party Size with Implications for Monitoring Angler Success
Authors: Miranda L. E. 
Published: June 2005

AbstractAngler catch rates often are used to monitor angler success, assess the need for additional management actions, and evaluate the effectiveness of management practices. Potential linkages between catch rate and angler party size were examined to assess how party size might affect the use of catch rate as an index of angler success in recreational fisheries. Data representing 22,355 completed interviews conducted at access points in lakes and reservoirs throughout Mississippi during 1987–2003 were analyzed. Total party catch was not proportional to total party effort; thus, catch rate decreased as party size increased. Depending on the taxa targeted, the average catch rate per angler decreased 40–50% between parties of one and parties of two, although subsequent decreases were less substantial. Because party size accounted for a considerable portion of the variability in catch rate over time and space, failure to remove this variability weakens the manager's ability to detect differences or changes in catch rates. Therefore, the use of catch rates to monitor fisheries may be inappropriate unless party size is taken into account. Party size may influence the angler's ability to catch fish through a variety of processes, including partitioning a limited number of catchable fish among members of a party and party composition. When catch rates are used to estimate total catch rather than to index angler success, party size is not a concern.