bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) isolates from major hospitals in Riyadh, Saudi Arabia
Authors: Baddour Manal M. , Abuelkheir Manal M. , Fatani Amal J. , Bohol Marie F. , Al-Ahdal Mohammad N. 
Published: September 2007

The few studies that have reported the incidence of methicillin-resistant Staphylococcus aureus (MRSA) in Saudi Arabia have indicated that a diverse number of circulating MRSA strains have been detected in several major hospitals. Thus, this study was designed to track the presence of MRSA strains in major hospitals in Riyadh, Saudi Arabia, and perform comparative chromosomal DNA analysis of MRSA strains for epidemiological investigation using pulsed-field gel electrophoresis (PFGE). Correlation of the PFGE types generated with microbiological and clinical data of the isolates was attempted. Screening for decreased susceptibility to vancomycin among the isolates was also done. A dendogram was generated using PFGE macrorestriction fragments and 6 types were identified (M1–M6) with M1 being predominant and widespread. A clear link between PFGE types and some clinical and microbiological data available for the strains was found. For example, M1 was statistically associated with male patients, whereas the unique types were associated with female patients, M2 was associated with isolates from wounds and age group <5 years, and M4 was associated with isolates from patients admitted to intensive care units. M5 was highly correlated with low sensitivity to linezolid. No vancomycin-resistant isolates were detected.
Differential regulation of interchromosomal copies of ToxR-induced genes
Authors: Nag Sanjay , Chaudhuri Keya 
Published: September 2007

In Vibrio cholerae , ToxR transcriptionally activates a number of virulence genes in response to various environmental signals. In the present study, transcription profiling by macroarray was carried out with 13 pairs of genes, one copy of which is present in each chromosome under ToxR-inducing (pH 6.5, osmolarity 66 mmol/L, 30 °C) and ToxR-repressing (pH 8.5, osmolarity 300 mmol/L, 37 °C) conditions followed by high pH (8.5) and low pH (6.5) conditions to eliminate pH effect. The genes dacAII, tagEII, secDII, pmmI, pmmII, and immII showed increased expression in the ToxR-inducing conditions, but not at low pH, suggesting that the expression of these genes might be regulated by ToxR. The expression of pmmII, dacAII, tagEII, secDII, and immII genes decreased significantly in the toxR insertion mutant as determined by RT–PCR, whereas the expression of the chromosome I copy of pmm increased in toxR mutant compared with wild-type cells. Thus, the chromosome II copy of these genes, which show increased expression under ToxR-inducing conditions, are all regulated by ToxR in V. cholerae, whereas the chromosome I copy of pmm may be regulated by other factors under ToxR-inducing conditions.
Carotenoid profiles of yeasts belonging to the genera Rhodotorula, Rhodosporidium, Sporobolomyces, and Sporidiobolus
Authors: Buzzini Pietro , Innocenti Marzia , Turchetti Benedetta , Libkind Diego , van Broock Maria , Mulinacci Nadia 
Published: September 2007

Eighteen yeast species of the genera Rhodotorula , Rhodosporidium , Sporobolomyces , and Sporidiobolus , each one represented by its type strain, were investigated with the objective of evaluating their carotenoid composition. The pigments were extracted from yeast cells, quantified by high pressure liquid chromatography diode array detector and the main compounds were confirmed by atmospheric pressure chemical ionization quadrupole mass spectrometry. Significant (P < 0.01) differences among several species and (or) genera were observed. Thirteen strains were seen to be able to produce carotenoids, from 16.4 to 184 μg/g cell dry mass and from 6.0 to 1993.4 μg/L culture. The main carotenoids produced were identified as torularhodin, torulene, γ-carotene, and β-carotene. The correlation matrix calculated on the basis of the carotenoid composition data matrix indicated significant (P < 0.01) relationships between torulene and torularhodin (r = 0.81), γ-carotene and torulene (r = 0.49), β-carotene and torulene (r = –0.72), as well as β-carotene and γ-carotene (r = 0.64). These significant correlation coefficients may suggest that species belonging to the genera Rhodosporidium, Sporobolomyces, and Sporidiobolus possess a carotenoid biosynthetic pathway analogous to that elsewhere postulated for Rhodotorula species.
Blood and gill responses to HCl infusions in the Pacific hagfish (Eptatretus stoutii)
Authors: Parks Scott K. , Tresguerres Martin , Goss Greg G. 
Published: September 2007

Pacific hagfish ( Eptatretus stoutii (Lockington, 1878)) were serially infused with HCl (6000 µmol·kg–1) every 6 h over a 24 h period to explore branchial acid secretion mechanisms. Blood pH recovered from a value ~2 pH units below that of resting pH. This pH regulatory mechanism was activated by 6 h and persisted over the 24 h time course. Western-blot analysis revealed an increased abundance (~2.3×) of NHE2-like immunoreactivity (NHE2 L-IR) in whole gill fractions from HCl-infused fish compared with control NaCl-infused fish. Membrane fractions isolated from the gills of HCl-infused fish also showed an increased abundance (~1.8×). Immunohistochemistry results demonstrated a significant redistribution of NHE2 L-IR to the apical region in HCl-infused fish. V-H+-ATPase abundance did not significantly increase in HCl-infused fish, while levels of Na+/K+-ATPase expression were unchanged. Immunohistochemistry of these transporters did not show any changes in cellular localization. We propose that the Pacific hagfish overcomes a metabolic acidosis via an increased synthesis of an NHE-like protein and an increased density of the transporter at the apical region of the mitochondria-rich cells of the gill.
In the mating system of the bat Saccopteryx bilineata, bioacoustic constraints impede male eavesdropping on female echolocation calls for their surveillance
Authors: Hoffmann F.F. , Hejduk J. , Caspers B. , Siemers B.M. , Voigt C.C. 
Published: September 2007

At night, bats utter loud echolocation calls at high repetition rates that may reveal the location and current behaviour of callers to eavesdropping bats. Given the strong attenuation of echolocation calls, we predicted that territorial males of a harem-polygynous species ought to forage at close distance to females to survey their movements by social eavesdropping. We estimated a maximum detection distance of 38 m for echolocation calls of Saccopteryx bilineata (Temminck, 1838) (Chiroptera; Emballonuridae) broadcasted within the forest under the sound transmission conditions of our study site and for an assumed signal detection threshold of 20 dB SPL (50 m for a threshold of 0 dB SPL). We then simultaneously radio-tracked the nocturnal movements of eight male–female pairs that each rested in the same harem territory during the day and measured the distances at which dyads foraged. Male–female pairs foraged at a median distance of 139 m. In the case of 90% of simultaneous bearings, males foraged at distances that prevented eavesdropping on 44 kHz echolocation calls (>38 m; 87% of radio fixes >50 m). Males and females of the same daytime territory roosted, on average, 226 ± 194 m apart from each other at night. Thus, males were most likely unaware of where females foraged as a result of the strong attenuation of female echolocation calls. In general, such acoustic constraints on social eavesdropping may promote extra-harem group paternities, female choice, and sperm competition in bats, and may therefore present an important selective force in the evolution of bat mating systems.
Fidelity to calving areas in moose (Alces alces) in the absence of natural predators
Authors: Tremblay J.-P. , Solberg E.J. , Sæther B.-E. , Heim M. 
Published: September 2007

We used long-term monitoring (1991–2005) data from a moose ( Alces alces (L., 1758)) population (i) to determine if moose cows are faithful to their calving sites and (ii) to examine the effect of previous recruitment success on calving-site fidelity. We generated null hypotheses from the distances between calving sites used by other individuals inside the home range of each cow. The calving sites used in successive years by individual cows were closer together (2.1 ± 0.2 km) than were calving sites used by other cows within their home range (3.9 ± 0.1 km; n = 30 cows, 148 sites). The former is similar to distances reported from areas where natural predators are present but females successfully weaned their calf or calves. We did not detect any effects of previous recruitment success, but the distances to the next calving sites of the only two cows that did not wean their calves (3.8 and 3.4 km) are analogous to values reported for cows that have lost their calf or calves to predators. Our data support the theory that fidelity to areas where parturition has been successful could be an evolutionary trade-off between reproductive success and risk of predation to maximize fitness. On an ecological scale, moose cows apparently perceived anthropogenic disturbances as a potential risk, influencing their choice of calving sites and ultimately their fidelity.
Analysis of navigability of Web applications for improving blind usability
Authors: Takagi Hironobu , Saito Shin , Fukuda Kentarou , Asakawa Chieko 
Published: September 2007

Various accessibility activities are improving blind access to the increasingly indispensable WWW. These approaches use various metrics to measure the Web's accessibility. “Ease of navigation” (navigability) is one of the crucial factors for blind usability, especially for complicated webpages used in portals and online shopping sites. However, it is difficult for automatic checking tools to evaluate the navigation capabilities even for a single webpage. Navigability issues for complete Web applications are still far beyond their capabilities.
This study aims at obtaining quantitative results about the current accessibility status of real world Web applications, and analyzes real users' behavior on such websites. In Study 1, an automatic analysis method for webpage navigability is introduced, and then a broad survey using this method for 30 international online shopping sites is described. The next study (Study 2) focuses on a fine-grained analysis of real users' behavior on some of these online shopping sites. We modified a voice browser to record each user's actions and the information presented to that user. We conducted user testing on existing sites with this tool. We also developed an analysis and visualization method for the recorded information. The results showed us that users strongly depend on scanning navigation instead of logical navigation. A landmark-oriented navigation model was proposed based on the results. Finally, we discuss future possibilities for improving navigability, including proposals for voice browsers.
Exploiting KAD
Authors: Steiner Moritz , En-Najjary Taoufik , Biersack Ernst W. 
Published: September 2007

Peer-to-peer systems have seen a tremendous growth in the last few years and peer-to-peer traffic makes a major fraction of the total traffic seen in the Internet. The dominating application for peer-to-peer is file sharing. Some of the most popular peer-to-peer systems for file sharing have been Napster, FastTrack, BitTorrent, and eDonkey, each one counting a million or more users at their peak time.
We got interested in kad since it is the only DHT that has been part of very popular peer-to-peer system with several million simultaneous users. As we have been studying kad over the course of the last 18 months we have been both, fascinated and frightened by the possibilities kad offers. Mounting a Sybil attack is very easy in kad and allows to compromise the privacy of kad users, to compromise the correct operation of the key lookup and to mount DDOS with very little resources.
In this paper, we will relate some of our findings and point out how kad can be used and misused.
Towards an active network architecture
Authors: Tennenhouse David L. , Wetherall David J. 
Published: September 2007

Active networks allow their users to inject customized programs into the nodes of the network. An extreme case, in which we are most interested, replaces packets with "capsules" -- program fragments that are executed at each network router/switch they traverse.
Active architectures permit a massive increase in the sophistication of the computation that is performed within the network. They will enable new applications, especially those based on application-specific multicast, information fusion, and other services that leverage network-based computation and storage. Furthermore, they will accelerate the pace of innovation by decoupling network services from the underlying hardware and allowing new services to be loaded into the infrastructure on demand.
In this paper, we describe our vision of an active network architecture, outline our approach to its design, and survey the technologies that can be brought to bear on its implementation. We propose that the research community mount a joint effort to develop and deploy a wide area ActiveNet.
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines
Authors: Bui Huynh-Hoa , Sidney John , Li Wei , Fusseder Nicolas , Sette Alessandro 
Published: September 2007

AbstractBackgroundIn an epitope-based vaccine setting, the use of conserved epitopes would be expected to provide broader protection across multiple strains, or even species, than epitopes derived from highly variable genome regions. Conversely, in a diagnostic and disease monitoring setting, epitopes that are specific to a given pathogen strain, for example, can be used to monitor responses to that particular infectious strain. In both cases, concrete information pertaining to the degree of conservancy of the epitope(s) considered is crucial.ResultsTo assist in the selection of epitopes with the desired degree of conservation, we have developed a new tool to determine the variability of epitopes within a given set of protein sequences. The tool was implemented as a component of the Immune Epitope Database and Analysis Resources (IEDB), and is directly accessible athttp://tools.immuneepitope.org/tools/conservancy.ConclusionAn epitope conservancy analysis tool was developed to analyze the variability or conservation of epitopes. The tool is user friendly, and is expected to aid in the design of epitope-based vaccines and diagnostics.
A multi-marker test based on family data in genome-wide association study
Authors: Zhang Zhaogong , Zhang Shuanglin , Sha Qiuying 
Published: September 2007

AbstractBackgroundComplex diseases are believed to be the results of many genes and environmental factors. Hence, multi-marker methods that can use the information of markers from different genes are appropriate for mapping complex disease genes. There already have been several multi-marker methods proposed for case-control studies. In this article, we propose a multi-marker test called a Multi-marker Pedigree Disequilibrium Test (MPDT) to analyze family data from genome-wide association studies. If the parental phenotypes are available, we also propose a two-stage test in which a genomic screening test is used to select SNPs, and then the MPDT is used to test the association of the selected SNPs.ResultsWe use simulation studies to evaluate the performance of the MPDT and the two-stage approach. The results show that the MPDT constantly outperforms the single marker transmission/disequilibrium test (TDT) [1]. Comparing the power of the two-stage approach with that of the one-stage approach, which approach is more powerful depends on the value of the prevalence; when the prevalence is no less than 10%, the two-stage approach may be more powerful than the one-stage approach. Otherwise, the one-stage approach is more powerful.ConclusionThe proposed MPDT, is more powerful than the single marker TDT. When the parental phenotypes are available and the prevalence is no less than 10%, the proposed two-stage approach is more powerful than the one-stage approach.
Dynamic remodelling of synapses can occur in the absence of the parent cell body
Authors: Bettini Natalia L , Moores Thomas S , Baxter Becki , Deuchars Jim , Parson Simon H 
Published: September 2007

Abstract

Background
Retraction of nerve terminals is a characteristic feature of development, injury and insult and may herald many neurodegenerative diseases. Although morphological events have been well characterized, we know relatively little about the nature of the underlying cellular machinery. Evidence suggests a strong local component in determining which neuronal branches and synapses are lost, but a greater understanding of this basic neurological process is required. Here we test the hypothesis that nerve terminals are semi-autonomous and able to rapidly respond to local stimuli in the absence of communication with their parent cell body.

Results
We used an isolated preparation consisting of distal peripheral nerve stumps, associated nerve terminals and post-synaptic muscle fibres, maintained in-vitro for up to 3 hrs. In this system synapses are intact but the presynaptic nerve terminal is disconnected from its cell soma. In control preparations synapses were stable for extended periods and did not undergo Wallerian degneration. In contrast, addition of purines triggers rapid changes at synapses. Using fluorescence and electron microscopy we observe ultrastructural and gross morphological events consistent with nerve terminal retraction. We find no evidence of Wallerian or Wallerian-like degeneration in these preparations. Pharmacological experiments implicate pre-synaptic P2X7 receptor subunits as key mediators of these events.

Conclusion
The data presented suggest; first that isolated nerve terminals are able to regulate connectivity independent of signals from the cell body, second that synapses exist in a dynamic state, poised to shift from stability to loss by activating intrinsic mechanisms and molecules, and third that local purines acting at purinergic receptors can trigger these events. A role for ATP receptors in this is not surprising since they are frequently activated during cellular injury, when adenosine tri-phosphate is released from damaged cells. Local control demands that the elements necessary to drive retraction are constitutively present. We hypothesize that pre-existing scaffolds of molecular motors and cytoskeletal proteins could provide the dynamism required to drive such structural changes in nerve terminals in the absence of the cell body.
Predictors of incident herpes simplex virus type 2 infections in young women at risk for unintended pregnancy in San Francisco
Authors: Moss Nicholas J , Harper Cynthia C , Ahrens Katherine , Scott Katherine , Kao Susan , Padian Nancy , Raine Tina , Klausner Jeffrey D 
Published: September 2007

Abstract

Background
Young women receiving family planning services are at risk for both unintended pregnancy and herpes simplex virus type 2 (HSV-2) infection.

Methods
We performed a secondary analysis using data from a previously published randomized controlled trial evaluating access to emergency contraception on reproductive health outcomes. Women aged 15 to 24 years were recruited from two Planned Parenthood clinics and two community health clinics in San Francisco. Demographic information and sexual history were obtained by interview. HSV-2 seropositivity was determined by fingerstick blood test. New pregnancies were measured by self-report, urine testing and medical chart review. Subjects were evaluated for incident HSV-2 infection and pregnancy at a 6-month follow-up appointment. Women who were pregnant or intending to become pregnant at enrolment were excluded.

Results
At enrolment 2,104 women were screened for HSV-2 and 170 (8.1%) were seropositive. Eighty-seven percent of initially seronegative women completed the study (n = 1,672) and 73 (4.4%) became HSV-2 seropositive. HSV-2 seroincidence was 7.8 cases per 100 person-years. One hundred and seventeen women (7%) became pregnant and 7 (6%) of these had a seroincident HSV-2 infection during the study. After adjustment for confounders, predictors of incident HSV-2 infection were African American race and having multiple partners in the last six months. Condom use at last sexual encounter was protective.

Conclusion
HSV-2 seroincidence and the unintended pregnancy rate in young women were high. Providers who counsel women on contraceptive services and sexually transmitted infection prevention could play an expanded role in counselling women about HSV-2 prevention given the potential sequelae in pregnancy. The potential benefit of targeted screening and future vaccination against HSV-2 needs to be assessed in this population.
Prognosis and serum creatinine levels in acute renal failure at the time of nephrology consultation: an observational cohort study
Authors: Perez-Valdivieso Jose Ramon , Bes-Rastrollo Maira , Monedero Pablo , de Irala Jokin , Lavilla Francisco Javier 
Published: September 2007

Abstract

Background
The aim of this study is to evaluate the association between acute serum creatinine changes in acute renal failure (ARF), before specialized treatment begins, and in-hospital mortality, recovery of renal function, and overall mortality at 6 months, on an equal degree of ARF severity, using the RIFLE criteria, and comorbid illnesses.

Methods
Prospective cohort study of 1008 consecutive patients who had been diagnosed as having ARF, and had been admitted in an university-affiliated hospital over 10 years. Demographic, clinical information and outcomes were measured. After that, 646 patients who had presented enough increment in serum creatinine to qualify for the RIFLE criteria were included for subsequent analysis. The population was divided into two groups using the median serum creatinine change (101%) as the cut-off value. Multivariate non-conditional logistic and linear regression models were used.

Results
A ≥ 101% increment of creatinine respect to its baseline before nephrology consultation was associated with significant increase of in-hospital mortality (35.6% vs. 22.6%, p < 0.001), with an adjusted odds ratio of 1.81 (95% CI: 1.08–3.03). Patients who required continuous renal replacement therapy in the ≥ 101% increment group presented a higher increase of in-hospital mortality (62.7% vs 46.4%, p = 0.048), with an adjusted odds ratio of 2.66 (95% CI: 1.00–7.21). Patients in the ≥ 101% increment group had a higher mean serum creatinine level with respect to their baseline level (114.72% vs. 37.96%) at hospital discharge. This was an adjusted 48.92% (95% CI: 13.05–84.79) more serum creatinine than in the < 101% increment group.

Conclusion
In this cohort, patients who had presented an increment in serum level of creatinine of ≥ 101% with respect to basal values, at the time of nephrology consultation, had increased mortality rates and were discharged from hospital with a more deteriorated renal function than those with similar Liano scoring and the same RIFLE classes, but with a < 101% increment. This finding may provide more information about the factors involved in the prognosis of ARF. Furthermore, the calculation of relative serum creatinine increase could be used as a practical tool to identify those patients at risk, and that would benefit from an intensive therapy.