bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproductive maturity in the edible Chilean crabCancer edwardsii:methodological and management considerations
Authors: Pardo Luis Miguel , Fuentes Juan Pablo , Olguín Andrés , Orensanz J.M. (Lobo) 
Published: May 2009

Size-at-maturity, often used by fisheries managers to specify reference points, was estimated forCancer edwardsii, the most intensely exploited brachyuran crab in Chile, using morphometric data and observation of the gonadal cycle. Sampling was conducted in Chiloé Island, the principal landing region. Several morphometric measurements of secondary sexual characters were recorded for both sexes. Their size-dependence was investigated in search of ontogenetic allometric changes. Six stages of maturity were established for females, and four for males, on the basis of macroscopic and histological observation of the reproductive system, allowing distinction between adults and juveniles. Females and males, on average, attained full development of secondary sexual characters at 106 and 118 mm carapace width (CW) respectively. The CW at which 50% of females and males have gonads of adult appearance was around 101 mm. Current minimum legal size is 120 mm CW, seemingly high enough for conservation purposes. This management control, however, is unlikely to provide effective protection due to the high proportion of crab of sub-legal size in the landings. Traps with escape vents could be introduced in this fishery in order to ensure its sustainability.
Multicenter Study of the Impact of Community-Onset Clostridium difficile Infection on Surveillance for C. difficile Infection
Authors: Dubberke Erik R. , Butler Anne M. , Hota Bala , Khan Yosef M. , Mangino Julie E. , Mayer Jeanmarie , Popovich Kyle J. , Stevenson Kurt B. , Yokoe Deborah S. , McDonald L. Clifford , Jernigan John , Fraser Victoria J. ,   Prevention Epicenters Program from the Centers for Disease Control and Prevention
Published: May 2009

Objective.To evaluate the impact of cases of community-onset, healthcare facility (HCF)-associated Clostridium difficile infection (CDI) on the incidence and outbreak detection of CDI.Design.A retrospective multicenter cohort study.Setting.Five university-affiliated, acute care HCFs in the United States.Methods.We collected data (including results of C. difficile toxin assays of stool samples) on all of the adult patients admitted to the 5 hospitals during the period from July I, 2000, through June 30, 2006. CDI cases were classified as HCF-onset if they were diagnosed more than 48 hours after admission or as community-onset, HCF-associated if they were diagnosed within 48 hours after admission and if the patient had recently been discharged from the HCF. Four surveillance definitions were compared: cases of HCF-onset CDI only (hereafter referred to as HCF-onset CDI) and cases of HCF-onset and community-onset, HCF-associated CDI diagnosed within 30, 60, and 90 days after the last discharge from the study hospital (hereafter referred to as 30-day, 60-day, and 90-day CDI, respectively). Monthly CDI rates were compared. Control charts were used to identify potential CDI outbreaks.Results.The rate of 30-day CDI was significantly higher than the rate of HCF-onset CDI at 2 HCFs (P < .01 ). The rates of 30-day CDI were not statistically significantly different from the rates of 60-day or 90-day CDI at any HCF. The correlations between each HCF's monthly rates of HCF-onset CDI and 30-day CDI were almost perfect (ρ range, 0.94-0.99; P < .001). Overall, 12 time points had a CDI rate that was more than 3 standard deviations above the mean, including 11 time points identified using the definition for HCF-onset CDI and 9 time points identified using the definition for 30-day CDI, with discordant results at 4 time points (k = 0.794; P < .001).Conclusions.Tracking cases of both community-onset and HCF-onset, HCF-associated CDI captures significantly more CDI cases, but surveillance of HCF-onset, HCF-associated CDI alone is sufficient to detect an outbreak.
Prospective Evaluation of Colonization with Extended-Spectrum β-Lactamase (ESBL)–Producing Enterobacteriaceae Among Patients at Hospital Admission and of Subsequent Colonization with ESBL-Producing Enterobacteriaceae Among Patients During Hospitalization
Authors: Friedmann Reuven , Raveh David , Zartzer Esther , Rudensky Bernard , Broide Ellen , Attias Denise , Yinnon Amos M. 
Published: May 2009

Objective.To determine the rates of and risk factors for carriage and acquisition of extended-spectrum (β-lactamase (ESBL)-producing Enterobacteriaceae during hospitalization.Design.Cohort study.Setting.Shaare Zedek Medical Center, a 550-bed teaching hospital.Methods.During a 5-month period (February 1-June 30, 2004), 167 (8%) of 1,985 newly admitted general medical patients were enrolled in our study. Nasal, oropharyngeal, and rectal swab specimens were obtained at admission and every 2-3 days until hospital discharge or death. Enterobacteriaceae isolates were tested for ESBL, andStaphylococcus aureusisolates were tested for methicillin resistance.Results.Of the 167 patients enrolled in our study, 15 (9%) were identified as nasal carriers of methicillin-resistantS. aureus(MRSA) at admission, and 13 (8%) were rectal carriers of ESBL-producing Enterobacteriaceae at admission. Univariate risk factors for rectal carriage of ESBL-producing Enterobacteriaceae included female sex (odds ratio [OR], 11 [95% confidence interval {CI}, 1.4—238];P< .05), nursing home residence (OR, 6.9 [95% CI, 1.8-27];P< .01), recent antibiotic treatment (OR, 9.8 [95% CI, 1.7-74];P< .05), and concomitant nasal carriage of MRSA and/or ESBL-producing Enterobacteriaceae (OR, 5.8 [95% CI, 1.2-26];P< .01). Multivariate risk factors were female sex and recent antibiotic treatment. During hospitalization, 35 (21%) of 167 patients had acquired rectal carriage of ESBL-producing Enterobacteriaceae (P= .002, for trend analysis). Of the 12 patients who were still in the hospital 2 weeks after admission, 4 (33%) were carriers of ESBL-producing Enterobacteriaceae. Univariate risk factors for acquisition included an age of older than 65 years (P< .005), nursing home residence (OR 2.6, [95% CI, 0.98-2.6]), impaired cognition (OR, 4.8 [95% CI, 1.9-12]), recent antibiotic treatment (OR, 2.7 [95% CI, 0.9-8.3]), respiratory assistance (OR, 4.2 [95% CI, 1.2-14]), and prolonged hospitalization. Multivariate risk factors were an age of older than 65 years and broad-spectrum antibiotic therapy.Conclusions.Rectal carriage of ESBL-producing Enterobacteriaceae occurred in 13 (8%) of 167 patients at admission to the medical departments of our hospital and in 4 (33%) of 12 patients still remaining in our hospital after 2 weeks.
Association Between Physician Caseload and Patient Outcome for Sepsis Treatment
Authors: Chen Chao-Hung , Chen Yi-Hua , Lin Hsiu-Chen , Lin Herng-Ching 
Published: May 2009

Objective.The purpose of this study was to investigate whether physicians with larger sepsis caseloads provide better outcomes, defined as lower in-hospital mortality rates, for patients with sepsis.Design.Retrospective cross-sectional study.Method.This study used pooled data from the 2002-2004 Taiwan National Health Insurance Research Database. A total of 48,336 patients hospitalized with a principal diagnosis of septicemia were selected and assigned to 1 of 4 caseload groups on the basis of their treating physician's sepsis caseload during the 3 years reflected in the pooled data (low caseload, less than 39 cases; medium caseload, 39–88 cases; high caseload, 89–176 cases; and very high caseload, more than 176 cases). Generalized estimating equation models were used for analysis.Results.Receipt of treatment from physicians in the very high, high, and medium caseload groups decreased patients' odds of inhospital mortality by 49% (95% confidence interval [CI], 0.41-0.67; P < .001 ), 40% (95% CI, 0.53-0.68; P < .001 ), and 18% (95% CI, 0.73-0.92; P < .001), respectively, compared with the odds for patients treated by low-caseload physicians. These findings persisted after partitioning out systematic physician-specific and hospital-specific variation and isolating the effects of most hospital, physician, and patient confounders.Conclusion.Patients treated by physicians who had a larger sepsis caseload had a substantially lower in-hospital mortality rate than did patients treated by physicians in the other caseload groups, and the difference was statistically significant. This result supports the “practice makes perfect” hypothesis.
Flexible structural protein alignment by a sequence of local transformations
Authors: Rocha Jairo , Segura Joan , Wilson Richard C. , Dasgupta Swagata 
Published: May 2009

Abstract
Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.
Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it.
Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/.
Contact: jairo@uib.es
Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online.
Efficient designs for sampling and subsampling in fisheries research based on ranked sets
Authors: Wang You-Gan , Ye Yimin , Milton David A. 
Published: May 2009

Abstract
Wang, Y-G., Ye, Y., and Milton, D. A. 2009. Efficient designs for sampling and subsampling in fisheries research based on ranked sets. – ICES Journal of Marine Science, 66: 928–934. Sampling strategies are developed based on the idea of ranked set sampling (RSS) to increase efficiency and therefore to reduce the cost of sampling in fishery research. The RSS incorporates information on concomitant variables that are correlated with the variable of interest in the selection of samples. For example, estimating a monitoring survey abundance index would be more efficient if the sampling sites were selected based on the information from previous surveys or catch rates of the fishery. We use two practical fishery examples to demonstrate the approach: site selection for a fishery-independent monitoring survey in the Australian northern prawn fishery (NPF) and fish age prediction by simple linear regression modelling a short-lived tropical clupeoid. The relative efficiencies of the new designs were derived analytically and compared with the traditional simple random sampling (SRS). Optimal sampling schemes were measured by different optimality criteria. For the NPF monitoring survey, the efficiency in terms of variance or mean squared errors of the estimated mean abundance index ranged from 114 to 199% compared with the SRS. In the case of a fish ageing study for Tenualosa ilisha in Bangladesh, the efficiency of age prediction from fish body weight reached 140%.
Cytokinin-Dependent Photorespiration and the Protection of Photosynthesis during Water Deficit
Authors: Rivero Rosa M. , Shulaev Vladimir , Blumwald Eduardo 
Published: May 2009

AbstractWe investigated the effects of PSARK∷IPT (for Senescence-Associated Receptor Kinase∷Isopentenyltransferase) expression and cytokinin production on several aspects of photosynthesis in transgenic tobacco (Nicotiana tabacum cv SR1) plants grown under optimal or restricted (30% of optimal) watering regimes. There were no significant differences in stomatal conductance between leaves from wild-type and transgenic PSARK-IPT plants grown under optimal or restricted watering. On the other hand, there was a significant reduction in the maximum rate of electron transport as well as the use of triose-phosphates only in wild-type plants during growth under restricted watering, indicating a biochemical control of photosynthesis during growth under water deficit. During water deficit conditions, the transgenic plants displayed an increase in catalase inside peroxisomes, maintained a physical association among chloroplasts, peroxisomes, and mitochondria, and increased the CO2 compensation point, indicating the cytokinin-mediated occurrence of photorespiration in the transgenic plants. The contribution of photorespiration to the tolerance of transgenic plants to water deficit was also supported by the increase in transcripts coding for enzymes involved in the conversion of glycolate to ribulose-1,5-bisphosphate. Moreover, the increase in transcripts indicated a cytokinin-induced elevation in photorespiration, suggesting the contribution of photorespiration in the protection of photosynthetic processes and its beneficial role during water stress.
The Ethylene Receptor ETR2 Delays Floral Transition and Affects Starch Accumulation in Rice
Authors: Wuriyanghan Hada , Zhang Bo , Cao Wan-Hong , Ma Biao , Lei Gang , Liu Yun-Feng , Wei Wei , Wu Hua-Jun , Chen Li-Juan , Chen Hao-Wei , Cao Yang-Rong , He Si-Jie , Zhang Wan-Ke , Wang Xiu-Jie , Chen Shou-Yi , Zhang Jin-Song 
Published: May 2009

AbstractEthylene regulates multiple aspects of plant growth and development in dicotyledonous plants; however, its roles in monocotyledonous plants are poorly known. Here, we characterized a subfamily II ethylene receptor, ETHYLENE RESPONSE2 (ETR2), in rice (Oryza sativa). The ETR2 receptor with a diverged His kinase domain is a Ser/Thr kinase, but not a His kinase, and can phosphorylate its receiver domain. Mutation of the N box of the kinase domain abolished the kinase activity of ETR2. Overexpression of ETR2 in transgenic rice plants reduced ethylene sensitivity and delayed floral transition. Conversely, RNA interference (RNAi) plants exhibited early flowering and the ETR2 T-DNA insertion mutant etr2 showed enhanced ethylene sensitivity and early flowering. The effective panicles and seed-setting rate were reduced in the ETR2-overexpressing plants, while thousand-seed weight was substantially enhanced in both the ETR2-RNAi plants and the etr2 mutant compared with controls. Starch granules accumulated in the internodes of the ETR2-overexpressing plants, but not in the etr2 mutant. The GIGANTEA and TERMINAL FLOWER1/CENTRORADIALIS homolog (RCN1) that cause delayed flowering were upregulated in ETR2-overexpressing plants but downregulated in the etr2 mutant. Conversely, the α-amylase gene RAmy3D was suppressed in ETR2-overexpressing plants but enhanced in the etr2 mutant. Thus, ETR2 may delay flowering and cause starch accumulation in stems by regulating downstream genes.
Dimensions of tasks: influences on information‐seeking and retrieving process
Authors: Xie Iris 
Published: May 2009

PurposePrevious research has demonstrated that task is the driving force for information retrieval (IR). However, few studies investigate how people engaged in work and search tasks define their decisions and behaviors in the IR process. The purpose of this paper is to investigate how dimensions of tasks affect the information‐seeking and retrieving process.Design/methodology/approachIn total, 40 participants are recruited for the two studies conducted in a corporate setting as well as an academic setting. Multiple methods are applied to collect data related to participants' tasks and the information‐seeking and retrieving process: web surveys, questionnaires, diaries, and telephone interviews. Both qualitative and quantitative data are analyzed.FindingsThis paper identifies nature (routine, typical, and unusual), stages (pre‐focus, formation, and post‐focus), and timeframe (extremely urgent, urgent, and non‐urgent) as dimensions of work tasks as well as origination (self‐generated and assigned), types (updating information, looking for specific information, looking for items with common characteristics, and looking for known items), and flexibility (very flexible, flexible, and inflexible) as dimensions of search tasks. Moreover, the relationships between dimensions of work and search tasks and the information‐seeking process – in particular, the extent of planning, the application of different types of information‐seeking strategies, and shifts in search‐task‐related goals – are explored.Originality/valueThis paper fills in a gap in current research – the impact of dimensions of task on the information‐seeking and ‐retrieving process.
Unanswerable questions at the IPL: user expectations of e‐mail reference
Authors: Westbrook Lynn 
Published: May 2009

PurposeIn a 31‐month period, 1,184 questions addressed to the Internet Public Library's (IPL) reference service remained unanswered on the grounds that they were “out of scope”. This paper aims to analyze the questions as artifacts of users' expectations to better chart the distinction between user and librarian views of reference service.Design/methodology/approachEach question is examined to identify two user expectations, i.e. what kinds of information librarians could provide and what kinds of needs librarians could help meet. Emergent coding with a code‐recode rate of 97 per cent identifies 23 types of expected librarian assistance and 28 characteristics of expected applications of that assistance.FindingsUsers expect IPL librarians to provide personal advice, analysis, facts, procedures, instruction, technology guidance and evaluation. IPL librarians are expected to help users in making decisions, solving problems, completing processes and developing understanding.Research limitations/implicationsLimitations include the use of a single coder and the use of single institution's data set. Mapping these user expectations suggests a need for librarians to consider further development of reference service in terms of its judgment, form, and involvement parameters.Practical implicationsReference service policies and training should be examined to enhance librarians' abilities to consider judgment, form, and involvement parameters primarily from the user's perspective.Originality/valueThis paper analyzes that which is rarely seen, i.e. e‐mail reference questions which are considered beyond the scope of service. Additionally, the IPL question pool provides a broader range of user mental models than would be found in any geographically bound institution.
Relationship among activities and problems causing uncertainty in information seeking and retrieval
Authors: Chowdhury Sudatta , Gibb Forbes 
Published: May 2009

PurposeThis paper aims to argue that different types of uncertainty are associated with information seeking and retrieval (IS&R), and that, with the proliferation of new and different search tools, channels and sources, uncertainty, whether positive or negative, continues to be a significant factor in the search process. The paper aims to report on one part of an ongoing research that aims to study correlations among a series of information‐seeking activities and information‐seeking problems that cause uncertainty amongst users in academic environment.Design/methodology/approachAn online questionnaire is used to collect data from users in the higher education sector. Quantitative analysis is carried out on the data collected through an online questionnaire distributed through eight online mailing lists comprising a total of 3,607 registered users. A total of 668 responses are returned from three categories of respondents: academic staff, research staff and research students. Pearson's correlation coefficient is used to study correlation among the activities and problems that cause uncertainty in IS&R.FindingsThis research shows that uncertainty may occur in course of a number of information‐seeking activities, and may also be created because of some problems associated with information seeking. Some of the activities and problems that caused uncertainty have significant correlations. There is also a correlation between information‐seeking activities and gender and disciplines, though there is little correlation between information‐seeking activities and age, information and communication technology (ICT) skills, and user categories. There is also a correlation between information‐seeking problems and ICT skills, gender and user categories, but there is less correlation between information‐seeking problems and age. Information‐seeking activities and information‐seeking problems that cause uncertainty have a significant correlation with disciplines and gender. Furthermore, it is noted that information‐seeking activities caused less uncertainty for users in the discipline of computer and information sciences compared to the other chosen disciplines such as business and management, and arts and humanities.Originality/valueThis research for the first time aimed to study which information‐seeking activities and problems cause uncertainty and how they are correlated.
Have we made any progress? Catalogues of the future revisited
Authors: Šauperl Alenka , Saye Jerry D. 
Published: May 2009

PurposeLibrary online public access catalogues (OPACs) are considered to be unattractive in comparison with popular internet sites. In 2000, the authors presented some suggestions on how library catalogues should change. Have librarians actually made their OPACs more user‐friendly by adopting techniques and technologies already present in other information resources? This paper aims to address these issues.Design/methodology/approachThe characteristics of four OPACs, one online bookstore and two internet search engines are analyzed. The paper reviews some of the changes and directions suggested by researchers and adds some of authors own. All this is in the hope that library catalogues will survive “Google attack.”FindingsChanges are identified in the information services studied over a seven‐year period. Least development is found in library catalogues. Suggestions are made for library catalogues of the future.Research limitations/implicationsA library catalogue, a web search engine and an internet bookstore cannot be compared directly because of differences in scope. But features from each could be fruitfully used in others.Practical implicationsOPACs must be both attractive and useful. They should be at least as easy to use as their competitors. With the results of research as well as the knowledge librarians have many years, the profession should be able to develop better OPACs than we have today and regain lost ground in the “competition” for those with information needs.Originality/valueA comparison of OPAC features in 2000 and 2007, even if subjective, can provide a panoramic view of the development of the field.