bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)
Authors: Chaudhuri Roy R , Allen Andrew G , Owen Paul J , Shalom Gil , Stone Karl , Harrison Marcus , Burgis Timothy A , Lockyer Michael , Garcia-Lara Jorge , Foster Simon J , Pleasance Stephen J , Peters Sarah E , Maskell Duncan J , Charles Ian G 
Published: July 2009

Abstract

Background
In recent years there has been an increasing problem with Staphylococcus aureus strains that are resistant to treatment with existing antibiotics. An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth.

Results
We have developed a robust microarray and PCR-based method, Transposon-Mediated Differential Hybridisation (TMDH), that uses novel bioinformatics to identify transposon inserts in genome-wide libraries. Following a microarray-based screen, genes lacking transposon inserts are re-tested using a PCR and sequencing-based approach. We carried out a TMDH analysis of the S. aureus genome using a large random mariner transposon library of around a million mutants, and identified a total of 351 S. aureus genes important for survival and growth in culture. A comparison with the essential gene list experimentally derived for Bacillus subtilis highlighted interesting differences in both pathways and individual genes.

Conclusion
We have determined the first comprehensive list of S. aureus essential genes. This should act as a useful starting point for the identification of potential targets for novel antimicrobial compounds. The TMDH methodology we have developed is generic and could be applied to identify essential genes in other bacterial pathogens.
Effects of clinical pathways in the joint replacement: a meta-analysis
Authors: Barbieri A , Vanhaecht K , Van Herck P , Sermeus W , Faggiano F , Marchisio S , Panella M 
Published: July 2009

Abstract

Background
A meta-analysis was performed to evaluate the use of clinical pathways for hip and knee joint replacements when compared with standard medical care. The impact of clinical pathways was evaluated assessing the major outcomes of in-hospital hip and knee joint replacement processes: postoperative complications, number of patients discharged at home, length of in-hospital stay and direct costs.

Methods
Medline, Cinahl, Embase and the Cochrane Central Register of Controlled Trials were searched. The search was performed from 1975 to 2007. Each study was assessed independently by two reviewers. The assessment of methodological quality of the included studies was based on the Jadad methodological approach and on the New Castle Ottawa Scale. Data analysis abided by the guidelines set out by The Cochrane Collaboration regarding statistical methods. Meta-analyses were performed using RevMan software, version 4.2.

Results
Twenty-two studies met the study inclusion criteria and were included in the meta-analysis for a total sample of 6,316 patients. The aggregate overall results showed significantly fewer patients suffering postoperative complications in the clinical pathways group when compared with the standard care group. A shorter length of stay in the clinical pathway group was also observed and lower costs during hospital stay were associated with the use of the clinical pathways. No significant differences were found in the rates of discharge to home.

Conclusion
The results of this meta-analysis show that clinical pathways can significantly improve the quality of care even if it is not possible to conclude that the implementation of clinical pathways is a cost-effective process, because none of the included studies analysed the cost of the development and implementation of the pathways. Based on the results we assume that pathways have impact on the organisation of care if the care process is structured in a standardised way, teams critically analyse the actual organisation of the process and the multidisciplinary team is highly involved in the re-organisation. Further studies should focus on the evaluation of pathways as complex interventions to help to understand which mechanisms within the clinical pathways can really improve the quality of care. With the need for knee and hip joint replacement on the rise, the use of clinical pathways might contribute to better quality of care and cost-effectiveness.
Clinical Implications of Microsatellite Instability and MLH1 Gene Inactivation in Sporadic Insulinomas
Authors: Mei Mei , Deng Dajun , Liu Tong-Hua , Sang Xin-Ting , Lu Xin , Xiang Hong-Ding , Zhou Jing , Wu HaiYan , Yang YingMai , Chen Jie , Lu Chong-Mei , Chen Yuan-Jia 
Published: July 2009

Context: The molecular pathogenesis of sporadic insulinomas is unknown. There is a lack of biomarker to distinguish benign and malignant form of insulinoma.
Objective: Our objective was to confirm the occurrence of microsatellite instability (MSI) in insulinomas, to identify alterations of mismatch repair (MMR) genes in the tumors, and to evaluate the possibility to distinguish benign and malignant insulinoma or to predict the clinical outcome of patients with these alterations.
Design and Patients: We detected MSI and inactivation of MLH1 gene in 55 sporadic insulinomas by PCR, immunohistochemical staining, allelic typing, analysis of promoter methylation, and exon mutations. Their correlations with clinicopathological characteristics were analyzed with univariate and multivariate statistic analysis.
Results: A high rate of MSI (MSI-H) was found in 33% of sporadic insulinomas. Reduced expression of mutL homolog 1 (MLH1) protein was observed in 36% of insulinomas and correlated with MSI-H (P = 0.008). Promoter methylation and loss of heterozygosity of MLH1 gene was found in 31 and 49% of insulinomas, respectively. Reduced expression of MLH1 and MSI-H were significantly associated with both tumor malignancy (P = 0.033 and P = 4.8 × 10−6, respectively) and incurable disease (P = 0.006 and P = 0.001, respectively).
Conclusion: High frequency of MSI occurred in sporadic insulinomas. The silencing of MLH1 gene may partially contribute to the MSI-H in the tumors. Assessing MSI-H and expressions of MLH1 could be used to distinguish benign and malignant insulinomas and to predict the outcome of patients.
Detecting of a high rate of microsatellite instability can be used to distinguish malignancy from benign, and predict clinical outcome of the sporadic insulinomas.
Adrenal Function during Childhood and Puberty in Daughters of Women with Polycystic Ovary Syndrome
Authors: Maliqueo Manuel , Sir-Petermann Teresa , Pérez Virginia , Echiburú Bárbara , Ladrón de Guevara Amanda , Gálvez Carla , Crisosto Nicolás , Azziz Ricardo 
Published: July 2009

Context: In some patients, PCOS may develop as a consequence of an exaggerated adrenarche during pubertal development.
Objective: The aim of the study was to assess adrenal function during childhood and pubertal development in daughters of women with PCOS (PCOSd).
Design: We included 98 PCOSd [64 during childhood (ages 4–8 yr) and 34 during the peripubertal period (ages 9–13 yr)] and 51 daughters of control women (Cd) [30 during childhood and 21 during the peripubertal period]. In both groups, an acute ACTH-(1–24) stimulation test (0.25 mg) and an oral glucose tolerance test were performed. Bone age and serum concentrations of cortisol, androstenedione, 17-hydroxyprogesterone, dehydroepiandrosterone (DHEA), DHEA sulfate (DHEAS), glucose, and insulin were determined.
Results: PCOSd and Cd were similar in age and body mass index. During the peripubertal period, basal and poststimulated DHEAS concentrations were higher in PCOSd compared to Cd. Among PCOSd, 12.5% of girls in childhood and 32.4% in peripuberty presented biochemical evidence of exaggerated adrenarche. Stimulated insulin was higher in PCOSd compared to Cd during childhood (P = 0.03) and peripuberty (P = 0.03). An advancement of 8 months between bone and chronological age was observed in peripubertal PCOSd compared to Cd.
Conclusions: In PCOSd, basal and stimulated DHEAS concentrations were higher during the onset of puberty. Around 30% of the PCOSd demonstrated an exacerbated adrenarche, which may reflect increased P450c17 activity. In addition, a modest advance in bone age was observed, probably secondary to the hyperinsulinemia and/or adrenal hyperandrogenism.
Daughters of women with PCOS exhibit increased dehydroepiandrosterone sulfate serum concentrations and biochemical evidence of an exacerbated adrenarche.
Physiological Thyroid Hormone Levels Regulate Numerous Skeletal Muscle Transcripts
Authors: Visser W. Edward , Heemstra Karen A. , Swagemakers Sigrid M. A. , Özgür Zeliha , Corssmit Eleonora P. , Burggraaf Jacobus , van Ijcken Wilfred F. J. , van der Spek Peter J. , Smit Johannes W. A. , Visser Theo J. 
Published: July 2009

Context: Skeletal muscle is an important target tissue for thyroid hormone (TH). It is currently unknown which genes are regulated by physiological TH levels.
Objective: We examined the effects of l-thyroxine on human skeletal muscle transcriptome.
Design: Microarray analysis of transcript levels was performed using skeletal muscle biopsies from patients under euthyroid and hypothyroid conditions.
Setting: The study was conducted in a university hospital laboratory.
Patients: We studied skeletal muscle obtained from 10 thyroidectomized patients with differentiated thyroid carcinoma on and after 4 wk off l-thyroxine replacement.
Mean Outcome Measures: Gene expression changes were measured using microarrays. Results were analyzed using dedicated statistical methods.
Results: We detected 607 differentially expressed genes on l-thyroxine treatment, of which approximately 60% were positively and approximately 40% were negatively regulated. Representative genes were validated by quantitative PCR. Genes involved in energy and fuel metabolism were overrepresented among the up-regulated genes, of which a large number were newly associated with thyroid state. l-thyroxine therapy induced a large down-regulation of the primary transcripts of the noncoding microRNA pair miR-206/miR-133b.
Conclusion: We demonstrated that physiological levels of TH regulate a myriad of genes in human skeletal muscle. The identification of novel putatively TH-responsive genes may provide the molecular basis of clinical effects in subjects with different TH status. The observation that TH regulates microRNAs reveals a new layer of complexity by which TH influences cellular processes.
Skeletal muscle has a major contribution to the metabolic rate in humans; data demonstrate that skeletal muscle transcriptome is largely changed in different thyroid states.
Book Review
Authors: Colquhoun‐Flannery Claire 
Published: June 2009

Corrections, mental health and social policy: International perspectivesEdited by Robert K. Ax and Thomas J. Fagan Springfield, IL: Charles C Thomas Publisher Ltd., 2007. pp. 418. 978‐0‐398‐07756‐3 (hard) 978‐0‐398‐07757‐0 (pbk)
Using postgraduate students' evaluations of research experience to benchmark departments and faculties: Issues and challenges
Authors: Ginns Paul , Marsh Herbert W. , Behnia Masud , Cheng Jacqueline H. S. , Scalas L. Francesca 
Published: July 2009

Background The introduction of the Australian Research Training Scheme has been a strong reason for assuring the quality of the research higher degree (RHD) experience; if students experience poor supervision, an unsupportive climate, and inadequate infrastructure, prior research suggests RHD students will be less likely to complete their degree, with negative consequences for the student, the university, and society at large.Aims The present study examines the psychometric properties of a survey instrument, the Student Research Experience Questionnaire (SREQ), for measuring the RHD experience of currently enrolled students. The core scales of the SREQ focus on student experiences of Supervision; Infrastructure; Intellectual and Social Climate; and Generic Skills Development.Sample Participants were 2,213 postgraduate research students of a large, research‐intensive Australian university.Results Preliminary factor analyses conducted at the student level supported the a priori four factors that the SREQ was designed to measure. However, multi‐level analyses indicated that there was almost no differentiation between faculties or departments nested with faculties, suggesting that the SREQ responses are not appropriate for benchmarking faculties or departments.Conclusions Consistent with earlier research based on comparisons across universities, the SREQ is shown to be almost completely unreliable in terms of benchmarking faculties or departments within a university.
“Born Under the Cruel Rigor of Captivity, The Supplicant Left it Unexpectedly by Committing a Crime”: Categorizing and Punishing Slave Convicts in Brazil, 1830-1897
Authors: Beatti Peter M. 
Published: June 2009

No presídio [de Fernando de Noronha] o bandido [Zé Moleque] criara fama de boa pessoa, de trabalhador. Os seus roçados de farinha eram sempre os maiores e nunca estivera em cela, nunca dera o que fazer aos diretores.In José Lins do Rego's 1936 novel,A Usina(the sugar refinery), the penal colony of Fernando de Noronha Island emerges as an incongruous Utopia. The novel's young black protoganist Ricardo serves a three year sentence there as a result of his involvement in a Recife labor strike. Upon his return, he is disillusioned by what he finds on the mainland. He recalls his penalcolony stint with a mixture of nostalgia and shame, especially the tender relationship he had had with the former black bandit Zé Moleque, the respected convict in the citation above. The island, some 220 miles off Brazil's northeast coast, initially appears to be an exotic criminal community of dishonored men, the antithesis of life on the mainland. But, as the plot progresses, it becomes a bucolic foil with which the author highlights hypocrisy, injustice, indifference, and corruption on the modernizing Brazilian mainland of the 1920s.
Isomorphism Types of Maximal Cofinitary Groups
Authors: Kastermans Bart 
Published: July 2009

AbstractA cofinitary group is a subgroup of Sym(ℕ) where all nonidentity elements have finitely many fixed points. A maximal cofinitary group is a cofinitary group, maximal with respect to inclusion. We show that a maximal cofinitary group cannot have infinitely many orbits. We also show, using Martin's Axiom, that no further restrictions on the number of orbits can be obtained. We show that Martin's Axiom implies there exist locally finite maximal cofinitary groups. Finally we show that there exists a uniformly computable sequence of permutations generating a cofinitary group whose isomorphism type is not computable.
Assessment of the acetaminophen absorption test as a diagnostic tool for the evaluation of the reticular groove reflex in lambs
Authors: Sharifi Kamran , Grünberg Walter , Soroori Sarang , Mohri Mehrdad , Ahrari-Khafi Mohamad Saeed 
Published: July 2009

Abstract
Objective—To assess the acetaminophen absorption test (APAT) for use in determining function of the reticular groove reflex in lambs.
Animals—12 Baluchi lambs.
Procedures—2 consecutive APATs were performed at each of 3 developmental stages (stage 1, before weaning; stage 2, at weaning; and stage 3, after weaning). Lambs suckled a test solution consisting of acetaminophen and barium sulfate and 1 week later were tube fed the same test solution. Abdominal radiographs were obtained immediately after administration of the test solution. Plasma acetaminophen concentrations were determined before and 30, 60, 90, 120, 150, and 180 minutes after intake of the test solution.
Results—Closure of the reticular groove after suckling the test solution was confirmed in all 12 lambs at stage 1, in 8 lambs at stage 2, and in 0 lambs at stage 3. Maximum plasma acetaminophen concentrations and area under the plasma acetaminophen concentration-time curves from 0 to 180 minutes were significantly higher in lambs suckling the test solution, compared with values for tube-fed lambs. Receiver operating characteristics analysis revealed that the plasma acetaminophen concentration at 60 minutes after administration was best suited to determine closure of the reticular groove in lambs.
Conclusions and Clinical Relevance—Results suggested that the APAT can be a useful diagnostic instrument to assess function of the reticular groove reflex in lambs. We propose a cutoff value for the plasma acetaminophen concentration of 25 μg/mL at 60 minutes after administration to determine function of the reticular groove mechanism in lambs.
Application of strong ion difference theory to urine and the relationship between urine pH and net acid excretion in cattle
Authors: Constable Peter D. , Gelfert Carl-Christian , Fürll Manfred , Staufenbiel Rudolf , Stämpfli Henry R. 
Published: July 2009

Abstract
Objective—To develop an equation expressing urine pH in terms of independent variables, derive an equation relating urine pH to net acid excretion (NAE), and apply this new knowledge to determine the role that monitoring urine pH should play when diets with low cationanion difference are fed to dairy cattle.
Animals—11 Holstein-Friesian cows.
Procedures—A physicochemical strong ion approach was used to develop a general electroneutrality equation for urine that involved urine pH and strong ion difference (SID [difference between strong cation and strong anion concentrations]), PCO2, the concentration of ammonium ([NH4+]) and phosphate ([PO4]), and 3 constants. The general electroneutrality equation was simplified for use in bovine urine and applied to 321 data points from 11 cows fed different diets.
Results—Urine pH was dependent on 4 independent variables (urine SID, [NH4+], PCO2, and [PO4]) and 3 constants. The simplified electroneutrality equation for bovine urine was pH ≈ {pK1′ − log10(S PCO2)} + log10([K+] + [Na+] + [Mg2+] + [Ca2+] + [NH4+] − [Cl−] − [SO42−]). The relationship between urine pH and NAE (in mEq/L) for cattle fed different diets was pH = 6.12 + log10(−NAE + [NH4+] + 2.6).
Conclusions and Clinical Relevance—A change in urine SID, [NH4+], PCO2, or [PO4] independently and directly led to a change in urine pH. Urinary [K+] had the greatest effect on urine pH in cattle, with high urine [K+] resulting in alkaline urine and low urine [K+] resulting in acidic urine. Urine pH provided an accurate assessment of NAE in cattle when pH was > 6.3.
Effect of National Football League games on small animal emergency room caseload
Authors: Rozanski Elizabeth A. , Rondeau Mark P. , Shaw Scott P. , Rush John E. 
Published: July 2009

Abstract
Objective—To evaluate whether games of popular professional football teams have an effect on small animal emergency room caseload and percentage of dogs and cats that subsequently are hospitalized, are euthanatized, or die following admission to veterinary emergency rooms located within a dedicated fan base.
Design—Prospective study.
Animals—818 dogs and cats admitted to the emergency room.
Procedures—During the 2007 New England Patriots (NEP) football season, small animal emergency room caseload was recorded for Sunday (4-hour blocks, 8:00 AM until 12:00 midnight) and Monday night (7:00 PM to 11:00 PM). Number of dogs and cats that subsequently were hospitalized, died, or were euthanatized was recorded. Mean game importance rating (GIR) was determined for NEP games (scale, 1 [mild] to 3 [great]).
Results—Percentage of dogs and cats admitted from 12:00 noon to 4:00 PM on Sundays during NEP games (mean GIR, 1.7) versus non-NEP games was not different. Mean ± SD percentage of dogs and cats admitted from 4:00 PM to 8:00 PM on Sundays during NEP games (mean GIR, 2.4) versus non-NEP games was significantly different (18 ± 5% and 25 ± 7% of daily caseload, respectively). Percentage of dogs and cats admitted from 8:00 PM to 12:00 midnight on Sundays during NEP games (mean GIR, 2.1) versus non-NEP games was not different. Game type (NEP vs non-NEP) during emergency room admission did not influence whether dogs and cats subsequently were hospitalized, died, or were euthanatized.
Conclusions and Clinical Relevance—Professional sporting events may influence veterinary emergency room caseloads.
Risk assessment in coronary patients undergoing abdominal nonvascular surgery
Authors: Karapandzic Vesna , Matic Mihailo , Pesko Predrag , Rankovic Vitomir , Milicic Biljana 
Published: July 2009

Abstract
The aim of our study was to establish that the incidence of perioperative cardiac complications were in direct correlation with level of operative risk in coronary patients undergoing open abdominal nonvascular surgery with general anesthesia. Our prospective observational clinical study was composed of a group of 111 consecutive patients with angiographically-verified coronary artery disease, who were operated on at the University Clinical Center of Serbia. The patients were classified into four stratification subgroups by “Goldman’s Cardiac Risk Index” (CRI) in relation to the incidence of perioperative cardiac complications. Electrocardiography was performed immediately after surgery, on postoperative days 1, 2, 7 and one day before discharge from the hospital. All patients were followed to postoperative day 30. Statistical design was presented by Pearson’s χ2 test and binomial logistic regression. The main result was significant difference between the four stratification subgroups of coronary patients in the incidence of cardiac death up to the 30th postoperative day: I — 0/17 (0.0%) vs. II — 0/40 (0.0%) vs. III — 1/37 (2.7%) vs. IV — 2/17 (11.8%), (p<0.05). We concluded that the incidence of perioperative cardiac complications significantly increased with the degree of Goldman’s CRI. There was significant difference in the incidence of perioperative cardiac complications between the four Goldman’s stratification subgroups.
Invasive giant basal cell carcinoma of the head: case report, reconstruction choice and literature review
Authors: Sakalauskaite M. , Vitkus K. , Balciunas D. , Sirsinaitis S. , Rocka S. 
Published: July 2009

Abstract
It is unusual to find a giant invasive basal cell carcinoma in the occipital region of the head. We are presenting a case of basal cell carcinoma invading and eroding occipital bone, managed with an unusual scalp reconstruction method. A 69-year-old female presented with a 16x19 cm diameter tumour in the occipital region. Preoperative biopsy revealed a basal cell carcinoma. A complete surgical excision of the tumour was performed in one-step surgery and tissue defect was reconstructed by a pedicle latissimus dorsi musculocutaneous flap. Our case shows that this distant pedicle flap is safe and reliable, and should be revised as the option for the occipital region reconstruction.
Have They Learnt to Swim?
Authors: Blühdorn Ingolfur 
Published: June 2009

“Liquid modernity” is a concept that Zygmunt Bauman suggested todescribe a certain condition in advanced modern societies where changeability,unpredictability, and unreliability have become core featuresdetermining individual life and social interaction.1 Diminishing party loyaltyand increasing voter volatility, erratic but often vociferous articulationof political preferences and participation, and a marked shift towards populismall belong to the political fallout from Bauman’s condition of liquidity.With his notion of the “fluid five-party system,” Oskar Niedermayer hasfurther developed the metaphor.2 On the one hand, his concept attemptsto capture the new structural characteristics of the German party system,i.e., its fragmentation and structural asymmetry. On the other hand, itseeks to capture the changed relationship between the individual parties,specifically their mutual demarcation and rapprochement in the context ofcoalition strategies. Indeed, having to compete in a five-party system andtrying to optimize their strategic position in a context of high unpredictabilityis the major new challenge Germany’s political parties are havingto confront.