bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA repair and recombination in higher plants: insights from comparative genomics of arabidopsis and rice
Authors: Singh Sanjay K , Roy Sujit , Choudhury Swarup Roy , Sengupta Dibyendu N 
Published: July 2010

Abstract

Background
The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them.

Results
We identified genes potentially involved in DRR mechanisms in Arabidopsis and rice using similarity searches and conserved domain analysis against proteins known to be involved in DRR in human, yeast and E. coli. As expected, many of DRR genes are very similar to those found in other eukaryotes. Beside these eukaryotes specific genes, several prokaryotes specific genes were also found to be well conserved in plants. In Arabidopsis, several functionally important DRR gene duplications are present, which do not occur in rice. Among DRR proteins, we found that proteins belonging to the nucleotide excision repair pathway were relatively more conserved than proteins needed for the other DRR pathways. Sub-cellular localization studies of DRR gene suggests that these proteins are mostly reside in nucleus while gene drain in between nucleus and cell organelles were also found in some cases.

Conclusions
The similarities and dissimilarities in between plants and other organisms' DRR pathways are discussed. The observed differences broaden our knowledge about DRR in the plants world, and raises the potential question of whether differentiated functions have evolved in some cases. These results, altogether, provide a useful framework for further experimental studies in these organisms.
Efficacy and safety of tigecycline monotherapy vs. imipenem/cilastatin in Chinese patients with complicated intra-abdominal infections: a randomized controlled trial
Authors: Chen Zhangjing , Wu Jufang , Zhang Yingyuan , Wei Junming , Leng Xisheng , Bi Jianwei , Li Rong , Yan Lunan , Quan Zhiwei , Chen Xiaoping , Yu Yunsong , Wu Zhiyong , Liu Dawei , Ma Xiaochun , Maroko Robert , Cooper Angel 
Published: July 2010

Abstract

Background
Tigecycline, a first-in-class broad-spectrum glycylcycline antibiotic, has broad-spectrum in vitro activity against bacteria commonly encountered in complicated intra-abdominal infections (cIAIs), including aerobic and facultative Gram-positive and Gram-negative bacteria and anaerobic bacteria. In the current trial, tigecycline was evaluated for safety and efficacy vs. imipenem/cilastatin in hospitalized Chinese patients with cIAIs.

Methods
In this phase 3, multicenter, open-label study, patients were randomly assigned to receive IV tigecycline or imipenem/cilastatin for ≤2 weeks. The primary efficacy endpoints were clinical response at the test-of-cure visit (12-37 days after therapy) for the microbiologic modified intent-to-treat and microbiologically evaluable populations. Because the study was not powered to demonstrate non-inferiority between tigecycline and imipenem/cilastatin, no formal statistical analysis was performed. Two-sided 95% confidence intervals (CIs) were calculated for the response rates in each treatment group and for differences between treatment groups for descriptive purposes.

Results
One hundred ninety-nine patients received ≥1 dose of study drug and comprised the modified intent-to-treat population. In the microbiologically evaluable population, 86.5% (45 of 52) of tigecycline- and 97.9% (47 of 48) of imipenem/cilastatin-treated patients were cured at the test-of-cure assessment (12-37 days after therapy); in the microbiologic modified intent-to-treat population, cure rates were 81.7% (49 of 60) and 90.9% (50 of 55), respectively. The overall incidence of treatment-emergent adverse events was 80.4% for tigecycline vs. 53.9% after imipenem/cilastatin therapy (P < 0.001), primarily due to gastrointestinal-related events, especially nausea (21.6% vs. 3.9%; P < 0.001) and vomiting (12.4% vs. 2.0%; P = 0.005).

Conclusions
Clinical cure rates for tigecycline were consistent with those found in global cIAI studies. The overall safety profile was also consistent with that observed in global studies of tigecycline for treatment of cIAI, as well as that observed in analyses of Chinese patients in those studies; no novel trends were observed.

Trial Registration
ClinicalTrials.gov NCT00136201
Sex difference in the association of metabolic syndrome with high sensitivity C-reactive protein in a Taiwanese population
Authors: Lai Ming-May , Li Chia-Ing , Kardia Sharon LR , Liu Chiu-Shong , Lin Wen-Yuan , Lee Yih-Dar , Chang Pei-Chia , Lin Cheng-Chieh , Li Tsai-Chung 
Published: July 2010

Abstract

Background
Although sex differences have been reported for associations between components of metabolic syndrome and inflammation, the question of whether there is an effect modification by sex in the association between inflammation and metabolic syndrome has not been investigated in detail. Therefore, the aim of this study was to compare associations of high sensitivity C-creative protein (hs-CRP) with metabolic syndrome and its components between men and women.

Methods
A total of 1,305 subjects aged 40 years and over were recruited in 2004 in a metropolitan city in Taiwan. The biochemical indices, such as hs-CRP, fasting glucose levels, lipid profiles, urinary albumin, urinary creatinine and anthropometric indices, were measured. Metabolic syndrome was defined using the American Heart Association and the National Heart, lung and Blood Institute (AHA/NHLBI) definition. The relationship between metabolic syndrome and hs-CRP was examined using multivariate logistic regression analysis.

Results
After adjustment for age and lifestyle factors including smoking, and alcohol intake, elevated concentrations of hs-CRP showed a stronger association with metabolic syndrome in women (odds ratio comparing tertile extremes 4.80 [95% CI: 3.31-6.97]) than in men (2.30 [1.65-3.21]). The p value for the sex interaction was 0.002. All components were more strongly associated with metabolic syndrome in women than in men, and all sex interactions were significant except for hypertension.

Conclusions
Our data suggest that inflammatory processes may be of particular importance in the pathogenesis of metabolic syndrome in women.
An antibiotic, heavy metal resistant and halotolerant Bacillus cereus SIU1 and its thermoalkaline protease
Authors: Singh Sanjay K , Tripathi Vinayak R , Jain Rakesh K , Vikram Surendra , Garg Satyendra K 
Published: July 2010

Abstract

Background
Many workers have reported halotolerant bacteria from saline conditions capable of protease production. However, antibiotic resistance and heavy metal tolerance pattern of such organisms is not documented very well. Similarly, only a few researchers have reported the pattern of pH change of fermentation medium during the course of protease production. In this study, we have isolated a halotolerant Bacillus cereus SIU1 strain from a non-saline environment and studied its antibiotic and heavy metal resistance pattern. The isolate produces a thermoalkaline protease and changes the medium pH during the course of fermentation. Thermostability of protease was also studied for 30 min.

Results
Seventy bacterial strains isolated from the soils of Eastern Uttar Pradesh, India were screened for protease production. All of them exhibited protease activity. However, 40% bacterial isolates were found good protease producers as observed by caseinolytic zones on milk agar plates. Among them, culture S-4 was adjudged as the best protease producer, and was identified as Bacillus cereus by morphological, biochemical and 16 S rDNA sequence analyses. The isolate was resistant to heavy metals (As2+, Pb2+, Cs1+) and antibiotics (penicillin, lincomycin, cloxacillin, pefloxacin). Its growth behavior and protease production was studied at 45°C and pH 9.0. The protease units of 88 ml-1 were noted in unoptimized modified glucose yeast extract (GYE) medium during early stationary phase at 20 h incubation period. The enzyme was stable in the temperature range of 35°-55°C.

Conclusions
An antibiotic and heavy metal resistant, halotolerant Bacillus cereus isolate is capable of producing thermoalkaline protease, which is active and stable at pH 9.0 and 35°-55°C. This isolate may be useful in several industrial applications owing to its halotolerance and antibiotic and heavy metal resistance characteristics.
A case of gastropericardial fistula of a gastric tube after esophagectomy: a case report and review
Authors: Kato Takehito , Mori Takahiro , Niibori Koki 
Published: July 2010

Abstract
A 65-year-old man who had received an esophagectomy 10 years earlier was admitted to our hospital for right chest pain. Preoperative examinations showed pneumopericardium, a retrosternal gastric tube, and an active gastric tube ulcer. We diagnosed gastropericardial fistula of the gastric tube ulcer. Emergency surgery included lavage and drainage of the pericardial cavity and plombage of the rectus abdominis muscle flap to the posterior space of the gastric tube. Total parental nutrition and/or enteric nutrition were provided. Due to minor leakage from the ulcer, the patient could start oral intake on the postoperative 49th day, and was discharged from the hospital on the postoperative 86th day after physical rehabilitation. He has been free from complications for more than 33 months after surgery. Here, we review the literature and discuss the etiology and treatment of choice for this rare yet lethal complication in the follow-up after esophagectomy.
A plausible mechanism for auxin patterning along the developing root
Authors: Mironova Victoria V , Omelyanchuk Nadezda A , Yosiphon Guy , Fadeev Stanislav I , Kolchanov Nikolai A , Mjolsness Eric , Likhoshvai Vitaly A 
Published: July 2010

Abstract

Background
In plant roots, auxin is critical for patterning and morphogenesis. It regulates cell elongation and division, the development and maintenance of root apical meristems, and other processes. In Arabidopsis, auxin distribution along the central root axis has several maxima: in the root tip, in the basal meristem and at the shoot/root junction. The distal maximum in the root tip maintains the stem cell niche. Proximal maxima may trigger lateral or adventitious root initiation.

Results
We propose a reflected flow mechanism for the formation of the auxin maximum in the root apical meristem. The mechanism is based on auxin's known activation and inhibition of expressed PIN family auxin carriers at low and high auxin levels, respectively. Simulations showed that these regulatory interactions are sufficient for self-organization of the auxin distribution pattern along the central root axis under varying conditions. The mathematical model was extended with rules for discontinuous cell dynamics so that cell divisions were also governed by auxin, and by another morphogen Division Factor which combines the actions of cytokinin and ethylene on cell division in the root. The positional information specified by the gradients of these two morphogens is able to explain root patterning along the central root axis.

Conclusion
We present here a plausible mechanism for auxin patterning along the developing root, that may provide for self-organization of the distal auxin maximum when the reverse fountain has not yet been formed or has been disrupted. In addition, the proximal maxima are formed under the reflected flow mechanism in response to periods of increasing auxin flow from the growing shoot. These events may predetermine lateral root initiation in a rhyzotactic pattern. Another outcome of the reflected flow mechanism - the predominance of lateral or adventitious roots in different plant species - may be based on the different efficiencies with which auxin inhibits its own transport in different species, thereby distinguishing two main types of plant root architecture: taproot vs. fibrous.
Unidirectional signaling triggered through 2B4 (CD244), not CD48, in murine NK cells
Authors: Kim Eun-Ok , Kim Nayoung , Kim Tae-Jin , Kim Kwanghee , Kim Tae Woo , Kumar Vinay , Lee Kyung-Mi 
Published: July 2010

Abstract
2B4 (CD244), not CD48, induces signaling in murine NK cells.
Engagement of 2B4 (CD244) with CD48 results in activation, costimulation, or inhibition of NK cell activities, depending on the cell types and the stage of differentiation. In vivo, 2B4+ NK cells can interact with CD48+ NK cells and also with surrounding CD48+ hematopoietic cells. Similarly, CD48+ NK cells may be triggered by adjacent 2B4+ NK cells or other hematopoietic cells expressing 2B4, e.g., monocytes, basophils, γδ T cells, etc. As CD48 was also shown to function as an activating receptor, 2B4/CD48 binding in the settings of NK-to-NK or NK-to-non-NK cell interactions may generate bidirectional signals. To address this question, we examined the consequence of CD48 or 2B4 ligation using two experimental settings: one with target (syngeneic EL4 and allogeneic P815) cells, ectopically expressing surface 2B4 or CD48, and the other with direct cross-linking with plate-bound mAb. Here, we report that ligation of CD48 with 2B4+ EL4 or 2B4+ P815 targets, in the absence of other receptor engagement, did not alter NK cell cytotoxicity or proliferation significantly. Similarly, cross-linking of NK cells with plate-bound anti-CD48 mAb in the absence or presence of a suboptimal dose of IL-2 did not modulate NK proliferation, cytotoxicity, or cytokine production. Nonetheless, 2B4 cross-linking promoted NK cell proliferation and effector functions consistently in both settings. Therefore, our results demonstrate unequivocally that CD48 on surrounding NK or non-NK cells serves primarily as a ligand to stimulate 2B4 on the adjacent NK cells in mice.
The Efficacy of a Neonatal Screening Programme in Decreasing the Hospitalization Rate of Patients with G6pd Deficiency in Southern Iran
Authors: Cohan Nader , Karimi Mehran , Khalili Amir Hossein , Falahzadeh Mohammad Hossein , Samadi Behrang , Mahdavi Reza Mohammad 
Published: July 2010

Objective To investigate whether a neonatal screening programme for G6PD deficiency has decreased hospitalization for acute haemolytic attack in the Fars province of southern Iran. Methods A total of 850 patients registered with G6PD deficiency were included in the study. Variables including age, sex, time and cause of hospitalization, cause of haemolytic crisis, positive history of blood transfusion, G6PD enzyme deficiency, blood urea nitrogen (BUN) and creatinine were recorded based on a standard questionnaire. All patients were analysed for G6PD enzyme level based on a quantitative test. Results Five hundred and fifty-three patients were hospitalized before the introduction of the neonatal screening programme (2001-2004) and 297 afterwards (2005-2008). Of those patients hospitalized after the introduction of the screening programme, 237 were wrongly classified as normal and 60 were recorded as having G6PD enzyme deficiency by the neonatal screening programme. The main causes of haemolytic crisis in G6PD-deficient patients were fava bean consumption (88.2%), underlying infection (10.9%) and drugs (0.8%). Conclusion Our study showed the effectiveness of the neonatal screening programme in decreasing the hospitalization rate.
Effect of Gender, Age and Deprivation on Key Performance Indicators in a Fobt-based Colorectal Screening Programme
Authors: Steele R J C , Kostourou I , Mcclements P , Watling C , Libby G , Weiler D , Brewster D H , Black R , Carey F A , Fraser C 
Published: July 2010

Objectives To assess the effect of gender, age and deprivation on key performance indicators in a colorectal cancer screening programme. Setting Between March 2000 and May 2006 a demonstration pilot of biennial guaiac faecal occult blood test (gFOBT) colorectal screening was carried out in North-East Scotland for all individuals aged 50-69 years. Methods The relevant populations were subdivided, by gender, into four age groups and into five deprivation categories according to the Scottish Index of Multiple Deprivation (SIMD), and key performance indicators analysed within these groups. Results In all rounds, uptake of the gFOBT increased with age ( P < 0.001), decreased with increasing deprivation in both genders ( P < 0.001), and was consistently higher in women than in men in all age and all SIMD groups. In addition, increasing deprivation was negatively associated with uptake of colonoscopy in men with a positive gFOBT ( P < 0.001) although this effect was not observed in women. Positivity rates increased with age ( P< 0.001) and increasing deprivation ( P > 0.001) in both genders in all rounds, although they were higher in men than in women for all age and SIMD categories. Cancer detection rates increased with age ( P < 0.001), were higher in men than in women in all age and SIMD categories, but were not consistently related to deprivation. In both genders, the positive predictive value (PPV) for cancer increased with age ( P < 0.001) and decreased with increasing deprivation ( P < 0.001) in all rounds and was consistently higher in men than in women in all age and SIMD categories. Conclusions In this population-based colorectal screening programme gender, age, and deprivation had marked effects on key performance indicators, and this has implications both for the evaluation of screening programmes and for strategies designed to reduce inequalities.
Improved Resolution of Diagnostic Problems in Selected Prostate Needle Biopsy Specimens by Using the ASAP Workup
Authors: Strand Calvin L. , Aponte Sandra L. , Chatterjee Monica , Engelbach Ludmila M. , Fromowitz Frank B. , Guo Yijun , Iorga Petronela G. , Kartika Gunawan , Li Rongshan , Mahapatro Darshana , Pai Usha L. , Romeroacaces Gloria M. , Sharaan Mona E. , Vara Manjula L. , Riba Ali K. 
Published: July 2010

Abstract
This study assessed the value of an atypical small acinar proliferation (ASAP) workup consisting of preparing new recut sections from the paraffin block and performing H&E-stained sections and immunostains (using the antibody cocktail for p63, cytokeratins 5 and 14, and α-methylacyl coenzyme A racemase) on the slides. We compared the ASAP workup with the interval workup, the common practice of performing the same immunostains on the saved interval sections, in 105 cases because of focal glandular atypia on the original H&E-stained sections. There were no specimens in which only the interval workup showed a changed diagnosis, but there were 23 specimens (21.9%) in which the preliminary diagnosis was changed to a definitive diagnosis of carcinoma (10 specimens) or a specific benign diagnosis (13 specimens) based solely on the findings of the ASAP workup. The ASAP workup is recommended as a very useful histologic tool for resolving diagnostic problems in prostate needle biopsy specimens.
“Double-Hit” Mature B-Cell Lymphomas Show a Common Immunophenotype by Flow Cytometry That Includes Decreased CD20 Expression
Authors: Wu David , Wood Brent L. , Dorer Russell , Fromm Jonathan R. 
Published: July 2010

Abstract
Lymphomas with 2 translocations involving c-MYC and BCL2 or BCL6 are a subset of biologically aggressive mature B-cell lymphomas now frequently categorized under the entity of B-cell lymphoma, unclassifiable, with features intermediate between Burkitt lymphoma and diffuse large B-cell lymphoma. We identified a cohort of these lymphomas in our databases and retrospectively reviewed corresponding in-house flow cytometric data to determine whether a common immunophenotype might be present. Herein we report on our findings on 10 lymphomas, each with translocations involving c-MYC and BCL2 or BCL6 and show that these cases frequently showed a common immunophenotype that includes decreased expression of CD20. Because these lymphomas often show aggressive biologic behavior and poor clinical outcome, recognition of this relatively common immunophenotype may be useful for identifying cases for confirmatory cytogenetic studies, as often, flow cytometry provides the first assessment of these clinical specimens.
High Percentage of JAK2 Exon 12 Mutation in Asian Patients With Polycythemia Vera
Authors: Yeh Yu-Min , Chen Yi-Lin , Cheng Hsieh-Yin , Su Wu-Chou , Chow Nan-Haw , Chen Tsai-Yun , Ho Chung-Liang 
Published: July 2010

Abstract
We examined the occurrence of JAK2V617F and JAK2 exon 12 mutations in a clinical cohort of polycythemia vera (PV) in Taiwan. Of 22 patients with PV, 17 (77%) had the V617F mutation, and all 5 V617F-negative patients (23%) had the exon 12 mutation. We found 3 different exon 12 mutations: 3 N542-E543del, 1 F537-K539delinsL, and 1 novel mutation, I540-E543delinsKK. Patients with V617F showed significantly higher WBC and platelet counts at diagnosis than patients with exon 12 mutations (P = .021 and P = .038, respectively). We report a surprisingly high incidence of exon 12 mutations in Taiwanese patients with PV, a result quite different from reports in the Western literature (P = .001). Our data suggest that exon 12 mutation of JAK2 in patients with PV may have an uneven geographic distribution. A clinical laboratory providing the V617F test alone may risk missing a substantial number of patients with PV in areas with a high incidence of exon 12 mutation.
Periodic Review of Pathology Training Program Teaching Files
Authors: Martin Matthew A. , Hallmark Kelly C. , Sharkey Francis E. 
Published: July 2010

Abstract
Pathology training programs typically retain teaching files of classic and unusual diagnostic cases. Since diagnostic criteria and terminology are mutable, we reviewed a surgical pathology teaching archive to determine if the materials continued to be acceptable for educational purposes. Each case (from 2001–2003) consisted of 1 to 3 slides and a 3 × 5 card with clinical information and the diagnosis. Cases were reviewed at a daily faculty consensus conference and categorized as follows: no diagnostic change; diagnosis added; or changed diagnosis. Slides were entirely missing from 79 (35.0%) of the 226 cases reviewed. Of the remaining 147 cases, 28 (19.0%) required additional clinical information and/or slides. The final disposition of the 147 cases was as follows: diagnosis unchanged, 126 (85.7%); diagnosis added, 15 (10.2%); and diagnosis changed, 6 (4.1%). Teaching files should be subject to prospective and retrospective controls to preserve the quality of the educational experience.
Special Commentary
Authors: Kinney Walter , Stoler Mark H. , Castle Philip E. 
Published: July 2010

Abstract
Human papillomavirus (HPV) testing is more sensitive for the detection of cervical precancer and cancer than cervical cytology. The increased sensitivity of HPV testing and cytology combined (“cotesting”) compared to cytology alone permitted professional societies to recommend 3-year screening intervals among the cotest-negative results. However, there is an increasing recognition that both clinical sensitivity and specificity of cervical cancer screening are important to patient safety and must be considered in the context of using current and future HPV DNA tests. Exquisite analytic sensitivity for HPV does not increase clinical sensitivity of an HPV test but does result in excessive test positivity and decreased clinical specificity. A recent US Food and Drug Administration (FDA)-approved HPV test, Cervista (Hologic, Bedford, MA), demonstrated excessive test positivity—2 to 4 times more positive than the other FDA-approved HPV test—from its premarketing approval trial. The poor specificity of Cervista raises questions about the safety and applicability of using this test in routine cervical cancer screening. These data provide a didactic example of the potential dangers of mistaking excellent analytic sensitivity and even clinical sensitivity for good clinical performance.