bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis
Authors: Chen Shun-Fu , Juang Yue-Li , Chou Wei-Kang , Lai Jin-Mei , Huang Chi-Ying F , Kao Cheng-Yan , Wang Feng-Sheng 
Published: December 2009

Abstract

Background
Network Component Analysis (NCA) is a network structure-driven framework for deducing regulatory signal dynamics. In contrast to principal component analysis, which can be employed to select the high-variance genes, NCA makes use of the connectivity structure from transcriptional regulatory networks to infer dynamics of transcription factor activities. Using the budding yeast Saccharomyces cerevisiae as a model system, we aim to deduce regulatory actions of cytokinesis-related genes, using precise spatial proximity (midbody) and/or temporal synchronicity (cytokinesis) to avoid full-scale computation from genome-wide databases.

Results
NCA was applied to infer regulatory actions of transcription factor activity from microarray data and partial transcription factor-gene connectivity information for cytokinesis-related genes, which were a subset of genome-wide datasets. No literature has so far discussed the inferred results through NCA are independent of the scale of the gene expression dataset. To avoid full-scale computation from genome-wide databases, four cytokinesis-related gene cases were selected for NCA by running computational analysis over the transcription factor database to confirm the approach being scale-free. The inferred dynamics of transcription factor activity through NCA were independent of the scale of the data matrix selected from the four cytokinesis-related gene sets. Moreover, the inferred regulatory actions were nearly identical to published observations for the selected cytokinesis-related genes in the budding yeast; namely, Mcm1, Ndd1, and Fkh2, which form a transcription factor complex to control expression of the CLB2 cluster (i.e. BUD4, CHS2, IQG1, and CDC5).

Conclusion
In this study, using S. cerevisiae as a model system, NCA was successfully applied to infer similar regulatory actions of transcription factor activities from two various microarray databases and several partial transcription factor-gene connectivity datasets for selected cytokinesis-related genes independent of data sizes. The regulated action for four selected cytokinesis-related genes (BUD4, CHS2, IQG1, and CDC5) belongs to the M-phase or M/G1 phase, consistent with the empirical observations that in S. cerevisiae, the Mcm1-Ndd1-Fkh2 transcription factor complex can regulate expression of the cytokinesis-related genes BUD4, CHS2, IQG1, and CDC5. Since Bud4, Iqg1, and Cdc5 are highly conserved between human and yeast, results obtained from NCA for cytokinesis in the budding yeast can lead to a suggestion that human cells should have the transcription regulator(s) as the budding yeast Mcm1-Ndd1-Fkh2 transcription factor complex in controlling occurrence of cytokinesis.
Spectral affinity in protein networks
Authors: Voevodski Konstantin , Teng Shang-Hua , Xia Yu 
Published: December 2009

Abstract

Background
Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length.

Results
We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks.

Conclusion
We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to quickly find nodes closest to a queried vertex in any protein network available from BioGRID or specified by the user.
Primary mucinous adenocarcinoma in a defunctionalized urinary bladder: a case report
Authors: Taneous Mary , Ramalingam Preetha , Mode Donald G , Heiner Jared G , Terris Martha K , Lee Jeffrey R 
Published: December 2009

Abstract

Introduction
Malignancies are rare in defunctionalized bladders and are thought to arise from metaplasia secondary to chronic inflammation. Transitional cell and squamous cell carcinomas are the most common but there are three reported cases of mucinous adenocarcinoma.

Case presentation
We report a 57-year-old Caucasian man presenting with penile discharge for 30 years following ileal conduit surgery for neurogenic bladder, and who was found to have primary mucinous adenocarcinoma of his defunctionalized bladder.

Conclusion
Although urinary diversion without cystectomy is less common in current urologic practice, there are many patients with longstanding defunctionalized bladders. While there are no established surveillance protocols, defunctionalized bladder patients with urethral discharge should be evaluated.
Influenza A (H1N1) in Rome, Italy in family: three case reports
Authors: Lisena Francesco , Bordi Licia , Carletti Fabrizio , Castilletti Concetta , Ferraro Federica , Lalle Eleonora , Lanini Simone , Ruscitti Luca Enrico , Fusco Francesco Maria 
Published: December 2009

Abstract

Introduction
A new Influenza A virus H1N1 appeared in March-April 2009, and thousands of cases are being reported worldwide. In the initial months, several imported cases were reported in many European countries, while some countries reported local chains of transmission. We describe the first cluster of in-country transmission of the new Influenza A H1N1 which occurred in Italy, involving 3 patients.

Case presentation
Patient 1, a 11-year-old male child developed fever, cough, and general malaise 4 days after returning from a travel to Mexico. Some days later, the 69-year-old grandfather (patient 2), who did not travel to Mexico, and the 33-month-old brother (patient 3) of patient 1 developed mild influenza symptoms. PCR tests resulted positive for Influenza A, and sequence analysis confirmed infection with the Influenza A (H1N1) strain for all three patients. Some problems were experienced in the administration of chemoprophylaxis and therapy in the patient 3. The chemoprophylaxis policies in other family members are described, too.

Conclusion
Some interesting facts emerge from the analysis of this cluster. The transmission of Influenza A H1N1 virus seems to be dependent on strict contacts. Patient 2 and patient 3 did not take the chemoprophylaxis properly. The problems in the administration of chemoprophylaxis and therapy to patient 3 suggest that in infants specific individual-based strategies for assuring the correct administration are advisable.
Prothrombin complex concentrate in surgical patients: retrospective evaluation of vitamin K antagonist reversal and treatment of severe bleeding
Authors: Schick Kerstin S , Fertmann Jan M , Jauch Karl-Walter , Hoffmann Johannes N 
Published: December 2009

Abstract
Introduction
Prothrombin complex concentrates are recommended for rapid reversal of vitamin K anticoagulants. As they normalize levels of vitamin K dependent clotting factors and re-establish hemostasis, they may also be used as adjunctive therapy in patients with major bleeding. The aim of this study was to retrospectively evaluate the efficacy of prothrombin complex concentrates in the surgical setting.

Methods
The case notes of 50 patients requiring urgent oral anticoagulation reversal (n = 12) or with severe perioperative coagulopathic bleeding (n = 38) who received an infusion of prothrombin complex concentrate (Beriplex P/N(R) 500) at the surgical department of the University of Munich Hospital, Germany were retrospectively reviewed. Efficacy of prothrombin complex concentrate application was evaluated using the Quick test, reported as an international normalized ratio, hemodynamic measurements and requirement for blood products. Safety assessments included whole blood hemoglobin levels and specific parameters of organ dysfunction.

Results
Baseline characteristics were comparable, except that mean baseline international normalized ratio and hemoglobin levels were significantly higher (P < 0.01) in anticoagulation reversal than in bleeding patients. In anticoagulation reversal, the international normalized ratio was significantly reduced (from 2.8 +/- 0.2 at baseline to 1.5 +/- 0.1, P < 0.001) after one prothrombin complex concentrate infusion (median dose 1500 IU; lower quartile 1,000, upper quartile 2,000). No major bleeding was observed during surgery after prothrombin complex concentrate administration. Only one patient received platelets and red blood cell transfusion after prothrombin complex concentrate administration. In bleeding patients, infusion of prothrombin complex concentrate (median dose 2,000 IU; lower quartile 2,000, upper quartile 3,000) significantly reduced the INR from 1.7 +/- 0.1 at baseline to 1.4 +/- 0.1 (P < 0.001). This decrease was unrelated to fresh frozen plasma or vitamin K administration. Bleeding stopped after prothrombin complex concentrate administration in 4/11 (36%) patients with surgical bleeding and 26/27 (96%) patients with diffuse bleeding. Hemoglobin levels increased significantly from baseline in bleeding patients (P < 0.05) and mean arterial pressure stabilized (P < 0.05). No thrombotic events or changes in organ function were reported in any patient.

Conclusions
Prothrombin complex concentrate application effectively reduced international normalized ratios in anticoagulation reversal, allowing surgical procedures and interventions without major bleeding. In bleeding patients, the improvement in coagulation after prothrombin complex concentrate administration was judged to be clinically significant.
Vestibulo-ocular monitoring as a predictor of outcome after severe traumatic brain injury
Authors: Schlosser Hans-Georg , Lindemann Jan-Nikolaus , Vajkoczy Peter , Clarke Andrew H 
Published: December 2009

Abstract
Introduction
Based on the knowledge that traumatic brainstem damage often leads to alteration in brainstem functions, including the vestibulo-ocular reflex, the present study is designed to determine whether prediction of outcome in the early phase after severe traumatic brain injury is possible by means of vestibulo-ocular monitoring.

Methods
Vestibulo-ocular monitoring is based on video-oculographic recording of eye movements during galvanic labyrinth polarization. The integrity of vestibulo-ocular reflex is determined from the eye movement response during vestibular galvanic labyrinth polarization stimulation. Vestibulo-ocular monitoring is performed within three days after traumatic brain injury and the oculomotor response compared to outcome after six months (Glasgow Outcome Score).

Results
Twenty-seven patients underwent vestibulo-ocular monitoring within three days after severe traumatic brain injury. One patient was excluded from the study. In 16 patients oculomotor response was induced, in the remaining 11 patients no oculomotor response was observed. The patients' outcome was classified as Glasgow Outcome Score 1-2 or as Glasgow Outcome Score 3 to 5. Statistical testing supported the hypothesis that those patients with oculomotor response tended to recover (exact two-sided Fisher-Test (P < 10-3)).

Conclusions
The results indicate that vestibulo-ocular monitoring with galvanic labyrinth polarization performed during the first days after traumatic brain injury helps to predict favourable or unfavourable outcome. As an indicator of brainstem function, vestibulo-ocular monitoring provides a useful, complementary approach to the identification of brainstem lesions by imaging techniques.
Kathleen Nolan
Authors: Mays Hoopes Laura L. 
Published: December 2009

Note from the Editor Educator Highlights for CBE-LSE show how professors at different kinds of institutions educate students in life sciences with inspiration and panache. If you have a particularly creative teaching portfolio yourself, or if you wish to nominate an inspiring colleague to be profiled, please email Laura Hoopes at lhoopes@pomona.edu .
Empirical typology of bipolar I mood episodes
Authors: Solomon David A. , Leon Andrew C. , Endicott Jean , Coryell William H. , Li Chunshan , Fiedorowicz Jess G. , Keller Martin B. 
Published: December 2009

BackgroundMuch remains unknown about the phenomenology of bipolar I disorder.AimsTo determine the type of bipolar I mood episodes that occur over time, and their relative frequency.MethodA total of 219 individuals with Research Diagnostic Criteria bipolar I disorder were prospectively followed for up to 25 years (median 20 years). Psychopathology was assessed with the Longitudinal Interval Follow-up Evaluation.ResultsOverall, 1208 mood episodes were prospectively observed. The episodes were empirically classified as follows: major depression, 30.9% (n= 373); minor depression, 13.0% (n= 157); mania, 20.4% (n= 246); hypomania, 10.4% (n= 126); cycling, 17.3% (n= 210); cycling plus mixed state, 7.8% (n= 94); and mixed, 0.2% (n= 2).ConclusionsCycling episodes constituted 25% of all episodes. Work groups revising ICD–10 and DSM–IV should add a category for bipolar I cycling episode.
Treatment of ischaemic heart disease and stroke in individuals with psychosis under universal healthcare
Authors: Kisely Stephen , Campbell Leslie Anne , Wang Yan 
Published: December 2009

BackgroundMost data on the quality of vascular care for individuals with psychiatric conditions come from countries without universal healthcare.AimsTo investigate the treatment of people with psychosis admitted for ischaemic heart disease or stroke under universal healthcare.MethodA population-based study of administrative data comparing Canadians with and without a history of schizophrenia or related psychosis (n= 65 039).ResultsOf 49 248 admissions for ischaemic heart disease, 1285 had a history of psychosis. Despite a higher 1-year mortality, they were less likely to receive guideline-consistent treatment: e.g. coronary artery bypass grafting (adjusted odds ratio (OR) = 0.35, 95% CI 0.25–0.48), beta-blockers (adjusted OR = 0.82, 95% CI 0.71–0.95) and statins (adjusted OR = 0.51, 95% CI 0.41–0.63). Of 15 791 admissions for stroke, 594 had a history of psychosis. Despite higher 1-year mortality rates, they were less likely to receive cerebrovascular arteriography or warfarin.ConclusionsPeople with a history of psychosis do not receive equitable levels of vascular care under universal healthcare.
Combined Resistance and Aerobic Exercise Program Reverses Muscle Loss in Men Undergoing Androgen Suppression Therapy for Prostate Cancer Without Bone Metastases: A Randomized Controlled Trial
Authors: Galvão Daniel A. , Taaffe Dennis R. , Spry Nigel , Joseph David , Newton Robert U. 
Published: December 2009

Purpose Androgen suppression therapy (AST) results in musculoskeletal toxicity that reduces physical function and quality of life. This study examined the impact of a combined resistance and aerobic exercise program as a countermeasure to these AST-related toxicities. Patients and Methods Between 2007 and 2008, 57 patients with prostate cancer undergoing AST (commenced > 2 months prior) were randomly assigned to a program of resistance and aerobic exercise (n = 29) or usual care (n = 28) for 12 weeks. Primary end points were whole body and regional lean mass. Secondary end points were muscle strength and function, cardiorespiratory capacity, blood biomarkers, and quality of life. Results Analysis of covariance was used to compare outcomes for groups at 12 weeks adjusted for baseline values and potential confounders. Patients undergoing exercise showed an increase in lean mass compared with usual care (total body, P = .047; upper limb, P < .001; lower limb, P = .019) and similarly better muscle strength (P < .01), 6-meter walk time (P = .024), and 6-meter backward walk time (P = .039). Exercise also improved several aspects of quality of life including general health (P = .022) and reduced fatigue (P = .021) and decreased levels of C-reactive protein (P = .008). There were no adverse events during the testing or exercise intervention program. Conclusion A relatively brief exposure to exercise significantly improved muscle mass, strength, physical function, and balance in hypogonadal men compared with normal care. The exercise regimen was well tolerated and could be recommended for patients undergoing AST as an effective countermeasure to these common treatment-related adverse effects.
Revised Tumor and Node Categorization for Rectal Cancer Based on Surveillance, Epidemiology, and End Results and Rectal Pooled Analysis Outcomes
Authors: Gunderson Leonard L. , Jessup John Milburn , Sargent Daniel J. , Greene Frederick L. , Stewart Andrew 
Published: December 2009

Purpose The sixth edition of the American Joint Committee on Cancer (AJCC) rectal cancer staging subdivided stage II into IIA (T3N0) and IIB (T4N0) and stage III into IIIA (T1-2N1M0), IIIB (T3-4N1M0), and IIIC (anyTN2M0). Subsequent analyses supported revised substaging of stage III as a result of improved survival with T1-2N2 versus T3-4N2 and survival of T4N1 more similar to T3-4N2 than T3N1. The AJCC Hindgut Taskforce sought population-based validation that depth of invasion interacts with nodal status to affect survival. Methods Surveillance, Epidemiology, and End Results (SEER) population-based data from January 1992 to December 2004 for 35,829 patients with rectal cancer were compared with rectal pooled analysis data (3,791 patients). T4N0 cancers were stratified by tumors that perforate visceral peritoneum (T4a) versus tumors that invade or are adherent to adjacent organs or structures (T4b). N1 and N2 were stratified by number of positive nodes as follows: N1a/N1b (one v two to three nodes) and N2a/N2b (four to six v ≥ seven nodes). Five-year observed and relative survival rates were obtained for each TN category. Results SEER rectal cancer analyses confirm that T1-2N2 cancers have better prognosis than T3-4N2, T4bN1 have similar prognosis to T4N2, T1-2N1 have similar prognosis to T2N0/T3N0, and T1-2N2a have similar prognosis to T2N0/T3N0 (T1N2a) or T4aN0 (T2N2a). Prognosis for T4a lesions is better than T4b by N category. The number of positive nodes affects prognosis. Conclusion This SEER population-based rectal cancer analysis validates the rectal pooled analyses and supports the shift of T1-2N2 lesions from IIIC to IIIA or IIIB and T4bN1 from IIIB to IIIC. SEER outcomes support subdividing T4, N1, and N2 and revised substaging of stages II and III. Survival by TN category suggests a complex biologic interaction between depth of invasion and nodal status.
Intravenous Immunoglobulin and Necrotizing Enterocolitis in Newborns With Hemolytic Disease
Authors: Figueras-Aloy Josep , Rodríguez-Miguélez José M. , Iriondo-Sanz Martin , Salvia-Roiges María-Dolores , Botet-Mussons Francesc , Carbonell-Estrany Xavier 
Published: December 2009

OBJECTIVE: The objective of this study was to assess whether the use of high-dose intravenous immunoglobulin (IVIG) in late-preterm and term newborns with severe isoimmune hemolytic jaundice caused by Rh and ABO incompatibility was a risk factor for necrotizing enterocolitis (NEC).
METHODS: An observational, retrospective study that encompassed 16 years was conducted. A total of 492 liveborn infants who were of ≥34 weeks' gestation and had severe isoimmune hemolytic jaundice caused by Rh (n = 91) and ABO (n = 401) incompatibility and were treated with phototherapy were included in the study. IVIG (500 mg/kg over 2–4 hours) was indicated when total serum bilirubin level plus 2 points reached 85% of the cutoff value for performing exchange transfusion.
RESULTS: A total of 167 (34%) infants received IVIG. NEC was diagnosed in 11 (2.2%) patients: 10 (6%) in the IVIG-treated group and 1 (0.3%) in the non–IVIG-treated group. Five patients required urgent operation, and 1 of them died as a result of massive intestinal necrosis. Another patient died 2 years later as a result of short bowel syndrome. In the multivariate analysis, cesarean delivery (odds ratio [OR]: 3.76 [95% confidence interval (CI): 1.10–12.90), Apgar test at 5 minutes (OR: 0.50 [95% CI: 0.40–0.64), and IVIG (OR: 31.66 [95% CI: 3.25–308.57]) were independent factors significantly associated with NEC.
CONCLUSIONS: The use of high-dose IVIG for severe isoimmune hemolytic jaundice in late-preterm and term infants was associated with a higher incidence of NEC.