bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells
Authors: Hummon Amanda B , Pitt Jason J , Camps Jordi , Emons Georg , Skube Susan B , Huppi Konrad , Jones Tamara L , Beissbarth Tim , Kramer Frank , Grade Marian , Difilippantonio Michael J , Ried Thomas , Caplen Natasha J 
Published: January 2012

Abstract

Background
Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival.

Results
A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway.

Conclusions
We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.
Detection of Hepatitis B virus in serum and liver of chickens
Authors: Tian Jijing , Xia Kangkang , She Ruiping , Li Wengui , Ding Ye , Wang Jiande , Chen Mingyong , Yin Jun 
Published: January 2012

AbstractHepatitis B virus (HBV) is one of the most important human pathogens. Its existence in food animals could present a significant threat to public health. The objective of this study was to determine if HBV is present in serum and liver of chickens. A total of 129 serum samples from broiler chickens were collected for the detection of HBV antigens and antibodies, and 193 liver samples were tested for HBV DNA sequence by PCR and for the existence of HBV antigens by immunohistochemistry. The overall prevalence of HBsAg, anti-HBs, anti-HBc was 28.68%, 53.49%, 17.05%, respectively, whereas HBeAg, anti-HBe were barely detectable. Three serum samples were found to be positive for both HBsAg and HBeAg. Further analysis of these samples with transmission electron microscopy (TEM) revealed two morphologic particles with 20 nm and 40 nm in diameter, which were similar to small spherical and Danes particles of HBV. The viral DNA sequence identified in two of the chicken livers shared 92.2% of one known HBV strain and 97.9% nucleotide sequence of another HBV strain. Our results showed the existence of HBV in chickens. This would present a significant risk to people who work with live chickens or chicken products if HBV found in chicken could be confirmed to be the same as human HBV.
Emergency incisional hernia repair: a difficult problem waiting for a solution
Authors: Zafar Hasnain , Zaidi Masooma , Qadir Irfan , Memon Ayaz Ahmed 
Published: January 2012

Abstract

Background
Emergency repair of incarcerated incisional hernia with associated bowel obstruction in potentially or contaminated field is technically challenging due to edematous, inflamed and friable tissues with occasional need for concurrent bowel resection and carries high rates of post-operative infectious complications. The aim of this study was to retrospectively assess the wound related morbidity of use of permanent prosthetic mesh in emergency repair of incarcerated incisional hernia with associated bowel obstruction. We also describe a new technique of leaving the mesh exposed to heal by secondary intention with granulation tissue.

Methods
Between 2000 and 2010 a total of 60 patients underwent emergency surgery for incarcerated incisional hernia with associated bowel obstruction with placement of permanent prosthetic mesh. The wound was closed after hernia repair in 55 patients while it was left open to granulate in 5 patients.

Results
In the group of patients with primary wound closure, 11 patients developed superficial surgical site infection, 5 developed deep wound infection and one patient had cellulitis. These patients were treated with wound debridement and antibiotics. Mesh removal was required in one patient. There were no infections in the group of patients who had their surgical wounds left open. One patient in this group died on the fifth postoperative day from septicemia.

Conclusion
Use of permanent prosthetic mesh in emergency repair of incarcerated incisional hernia with associated bowel obstruction. in contaminated field is associated with high risk of wound infection.
The Role of the Drug Information Center in Disaster and Emergency Preparedness
Authors: Wesley T. Lindsey , Charles C. Thomas 
Published: January 2012

Purpose The objective of this article is to describe an innovative practice model that involves the drug information centers and drug information specialists in the Alabama Department of Public Health's (ADPH) response procedure to a terrorism event or natural disaster that requires mass dispensing of a pharmaceutical product. Summary A descriptive account is provided of a strategic partnership between the ADPH and the drug information centers located in the state of Alabama. These sites have been contracted to supply information services to patients during an event where a disaster response is required and adequate patient information regarding the disease state and drug product may be lacking. These sites are utilized on a rotating basis, with the ADPH obligated to provide infrastructure and access to the drug information specialists providing information and counseling over the telephone to patients. These services can be funded through federal and state agencies to support the equipment and personnel needed during a response. Conclusion Drug information centers in Alabama play a key role in the plan for providing reliable and unbiased information to patients during a disaster event where an ADPH response is needed.
RCT of Montelukast as Prophylaxis for Upper Respiratory Tract Infections in Children
Authors: Kozer Eran , Lotem Zachi , Elgarushe Mahmud , Torgovicky Rafael , Cohen Raanan , Cohen Herman A. , Berkovitch Matitiahu 
Published: January 2012

BACKGROUND:Infections with viruses causing upper respiratory tract infection (URI) are associated with increased leukotriene levels in the upper airways. Montelukast, a selective leukotriene-receptor antagonist, is an effective treatment of asthma and allergic rhinitis.OBJECTIVE:To determine whether prophylactic treatment with montelukast reduces the incidence and severity of URI in children.METHODS:A randomized, double-blind, placebo-controlled study was performed in 3 primary care pediatric ambulatory clinics in Israel. Healthy children aged 1 to 5 years were randomly assigned in a 1:1 ratio to receive 12-week treatment with 4 mg oral montelukast or look-alike placebo. Patients were excluded if they had a previous history of reactive airway disease. A study coordinator contacted the parents by phone once a week to obtain information regarding the occurrence of acute respiratory episodes. The parents received a diary card to record any acute symptoms of URI. The primary outcome measure was the number of URI episodes.RESULTS:Three hundred children were recruited and randomly assigned into montelukast (n = 153) or placebo (n = 147) groups. One hundred thirty-one (85.6%) of the children treated with montelukast and 129 (87.7%) of the children treated with placebo completed 12 weeks of treatment. The number of weeks in which URI was reported was 30.4% in children treated with montelukast and 30.7% in children treated with placebo. There was no significant difference in any of the secondary variables between the groups.CONCLUSIONS:In preschool-aged children, 12-week treatment with montelukast, compared with placebo, did not reduce the incidence of URI.
The Helminths of Wild Predatory Mammals of Ukraine. Cestodes
Authors: Kornyushin V. , (Varodi) E. , Malega A. 
Published: January 2012

The Helminths of Wild Predatory Mammals of Ukraine. Cestodes
Data related to cestodes (totally 17 species), registered in predatory mammals in Ukraine are given and summarized. The richest cestode fauna was found in the Polissya region (Zhitomir, Kiev, Chernigov, Sumy Oblasts), Carpathian region and Transcarpathia. A wide host range characterizes the majority of cestodes occurring in predatory mammals of Ukraine. They are registered in both canines (Canidae) and felines (Felidae). Cestodes of the fox (9 species) and wolf (11 species) were studied more comprehensively. Other species of predatory mammals were infected with 1 to 3 species of cestodes.
Cancers with increasing incidence trends in the United States: 1999 through 2008
Authors: Simard Edgar P. , Ward Elizabeth M. , Siegel Rebecca , Jemal Ahmedin 
Published: January 2012

AbstractDespite declines in incidence rates for the most common cancers, the incidence of several cancers has increased in the past decade, including cancers of the pancreas, liver, thyroid, and kidney and melanoma of the skin, as well as esophageal adenocarcinoma and certain subsites of oropharyngeal cancer associated with human papillomavirus (HPV) infection. Population‐based incidence data compiled by the North American Association of Central Cancer Registries were used to examine trends in incidence rates from 1999 through 2008 for the 7 cancers listed by sex, age group, race/ethnicity, and stage at diagnosis. Joinpoint regression was used to calculate average annual percent changes in incidence rates (1999‐2008). Rates for HPV‐related oropharyngeal cancer, esophageal adenocarcinoma, cancer of the pancreas, and melanoma of the skin increased only in whites, except for esophageal adenocarcinoma, which also increased in Hispanic men. Liver cancer rates increased in white, black, and Hispanic men and in black women only. In contrast, incidence rates for thyroid and kidney cancers increased in all racial/ethnic groups, except American Indian/Alaska Native men. Increases in incidence rates by age were steepest for liver and HPV‐related oropharyngeal cancers among those aged 54 to 64 years and for melanoma of the skin in those aged 65 years and older. Notably, for HPV‐related oropharyngeal cancer in men and thyroid cancer in women, incidence rates were higher in those aged 55 to 64 years than in those aged 65 years and older. Rates increased for both local and advanced stage diseases for most cancer sites. The reasons for these increasing trends are not entirely known. Part of the increase (for esophageal adenocarcinoma and cancers of the pancreas, liver, and kidney) may be linked to the increasing prevalence of obesity as well as increases in early detection practices for some cancers. These rising trends will exacerbate the growing cancer burden associated with population expansion and aging. Additional research is needed to determine the underlying reasons for these increasing trends. CA Cancer J Clin 2012. © 2012 American Cancer Society.
Trend of herbicide loads in the river Rhine and its tributaries
Authors: Bach Martin , Frede Hans-Georg 
Published: January 2012

Abstract
Many policies have been established and actions have been taken to reduce pesticide pollution of surface waters. However, the effectiveness of these initiatives was rarely tested on an empirical basis. This study suggests that evidence on the policy effects can be evaluated by analyzing the temporal changes in the loads rather than the concentrations of active ingredients in rivers. It is shown that the long-term change of pesticide emissions into surface waters can be tested statistically by the number of upward versus downward trends in river load. To evaluate the situation in Germany, 57 concentration time series of 14 herbicide substances at 7 river monitoring stations with a minimum of 24 analyses per year were assembled and annual substance river loads were calculated. The longest time course was 17 years (1990–2006). The significance of trends of data rows was analyzed by an univariate Mann–Kendall test that evaluates 27 (47.4%) of the 57 time series as statistically significant downward trended. It took a period of 10 years and longer before the high annual atrazine and simazine loads measured in the years 1990–1991 had been diminished to a drastically lowered level after ban of the herbicides. Data are available on the yearly consumption of 8 substances used in German agriculture. A total of 36 time series for this subset were tested with a partial Mann–Kendall test with the consumption as covariance factor, which reduces the number of significant trends in river load noticeably. Based on this test, only 7 (19.4% of 36) declining time series remain. As a result, the intended effect of measures to reduce surface water contamination by the use of pesticides seems to be only partially successful, however, the database to justify this statement is small. For the water monitoring strategies in Germany, it is recommend to enhance the sampling frequency at river stations. A minimum of a semimonthly sampling interval would facilitate the calculation of valuable annual river loads and would therefore allow a pronounced validation of the long-term change of pesticide emission into rivers. Integr Environ Assess Manag 2012; 8: 543–552. © 2012 SETAC
Data and literature gathering in chemical cancer risk assessment
Authors: Silins Ilona , Korhonen Anna , Högberg Johan , Stenius Ulla 
Published: January 2012

Abstract
In recent years, chemical cancer risk assessment has faced major challenges: the demand for cancer risk assessment has grown considerably with strict legislation regarding chemical safety, whereas cancer hazard identification has turned increasingly complex due to the rapid development and high publication rate in biomedical sciences. Thus, much of the scientific evidence required for hazard identification is hidden in large collections of biomedical literature. Extensive guidelines have been produced to support cancer risk assessment under these circumstances. We evaluated whether these guidelines support the first, critical step of this task—data and literature gathering—and found that the guidance is vague. We propose ways to improve data and literature gathering for cancer risk assessment and suggest developing a computational literature search and analysis tool dedicated to the task. We describe the first prototype tool we have developed and discuss how it could help to improve the quality, consistency, and effectiveness of cancer risk assessment when developed further. Fully reliable automatic data and literature gathering may not be realistic; the retrieved articles will always need to be examined further by risk assessors. However, our proposal offers a starting point for improved data and literature gathering that can benefit the whole cancer risk assessment process. Integr Environ Assess Manag 2012; 8: 412–417. © 2012 SETAC
ANN‐BASED MODEL FOR PLANNING OF GROUNDWATER DEVELOPMENT FOR AGRICULTURAL USAGE
Authors: Ghosh Susmita , Kashyap Deepak 
Published: January 2012

ABSTRACTA computationally inexpensive linked ANN‐optimization model for planning of groundwater development for agricultural usage is presented and illustrated on a canal command area in India. The planning ensures optimization of zonal crop areas subject to the constraints on maximum groundwater table depth and stream–aquifer interflow under dynamic equilibrium. The data required for developing the ANN models of the envisaged state variables comprise an array of zonal crop areas and the corresponding state variables. These data are generated invoking a pre‐calibrated simulation model of groundwater flow. Copyright © 2012 John Wiley & Sons, Ltd.
Effects of ethnicity and socioeconomic status on survival and severity of fibrosis in liver transplant recipients with hepatitis C virus#
Authors: Verna Elizabeth C. , Valadao Rosa , Farrand Erica , Pichardo Elsa M. , Lai Jennifer C. , Terrault Norah A. , Brown Robert S. 
Published: January 2012

Abstract
The ethnicity and socioeconomic status of the host may affect the progression of hepatitis C virus (HCV). We aimed to compare survival and fibrosis progression in Hispanic white (HW) and non-Hispanic white (NHW) recipients of liver transplantation (LT) with HCV. All HW and NHW patients with HCV who underwent transplantation between January 2000 and December 2007 at 2 centers were retrospectively assessed. The primary outcomes were the time to death, death or graft loss due to HCV, and significant fibrosis [at least stage 2 of 4]. Five hundred eleven patients were studied (159 HW patients and 352 NHW patients), and the baseline demographics were similar for the 2 groups. NHW patients were more likely to be male, to have attended college, and to have private insurance, and they had a higher median household income (MHI). The unadjusted rates of survival (log-rank P = 0.93), death or graft loss due to HCV (P = 0.89), and significant fibrosis (P = 0.95) were similar between groups. In a multivariate analysis controlling for center, age [hazard ratio (HR) per 10 years = 1.43, P = 0.01], donor age (HR per 10 years = 1.25, P < 0.001), and rejection (HR = 1.47, P = 0.048) predicted death, whereas HW ethnicity (HR = 1.06, P = 0.77) was not significant. Independent predictors of significant fibrosis were HW ethnicity (HR = 2.42, P = 0.046), MHI (HR per $10,000 = 1.11, P = 0.01), donor age (HR per 10 years = 1.13, P = 0.02), cold ischemia time (HR = 1.06, P = 0.03), and the interaction between ethnicity and MHI (HR = 0.82, P = 0.03). In conclusion, there is no difference in post-LT survival or graft loss due to HCV between HW patients and NHW patients. Socioeconomic factors may influence disease severity; this is suggested by our findings of more significant fibrosis in HW patients with a low MHI. Liver Transpl 18:461–467, 2012. © 2012 AASLD.
Azithromycin maintenance therapy in patients with cystic fibrosis: A dose advice based on a review of pharmacokinetics, efficacy, and side effects
Authors: Wilms Erik B. , Touw Daniel J. , Heijerman Harry G.M. , van der Ent Cornelis K. 
Published: January 2012

AbstractAzithromycin maintenance therapy results in improvement of respiratory function in patients with cystic fibrosis (CF). In azithromycin maintenance therapy, several dosing schemes are applied. In this review, we combine current knowledge about azithromycin pharmacokinetics with the dosing schedules used in clinical trials in order to come to a dosing advise which could be generally applicable. We used data from a recently updated Cochrane meta analysis (2011), the reports of clinical trials and pharmacokinetic studies. Based on these data, it was concluded that a dose level of 22–30 mg/kg/week is the lowest dose level with proven efficacy. Due to the extended half‐life in patients with CF, the weekly dose of azithromycin can be divided in one to seven dosing moments, depending on patient preference and gastro‐intestinal tolerance. No important side effects or interactions with other CF‐related drugs have been documented so far. Pediatr Pulmonol. 2012; 47:658–665. © 2011 Wiley Periodicals, Inc.
Posterior representation with a multi‐modal likelihood using the gaussian sum filter for localization in a known map
Authors: Schoenberg Jonathan R. , Campbell Mark , Miller Isaac 
Published: January 2012

AbstractA Gaussian sum filter (GSF) with component extended Kalman filters (EKF) is proposed as an approach to localizing an autonomous vehicle in an urban environment with limited GPS availability. The GSF uses vehicle‐relative vision‐based measurements of known map features coupled with inertial navigation solutions to accomplish localization in the absence of GPS. The vision‐based measurements have multimodal measurement likelihood functions that are well represented as weighted sums of Gaussian densities. The GSF is used because of its ability to represent the posterior distribution of the vehicle pose with better efficiency (fewer terms, less computational complexity) than a corresponding bootstrap particle filter with various numbers of particles because of the interaction with measurement hypothesis tests. The expectation‐maximization algorithm is used off line to determine the representational efficiency of the particle filter in terms of an effective number of Gaussian densities. In comparison, the GSF, which uses an iterative condensation procedure after each iteration of the filter to maintain real‐time capabilities, is shown through a series of in‐depth empirical studies to more accurately maintain a representation of the posterior distribution than the particle filter using 37 min of recorded data from Cornell University's autonomous vehicle driven in an urban environment, including a 32 min GPS blackout. © 2012 Wiley Periodicals, Inc.
Hope, older adults, and chronic illness: a metasynthesis of qualitative research
Authors: Duggleby Wendy , Hicks Deborah , Nekolaichuk Cheryl , Holtslander Lorraine , Williams Allison , Chambers Thane , Eby Jeannette 
Published: January 2012

duggleby w., hicks d., nekolaichuk c., holtslander l., williams a., chambers t. & eby j. (2012) Hope, older adults, and chronic illness: a metasynthesis of qualitative research. Journal of Advanced Nursing68(6), 1211–1223.AbstractAim.  To report a metasynthesis review of qualitative research studies exploring the hope experience of older persons with chronic illness.Background.  Hope is a psychosocial resource used by persons to deal with their chronic illness experience.Data sources.  A comprehensive search of multiple databases for studies of the hope experience (published 1980–2010) was completed. Inclusion criteria were included qualitative studies of the hope experience of persons (all genders; mean age 60 years and older), with chronic illnesses, and publications in any language and country.Review methods.  The metasynthesis followed four procedural steps: (a) comprehensive search, (b) quality appraisal, (c) classification of studies, and (d) synthesis of findings.Results.  Twenty studies were included in the metasynthesis representing research from a variety of different countries and populations with differing medical diagnoses. The characteristics of hope included: (a) dynamic or situational nature, (b) multiple co‐existing types, (c) objects that were desirable realistic possibilities, (d) future‐focused, and (e) involvement of choice/will. Hope as ‘transcending possibilities’ represented the integration of two processes of transcendence and positive reappraisal. Reaching inwardly and outwardly and finding meaning and purpose were sub‐processes of transcendence, whereas re‐evaluating hope in light of illness and finding positive possibilities were sub‐processes of positive reappraisal.Conclusions.  The concept of hope may differ for older adults vs. younger adults in its interaction with suffering. Resources for hope are both internal and external. Finding meaning and positive reappraisal are important strategies to help older adults with chronic illness maintain their hope.