bluuebunny/crossref_metadata_2025_split huggingface dataset:
The intestinal microbiome of fish under starvation
Authors: Xia Jun Hong , Lin Grace , Fu Gui Hong , Wan Zi Yi , Lee May , Wang Le , Liu Xiao Jun , Yue Gen Hua 
Published: April 2014

AbstractBackgroundStarvation not only affects the nutritional and health status of the animals, but also the microbial composition in the host’s intestine. Next-generation sequencing provides a unique opportunity to explore gut microbial communities and their interactions with hosts. However, studies on gut microbiomes have been conducted predominantly in humans and land animals. Not much is known on gut microbiomes of aquatic animals and their changes under changing environmental conditions. To address this shortcoming, we determined the microbial gene catalogue, and investigated changes in the microbial composition and host-microbe interactions in the intestine of Asian seabass in response to starvation.ResultsWe found 33 phyla, 66 classes, 130 orders and 278 families in the intestinal microbiome. Proteobacteria (48.8%), Firmicutes (15.3%) and Bacteroidetes (8.2%) were the three most abundant bacteria taxa. Comparative analyses of the microbiome revealed shifts in bacteria communities, with dramatic enrichment of Bacteroidetes, but significant depletion of Betaproteobacteria in starved intestines. In addition, significant differences in clusters of orthologous groups (COG) functional categories and orthologous groups were observed. Genes related to antibiotic activity in the microbiome were significantly enriched in response to starvation, and host genes related to the immune response were generally up-regulated.ConclusionsThis study provides the first insights into the fish intestinal microbiome and its changes under starvation. Further detailed study on interactions between intestinal microbiomes and hosts under dynamic conditions will shed new light on how the hosts and microbes respond to the changing environment.
Deregulated expression of circadian clock genes in gastric cancer
Authors: Hu Ming-Luen , Yeh Kun-Tu , Lin Pai-Mei , Hsu Cheng-Ming , Hsiao Hui-Hua , Liu Yi-Chang , Lin Hugo You-Hsien , Lin Sheng-Fung , Yang Ming-Yu 
Published: April 2014

Abstract

Background
Gastric cancer (GC), an aggressive malignant tumor of the alimentary tract, is a leading cause of cancer-related death. Circadian rhythm exhibits a 24-hour variation in physiological processes and behavior, such as hormone levels, metabolism, gene expression, sleep and wakefulness, and appetite. Disruption of circadian rhythm has been associated with various cancers, including chronic myeloid leukemia, head and neck squamous cell carcinoma, hepatocellular carcinoma, endometrial carcinoma, and breast cancer. However, the expression of circadian clock genes in GC remains unexplored.

Methods
In this study, the expression profiles of eight circadian clock genes (PER1, PER2, PER3, CRY1, CRY2, CKIϵ, CLOCK, and BMAL1) of cancerous and noncancerous tissues from 29 GC patients were investigated using real-time quantitative reverse-transcriptase polymerase chain reaction and validated through immunohistochemical analysis.

Results
We found that PER2 was significantly up-regulated in cancer tissues (p < 0.005). Up-regulated CRY1 expression was significantly correlated with more advanced stages (stage III and IV) (p < 0.05).

Conclusions
Our results suggest deregulated expressions of circadian clock genes exist in GC and circadian rhythm disturbance may be associated with the development of GC.
The impact of HBV or HCV infection in a cohort of HIV-infected pregnant women receiving a nevirapine-based antiretroviral regimen in Malawi
Authors: Andreotti Mauro , Pirillo Maria Franca , Liotta Giuseppe , Jere Haswell , Maulidi Martin , Sagno Jean-Baptiste , Luhanga Richard , Amici Roberta , Mancini Maria Grazia , Gennaro Elisabetta , Marazzi Maria Cristina , Vella Stefano , Giuliano Marina , Palombi Leonardo , Mancinelli Sandro 
Published: April 2014

Abstract

Background
Coinfection with the hepatitis viruses is common in the HIV population in sub-Saharan Africa. The aim of this study was to assess, in a cohort of HIV-infected pregnant women receiving antiretroviral drugs (ARVs), the prevalence of HBV and HCV infections and to determine the impact of these infections on the occurrence of liver toxicity and on the viro-immunological response.

Methods
Women were screened for HBsAg and HCV-RNA before starting, at week 25 of gestational age, an antiretroviral regimen consisting of lamivudine and nevirapine plus either stavudine or zidovudine. Women with CD4+ < 350/mm3 continued ARVs indefinitely, while the other women interrupted treatment 6 months postpartum (end of breastfeeding period). Both groups were followed for 2 years after delivery. Liver function was monitored by alanine aminotransferase (ALT) measurement. The Cox proportional hazards model was used to identify factors associated with the emergence of liver toxicity.

Results
A total of 28 women out of the 309 enrolled in the study (9.1%) were coinfected with HBV (n. 27), or HCV (n. 1). During follow-up 125 women (40.4%) developed a grade ≥ 1 ALT elevation, 28 (9.1%) a grade ≥ 2 and 6 (1.9%) an elevation defining grade 3 toxicity. In a multivariate model including age, baseline CD4+ count and hemoglobin level, the presence of either HBV or HCV infection was significantly associated with the development of an ALT increase of any grade (P = 0.035). Moderate or severe liver laboratory toxicity (grade ≥ 2) was more frequent among women with baseline CD4+ > 250/mm3 (P = 0.030). In HBV-infected women a baseline HBV-DNA level above 10,000 IU/ml was significantly associated to the development of liver toxicity of grade ≥ 1 (P = 0.040). Coinfections had no impact on the immunological and virological response to antiretroviral drugs up to 2 years after delivery.

Conclusions
In this cohort of nevirapine-treated women the presence of HBV or HCV was associated only to the development of mild liver toxicity, while the occurrence of moderate or severe hepatoxicity was correlated to a baseline CD4+ count > 250/mm3. No statistically significant effect of the coinfections was observed on the efficacy of antiretroviral therapy.
p21 and CD166 as predictive markers of poor response and outcome after fluorouracil-based chemoradiotherapy for the patients with rectal cancer
Authors: Sim Sung Hoon , Kang Mi-Hyun , Kim Yu Jung , Lee Keun-Wook , Kim Duck-Woo , Kang Sung-Bum , Eom Keun-Yong , Kim Jae-Sung , Lee Hye Seung , Kim Jee Hyun 
Published: April 2014

Abstract

Background
Pre-operative chemoradiotherapy (CRT) is the standard treatment in clinical stage T3/4 or node positive rectal cancer. However, there are no established biomarkers that can predict the pathological response and clinical outcome to CRT.

Methods
Immunohistochemical staining was performed in tissue arrays constructed from core tissue specimens taken before treatment and from operative specimens from 112 patients who received 5-FU based pre-operative CRT and surgery. Expression of Ki67, TS, BAX, EpCAM, p53, p21, EGFR, CD44, CD133, CD166, HIF1α and ALDH1 were assessed and correlated with tumor regression grades and disease free survival.

Results
Of the 112 patients (M/F 74/38, median age: 62), 20 (17.9%) patients achieved pathologic complete remission (pCR). In analyzing the associations between marker expressions and tumor regression grades, high p21 expression at the pretreatment biopsy was significantly associated with non-pCR (p = 0.022) and poor disease free survival (median DFS - low vs high p21: 75.8 vs 58.1 months, p = 0.002). In the multivariate analysis, high p21 expression level at the pre-treatment biopsy was significantly associated with poor DFS (p = 0.001, HR 6.14; 95% CI 2.03, 18.55). High CD166 expression level at the pretreatment biopsy was also associated with poor DFS (p = 0.003; HR 5.61; 95% CI 1.81, 17.35).

Conclusion
These show high p21 and CD166 expression at the pretreatment biopsy were associated with tumor regression and poor prognosis in patients treated with 5-FU based CRT. Larger, prospective and functional studies are warranted to determine the role of p21 and CD166 as predictive biomarker of response to CRT.
Effects of honey supplementation combined with different jumping exercise intensities on bone mass, serum bone metabolism markers and gonadotropins in female rats
Authors: Mosavat Maryam , Ooi Foong Kiew , Mohamed Mahaneem 
Published: April 2014

Abstract

Background
The effects of high and low jumping exercise intensities combined with honey on bone and gonadotrophins were investigated in eighty four 9 week-old female rats.

Methods
The experimental groups were 20 or 80 jumps per day combined with or without honey supplementation (HJ20, HJ80, J20 and J80), honey supplementation (H), sedentary without supplementation control (C), and baseline control (C0) groups.

Results
Study results showed that HJ80 elicited greatest beneficial effects on tibial and femoral mass, serum total calcium and alkaline phosphatase concentrations. There were significantly (p < 0.05) lower levels of serum follicle stimulating hormone concentrations in H, J20, J80 compared to C, with exception of HJ20 and HJ80. Serum luteinizing hormone concentrations were significantly (p < 0.05) greater in HJ20, HJ80 and J20 compared to J80.

Conclusions
It appears that high intensity jumping exercise combined with honey supplementation resulted more discernable effects on bone. Meanwhile, honey may protect against the adverse effects induced by jumping exercise on gonadotropins in female rats.
IMPACT - Integrative Medicine PrimAry Care Trial: protocol for a comparative effectiveness study of the clinical and cost outcomes of an integrative primary care clinic model
Authors: Herman Patricia M , Dodds Sally E , Logue Melanie D , Abraham Ivo , Rehfeld Rick A , Grizzle Amy J , Urbine Terry F , Horwitz Randy , Crocker Robert L , Maizes Victoria H 
Published: April 2014

Abstract

Background
Integrative medicine (IM) is a patient-centered, healing-oriented clinical paradigm that explicitly includes all appropriate therapeutic approaches whether they originate in conventional or complementary medicine (CM). While there is some evidence for the clinical and cost-effectiveness of IM practice models, the existing evidence base for IM depends largely on studies of individual CM therapies. This may in part be due to the methodological challenges inherent in evaluating a complex intervention (i.e., many interacting components applied flexibly and with tailoring) such as IM.

Methods/Design
This study will use a combination of observational quantitative and qualitative methods to rigorously measure the health and healthcare utilization outcomes of the University of Arizona Integrative Health Center (UAIHC), an IM adult primary care clinic in Phoenix, Arizona. There are four groups of study participants. The primary group consists of clinic patients for whom clinical and cost outcomes will be tracked indicating the impact of the UAIHC clinic (n = 500). In addition to comparing outcomes pre/post clinic enrollment, where possible, these outcomes will be compared to those of two matched control groups, and for some self-report measures, to regional and national data. The second and third study groups consist of clinic patients (n = 180) and clinic personnel (n = 15-20) from whom fidelity data (i.e., data indicating the extent to which the IM practice model was implemented as planned) will be collected. These data will be analyzed to determine the exact nature of the intervention as implemented and to provide covariates to the outcomes analyses as the clinic evolves. The fourth group is made up of patients (n = 8) whose path through the clinic will be studied in detail using qualitative (periodic semi-structured interviews) methods. These data will be used to develop hypotheses regarding how the clinic works.

Discussion
The US health care system needs new models of care that are more patient-centered and empower patients to make positive lifestyle changes. These models have the potential to reduce the burden of chronic disease, lower the cost of healthcare, and offer a sustainable financial paradigm for our nation. This protocol has been designed to test whether the UAIHC can achieve this potential.

Trial registration
Clinical Trials.gov NCT01785485.
Relative efficiency and productivity: a preliminary exploration of public hospitals in Beijing, China
Authors: Li Hao , Dong Siping , Liu Tingfang 
Published: April 2014

Abstract

Background
Third-grade hospitals in Beijing have been rapidly developing in capacity and scale for many years. These hospitals receive a large number of patients, and ensuring their efficient operation is crucial in meeting people’s healthcare needs. In this context, a study of their relative efficiency and productivity would be helpful to identify the driving factors and further improve their performance.

Methods
After a review of literature, the current numbers of open beds and employees were selected as input variables. The number of outpatient and emergency visits and the number of discharged patients were selected as output variables. A total of 12 third-grade Class A general public hospitals in Beijing were selected for a preliminary study. The panel data from 2006–2009 were collected by the National Institute of Hospital Administration, Ministry of Health of P.R. China. Descriptive analysis and data envelopment analysis were used to analyze the data using Stata 10.0 and DEAP(V2.1) software.

Results
In the 2006–2009 period, descriptive results show that sample hospitals continuously expanded their capacity and scale, with growth rate of total revenue being the highest among all variables. The DEA results show that the average annual growth rate of productivity was 26.7%, and the rates were 47.3%, 21.3% and 13.8% respectively for two consecutive years. The average annual growth rate of technological change was 28.3%, and the rates were 49.4%, 21.5% and 16.4% respectively for two consecutive years. The average annual growth rate of technical efficiency change was -1.3%, and the rates were -1.4%, -0.02% and -2.2% respectively for two consecutive years.

Conclusions
The sample hospitals in Beijing experienced substantial productivity growth, but annual growth rates were declining. Substantial technological change was the main contributor to the growth. Although some hospitals exhibited improvements in technical efficiency, there was a slight decline in general. To improve overall efficiency and productivity, both government and hospitals need to further drive positive technological change, technical change, and allocative efficiency of public hospitals. More empirical studies are needed to include more hospitals of all three grades at a larger scale.
Slit2N and Robo4 regulate lymphangiogenesis through the VEGF-C/VEGFR-3 pathway
Authors: Yu Jinlong , Zhang Xuefeng , Kuzontkoski Paula M , Jiang Shuxian , Zhu Weiquan , Li Dean Y , Groopman Jerome E 
Published: April 2014

Abstract

Background
Signaling through vascular endothelial growth factor C (VEGF–C) and VEGF receptor 3 (VEGFR-3) plays a central role in lymphangiogenesis and the metastasis of several cancers via the lymphatics. Recently, the Slit2/Robo4 pathway has been recognized as a modulator of vascular permeability and integrity. Signaling via the Robo receptor inhibits VEGF-mediated effects; however, its effects on lymphatic endothelial cell function have not been well characterized.

Results
We found that pretreatment with Slit2N, an active fragment of Slit2, inhibited VEGF-C-mediated lung-derived lymphatic endothelial cell (L-LEC) proliferation, migration, and in vitro tube formation. Slit2N induced the internalization of VEGFR-3, which blocked its activation, and inhibited the activation of the PI3K/Akt pathway by VEGF-C in L-LECs. Moreover, we found that inhibition of VEGF-C-induced effects by Slit2N was Robo4-dependent.

Conclusion
These results indicate that Slit2N/Robo4 modulates several key cellular functions, which contribute to lymphangiogenesis, and identify this ligand-receptor pair as a potential therapeutic target to inhibit lymphatic metastasis of VEGF-C-overexpressing cancers and manage lymphatic dysfunctions characterized by VEGF-C/VEGFR-3 activation.
Preparation of uniform magnetic recoverable catalyst microspheres with hierarchically mesoporous structure by using porous polymer microsphere template
Authors: Ren Lianbing , Teng Chao , Zhu Lili , He Jie , Wang You , Zuo Xinbing , Hong Mei , Wang Yong , Jiang Biwang , Zhao Jing 
Published: April 2014

Abstract
Merging nanoparticles with different functions into a single microsphere can exhibit profound impact on various applications. However, retaining the unique properties of each component after integration has proven to be a significant challenge. Our previous research demonstrated a facile method to incorporate magnetic nanoparticles into porous silica microspheres. Here, we report the fabrication of porous silica microspheres embedded with magnetic and gold nanoparticles as magnetic recoverable catalysts. The as-prepared multifunctional composite microspheres exhibit excellent magnetic and catalytic properties and a well-defined structure such as uniform size, high surface area, and large pore volume. As a result, the very little composite microspheres show high performance in catalytic reduction of 4-nitrophenol, special convenient magnetic separability, long life, and good reusability. The unique nanostructure makes the microspheres a novel stable and highly efficient catalyst system for various catalytic industry processes.

PACS: 61.46.-w; 75.75.-c; 81.07.-b
Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
Authors: Kuppuswamy Usha , Ananthasubramanian Seshan , Wang Yanli , Balakrishnan Narayanaswamy , Ganapathiraju Madhavi K 
Published: April 2014

Abstract

Background
The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating these findings into biomedically useful information is to find out the mechanism of the action of these genes. However, GWAS studies often implicate genes whose functions are currently unknown; for example, MYEOV, ANKLE1, TMEM45B and ORAOV1 are found to be associated with breast cancer, but their molecular function is unknown.

Results
We carried out Bayesian inference of Gene Ontology (GO) term annotations of genes by employing the directed acyclic graph structure of GO and the network of protein-protein interactions (PPIs). The approach is designed based on the fact that two proteins that interact biophysically would be in physical proximity of each other, would possess complementary molecular function, and play role in related biological processes. Predicted GO terms were ranked according to their relative association scores and the approach was evaluated quantitatively by plotting the precision versus recall values and F-scores (the harmonic mean of precision and recall) versus varying thresholds. Precisions of ~58% and ~ 40% for localization and functions respectively of proteins were determined at a threshold of ~30 (top 30 GO terms in the ranked list). Comparison with function prediction based on semantic similarity among nodes in an ontology and incorporation of those similarities in a k-nearest neighbor classifier confirmed that our results compared favorably.

Conclusions
This approach was applied to predict the cellular component and molecular function GO terms of all human proteins that have interacting partners possessing at least one known GO annotation. The list of predictions is available at http://severus.dbmi.pitt.edu/engo/GOPRED.html. We present the algorithm, evaluations and the results of the computational predictions, especially for genes identified in GWAS studies to be associated with diseases, which are of translational interest.
Video-assisted thoracic bronchial sleeve lobectomy with bronchoplasty for treatment of lung cancer confined to a single lung lobe: a case series of Chinese patients
Authors: Yu Daping , Han Yi , Zhou Shijie , Song Xiaoyun , Li Yunsong , Xiao Ning , Liu Zhidong 
Published: April 2014

Abstract

Background
The outcomes of video-assisted thoracic bronchial sleeve lobectomy (VABSL), a minimally invasive video-assisted thoracoscopic (VATS) lobectomy, are mostly unknown in Chinese patients.

Objectives
To investigate operative and postoperative outcomes of VABSL in a cases series of Chinese patients with lung cancer.

Methods
Retrospective study of 9 patients (male:female 8:1; mean age 59.4 ± 17.6 years, ranging 21–79 years) diagnosed with lung cancer of a single lobe, treated with VABSL between March 2009 and November 2011, and followed up for at least 2 months (mean follow-up: 14.17 ± 12.91 months). Operative outcomes (tumor size, operation time, estimated blood loss and blood transfusion), postoperative outcomes (intensive care unit [ICU] stay, hospitalization length and pathological tumor stage), death, tumor recurrence and safety were assessed.

Results
Patients were diagnosed with carcinoid cancer (11.1%), squamous carcinoma (66.7%) or small cell carcinoma (22.2%), affecting the right (77.8%) or left (22.2%) lung lobes in the upper (55.6%), middle (11.1%) or lower (33.3%) regions. TNM stages were T2 (88.9%) or T3 (11.1%); N0 (66.7%), N1 (11.1%) or N2 (22.2%); and M0 (100%). No patient required conversion to thoracotomy. Mean tumor size, operation time and blood loss were 2.50 ± 0.75 cm, 203 ± 20 min and 390 ± 206 ml, respectively. Patients were treated in the ICU for 18.7 ± 0.7 hours, and overall hospitalization duration was 20.8 ± 2.0 days. No deaths, recurrences or severe complications were reported.

Conclusions
VABSL surgery is safe and effective for treatment of lung cancer by experienced physicians, warranting wider implementation of VABSL and VATS training in China.