bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bu-Zhong-Yi-Qi pill alleviate the chemotherapy-related fatigue in 4 T1 murine breast cancer model
Authors: Ouyang Mingzi , Liu Yanyan , Tan Wei , Xiao Ya , Yu Keqiang , Sun Xiaomin , Huang Ying , Cheng JingRu , Luo Ren , Zhao Xiaoshan 
Published: June 2015

Abstract

Background
Paclitaxel induced fatigue still remains underrecognized and undertreated, partly because of limited understanding of its pathophysiology and lack of effective treatments. This study is aim to evaluate the anti-fatigue effects and mechanism of Bu-Zhong-Yi-Qi pill in murine 4 T1 breast cancer mice were treated with paclitaxel.

Methods
Breast cancer mice established with murine 4 T1 cells were randomly and repectively divided into five groups: negative control group (NC), tumor control group (TC), paclitaxel group (PTX), Bu-Zhong-Yi-Qi pill group (BZYQ) and Bu-Zhong-Yi-Qi pill plus paclitaxel group (BZYQ + PTX). The mice were administered for 21 days. During this period, the tumor volume, body weight and the weight-loaded swimming time were measured. After the last administration, all mice were sacrificed, weighted the tumor, measured immune cell cytokines and oxidative stress indicator. The remaining 10 mice in each group were observed for survival analysis.

Results
Treatments with BZYQ + PTX and PTX significantly reduced the rates of tumor volume in comparison with TC starting on the 9th day and the 18th day respectively (P < 0.05-0.01), and presented decreased tumor weight compared to TC (P < 0.05-0.01). Compared with mice in TC group, the median survival time and the average survival time in BZYQ + PTX group, BZYQ group and PTX group were significantly prolonged (P < 0.05-0.01). The swimming time of the BZYQ + PTX group gradually increased, which is longer than the PTX group on Day 14 and Day 21 (P < 0.01). The level of TNF-α was lower in BZYQ + PTX group than PTX group (P < 0.01). The level of SOD activity in BZYQ + PTX group was lower than the NC group (P <0.01), but much higher than the PTX group (P < 0.01). The level of MDA of BZYQ + PTX group was higher than the NC group (P < 0.01), but significant lower than the PTX group (P < 0.01).

Conclusions
BZYQ has the potential of alleviating paclitaxel chemotherapy-related fatigue in 4 T1 breast cancer mice by reducing the serum levels of TNF-α and modulating the level of MDA and the SOD activity.
Existence of solutions for fractional q-difference equation with mixed nonlinear boundary conditions
Authors: Li Xinhui , Han Zhenlai , Sun Shurong , Zhao Ping 
Published: June 2015

Abstract
In this paper, we study the boundary value problem for a class of nonlinear fractional q-difference equation with mixed nonlinear conditions involving the fractional q-derivative of Riemann-Liouuville type. By means of the Guo-Krasnosel’skii fixed point theorem on cones, some results concerning the existence of solutions are obtained. Finally, examples are presented to illustrate our main results.

MSC:39A13, 34B18, 34A08.
tmChem: a high performance approach for chemical named entity recognition and normalization
Authors: Leaman Robert , Wei Chih-Hsuan , Lu Zhiyong 
Published: June 2015

Abstract
Chemical compounds and drugs are an important class of entities in biomedical research with great potential in a wide range of applications, including clinical medicine. Locating chemical named entities in the literature is a useful step in chemical text mining pipelines for identifying the chemical mentions, their properties, and their relationships as discussed in the literature.
We introduce the tmChem system, a chemical named entity recognizer created by combining two independent machine learning models in an ensemble. We use the corpus released as part of the recent CHEMDNER task to develop and evaluate tmChem, achieving a micro-averaged f-measure of 0.8739 on the CEM subtask (mention-level evaluation) and 0.8745 f-measure on the CDI subtask (abstract-level evaluation). We also report a high-recall combination (0.9212 for CEM and 0.9224 for CDI). tmChem achieved the highest f-measure reported in the CHEMDNER task for the CEM subtask, and the high recall variant achieved the highest recall on both the CEM and CDI tasks.
We report that tmChem is a state-of-the-art tool for chemical named entity recognition and that performance for chemical named entity recognition has now tied (or exceeded) the performance previously reported for genes and diseases. Future research should focus on tighter integration between the named entity recognition and normalization steps for improved performance.
The source code and a trained model for both models of tmChem is available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmChem. The results of running tmChem (Model 2) on PubMed are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator
Dynamics of natural populations of the dertitivorous mudsnail Potamopyrgus antipodarum (Gray) (Hydrobiidae) in two interconnected Lakes differing in trophic state
Authors: Dorgelo Jaap , van der Geest Harm G , Hunting Ellard R 
Published: June 2015

Abstract
Here we investigate the allocation of resources between growth and reproduction by surveying the dynamics of natural populations of the aquatic detritivorous mudsnail Potamopyrgus antipodarum from two interconnected lakes that differ in trophic state. The size distributions and reproductive output of the snail populations was analyzed monthly by field surveys spanning 3 years, and in a controlled microcosm experiment to evaluate the reproductive potential under laboratory conditions. Snails in the meso-oligotrophic lake showed reduced growth and a smaller size compared to snails in the eutrophic lake. However, the numbers of eggs and nearly-neonates per adult snail did not differ significantly between the two populations. It is speculated that P. antipodarum populations living under meso-oligotrophic conditions may consistently invest more internal energy in reproduction at the expense of growth and that food quantity may be an important driver for macro-invertebrate resource allocation in detrital food webs.
Microbiological profiling and the demonstration of in vitro anti-bacterial traits of the major oral herbal medicines used in Dhaka Metropolis
Authors: Sharmin Marufa , Nur Ifra Tun , Acharjee Mrityunjoy , Munshi Saurab Kishore , Noor Rashed 
Published: June 2015

Abstract
Present study attempted to assess the level of microbiological contamination in oral herbal medicines, frequently used for medications, through conventional cultural and biochemical tests along with the antibiogram of the isolates. Moreover, the anti-bacterial potential of the herbal medicines was also aimed to be checked by the agar well diffusion method and minimum inhibitory concentration (MIC) assay. Out of 10 categories of liquid oral herbal medicine samples (n = 50) studied, all were found to be contaminated with bacteria (103-105 cfu/mL), specifically with Staphylococcus spp. in 8 samples; while 2 samples harbored Klebsiella spp. Fungal presence was observed only in one sample. Study of antibiogram revealed Klebsiella spp. to be strongly resistant against penicillin G and erythromycin, whereas S. aureus possessed 80% sensitivity. The in vitro anti-bacterial activity was observed in 7 samples. Of them, one sample was found to exhibit the activity against almost all the test bacteria and another was found effective against 5 out of 8 test bacteria. Five samples showed the activity within a minor range while 3 samples were devoid of such trait. Samples 2 and 4 were found to stall the bacterial growth below 10 mg/mL of concentration in MIC test. Overall, the prevalence of specific pathogens was not so significant in the samples studied as well as only one drug-resistant isolate was identified. Besides, the anti-bacterial trait of 5 samples indicated that most of herbal medicines might be considered effective for medication.
The potential utility of urinary biomarkers for risk prediction in combat casualties: a prospective observational cohort study
Authors: Stewart Ian J. , Glass Kristen R. , Howard Jeffrey T. , Morrow Benjamin D. , Sosnov Jonathan A. , Siew Edward D. , Wickersham Nancy , Latack Wayne , Kwan Hana K. , Heegard Kelly D. , Diaz Christina , Henderson Aaron T. , Saenz Kristin K. , Ikizler T. Alp , Chung Kevin K. 
Published: June 2015

Abstract
Introduction
Traditional risk scoring prediction models for trauma use either anatomically based estimations of injury or presenting vital signs. Markers of organ dysfunction may provide additional prognostic capability to these models. The objective of this study was to evaluate if urinary biomarkers are associated with poor outcomes, including death and the need for renal replacement therapy.

Methods
We conducted a prospective, observational study in United States Military personnel with traumatic injury admitted to the intensive care unit at a combat support hospital in Afghanistan.

Results
Eighty nine patients with urine samples drawn at admission to the intensive care unit were studied. Twelve patients subsequently died or needed renal replacement therapy. Median admission levels of urinary cystatin C (CyC), interleukin 18 (IL-18), L-type fatty acid binding protein (LFABP) and neutrophil gelatinase-associated lipocalin (NGAL) were significantly higher in patients that developed the combined outcome of death or need for renal replacement therapy. Median admission levels of kidney injury molecule-1 were not associated with the combined outcome. The area under the receiver operating characteristic curves for the combined outcome were 0.815, 0.682, 0.842 and 0.820 for CyC, IL-18, LFABP and NGAL, respectively. Multivariable regression adjusted for injury severity score, revealed CyC (OR 1.97, 95 % confidence interval 1.26-3.10, p = 0.003), LFABP (OR 1.92, 95 % confidence interval 1.24-2.99, p = 0.004) and NGAL (OR 1.80, 95 % confidence interval 1.21-2.66, p = 0.004) to be significantly associated with the composite outcome.

Conclusions
Urinary biomarker levels at the time of admission are associated with death or need for renal replacement therapy. Larger multicenter studies will be required to determine how urinary biomarkers can best be used in future prediction models.
Anti-high mobility group box-1 monoclonal antibody treatment provides protection against influenza A virus (H1N1)-induced pneumonia in mice
Authors: Nosaka Nobuyuki , Yashiro Masato , Yamada Mutsuko , Fujii Yosuke , Tsukahara Hirokazu , Liu Keyue , Nishibori Masahiro , Matsukawa Akihiro , Morishima Tsuneo 
Published: June 2015

AbstractIntroductionProvision for the emergence of an influenza pandemic is an urgent issue. The discovery of a novel anti-influenza therapeutic approach would increase the effectiveness of traditional virus-based strategies. This study was undertaken to evaluate the therapeutic effects of anti-high mobility group box-1 (HMGB1) monoclonal antibody (mAb) treatment on influenza A virus (H1N1)-induced pneumonia in mice.MethodsNine-week-old male C57BL/6 mice were inoculated with H1N1, then anti-HMGB1 mAb or control mAb were administered intravenously at 1, 24 and 48 hours after H1N1 inoculation and the survival rate was analyzed. Lung lavage and histopathological analysis were performed on days 3, 5, 7 and 10 after inoculation.ResultsAnti-HMGB1 mAb significantly improved the survival rate of H1N1-inoculated mice (1 out of 15 versus 8 out of 15 deaths in the anti-HMGB1 mAb-treated group versus the control mAb-treated group,p < 0.01), although the treatment did not affect virus propagation in the lungs. The treatment also significantly attenuated histological changes and neutrophil infiltration in the lungs of H1N1-inoculated mice. This was associated with inhibition of HMGB1 and suppression of inflammatory cytokine/chemokine expression and oxidative stress enhancement, which were observed in H1N1-inoculated mice. The expression of receptor for advanced glycation end products and nuclear factor κB was attenuated by the treatment.ConclusionsAnti-HMGB1 mAb may provide a novel and effective pharmacological strategy for severe influenza virus infection in humans by reducing the inflammatory responses induced by HMGB1.
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation
Authors: Dueck Hannah , Khaladkar Mugdha , Kim Tae Kyung , Spaethling Jennifer M. , Francis Chantal , Suresh Sangita , Fisher Stephen A. , Seale Patrick , Beck Sheryl G. , Bartfai Tamas , Kuhn Bernhard , Eberwine James , Kim Junhyong 
Published: June 2015

Abstract
Background
Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotypes. Additionally, single-cell transcriptomics presents unique analysis challenges that need to be addressed to answer this question.

Results
We present high quality deep read-depth single-cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within-cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single-cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved.

Conclusions
Single-cell RNA-sequencing data provide a unique view of transcriptome function; however, careful analysis is required in order to use single-cell RNA-sequencing measurements for this purpose. Technical variation must be considered in single-cell RNA-sequencing studies of expression variation. For a subset of genes, biological variability within each cell type appears to be regulated in order to perform dynamic functions, rather than solely molecular noise.
Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Authors: Kim Kyu-Tae , Lee Hye Won , Lee Hae-Ock , Kim Sang Cheol , Seo Yun Jee , Chung Woosung , Eum Hye Hyeon , Nam Do-Hyun , Kim Junhyong , Joo Kyeung Min , Park Woong-Yang 
Published: June 2015

Abstract
Background
Intra-tumoral genetic and functional heterogeneity correlates with cancer clinical prognoses. However, the mechanisms by which intra-tumoral heterogeneity impacts therapeutic outcome remain poorly understood. RNA sequencing (RNA-seq) of single tumor cells can provide comprehensive information about gene expression and single-nucleotide variations in individual tumor cells, which may allow for the translation of heterogeneous tumor cell functional responses into customized anti-cancer treatments.

Results
We isolated 34 patient-derived xenograft (PDX) tumor cells from a lung adenocarcinoma patient tumor xenograft. Individual tumor cells were subjected to single cell RNA-seq for gene expression profiling and expressed mutation profiling. Fifty tumor-specific single-nucleotide variations, including KRAS
G12D
, were observed to be heterogeneous in individual PDX cells. Semi-supervised clustering, based on KRAS
G12D
mutant expression and a risk score representing expression of 69 lung adenocarcinoma-prognostic genes, classified PDX cells into four groups. PDX cells that survived in vitro anti-cancer drug treatment displayed transcriptome signatures consistent with the group characterized by KRAS
G12D
and low risk score.

Conclusions
Single-cell RNA-seq on viable PDX cells identified a candidate tumor cell subgroup associated with anti-cancer drug resistance. Thus, single-cell RNA-seq is a powerful approach for identifying unique tumor cell-specific gene expression profiles which could facilitate the development of optimized clinical anti-cancer strategies.
Brave new epigenomes: the dawn of epigenetic engineering
Authors: Köferle Anna , Stricker Stefan H. , Beck Stephan 
Published: June 2015

Editorial summaryNew methods for epigenome editing now make it possible to manipulate the epigenome in living cells with unprecedented specificity and efficiency. These ground-breaking approaches are beginning to yield novel insights into the function of individual chromatin marks in the context of cellular phenotype.
Stress Doppler echocardiography for early detection of systemic sclerosis-associated pulmonary arterial hypertension
Authors: Nagel Christian , Henn Philipp , Ehlken Nicola , D’Andrea Antonello , Blank Norbert , Bossone Eduardo , Böttger Anke , Fiehn Christoph , Fischer Christine , Lorenz Hanns-Martin , Stöckl Frank , Grünig Ekkehard , Egenlauf Benjamin 
Published: June 2015

Abstract
Introduction
In patients with systemic sclerosis (SSc), associated pulmonary arterial hypertension (SSc-APAH) is the leading cause of death. The objective of this prospective screening study was to analyse sensitivity and specificity of stress Doppler echocardiography (SDE) in detecting pulmonary hypertension (PH).

Methods
Pulmonary artery pressures and further parameters of PH were assessed by echocardiography and right heart catheterisation (RHC) at rest and during exercise in patients with SSc. Investigators of RHC were blinded to the results of non-invasive measurements.

Results
Of 76 patients with SSc (64 were female and mean age was 58±14 years), 22 (29 %) had manifest PH confirmed by RHC: four had concomitant left heart diseases, three had lung diseases, and 15 had SSc-APAH. Echocardiography at rest missed PH diagnosis in five of 22 patients with PH when a cutoff value for systolic pulmonary arterial pressure (PASP) was more than 40 mm Hg at rest. The sensitivity of echocardiography at rest was 72.7 % (95 % confidence interval (CI) 0.52–0.88), and specificity was 88.2 % (95 % CI 0.78–0.95). When a cutoff value for PASP was more than 45 mm Hg during low-dose exercise, SDE missed PH diagnosis in one of the 22 patients with PH and improved sensitivity to 95.2 % (95 % CI 0.81–1.0) but reduced specificity to 84.9 % (95 % CI 0.74–0.93). Reduction of specificity was partly due to concomitant left heart disease.

Conclusions
The results of this prospective cross-sectional study using RHC as gold standard in all patients showed that SDE markedly improved sensitivity in detecting manifest PH to 95.2 % compared with 72.7 % using echocardiography at rest only. Thus, for PH screening in patients with SSc, echocardiography should be performed at rest and during exercise.

Trial registration
ClinicalTrials.gov NCT01387035. Registered 29 June 2011.
Generation of human iPSCs from cells of fibroblastic and epithelial origin by means of the oriP/EBNA-1 episomal reprogramming system
Authors: Drozd Anna M. , Walczak Maciej P. , Piaskowski Sylwester , Stoczynska-Fidelus Ewelina , Rieske Piotr , Grzela Dawid P. 
Published: June 2015

Abstract
Introduction
The prospect of therapeutic applications of the induced pluripotent stem cells (iPSCs) is based on their ability to generate virtually any cell type present in human body. Generation of iPSCs from somatic cells has opened up new possibilities to investigate stem cell biology, to better understand pathophysiology of human diseases, and to design new therapy approaches in the field of regenerative medicine. In this study, we focus on the ability of the episomal system, a non-viral and integration-free reprogramming method to derive iPSCs from somatic cells of various origin.

Methods
Cells originating from neonatal and adult tissue, renal epithelium, and amniotic fluid were reprogrammed by using origin of replication/Epstein-Barr virus nuclear antigen-1 (oriP/EBNA-1)-based episomal vectors carrying defined factors. The iPSC colony formation was evaluated by using immunocytochemistry and alkaline phosphatase assay and by investigating gene expression profiles. The trilineage formation potential of generated pluripotent cells was assessed by embryoid body-mediated differentiation. The impact of additionally introduced factors on episome-based reprogramming was also investigated.

Results
Reprogramming efficiencies were significantly higher for the epithelial cells compared with fibroblasts. The presence of additional factor miR 302/367 in episomal system enhanced reprogramming efficiencies in fibroblasts and epithelial cells, whereas the downregulation of Mbd3 expression increased iPSC colony-forming efficiency in fibroblasts solely.

Conclusions
In this study, we performed a side-by-side comparison of iPSC colony-forming efficiencies in fibroblasts and epithelial cells transiently transfected with episomal plasmids and demonstrated that iPSC generation efficiency was highest when donor samples were derived from epithelial cells. We determined that reprogramming efficiency of episomal system could be further improved. Considering results obtained in the course of this study, we believe that episomal reprogramming provides a simple, reproducible, and efficient tool for generating clinically relevant pluripotent cells.
Monitoring serum HER2 levels in breast cancer patients
Authors: Tchou Julia , Lam Lian , Li Yun Rose , Edwards Claire , Ky Bonnie , Zhang Hongtao 
Published: June 2015

Abstract

Background
We have developed a new approach to reduce the serum interference for ELISA. The purpose of this study is to investigate if we can use the optimized ELISA (MBB-ELISA) to detect serum soluble HER2/neu (sHER2) in early stage primary breast cancer and monitor its change during treatments.

Findings
We collected sera preoperatively from 118 primary breast cancer patients. Serum samples were also collected sequentially from a subset of patients during and after adjuvant treatment. sHER2 in these samples was measured by the MBB-ELISA. Only 16.7 % of tissue HER2 (tHER2) positive patients had significantly elevated sHER2 levels in serum. Interestingly, sera of some patients with tHER2 negative tumors, including those that were 2+ by IHC but negative by FISH, demonstrated slightly elevated sHER2 levels. Multivariate analysis demonstrated that patients with elevated sHER2 (> = 7 ng/ml) had significantly worse disease free survival. During treatments, sHER2 levels consistently fell in response to adjuvant therapies. Nevertheless, in all 4 patients who developed metastases, a steady rise in sHER2 levels was noted before metastatic disease became clinically evident.

Conclusions
For early stage breast cancers, sHER2 is a poor biomarker to predict tHER2 status, but may have value to supplement tissue tests to identify patients with HER2 tumors. Our results also suggest that sHER2 is worth further study as a biomarker to monitor breast cancer patients during treatments.
Stability study of docetaxel solution (0.9%, saline) using Non-PVC and PVC tubes for intravenous administration
Authors: Park Kang Hoon , Chung Dong June 
Published: June 2015

Abstract

Background
Di-2-ethylhexyl phthalate (DEHP) are added to poly(vinyl chloride)(PVC) infusion tubes as a plasticizer to ensure tube flexibility. In addition to previously reported disadvantages of DEHP, released DEHP molecules from PVC tubes can easily interact with surfactants in anticancer drug solutions (i.e., polysorbate 80 for Taxotere®-Inj) and reduce the solubility of docetaxel in aqueous solution during anticancer drug administration.

Results

In this study, we investigated the
in vitro
stability of docetaxel in a 0.9% saline solution under an intravenous administration condition using a PVC tube (high DEHP content) and non-PVC infused tube.

Conclusion
The docetaxel solution circulating through the non-PVC tube had better solution stability than through the PVC tube(high DEHP content).