Miracle-dz/UniFAR-FTUs huggingface dataset:
Doxorubicin plus sorafenib vs doxorubicin alone in patients with advanced hepatocellular carcinoma: a randomized trial.

CONTEXT In a randomized phase 3 trial, 400 mg of sorafenib twice daily prolonged overall survival of patients with advanced hepatocellular carcinoma (HCC) and Child-Pugh A disease. In a phase 1 study, sorafenib combined with doxorubicin, 60 mg/m(2), was well tolerated by patients with refractory solid tumors. The combination of sorafenib and doxorubicin in patients with advanced HCC has not been evaluated in a phase 2 or 3 trial. OBJECTIVE To evaluate the efficacy and safety of doxorubicin plus sorafenib compared with doxorubicin alone in patients with advanced HCC and Child-Pugh A disease. DESIGN, SETTING, AND PATIENTS In a double-blind phase 2 multinational study, conducted from April 2005 to October 2006, 96 patients (76% male; median age, 65 years [range, 38-82 years]) with advanced HCC, Eastern Cooperative Oncology Group performance status 0 to 2, Child-Pugh A status, and no prior systemic therapy were randomly assigned to receive 60 mg/m(2) of doxorubicin intravenously every 21 days plus either 400 mg of sorafenib or placebo orally twice a day. The date of the last patient's follow-up was April 2008. MAIN OUTCOME MEASURE Time to progression as determined by independent review. RESULTS Following complete accrual, an unplanned early analysis for efficacy was performed by the independent data monitoring committee, so the trial was halted. The 2 patients remaining in the placebo group at that time were offered sorafenib. Based on 51 progressions, 63 deaths, and 70 events for progression-free survival, median time to progression was 6.4 months in the sorafenib-doxorubicin group (95% confidence interval [CI], 4.8-9.2), and 2.8 months (95% CI, 1.6-5) in the doxorubicin-placebo monotherapy group (P = .02). Median overall survival was 13.7 months (95% CI, 8.9--not reached) and 6.5 months (95% CI, 4.5-9.9; P = .006), and progression-free survival was 6.0 months (95% CI, 4.6-8.6) and 2.7 months (95% CI, 1.4-2.8) in these groups, respectively (P = .006). Toxicity profiles were similar to those for the single agents. CONCLUSIONS Among patients with advanced HCC, treatment with sorafenib plus doxorubicin compared with doxorubicin monotherapy resulted in greater median time to progression, overall survival, and progression-free survival. The degree to which this improvement may represent synergism between sorafenib and doxorubicin remains to be defined. The combination of sorafenib and doxorubicin is not yet indicated for routine clinical use. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00108953.
Empirical advantages of adeno associated viral vectors in vivo gene therapy for arthritis.

OBJECTIVE To evaluate the utility of the adeno associated viral (AAV) vector for gene delivery to joint cells in vivo and in vitro, and to assess its potential as a vector for arthritis gene therapy. METHODS A recombinant AAV (rAAV) vector expressing the bacterial beta-galactosidase (beta-gal) gene (rAAV-CMV-LacZ) was directly introduced into healthy-normal mouse knees, or arthritic knees in mice overexpressing tumor necrosis factor-alpha (hTNFalpha-Tg). Beta-gal expression levels were determined by immunohistochemistry and chemiluminescence. The transduction efficiency of this vector on primary fibroblast-like synoviocytes (FLS) in vitro was determined by FACS. The effects of UV and gamma-irradiation as well as TNF-alpha on transduction efficiency were determined using the same methods. RESULTS We found little evidence of rAAV transduction in the joint cells of healthy mice. Target gene expression was detected in all animals at Day 3, and peaked at Day 7 before returning to baseline levels 21 days after injection. In contrast, synoviocytes, articular chondrocytes, and meniscal cells of diseased mice were transduced by rAAV-CMV-LacZ in hTNFalpha-Tg animals. Transduction efficiencies correlated with joint damage, and target gene expression was up to 10-fold greater than that seen in the normal mice. In vitro, we found that rAAV transduction of FLS can be enhanced by pretreatment with UV or gamma-irradiation and TNF-alpha stimulation. CONCLUSION We find that rAAV vectors have several empirical advantages for in vivo gene therapy for arthritis: (1) rAAV preferentially transduces arthritic joint cells in vivo. (2) rAAV can transduce both FLS and chondrocytes in vivo. (3) rAAV transduction of FLS can be augmented by pretreatment with agents that induce DNA repair enzymes.
Multiple introductions of the eastern fox squirrel (Sciurus niger) in California

Abstract Eastern fox squirrels (Sciurus niger) have been introduced into California within the past 130 years. Recently, their range has been expanding at an alarming rate. Genetic diversity was assessed in 101 control region sequences of eastern fox squirrels from three geographic regions within California (Los Angeles County, Alameda and Contra Costa counties and Sacramento County) to determine if a single or multiple introductions occurred within California, as indicated by the detection of multiple haplotypes. A total of 11 haplotypes were discovered, with haplotypes rarely shared among geographic regions and no clustering by region in a haplotype network. This suggests that the introduction to different regions within California came from different source populations within the native range of the species. Haplotype diversity was highest in Los Angeles County. Due to a lack of phylogeographic structure in fox squirrels in their native range, it is difficult to identify the sources of all introductions.
Evaluation of methods to assess physical activity in free-living conditions.

PURPOSE The purpose of this study was to compare different methods of measuring physical activity (PA) in women by the doubly labeled water method (DLW). METHODS Thirteen subjects participated in a 7-d protocol during which total daily energy expenditure (TDEE) was measured with DLW. Body composition, basal metabolic rate (BMR), and peak oxygen consumption were also measured. Physical activity-related energy expenditure (PAEE) was then calculated by subtracting measured BMR and the estimated thermic effect of food from TDEE. Simultaneously, over the 7 d, PA was assessed via a 7-d Physical Activity Recall questionnaire (PAR), and subjects wore secured at the waist, a Tritrac-R3D (Madison, WI), a Computer Science Application Inc. activity monitor (CSA; Shalimar, FL), and a Yamax Digi Walker-500 (Tokyo, Japan). Pearson-product moment correlations were calculated to determine the relationships among the different methods for estimating PAEE. Paired t-tests with appropriate adjustments were used to compare the different methods with DLW-PAEE. RESULTS There was no significant difference between PAEE determined from PAR and DLW. The differences between the two methods ranged from -633 to 280 kcal.d(-1). Compared with DLW, PAEE determined from CSA, Tritrac, and Yamax was significantly underestimated by 59% (-495 kcal.d(-1)), 35% (-320 kcal.d(-1)) and 59% (-497 kcal.d(-1)), respectively. VO2peak explained 43% of the variation in DLW-PAEE. CONCLUSION Although the group average for PAR-PAEE agreed with DLW-PAEE, there were differences in the methods among the subjects. PAEE determined by Tritrac, CSA, and Yamax significantly underestimate free-living PAEE in women.
Interoperable Document Collaboration

To provide office applications with an easy interoperable document merge capability and to enable the usage of document revision across applications, it is necessary to not only standardize the representations of a document state, but also of the changes made to the document during the editing process. Tracking the changes during editing retains the information usually being recovered afterwards. This avoids costly and time consuming processes like document comparison and diff heuristics [1]. To this day, file formats such as the OpenDocument file format (ODF) do only specify all possible document variations of a document representing the final state of user data. Interoperability is therefore only given on a document level: One ODF application saves a document and a different application is able to load and continue work on the same document state. Common scenarios of document exchange have been by floppy disc, attached to email and exchange across networks via file services such as Dropbox. Nowadays, the Internet is ubiquitous and multiple users want to work simultaneously on the same document. In that context the transfer of a whole document from user to user is inefficient. Additionally, finding and merging changes in XML-based documents appears to be complex and possibly error-prone [2]. For this reason, the OASIS Advanced Document Collaboration subcommittee has started to simplify collaboration by specifying the changes applicable to an ODF document and raising ODF application interoperability from a full document level to a more granular document change level. In this paper, we present an approach to ODF change representation called "Merge enabled Change-Tracking" (MCT), which is based on the Operational Transformation approach [3].
La jachère et le fonctionnement des sols tropicaux : rôle de l'activité biologique et des matières organiques : quelques éléments de réflexion

FALLOWING AND FUNCTIONING OF TROPICAL SOILS. ROLE OF BIOLOGICAL ACTIVlTY AND ORGANIC MATTER. SOME ELEMENTS FOR STUDY Fallowing after cultivation induces a high modification in biological activity and in the levels of organic restitution to the soil. It brings about a modification in the functioning of the soil : distribution of the constituents, bio-geochemical cycles and water dynamics. Some of these aspects are illustrated through examples from the West Indies and the West Africa : storage and dynam'cs of organic matter (C,.N), activity of the soil macro-fauna, physical properties of suvace horizons The authors emphasize the analysis of bioorgano-minera1 interactions and the possible effect of a fallow shortening .
Feature selection for multi-label classification using neighborhood preservation

Multi-label learning deals with data associated with a set of labels simultaneously. Dimensionality reduction is an important but challenging task in multi-label learning. Feature selection is an efficient technique for dimensionality reduction to search an optimal feature subset preserving the most relevant information. In this paper, we propose an effective feature evaluation criterion for multi-label feature selection, called neighborhood relationship preserving score. This criterion is inspired by similarity preservation, which is widely used in single-label feature selection. It evaluates each feature subset by measuring its capability in preserving neighborhood relationship among samples. Unlike similarity preservation, we address the order of sample similarities which can well express the neighborhood relationship among samples, not just the pairwise sample similarity. With this criterion, we also design one ranking algorithm and one greedy algorithm for feature selection problem. The proposed algorithms are validated in six publicly available data sets from machine learning repository. Experimental results demonstrate their superiorities over the compared state-of-the-art methods.
Improved software current-limiting protection strategy for starting the high-power motor

The current is limited within a certain range with poor waveforms by fast response of hardware current limiting. The current limiting with software can produce good waveforms. The emphasis is the switch between the voltage loop and the current. In order to switch smoothly without shock waves, the traditional method is used to switch into the current loop, when current exceeds the upper limit point of the threshold. It switches into the voltage loop when the voltage rises to the rated value. However, for starting the high-power motor, it is necessary to set a high threshold of the current entering the current loop. Nevertheless, for the reliable protection of breakdown, such as short circuit, the value of threshold is expected to be small. To solve the contradiction, a method of relying on their own characteristics to enter current loop is presented in this paper. The contrastive experiments are made on the 400 KVA/50 HZ experimental machines. The experimental results show that the method presented in this paper can not only limit reliably current for the instantaneous impact, but also escape going into the current loop at the moment of starting the high-power motor. The desirable effects are achieved.
Dopaminergic differentiation using pluripotent stem cells

Parkinson's disease (PD) is the second most common neurodegenerative disorder. The motor symptoms of PD are caused by the loss of dopaminergic (DA) neurons in the substantia nigra pars compacta of mesencephalon. The causes for death of DA neurons are not well understood, but the strongest risk factor is increasing age. There is no cure currently available for PD, and treatment is limited to management of PD symptoms in patients. Primary DA neurons are virtually unobtainable from living patients and animal studies have proven inadequate for studying the mechanism of PD development. Pluripotent stem cells (PSC) are primary self‐renewing cells capable of differentiating into all cell types of an organism, including DA neurons. PSCs represent an abundant source of cells that can be genetically modified or isolated from patients with complex diseases, enabling the production of large quantities of DA neurons for disease modeling, drug screening, and gene function studies. Furthermore, since PD arises as a result of deterioration of DA neurons in a specific brain region, it has been suggested that a relatively small number of cells could restore normal function. PSCs could provide a source of DA neurons for cell replacement therapy. In this Prospects article, we focus on the development and in vitro derivation of DA neurons from PSCs, as well as current applications of the technological advances, with the emphasis on future directions and efforts in the field. J. Cell. Biochem. 113: 3610–3619, 2012. © 2012 Wiley Periodicals, Inc.
Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis1

A salt-related transcription factor regulates abscisic acid synthesis and signaling genes in germinating Arabidopsis seeds under saline conditions. Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance.
Expression of CCR7 in multiple sclerosis: Implications for CNS immunity

It is unclear how immune cells traffic between the lymphoid compartment and the central nervous system (CNS), which lacks lymphatic vessels and is shielded by the blood–brain barrier. We studied the expression of CCR7, a chemokine receptor required for migration of T cells and dendritic cells (DCs) to lymphoid organs, in the CNS of patients with multiple sclerosis (MS) to gain insight into pathways for CNS immune cell trafficking. Inflamed MS lesions contained numerous CCR7+ myeloid cells expressing major histocompatibility complex class II, CD68 and CD86, consistent with maturing DCs. CCR7+ DCs also were identified in cerebrospinal fluid (CSF). These observations suggested that the afferent limb of CNS immunity is comprised, in part, of DCs, which are generated within the CNS and migrate to deep cervical lymph nodes through the CSF after antigen capture. Ninety percent of CSF T cells expressed CCR7 and CSF from patients with MS was relatively depleted of CCR7‐negative effector‐memory T cells. In contrast, all T cells in parenchymal MS lesions lacked CCR7, indicating local retention and differentiation of central‐memory T cells upon restimulation by antigen within the CNS. These data suggested that the efferent limb of CNS immunity is executed by central‐memory T cells, which enter CSF directly from the circulation. Ann Neurol 2004
Thrombin peptide, TP508, induces differential gene expression in fibroblasts through a nonproteolytic activation pathway.

Prior studies have shown that synthetic peptides representing the domain of thrombin responsible for high-affinity binding to fibroblasts stimulate chemotactic and cell proliferative signals through a nonproteolytic mechanism. One of these peptides, TP508, has recently been shown to be chemotactic for neutrophils, to enhance collagen accumulation in wounds, to enhance revascularization of wounds, and to accelerate the healing of incisional and open wounds in normal animals and in animals with impaired healing. To determine whether TP508 activates the proteolytically activated receptor for thrombin (PAR1), or the signals that are activated by PAR1, we treated human fibroblasts with TP508 and the PAR1-activating peptide, SFLLRNP, and analyzed the effects of these peptides on gene expression using differential display reverse transcriptase polymerase chain reaction. TP508 induces expression of a number of specific message fragments with short tyrosine kinase-like domains that are not induced by SFLLRNP. Sequencing full-length clones prepared by Marathon extension of TP508-induced fragments revealed that among the induced transcripts, there was a sequence with 88% homology to human annexin V. Northern analysis with authentic annexin V cDNA confirms that TP508, but not SFLLRNP, induces expression of annexin V in human fibroblasts. These results demonstrate that TP508 activates a cellular response separate from that activated through PAR1 and supports the hypothesis that TP508 acts through a separate nonproteolytically activated thrombin receptor that may be responsible for high-affinity thrombin binding and for nonproteolytic signals that are required for thrombin stimulation of cell proliferation.
Origin and evolution of chloroplast group I introns in lichen algae

The history of group I introns is characterized by repeated horizontal transfers, even among phylogenetically distant species. The symbiogenetic thalli of lichens are good candidates for the horizontal transfer of genetic material among distantly related organisms, such as fungi and green algae. The main goal of this study was to determine whether there were different trends in intron distribution and properties among Chlorophyte algae based on their phylogenetic relationships and living conditions. Therefore, we investigated the occurrence, distribution and properties of group I introns within the chloroplast LSU rDNA in 87 Chlorophyte algae including lichen and free‐living Trebouxiophyceae compared to free‐living non‐Trebouxiophyceae species. Overall, our findings showed that there was high diversity of group I introns and homing endonucleases (HEs) between Trebouxiophyceae and non‐Trebouxiophyceae Chlorophyte algae, with divergence in their distribution patterns, frequencies and properties. However, the differences between lichen Trebouxiophyceae and free‐living Trebouxiophyceae were smaller. An exception was the cL2449 intron, which was closely related to ω elements in yeasts. Such introns seem to occur more frequently in lichen Trebouxiophyceae compared to free‐living Trebouxiophyceae. Our data suggest that lichenization and maintenance of lichen symbiosis for millions of years of evolution may have facilitated horizontal transfers of specific introns/HEs between symbionts. The data also suggest that sequencing of more chloroplast genes harboring group I introns in diverse algal groups may help us to understand the group I intron/HE transmission process within these organisms.
Expectations predict chronic pain treatment outcomes

Abstract Accumulating evidence suggests an association between patient pretreatment expectations and numerous health outcomes. However, it remains unclear if and how expectations relate to outcomes after treatments in multidisciplinary pain programs. The present study aims at investigating the predictive association between expectations and clinical outcomes in a large database of chronic pain patients. In this observational cohort study, participants were 2272 patients treated in one of 3 university-affiliated multidisciplinary pain treatment centers. All patients received personalized care, including medical, psychological, and/or physical interventions. Patient expectations regarding pain relief and improvements in quality of life and functioning were measured before the first visit to the pain centers and served as predictor variables. Changes in pain intensity, depressive symptoms, pain interference, and tendency to catastrophize, as well as satisfaction with pain treatment and global impressions of change at 6-month follow-up, were considered as treatment outcomes. Structural equation modeling analyses showed significant positive relationships between expectations and most clinical outcomes, and this association was largely mediated by patients' global impressions of change. Similar patterns of relationships between variables were also observed in various subgroups of patients based on sex, age, pain duration, and pain classification. Such results emphasize the relevance of patient expectations as a determinant of outcomes in multimodal pain treatment programs. Furthermore, the results suggest that superior clinical outcomes are observed in individuals who expect high positive outcomes as a result of treatment.