Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding Angiosperm Diversification Using Small and Large Phylogenetic Trees 1

Is the global success of the fl owering plants a function of some feature of the group as a whole, or does it really refl ect the success of one or more angiosperm subgroups (e.g., Sanderson and Donoghue, 1994)? Are such apparent successes, at whatever level they occur, best explained by key innovations or by key opportunities (e.g., Moore and Donoghue, 2007), and how has differential extinction infl uenced our perception of the problem? Answers to these questions depend on insights about phylogenetic relationships and about how species richness is distributed throughout the tree. Fortunately, our knowledge of angiosperm phylogeny has improved dramatically over the past decade (e.ever, it will still be a long time before we know the relationships of every angiosperm species with any level of confi dence. In view of our incomplete knowledge for the foreseeable future, what are the best strategies for studying shifts in diversifi cation rate? One approach has been to base such analyses on a backbone tree that depicts " established " relationships among the major lineages within a clade of interest. In this case, each terminal is assigned the number of species thought to be represented by an " exemplar species, " and the analysis necessarily bypasses how diversity is distributed within these terminal lineages (e. This has the obvious drawback of not being able to identify where shifts in diversifi cation may have occurred within a large terminal clade, and it can result in a particular kind of mistake: a shift in diversifi cation attributed to such a composite terminal might actually be due to a shift that occurred within that clade (a form of the " trickle-down " effect; Moore et al., 2004). Another possible approach, which has not yet been explored in detail, is to use a phylogenetic tree that includes all species for which relevant phylogenetic data are available, simply treating each terminal as a single species. In using this approach, one has to hope that there are enough representatives of the clade of interest for which data are available and that the sample of species available for phylogenetic analysis more-or-less accurately refl ects the distribution of the underlying species diversity. This approach has the obvious drawback of potentially biasing the results due to the over-or underrepresentation of particular clades in the underlying data set. One would hope that these two different approaches would largely yield similar results, …
Probe, count, and classify: categorizing hidden web databases

The contents of many valuable web-accessible databases are only accessible through search interfaces and are hence invisible to traditional web “crawlers. ” Recent studies have estimated the size of this “hidden web” to be 500 billion pages, while the size of the “crawlable” web is only an estimated two billion pages. Recently, commercial web sites have started to manually organize web-accessible databases into Yahoo! -like hierarchical classification schemes. In this paper, we introduce a method for automating this classification process by using a small number of query probes. To classify a database, our algorithm does not retrieve or inspect any documents or pages from the database, but rather just exploits the number of matches that each query probe generates at the database in question. We have conducted an extensive experimental evaluation of our technique over collections of real documents, including over one hundred web-accessible databases. Our experiments show that our system has low overhead and achieves high classification accuracy across a variety of databases.
Effect of weight reduction on liver histology and biochemistry in patients with chronic hepatitis C

Background: Steatosis occurs in more than 50% of patients with chronic hepatitis C and is associated with increased hepatic fibrosis. In many of these patients the pathogenesis of steatosis appears to be the same as for patients with non-alcoholic fatty liver disease—that is, related to visceral adiposity and obesity. Methods: The effect of a three month weight reduction programme on liver biochemistry and metabolic parameters was examined in 19 subjects with steatosis and chronic hepatitis C. Paired liver biopsies were performed in 10 subjects, prior to and 3–6 months following the intervention, to determine the effect of weight loss on liver histology. Results: There was a mean weight loss of 5.9 (3.2) kg and a mean reduction in waist circumference of 9.0 (5.0) cm. In 16 of the 19 patients, serum alanine aminotransferase levels fell progressively with weight loss. Mean fasting insulin fell from 16 (7) to 11 (4) mmol/l (p<0.002). Nine of 10 patients with paired liver biopsies had a reduction in steatosis irrespective of viral genotype. In these subjects the median modified Knodell fibrosis score decreased from 3 to 1 (p=0.04) and activated stellate cells significantly decreased (p<0.004). Conclusions: Weight loss in patients with chronic hepatitis C may be associated with a reduction in steatosis and abnormal liver enzymes and an improvement in fibrosis, despite the persistence of the virus. Weight reduction may provide an important adjunct treatment strategy for patients with chronic hepatitis C.
Stability of closedness of convex cones under linear mappings II

In this paper we reconsider the question of when the continuous linear image of a closed convex cone is closed in Euclidean space. In particular, we show that although it is not true that the closedness of the image is preserved under small perturbations of the linear mappings it is “almost” true that the closedness of the image is preserved under small perturbations, in the sense that, for “almost all” linear mappings from $R^n$ into $R^m$ if the image of the cone is closed then there is a small neighbourhood around it whose members also preserve the closedness of the cone.
Apoptosis-related gene expression in benign prostatic hyperplasia and prostate carcinoma.

BACKGROUND The aim of this study was to examine the expressions of the bcl-2, bax, fas and c-myc apoptosis-related genes in benign prostatic hyperplasia (BPH) and prostate carcinoma (CaP) to determine whether significant differences exist within each disease and between the two groups of patients. The correlation between gene expression and tumour diameter, stage, Gleason score and serum PSA was also investigated. PATIENTS AND METHODS Tissue specimens from 51 cases of BPH and 27 cases of CaP were examined for bcl-2, bax, fas and c-myc expression by reverse transcriptase-PCR (RT-PCR). RESULTS In BPH, bcl-2 and bax gave the weakest signals (p < 0.001). In CaP, bcl-2 was the least expressed gene (p < 0.001). In both patient groups, fas and c-myc were the most highly expressed genes (p < 0.05). Both bcl-2 and bax were expressed at higher levels in CaP than in BPH (p < 0.02). The bcl-2/bax ratio was lower in CaP than in BPH (p < 0.001). Bcl-2 was more highly expressed in high Gleason grade (> 7) tumours (p < 0.05). In the BPH group, bax showed a positive relationship with fas (p < 0.01), while the bcl-2 level inversely correlated with that of c-myc (p < 0.05). CONCLUSION Our data showed that all the apoptosis-related genes were expressed in both BPH and CaP. The stronger expression of bax and the lower bcl-2/bax ratio observed in CaP may suggest a pro-apoptotic stimulus, while the higher bcl-2 levels appear to counterbalance the tendency to cell death.
General solutions to consistency problems in multiple hypothesis testing

Coherence and consonance are the two important concepts to ensure consistent conclusions drawn from multiple tests. Unlike coherence, consonance of a multiple testing procedure (MTP) has not yet received much attention. Although most of the MTPs used in practice are consonant, cases still exist that dissonant tests have to be used due to their unique advantages, for example, the likelihood ratio tests and sum tests. Consonance adjustments are necessary for such tests to avoid difficulty in interpretation. Moreover, in terms of detecting elementary hypotheses, a consonant test procedure is uniformly more powerful than the corresponding dissonant one. In this paper, several general methods using the partitioning principle to construct (strongly) consonant and strongly coherent MTPs are proposed. As a result, any dissonant (but coherent) multiple level α test can be improved by a consonant one without any cost in terms of inferences on elementary hypotheses.
Social robots in advanced dementia

Aims: Pilot studies applying a humanoid robot (NAO), a pet robot (PARO) and a real animal (DOG) in therapy sessions of patients with dementia in a nursing home and a day care center. Methods:In the nursing home, patients were assigned by living units, based on dementia severity, to one of the three parallel therapeutic arms to compare: CONTROL, PARO and NAO (Phase 1) and CONTROL, PARO, and DOG (Phase 2). In the day care center, all patients received therapy with NAO (Phase 1) and PARO (Phase 2). Therapy sessions were held 2 days per week during 3 months. Evaluation, at baseline and follow-up, was carried out by blind raters using: the Global Deterioration Scale (GDS), the Severe Mini Mental State Examination (sMMSE), the Mini Mental State Examination (MMSE), the Neuropsychiatric Inventory (NPI), the Apathy Scale for Institutionalized Patients with Dementia Nursing Home version (APADEM-NH), the Apathy Inventory (AI) and the Quality of Life Scale (QUALID). Statistical analysis included descriptive statistics and non-parametric tests performed by a blinded investigator. Results: In the nursing home, 101 patients (Phase 1) and 110 patients (Phase 2) were included. There were no significant differences at baseline. The relevant changes at follow-up were: (Phase 1) patients in the robot groups showed an improvement in apathy; patients in NAO group showed a decline in cognition as measured by the MMSE scores, but not the sMMSE; the robot groups showed no significant changes between them; (Phase 2) QUALID scores increased in the PARO group. In the day care center, 20 patients (Phase 1) and 17 patients (Phase 2) were included. The main findings were: (Phase 1) improvement in the NPI irritability and the NPI total score; (Phase 2) no differences were observed at follow-up.
Robot-assisted therapy for neuromuscular training of sub-acute stroke patients. A feasibility study.

AIM Several studies have described the contribution of robotics technology in providing effective treatment options for improving upper-extremity functions in patients with hemiparesis following stroke. The aim of this study was to conduct a preliminary assessment of patient acceptance of an upper extremity robot, the Reo Therapy System (Motorika Ltd., Israel), developed specifically for neuromuscular training of upper extremities for use in rehabilitation centers and outpatient clinics. METHODS Ten in-patient sub-acute stroke patients aged 30-60 years participated in the study. They received 15 sessions of forty five minutes training with the Reo Therapy System, in addition to traditional occupational and physical therapy. A feedback questionnaire of the patients' satisfaction, the Fugl-Meyer test and the Manual Function Test (MFT) were used as outcome measures. RESULTS Patient satisfaction with the robot-assisted therapy program and acceptance of working with Reo Therapy System was very good. Arm impairment and functionality as measured with the Fugl-Meyer and the MFT increased significantly after treatment. CONCLUSION The Reo Therapy System was found to be valued by patients. Further research is necessary in order to identify the most efficient balance of Reo Therapy and traditional therapy methods.
Introduction to the Special Issues on Longitudinal Research on Substance Abuse and Health Services

In recent years, a perspective of chronic disease management in the treatment of alcohol or drug dependencies has emerged as the field embraces the concept of substance use disorders as a persistent or recurring condition (Compton, Glantz, and Delany 2003; Leshner 2001; McLellan 2002, 2004). Scientific investigation of substance abuse has increasingly documented the often chronic nature of addiction through both clinical observations and empirical data that reveal high relapse rates and protracted use across long periods of time. Along with the recognition of substance abuse as a chronic condition is the concern about the frequent and repeated encounters of substance abusers with social, health service, and criminal justice systems. Still, the lack of scientific understanding of how chronic drug use patterns evolve and interact with service systems over time has limited the field’s ability to develop optimal clinical and policy strategies. Reviews of the substance abuse field by both the Institute of Medicine (Lamb, Greenlick, and McCarty 1998) and the National Institute on Drug Abuse’s Blue Ribbon Task Force on Health Services Research (2004) call for broad and long-term research to address the current disconnect between knowledge of long-term drug abuse patterns and clinical and services research. In an effort to facilitate this movement, the Center for Advancing Longitudinal Drug Abuse Research (CALDAR) at the University of California, Los Angeles, has prepared two special issues assessing current knowledge on the life course of substance abuse (and their related HIV risks) and its interplay with the social, health, and criminal justice systems. By examining current knowledge, we delineate the gaps in our understanding of Evaluation Review Volume 31 Number 6 December 2007 511-514 © 2007 Sage Publications 10.1177/0193841X07308155 http://erx.sagepub. com hosted at http://online.sagepub. com
Potential and Pitfalls of Domain-Specific Information Extraction at Web Scale

In many domains, a plethora of textual information is available on the web as news reports, blog posts, community portals, etc. Information extraction (IE) is the default technique to turn unstructured text into structured fact databases, but systematically applying IE techniques to web input requires highly complex systems, starting from focused crawlers over quality assurance methods to cope with the HTML input to long pipelines of natural language processing and IE algorithms. Although a number of tools for each of these steps exists, their seamless, flexible, and scalable combination into a web scale end-to-end text analytics system still is a true challenge. In this paper, we report our experiences from building such a system for comparing the "web view" on health related topics with that derived from a controlled scientific corpus, i.e., Medline. The system combines a focused crawler, applying shallow text analysis and classification to maintain focus, with a sophisticated text analytic engine inside the Big Data processing system Stratosphere. We describe a practical approach to seed generation which led us crawl a corpus of ~1 TB web pages highly enriched for the biomedical domain. Pages were run through a complex pipeline of best-of-breed tools for a multitude of necessary tasks, such as HTML repair, boilerplate detection, sentence detection, linguistic annotation, parsing, and eventually named entity recognition for several types of entities. Results are compared with those from running the same pipeline (without the web-related tasks) on a corpus of 24 million scientific abstracts and a third corpus made of ~250K scientific full texts. We evaluate scalability, quality, and robustness of the employed methods and tools. The focus of this paper is to provide a large, real-life use case to inspire future research into robust, easy-to-use, and scalable methods for domain-specific IE at web scale.
EFFECTS OF REACTIVE OXYGEN SPECIES SCAVENGER ON THE PROTECTIVE ACTION OF 100% OXYGEN TREATMENT AGAINST STERILE INFLAMMATION IN MICE

Sepsis/multiple organ dysfunction syndrome (MODS) is a major cause of high mortality in the intensive care unit. We have recently reported that 100% oxygen treatment is beneficial to mice with zymosan-induced sterile inflammation by increasing antioxidant enzymatic activities. Yet, the use of hyperoxia is hindered by concerns that it could exacerbate organ injury by increasing free radical formation. It is believed that systemic inflammation and overproduction of reactive oxygen species (ROS) contribute to the mechanism underlying sepsis/MODS. A ROS scavenger has been proven to protect against sepsis/MODS in some animal models. Therefore, we hypothesized that ROS scavenger pretreatment might enhance the protective action of 100% oxygen treatment against zymosan-induced sterile inflammation in mice. In the present study, we showed that 100% oxygen treatment prevented the abnormal changes in serum biochemical parameters, tissue oxygenation, and organ histopathology, and improved the 14-day survival rate in zymosan-stimulated mice, indicating that 100% oxygen treatment had a protective action on sterile inflammation. We found that pretreatment with a ROS scavenger (N-acetylcysteine, vitamin C, or dimethylthiourea) abolished this protective action of 100% oxygen treatment. We also showed that 100% oxygen treatment decreased the levels of serum proinflammatory cytokines (TNF-&agr;, IL-6, and high-mobility group box 1), increased the level of serum anti-inflammatory cytokine (IL-10), and upregulated the activities of serum and tissue antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase) in zymosan-stimulated mice, which were reversed by the pretreatment with a ROS scavenger (N-acetylcysteine, vitamin C, or dimethylthiourea). We thus conclude that ROS scavenger pretreatment partly abolishes the protective effects of 100% oxygen treatment on sterile inflammation in mice by regulating inflammatory cytokines as well as antioxidant enzymes.ABBREVIATIONS-ALT-alanine aminotransferase; AST-aspartate aminotransferase; BUN-blood urea nitrogen; CAT-catalase; cTnI-cardiac troponin I; Cr-creatinine; DMTU-dimethylthiourea; GSH-Px-glutathione peroxidase; HBO-hyperbaric oxygen; HMGB1-high-mobility group box 1; ICU-intensive care unit; MODS-multiple organ dysfunction syndrome; NAC-N-acetylcysteine; NS-normal saline; Oxy-oxygen; SOD-superoxide dismutase; Vit C-vitamin C; Veh-vehicle; ZY-zymosan
How to Survey Patient Satisfaction

AMONG THE CONCEPTS most frequently discussed by those interested in health and medical care services is patient satisfaction. Debate continues regarding the many methodological difficulties that can make interpretation of patient ratings and reports problematic, as well as the use of patient satisfaction data in formulating public policy. This article presents an overview of how one might approach the construction of a patient satisfaction survey. We focus on those issues that have been raised most frequently and offer our best advice about how they should be handled. In addition to a brief overview of the general goals of measurement and techniques of measurement evaluation, we offer some specific suggestions about how to determine the content of a patient satisfaction survey, an example of how to construct and test multi-item scales, and some recommendations regarding other important issues including reliability, validity, and the uses of satisfaction surveys in research and evaluation projects. Thus, we focus first and foremost on basic measurement considerations that are prerequisites to a successful satisfaction survey. These comments are based on the experiences of
[Treatment of femoral shaft fractures with interlocking intramedullary nailing].

OBJECTIVES Fractures of the femoral shaft are one of the most common fractures and may result in extensive disability, prolonged morbidity, or mortality unless appropriate treatment is applied. There are several treatment alternatives. In this study, we evaluated early results of interlocking intramedullary nailing in patients with femoral shaft fractures. METHODS Femoral fractures of 42 patients (34 males, 8 females; mean age 32 years; range 16 to 67 years) were treated with interlocking intramedullary nailing. The mean follow-up was 14.4 months (range 8 to 32 months). Radiologic and clinical results were evaluated. RESULTS Union was obtained in all but one patient within a mean duration of 18.2 weeks. Discrepancy of leg length was measured as 10 mm in six patients, and 25 mm in one patient. One patient (2.38%) developed deep infection. Knee flexion was more than 120 degrees in 95.23%. According to Thoresen's criteria, the results were excellent and good in 89% of patients. CONCLUSION Interlocking intramedullary nailing proved an acceptable alternative in the treatment of femoral shaft fractures.
Remote Acoustic Monitoring of North Atlantic Right Whales (Eubalaena glacialis) Reveals Seasonal and Diel Variations in Acoustic Behavior

Remote acoustic monitoring is a non-invasive tool that can be used to study the distribution, behavior, and habitat use of sound-producing species. The North Atlantic right whale (Eubalaena glacialis) is an endangered baleen whale species that produces a variety of stereotyped acoustic signals. One of these signals, the “gunshot” sound, has only been recorded from adult male North Atlantic right whales and is thought to function for reproduction, either as reproductive advertisement for females or as an agonistic signal toward other males. This study uses remote acoustic monitoring to analyze the presence of gunshots over a two-year period at two sites on the Scotian Shelf to determine if there is evidence that North Atlantic right whales may use these locations for breeding activities. Seasonal analyses at both locations indicate that gunshot sound production is highly seasonal, with an increase in the autumn. One site, Roseway West, had significantly more gunshot sounds overall and exhibited a clear diel trend in production of these signals at night. The other site, Emerald South, also showed a seasonal increase in gunshot production during the autumn, but did not show any significant diel trend. This difference in gunshot signal production at the two sites indicates variation either in the number or the behavior of whales at each location. The timing of the observed seasonal increase in gunshot sound production is consistent with the current understanding of the right whale breeding season, and our results demonstrate that detection of gunshots with remote acoustic monitoring can be a reliable way to track shifts in distribution and changes in acoustic behavior including possible mating activities.
Revised North Star Ambulatory Assessment for Young Boys with Duchenne Muscular Dystrophy

The advent of therapeutic approaches for Duchenne muscular dystrophy (DMD) has highlighted the need to identify reliable outcome measures for young boys with DMD. The aim of this study was to develop a revised version of the North Star Ambulatory Assessment (NSAA) suitable for boys between the age of 3 and 5 years by identifying age appropriate items and revising the scoring system accordingly. Using the scale in 171 controls between the age of 2.9 and 4.8 years, we identified items that were appropriate at different age points. An item was defined as age appropriate if it was completed, achieving a full score, by at least 85% of the typically developing boys at that age. At 3 years (±3months) there were only 8 items that were age appropriate, at 3 years and 6 months there were 13 items while by the age of 4 years all 17 items were appropriate. A revised version of the scale was developed with items ordered according to the age when they could be reliably performed. The application of the revised version of the scale to data collected in young DMD boys showed that very few of the DMD boys were able to complete with a full score all the age appropriate items. In conclusion, our study suggests that a revised version of the NSAA can be used in boys from the age of 3 years to obtain information on how young DMD boys acquire new abilities and how this correlates with their peers.