LLukas22/scidocs huggingface dataset:
Small nodules detected on chest radiography: does size predict calcification?

STUDY OBJECTIVES
To determine whether the likelihood of lung nodule calcification can be predicted from nodule size as measured on a chest radiograph (CXR).


DESIGN
Retrospective review of CXRs of patients with lung nodules < or =1 cm in size detected on CT scanning. CT images were used to identify calcifications and to provide spatial localization for readers to visualize nodules on a CXR and to measure their size. A subset of these nodules then was reexamined by different readers who did not view the CT scans


SETTING
Two university hospitals (Albuquerque, NM; Dallas, TX) and a US Air Force/Veterans Administration medical center (Albuquerque, NM).


PATIENTS
Two hundred thirty-six nodules in 185 patients


RESULTS
One half of the nodules (118) seen on CT scans could not be located on CXR, of which 8 (7%) were calcified. The prevalence of calcifications in the other 118 nodules visualized on CXRs was much higher (71 of 118 nodules [60%]; p<0.005). Among the nodules visualized on CXRs, those < 7 mm in diameter (44 of 57 nodules [77%]) were more likely to be calcified than those > or = 7 mm in diameter (27 of 61 nodules [44%]; p<0.005). Radiographs of 42 of the smallest nodules visualized on CXRs by the initial readers later were examined prospectively by different readers who did not have access to the CT images. Thirty of 33 of the calcified nodules (91%) but only 3 of 9 of the noncalcified nodules (33%) were detected (p<0.005). These readers also recorded 40 additional small nodules that were not seen on CT scans, which were considered to be false-positives.


CONCLUSIONS
Nodules detected on CXRs that measure <7 mm in size are likely to be calcified or to represent a false-positive finding.
Methylphenidate reduces mental fatigue and improves processing speed in persons suffered a traumatic brain injury.

OBJECTIVE
Post-traumatic brain injury symptoms, such as mental fatigue, have considerable negative impacts on quality-of-life. In the present study the effects of methylphenidate in two different dosages were assessed with regard to mental fatigue, pain and cognitive functions in persons who had suffered a traumatic brain injury.


METHODS
Fifty-one subjects were included and 44 completed the study. The treatment continued for 12 weeks, including three treatment periods with no medication for 4 weeks, administration of low dose methylphenidate (up to 5 mg × 3) for 4 weeks and normal dose methylphenidate (up to 20 mg × 3) for a further 4 weeks. The patients were randomized into three groups where all groups were given all treatments.


RESULTS
Significantly reduced mental fatigue, assessed with the Mental Fatigue Scale (MFS) and increased information processing speed (coding, WAIS-III), were detected. The SF-36 vitality and social functioning scales were also improved significantly. Pain was not reduced by methylphenidate. The positive effects of treatment were dose-dependent, with the most prominent effects being at 60 mg methylphenidate/day spread over three doses. Observed side-effects were increased blood pressure and increased heart rate.


CONCLUSIONS
Methylphenidate was generally well-tolerated and it improved long-lasting mental fatigue and processing speed after traumatic brain injury.
Obsessive-compulsive disorder across developmental trajectory: cognitive processing of threat in children, adolescents and adults.

BACKGROUND
While the cognitive theory of obsessive-compulsive disorder (OCD) is one of the most widely accepted accounts of the maintenance of the disorder in adults, no study to date has systematically evaluated the theory across children, adolescence and adults with OCD.


METHOD
This paper investigated developmental differences in the cognitive processing of threat in a sample of children, adolescents and adults with OCD. Using an idiographic assessment approach, as well as self-report questionnaires, this study evaluated cognitive appraisals of responsibility, probability, severity, thought-action fusion (TAF), thought-suppression, self-doubt and cognitive control. It was hypothesised that there would be age related differences in reported responsibility for harm, probability of harm, severity of harm, thought suppression, TAF, self-doubt and cognitive control.


RESULTS
Results of this study demonstrated that children with OCD reported experiencing fewer intrusive thoughts, which were less distressing and less uncontrollable than those experienced by adolescents and adults with OCD. Furthermore, responsibility attitudes, probability biases and thought suppression strategies were higher in adolescents and adults with OCD. Cognitive processes of TAF, perceived severity of harm, self-doubt and cognitive control were found to be comparable across age groups.


CONCLUSIONS
These results suggest that the current cognitive theory of OCD needs to address developmental differences in the cognitive processing of threat. Furthermore, for a developmentally sensitive theory of OCD, further investigation is warranted into other possible age related maintenance factors. Implications of this investigation and directions for future research are discussed.
A randomised controlled feasibility trial of Group Cognitive Behavioural Therapy for people with severe asthma.

OBJECTIVES
Evidence for the efficacy of Cognitive Behavioural Therapy (CBT) in asthma is developing but it is not known if this translates to benefits in severe asthma or if a group approach is acceptable to this patient group. This study aimed to assess the feasibility and acceptability of Group-CBT in severe asthma.


METHOD
This was a two-centre, randomised controlled parallel group feasibility study. Eligible participants (patients with severe asthma and a clinically significant diagnosis of anxiety and/or depression - Hospital Anxiety and Depression Scale (HAD) score greater than 8 for the anxiety or depression sub-scale) received Group-CBT in weekly sessions for eight consecutive weeks and usual care or usual care only. Follow-up was for 16 weeks and end points were: Asthma Quality of Life Questionnaire, Asthma Control Questionnaire, HAD, Dyspnoea-12, EuroQual-5D and EuroQuol-VAS.


RESULTS
51 patients were randomised: 36% (51 out of 140) consent rate and attrition at week 16 was 12. Screening logs indicated that study take-up was influenced by patients living long distances from the treatment centre and inability to commit to the weekly demands of the programme. Drop-out was higher in Group-CBT compared due to inability to commit to the weekly programme because of poor health. Participants who contributed to focus group discussions reported that Group-CBT contributed to a better understanding of their illness and related approaches to anxiety management and acceptance of their asthma condition. Although weekly face-to-face sessions were challenging, this was the preferred method of delivery for these participants.


CONCLUSIONS
This feasibility study shows that Group-CBT warrants further investigation as a potentially promising treatment option for patients with severe asthma. It has been possible but not easy to recruit and retain the sample. Options for a less demanding intervention schedule, such as less frequent face-to-face visits and the use of web-based interventions, require careful consideration.
Pattern Recognition and Machine Learning Solutions to the Exercises : Web-Edition

This is the solutions manual (web-edition) for the book Pattern Recognition and Machine Learning (PRML; published by Springer in 2006). It contains solutions to the www exercises. This release was created September 8, 2009. Future releases with corrections to errors will be published on the PRML web-site (see below). The authors would like to express their gratitude to the various people who have provided feedback on earlier releases of this document. In particular, the " Bishop Reading Group " , held in the Visual Geometry Group at the University of Oxford provided valuable comments and suggestions. The authors welcome all comments, questions and suggestions about the solutions as well as reports on (potential) errors in text or formulae in this document; please send any such feedback to
Preconditioning chemotherapy with paclitaxel and cisplatin enhances the antitumor activity of cytokine induced-killer cells in a murine lung carcinoma model.

Adoptive cell therapy involving the use of ex vivo generated cytokine-induced killer cells (CIKs) provides a promising approach to immunotherapy. However, the therapeutic activity of CIKs is limited by the immunosuppressive factors active in the host. It has become increasingly apparent that manipulation of the recipient immune system with the preconditioning regimen is essential to guarantee the antitumor effect of subsequent adoptive cell therapy. In our study, paclitaxel (PTX) and cisplatin (DDP) were used as preconditioning drugs combined with CIKs to illustrate the potential mechanisms underlying the synergic antitumor effect against Lewis lung cancer cells in vitro and in vivo. We found that 3LL cells displayed an increased sensitization to CIKs-induced lysis after treatment with PTX or DDP in vitro. Significant inhibition of tumor growth was observed in mice treated with combinatorial chemo-immunotherapy with respect to untreated or single regimen treated ones. Prior chemotherapy markedly enhanced the intratumoral accumulation of CD3(+) T lymphocytes and the homing of CIKs to the spleen and tumor. Moreover, the frequencies of intratumoral and splenic regulatory T cells (Tregs) were significantly decreased after chemotherapy pretreatment. Our findings provide a new rationale for combining immunotherapy and chemotherapy to induce a synergistic antitumor response in patients with lung cancer.
Epirubicin and cyclophosphamide, methotrexate, and fluorouracil as adjuvant therapy for early breast cancer.

BACKGROUND
The National Epirubicin Adjuvant Trial (NEAT) and the BR9601 trial examined the efficacy of anthracyclines in the adjuvant treatment of early breast cancer.


METHODS
In NEAT, we compared four cycles of epirubicin followed by four cycles of cyclophosphamide, methotrexate, and fluorouracil (CMF) with six cycles of CMF alone. In the BR9601 trial, we compared four cycles of epirubicin followed by four cycles of CMF, with eight cycles of CMF alone every 3 weeks. The primary end points were relapse-free and overall survival. The secondary end points were adverse effects, dose intensity, and quality of life.


RESULTS
The two trials included 2391 women with early breast cancer; the median follow-up was 48 months. Relapse-free and overall survival rates were significantly higher in the epirubicin-CMF groups than in the CMF-alone groups (2-year relapse-free survival, 91% vs. 85%; 5-year relapse-free survival, 76% vs. 69%; 2-year overall survival, 95% vs. 92%; 5-year overall survival, 82% vs. 75%; P<0.001 by the log-rank test for all comparisons). Hazard ratios for relapse (or death without relapse) (0.69; 95% confidence interval [CI], 0.58 to 0.82; P<0.001) and death from any cause (0.67; 95% CI, 0.55 to 0.82; P<0.001) favored epirubicin plus CMF over CMF alone. Independent prognostic factors were nodal status, tumor grade, tumor size, and estrogen-receptor status (P<0.001 for all four factors) and the presence or absence of vascular or lymphatic invasion (P=0.01). These factors did not significantly interact with the effect of epirubicin plus CMF. The overall incidence of adverse effects was significantly higher with epirubicin plus CMF than with CMF alone but did not significantly affect the delivered-dose intensity or the quality of life.


CONCLUSIONS
Epirubicin plus CMF is superior to CMF alone as adjuvant treatment for early breast cancer. (ClinicalTrials.gov number, NCT00003577 [ClinicalTrials.gov].).
Enterococcal peritonitis in children receiving chronic peritoneal dialysis.

BACKGROUND
Peritonitis is a common complication of chronic peritoneal dialysis (CPD) and can be associated with technique failure. Enterococcus is an uncommon peritoneal pathogen in children receiving CPD but represents a potential therapeutic challenge due to its innate resistance to cephalosporins and emerging resistance to glycopeptides.


METHODS
The International Pediatric Peritonitis Registry is a global consortium of 47 paediatric dialysis centres designed to address validation of the International Society for Peritoneal Dialysis paediatric peritonitis treatment guidelines. Between 2001 and 2004, peritonitis episodes were assessed in 392 participating children receiving CPD.


RESULTS
Among the 392 patients, 340 episodes of culture-positive peritonitis were evaluated. Twenty of these episodes were due to Enterococcus species (5.9%). There were no clinical characteristics uniquely associated with enterococcal peritonitis at presentation. After 3 days of therapy, 75% of patients were pain free, 95% had decreased effluent cloudiness and 90% were afebrile. Only one patient required a catheter exchange, and all patients experienced full functional recovery. Despite broad in vitro resistance to cephalosporins and 21% resistance to glycopeptides, neither in vitro resistance pattern nor choice of empiric antibiotic regimen affected short- or long-term outcomes.


CONCLUSIONS
Enterococci are likely responsible for ∼6% of culture-positive peritonitis episodes in children receiving CPD. Although it was not possible to identify patients with enterococcal peritonitis based on presentation, clinical response was not associated with in vitro resistance patterns, and patients who initially received a cephalosporin-based empiric regimen until culture results are available are likely to respond quickly and have full functional recovery.
Treatment of depression and anxiety with internet-based cognitive behavior therapy in patients with a recent myocardial infarction (U-CARE Heart): study protocol for a randomized controlled trial

BACKGROUND
Major depression and depressive symptoms are common in patients with a recent myocardial infarction (MI), and depression is associated with adverse cardiovascular outcomes. Anxiety post-MI is less studied, but occurs commonly in patients with heart disease, and is also considered a risk factor for recurrence of cardiac events. Cognitive behavior therapy (CBT) is an established therapy for depression and anxiety disorders. To the best of our knowledge, there have not been any studies to determine if internet-based CBT (iCBT) can reduce the symptoms of depression and anxiety in patients with a recent MI. The main aim of the U-CARE Heart trial is to evaluate an iCBT intervention for patients with a recent MI.


METHODS/DESIGN
This is a randomized, controlled, prospective study with a multicenter design. A total of 500 participants will be randomized at a 1:1 ratio, around two months after an acute MI, to either iCBT or to a control group. Both groups will receive an optimal standard of care according to guidelines. The intervention consists of a self-help program delivered via the internet with individual online support from a psychologist. Treatment duration is 14 weeks. The primary outcome is change in patients' self-rated anxiety and depression symptoms from baseline to end of treatment. An internal pilot study was conducted indicating sufficient levels of study acceptability and engagement in treatment.


DISCUSSION
The present study is designed to evaluate an iCBT intervention targeting symptoms of depression and anxiety in a post-MI population. If effective, iCBT has several advantages, and will potentially be implemented as an easily accessible treatment option added to modern standard of care.


TRIAL REGISTRATION
This trial was registered with Clinicaltrials.gov (identifier: NCT01504191 ) on 19 December 2011.
Monotherapy with infliximab versus combination therapy in the maintenance of clinical remission in children with moderate to severe Crohn disease.

OBJECTIVES
The aim of the present study was to compare the efficacy and safety of 2 protocols of maintenance therapy with infliximab (IFX) and an immunomodulatory agent in pediatric patients with Crohn disease (CD): withdrawal of immunomodulators versus continuation of immunosuppressants.


METHODS
The present multicenter randomized open-label trial included 99 patients with CD (ages 14.5 ± 2.6 years) who were administered IFX (5 mg/kg body weight) along with an immunomodulatory agent (azathioprine 1.5-3 mg/kg body weight per day, methotrexate 10-25 mg/week). After 10 weeks of the induction therapy, 84 responders were centrally randomized into 1 of the following groups: group I (n = 45) in which IFX and an immunomodulatory agent were continued up to week 54 and group II (n = 39) in which the immunomodulatory agent was discontinued after 26 weeks.


RESULTS
The induction therapy was reflected by a significant decrease in Pediatric Crohn's Disease Activity Index (PCDAI) and Simplified Endoscopic Activity Score for Crohn's Disease (SES-CD) values. After the maintenance phase, the analyzed groups did not differ significantly in terms of the clinical response loss rates and final PCDAI and SES-CD scores. Furthermore, no significant intragroup differences were documented between mean PCDAI scores determined at the end of induction and maintenance phases. Intensification/modification of the treatment was required in 13 of 45 (29%) and 11 of 39 (28%) patients of groups I and II, respectively. A total of 9 serious adverse events were documented; none of the patients died during the trial.


CONCLUSIONS
Twenty-six weeks likely represent the safe duration of combined IFX/immunomodulatory therapy in our sample of pediatric patients with CD.
LEARNING TO PREDICT FOREST FIRES WITH DIFFERENT DATA MINING TECHNIQUES

The motive for this study was to learn to predict forest fires in Slovenia using different data mining techniques. We used predictive models based on the forest structure GIS (geographical information system), the weather prediction model Aladin and MODIS satellite data. We examined three different datasets: one for the Kras region, one for Primorska region and one for continental Slovenia because of the climate differences. On these datasets we applied logistic regression and decision trees (J48), as well as random forests, bagging and boosting of decision trees, in order to obtain predictive models of fire occurrence. Best results in terms of predictive accuracy were obtained by bagging decision trees.
Algorithms for Graph Similarity and Subgraph Matching

We deal with two independent but related problems, those of graph similarity and subgraph matching, which are both important practical problems useful in several fields of science, engineering and data analysis. For the problem of graph similarity, we develop and test a new framework for solving the problem using belief propagation and related ideas. For the subgraph matching problem, we develop a new algorithm based on existing techniques in the bioinformatics and data mining literature, which uncover periodic or infrequent matchings. We make substantial progress compared to the existing methods for both problems. 1 Problem Definitions and Statement of Contributions 1.1 Graph Similarity Problem 1 1 Given: two graphs G1(n1, e1) and G2(n2, e2), with possibly different number of nodes and edges, and the mapping between the graphs’ nodes. Find: (a) an algorithm to calculate the similarity of the two graphs, which returns (b) a measure of similarity (a real number between 0 and 1) that captures intuition well. Innovations: a) We develop a method involving belief propagation, unseen in literature, to solve this problem b) The method (and its fast linearized approximate version) gives extremely agreeable results c) Except for scalability, we know of no shortcomings of this method. 1.2 Subgraph Matching Problem 2 Given: a graph time series, where there are T number of graphs. Find: (a) An algorithm to find approximate subgraphs that occur in a subset of the T graphs. (b) Where the approximate subgraphs may not occur in the majority of the time points, but in local sections of the time series Innovations: a) We develop a principled approach to selecting the important time components from which subgraphs should be mined. Our method is also tailored for the problem of selecting subgraphs in biological networks. For this, we use sparse PCA which has not been for this application domain. b) Scalability: Our method is both fast and scalable to real biological data (1000s of nodes). However, it has not been demonstrated whether it can scale to extremely large networks of more than 10 000 nodes. c) The method gives results that are easy to interpret and biologically sensible. Disclaimer of interests intersecting with course project Aaditya may use the PhoneCall dataset for his DAP. Danai is interested in graph similarity and belief propagation for research. Ankur has used tensors for his research, but in a different context. Jing has used CODENSE before, and is interested in improving it for research purposes. None of the authors have other course projects this term. The following are the papers read for this course (refer to the numbering in the references section): Jing [21], [28], [22], Ankur [20], [18], [9], Aaditya [5], [26], [27], Danai [10], [14], [15].