LLukas22/scidocs huggingface dataset:
Tumor cytogenetics revisited: comparative genomic hybridization and spectral karyotyping

 Fluorescence in situ hybridization techniques allow the visualization and localization of DNA target sequences on the chromosomal and cellular level and have evolved as exceedingly valuable tools in basic chromosome research and cytogenetic diagnostics. Recent advances in molecular cytogenetic approaches, namely comparative genomic hybridization and spectral karyotyping, now allow tumor genomes to be surveyed for chromosomal aberrations in a single experiment and permit identification of tumor-specific chromosomal aberrations with unprecedented accuracy. Comparative genomic hybridization utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes. Comparative genomic hybridization is an ideal tool for analyzing chromosomal imbalances in archived tumor material and for examining possible correlations between these findings and tumor phenotypes. Spectral karyotyping is based on the simultaneous hybridization of differentially labeled chromosome painting probes (24 in human), followed by spectral imaging that allows the unique display of all human (and other species) chromosomes in different colors. Spectral karyotyping greatly facilitates the characterization of numerical and structural chromosomal aberrations, therefore improving karyotype analysis considerably. We review these new molecular cytogenetic concepts, describe applications of comparative genomic hybridization and spectral karyotyping for the visualization of chromosomal aberrations as they relate to human malignancies and animal models thereof, and provide evidence that fluorescence in situ hybridization has developed as a robust and reliable technique which justifies its translation to cytogenetic diagnostics.
Thermo-chemotherapy for intermediate or high-risk recurrent superficial bladder cancer patients.

BACKGROUND
The purpose of this study was to evaluate the efficacy of combined local hyperthermia and intravesical mitomycin-C (MMC) in a selected group of patients with intermediate or high-risk recurrent transitional cell carcinoma (TCC) of bladder.


PATIENTS AND METHODS
Forty-seven patients with multiple or recurrent Ta or T1 TCC of the bladder were treated with intravesical MMC and local hyperthermia of the bladder wall. Patients were treated with either a prophylactic protocol (40 mg MMC) after complete transurethral resection of all tumours or with an ablative protocol (80 mg MMC) in patients with viable tumours.


RESULTS
Thirty-two patients were eligible for analysis. The prophylactic protocol was administered to 22 patients. After a mean follow-up of 289 days, 20 patients (91%) were recurrence free. Two patients (9%) had tumour recurrence after a mean period of 431 days. The ablative protocol was administered to 10 patients. Complete tumour ablation was achieved in eight patients (80%) after a mean follow up of 104.5 days.


CONCLUSIONS
Our efficacy and safety results confirm those reported in previously published studies, suggesting the promising value of this combined treatment modality for both prophylactic and ablative patients. The ablative protocol offers an alternative therapy for a selected patient population for whom no other treatment option exists.
Bronfenbrenner’s bioecological theory for modelling community resilience to natural disasters

This paper advocates the use of Bronfenbrenner’s bioecological theory as a framework to analyse resilience at diverse scales. Bronfenbrenner’s bioecological theory can be employed to (a) benchmark social resilience, (b) target the priority interventions required and (c) measure progress arising from these interventions to enhance resilience to natural disasters. First, the paper explores resilience to natural disasters in the context of climatic change as building resilience is seen as a way to mitigate impacts of natural disasters. Second, concepts of resilience are systematically examined and documented, outlining resilience as a trait and resilience as a process. Third, issues arising in relation to the measurement of resilience are discussed. Fourth, Bronfenbrenner’s bioecological systems theory is described and proffered to model and assess resilience at different scales. Fifth, studies are described which have supported the use of the bioecological systems theory for the study of resilience. Sixth, an example of the use of Bronfenbrenner’s theory is offered and the paper concludes with suggestions for future research using Bronfenbrenner’s theory.
Effect of sow and piglet porcine circovirus type 2 (PCV2) vaccination on piglet mortality, viraemia, antibody titre and production parameters.

The present study describes the effects of sow and/or piglet porcine circovirus type 2 (PCV2) vaccination on viraemia, antibody response and production parameters (average daily weight gain [ADWG] and mortality) of piglets from a PCV2 subclinically infected farm. Four hundred seventy-six piglets born from vaccinated (V) or non-vaccinated (NV) sows were further subdivided in a total of four groups: NV sows-NV pigs (NV-NV, n=134), NV sows-V pigs (NV-V, n=135);V sows-NV pigs (V-NV, n=104) and V sows-V pigs (V-V, n=103). A single vaccination of sows before mating was able to confer significantly higher antibody titres to their piglets at 4 weeks of age and a different PCV2 dynamics infection compared to piglets coming from NV sows. Piglet vaccination (independently of sow treatment) caused an earlier seroconversion and lower percentages of PCV2 infected pigs compared to the NV ones throughout their life. The double PCV2 vaccination strategy was able to reduce PCV2 infection but apparently caused some interference in piglet humoral response development. PCV2 vaccination was able to overcome this interference since the ADWG was improved in both groups of vaccinated piglets, independently of the sow treatment, being the highest ones obtained in the double vaccination group.
Predicting 12-month mortality for persons with dementia.

OBJECTIVES
We develop and test a model of 12-month mortality among persons (N=3858) with organic dementia.


METHODS
Data are from caregiver interviews and claims records for persons enrolled in the Medicare Alzheimer's Disease Demonstration Evaluation. Information covers the year prior to enrollment through 36 months. We used Proportional hazards models to predict time to death. We estimated two starting points: first, the date of randomization, and second, the date of maximum difficulty in performing two or more activities of daily living (ADLs).


RESULTS
The final model includes age, gender, ADL difficulty, medical conditions, prior year hospitalizations, and whether a daughter was the primary caregiver. We combined hazard ratios to produce a cumulative mortality risk score. Model discrimination is reasonable for both models (c statistics of.72 and.69, respectively), and calibration tests were nonsignificant.


DISCUSSION
The model's efficiency, as measured by the ratio of false positives (those predicted to die, but who lived) to true positives (those predicted to die and who did die) ranged from fewer than 1:1 to more than 4:1 as the model's sensitivity increased. This ratio was lower in the two or more ADL difficulty model. A validation test of the prediction model found comparable sensitivity and specificity (c statistic of.69) to the reference model.
1 Multiresolution Signal Decomposition Schemes . Part 2 : Morphological Wavelets

In its original form, the wavelet transform is a linear tool. However, it has been increasingly recognized that nonlinear extensions are possible. A major impulse to the development of nonlinear wavelet transforms has been given by the introduction of the lifting scheme by Sweldens. The aim of this report, which is a sequel to a previous report devoted exclusively to the pyramid transform, is to present an axiomatic framework encompassing most existing linear and nonlinear wavelet decompositions. Furthermore, it introduces some, thus far unknown, wavelets based on mathematical morphology, such as the morphological Haar wavelet, both in one and two dimensions. A general and flexible approach for the construction of nonlinear (morphological) wavelets is provided by the lifting scheme. This paper discusses one example in considerable detail, the max-lifting scheme, which has the intriguing property that it preserves local maxima in a signal over a range of scales, depending on how local or global these maxima are. 1991 Mathematics Subject Classification: 68U10, 94A12
Incidence of left atrial abnormalities under treatment with dabigatran, rivaroxaban, and vitamin K antagonists

BACKGROUND
Non-vitamin K antagonist oral anticoagulants (NOACs) such as dabigatran or rivaroxaban are alternatives to vitamin K antagonists (VKAs) for prevention of stroke and systemic embolism in patients with atrial fibrillation (AF) and atrial flutter (AFL). Incidences of risk factors for left atrium (LA) and left atrial appendage (LAA) thrombus formation, such as dense spontaneous echo contrast (SEC), low LAA velocity (LAAV) <20 cm/s under treatment with dabigatran and rivaroxaban in comparison with VKAs are unknown.


METHODS
We studied 306 patients with AF (94 %) and AFL (6 %) undergoing transesophageal echocardiography. Patients received VKAs (n = 138), dabigatran (n = 68), or rivaroxaban (n = 100) for at least 3 weeks prior to investigation. Time in therapeutic range was 67 % for VKA. Mean CHADS2 score and CHA2DS2-VASc score were 1.3 and 2.5, respectively. Left atrial abnormality was defined as either dense SEC, low LAAV <20 cm/s, or thrombus.


RESULTS
Any LA abnormality occurred in 9, 3, and 5 % of patients receiving VKA, dabigatran, and rivaroxaban, respectively. The most frequent abnormality was LAA thrombus (VKA: 4 %, dabigatran: 0 %, rivaroxaban: 2 %) and low LAAV of less than 20 cm/s (VKA: 4 %, dabigatran: 1 %, rivaroxaban: 1 %), followed by dense SEC (VKA: 2 %, dabigatran: 1 %, rivaroxaban: 2 %). Results of uni- and multivariate analyses revealed a numerically lower but not significantly different frequency of any LA abnormality under dabigatran (OR 0.4, 95 % Cl 0.08 - 1.88, p = 0.25) and rivaroxaban (OR 0.65, 95 % Cl 0.22 - 1.98, p = 0.45) compared to VKA.


CONCLUSION
With respect to the incidence of LA abnormalities, dabigatran and rivaroxaban are not inferior to VKA.
A systematic analysis of performance measures for classification tasks

Article history: Received 14 February 2008 Received in revised form 21 November 2008 Accepted 6 March 2009 Available online 8 May 2009
Multiscale Design of Cell-Type–Specific Pharmacokinetic/Pharmacodynamic Models for Personalized Medicine: Application to Temozolomide in Brain Tumors

Optimizing anticancer therapeutics needs to account for variable drug responses in heterogeneous cell populations within the tumor as well as in organs of toxicity. To address cell heterogeneity, we propose a multiscale modeling approach-from in vitro to preclinical and clinical studies-to develop cell-type-specific pharmacokinetic-pharmacodynamic (PK-PD) models. A physiologically based mechanistic modeling approach integrating data from aqueous solutions, U87 glioma cells, mice, and cancer patients was utilized to characterize the brain disposition of temozolomide (TMZ), the cornerstone of chemotherapy against glioblastoma multiforme. The final model represented intracellular normal brain and brain tumor compartments in which TMZ pH-dependent conversion to the DNA-alkylating species leads to the formation of DNA adducts that serve as an entry point for a PD model. This multiscale protocol can be extended to account for TMZ PK-PD in different cell populations, thus providing a critical tool to personalize TMZ-based chemotherapy on a cell-type-specific basis.
Structured self-management education maintained over two years in insufficiently controlled type 2 diabetes patients: the ERMIES randomised trial in Reunion Island

BACKGROUND
Self-management education programs can reduce the complications and mortality in type 2 diabetes. The need to structure these programs for outpatient and community care with a vision for long-term maintenance has been recognised. In Reunion Island, an area affected by epidemiological and nutritional transition, diabetes affects 18% of the adult population over 30 years, with major social disparities, poor glycaemic control and frequent cardiovascular complications.


METHODS/DESIGN
ERMIES is a randomised controlled trial designed to test the efficacy of a long-term (2 years) structured group self management educational intervention in improving blood glucose in non-recent, insufficiently controlled diabetes. After an initial structured educational cycle carried out blind for the intervention arm, patients will be randomised in two parallel group arms of 120 subjects: structured on-going group with educational intervention maintained over two years, versus only initial education. Education sessions are organised through a regional diabetes management network, and performed by trained registered nurses at close quarters. The educational approach is theoretically based (socio-constructivism, social contextualisation, empowerment, action planning) and reproducible, thanks to curricula and handouts for educators and learners. The subjects will be recruited from five hospital outpatient settings all over Reunion Island. The main eligibility criteria include: age ≥18 years, type 2 diabetes treated for more than one year, HbA1c ≥ 7.5% for ≥3 months, without any severe evolving complication (ischaemic or proliferative retinopathy, severe renal insufficiency, coronaropathy or evolving foot lesion), and absence of any major physical or cognitive handicap. The primary outcome measure is HbA1c evolution between inclusion and 2 years. The secondary outcome measures include anthropometric indicators, blood pressure, lipids, antidiabetic medications, level of physical activity, food ingestion, quality of life, social support, anxiety, depression levels and self-efficacy. An associated nested qualitative study will be conducted with 30 to 40 subjects in order to analyse the learning and adaptation processes during the education cycles, and throughout the study.


CONCLUSIONS
This research will help to address the necessary but difficult issue of structuring therapeutic education in type 2 diabetes based on: efficacy and potential interest of organising on-going empowerment group-sessions, at close quarters, over the long term, in a heterogeneous socioeconomic environment.


TRIAL REGISTRATION
ID_RCB number: 2011-A00046-35Clinicaltrials.gov number: NCT01425866.
Re-stor(y)ing North West Sutherland, Scotland

Abstract This paper focuses on two high profile projects initiated by communities in north west Sutherland as part of Highland 2007. The first concerns the Ceannabeinne Township Trail near Durness which involves the telling of the story of reistance to the Clearances of the nineteenth century. The second, Summer in the Straths, retraces the route of the Summer Walkers and highlights their contribution to social and economic life in the Highlands. The paper argues that the projects remap the land in ways that suggest an alternative imaginary to that aligned with processes of dispossession that have for so long defined social and economic practice in the area. Literally and figuratively, the projects map openings which challenge the norms through which the land is frequently cast.
Face Recognition Based on Curvelet Transform and LS-SVM

As a latest multiresolution analysis method, curvelet transform has improved directional elements with anisotropy and better ability to represent sparsely edges and other singularities along curves. To reduce the dimensionality of facial image and improve the recognition rate, a face recognition system based on curvelet transform and Least Square Support Vector Machine (LS-SVM) has been developed in this paper, which uses curvelet transform to extract features from facial images first, and then uses LS-SVM to classify facial images based on features. The proposed method has been evaluated by carrying out experiments on the well-known ORL face database. The results show that the correct recognition rate is up to 96%, and the computational speed is faster. Index Terms —curvelet transform, LS-SVM, face recognit –ion, ORL face database
HAMILTONIAN FLOW EQUATIONS FOR A DIRAC PARTICLE IN AN EXTERNAL POTENTIAL

Abstract We derive and solve the Hamiltonian flow equations for a Dirac particle in an external static potential. The method shows a general procedure for the set up of continuous unitary transformations to reduce the Hamiltonian to a quasidiagonal form.
Hypoglycemic effect of bitter melon compared with metformin in newly diagnosed type 2 diabetes patients.

ETHNOPHARMACOLOGICAL RELEVANCE
Bitter melon (Momordica charantia L.) has been widely used as an traditional medicine treatment for diabetic patients in Asia. In vitro and animal studies suggested its hypoglycemic activity, but limited human studies are available to support its use.


AIM OF STUDY
This study was conducted to assess the efficacy and safety of three doses of bitter melon compared with metformin.


MATERIALS AND METHODS
This is a 4-week, multicenter, randomized, double-blind, active-control trial. Patients were randomized into 4 groups to receive bitter melon 500 mg/day, 1,000 mg/day, and 2,000 mg/day or metformin 1,000 mg/day. All patients were followed for 4 weeks.


RESULTS
There was a significant decline in fructosamine at week 4 of the metformin group (-16.8; 95% CI, -31.2, -2.4 μmol/L) and the bitter melon 2,000 mg/day group (-10.2; 95% CI, -19.1, -1.3 μmol/L). Bitter melon 500 and 1,000 mg/day did not significantly decrease fructosamine levels (-3.5; 95% CI -11.7, 4.6 and -10.3; 95% CI -22.7, 2.2 μmol/L, respectively).


CONCLUSIONS
Bitter melon had a modest hypoglycemic effect and significantly reduced fructosamine levels from baseline among patients with type 2 diabetes who received 2,000 mg/day. However, the hypoglycemic effect of bitter melon was less than metformin 1,000 mg/day.
Use of thoracic radiotherapy for extensive stage small-cell lung cancer: a phase 3 randomised controlled trial

BACKGROUND
Most patients with extensive stage small-cell lung cancer (ES-SCLC) who undergo chemotherapy, and prophylactic cranial irradiation, have persistent intrathoracic disease. We assessed thoracic radiotherapy for treatment of this patient group.


METHODS
We did this phase 3 randomised controlled trial at 42 hospitals: 16 in Netherlands, 22 in the UK, three in Norway, and one in Belgium. We enrolled patients with WHO performance score 0-2 and confirmed ES-SCLC who responded to chemotherapy. They were randomly assigned (1:1) to receive either thoracic radiotherapy (30 Gy in ten fractions) or no thoracic radiotherapy. All underwent prophylactic cranial irradiation. The primary endpoint was overall survival at 1 year in the intention-to-treat population. Secondary endpoints included progression-free survival. This study is registered with the Nederlands Trial Register, number NTR1527.


FINDINGS
We randomly assigned 498 patients between Feb 18, 2009, and Dec 21, 2012. Three withdrew informed consent, leaving 247 patients in the thoracic radiotherapy group and 248 in the control group. Mean interval between diagnosis and randomisation was 17 weeks. Median follow-up was 24 months. Overall survival at 1 year was not significantly different between groups: 33% (95% CI 27-39) for the thoracic radiotherapy group versus 28% (95% CI 22-34) for the control group (hazard ratio [HR] 0.84, 95% CI 0.69-1.01; p=0.066). However, in a secondary analysis, 2-year overall survival was 13% (95% CI 9-19) versus 3% (95% CI 2-8; p=0.004). Progression was less likely in the thoracic radiotherapy group than in the control group (HR 0.73, 95% CI 0.61-0.87; p=0.001). At 6 months, progression-free survival was 24% (95% CI 19-30) versus 7% (95% CI 4-11; p=0.001). We recorded no severe toxic effects. The most common grade 3 or higher toxic effects were fatigue (11 vs 9) and dyspnoea (three vs four).


INTERPRETATION
Thoracic radiotherapy in addition to prophylactic cranial irradiation should be considered for all patients with ES-SCLC who respond to chemotherapy.


FUNDING
Dutch Cancer Society (CKTO), Dutch Lung Cancer Research Group, Cancer Research UK, Manchester Academic Health Science Centre Trials Coordination Unit, and the UK National Cancer Research Network.
The panorama of animal leptospirosis in Rio de Janeiro, Brazil, regarding the seroepidemiology of the infection in tropical regions

BACKGROUND
Leptospirosis is an important disease caused by various serovars of Leptospira sp. It can affect humans as well as domestic and wild animals; therefore, it has importance for public health, animal production, and wild species. The aim of this paper is to discuss the epidemiology of animal leptospirosis in Rio de Janeiro, Brazil, as a possible model for other tropical regions. In several studies conducted in the last 20 years, a total of 47 rats, 120 dogs, 875 cows, 695 horses, 1,343 goats, 308 sheep and 351 pigs from all regions of the state, in addition to 107 wild mammals and 73 golden-lion tamarins were tested (MAT) for anti-Leptospira antibodies.


RESULTS
Seroreactivity was frequent in all studied species, confirming that the infection is endemic in Rio de Janeiro. Serogroups Icterohaemorrhagiae and Sejroe were the most prevalent in urban and rural scenarios, respectively. This paper reviews the current knowledge on animal leptospirosis in Rio de Janeiro and describes important differences between urban versus rural cycles of the infection in various species.


CONCLUSION
Identification of the prevailing serogroups and their reservoirs is essential for understanding agent-host-environment interactions under tropical conditions.
STUDY TOWARDS A 21ST-CENTURY INTELLIGENT SHIP

Recent technological developments and the emergence of new, high-tech materials have led to the concept of a new type of ship and to innovations in ship operation. A Japanese research team is studying ways of designing a ship for the future. This paper focuses on the optimum automatic operation system for oceanic navigation in a future ship. See also the following abstract.