Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive designs: Looking for a needle in the haystack—A new challenge in medical research

The statistical principles of fully adaptive designs are outlined. The options of flexibility and the price to be paid in terms of statistical properties of the test procedures are discussed. It is stressed that controlled inference after major design modifications (changing hypotheses) will include a penalty: Intersections among all the hypotheses considered throughout the trial have to be rejected before testing individual hypotheses. Moreover, feasibility in terms of integrity and persuasiveness of the results achieved after adaptations based on unblinded data is considered as the crucial issue in practice. In the second part, sample size adaptive procedures are considered testing a large number of hypotheses under constraints on total sample size as in genetic studies. The advantage of sequential procedures is sketched for the example of two‐stage designs with a pilot phase for screening promising hypotheses (markers) and controlling the false discovery rate. Finally, we turn to the clinical problem how to select markers and estimate a score from limited samples, e.g. for predicting the response to therapy of a future patient. The predictive ability of such scores will be rather poor when investigating a large number of hypotheses and truly large marker effects are lacking. An obvious dilemma will show up: More optimistic selection rules may be superior if in fact effective markers exist, but will produce more nuisance prediction if no effective markers exist compared with more cautious strategies, e.g. aiming at some control of type I error probabilities. Copyright © 2007 John Wiley & Sons, Ltd.
Further developments in the use of semipermeable membrane devices as passive air samplers: application to PCBs.

There are several incentives for developing passive air sampling techniques for persistent organic pollutants (POPs). This paper reports on studies to further calibrate and optimize semipermeable membrane devices (SPMDs) for use as "integrated" air samplers of gas-phase POPs. These samplers are deployed over weeks/months/years. Polychlorinated biphenyls (PCBs) were used as the test compounds in this study, with three specific objectives: (i) to determine whether ambient wind speed limits the rate of uptake during typical deployment conditions; (ii) to monitor uptake and SPMD-air equilibrium for a range of compounds; and (iii) to assess the application of performance reference compounds (PRCs) in air sampling, to "correct" for site-specific differences in uptake rates. When deployed in Stevensons screens under ambient conditions, wind speed did not significantly affect uptake rates. Rather, differences in summer/winter uptake rates reported previously, using the same deployment devices as here, are due to temperature affecting compound permeability through the membrane. Results from the use of PRCs indicate that SPMDs should be spiked prior to exposure with a range of compounds that are not present in the atmosphere, so that uptake rates can be estimated from depuration rates during a particular deployment. Short-term deployments (e.g. days; few weeks) would need to use compound(s) with a low octanol:air partition coefficient (K(OA)) (e.g. 13C12 labeled PCB-28); long-term deployments (of many months to years) would need to use intermediate K(OA) compounds (e.g. 13C12 PCB-101; 13C12 PCB-153).
Evaluation of Maxillary Alveolar Reconstruction Using a Resorbable Collagen Sponge with Recombinant Human Bone Morphogenetic Protein-2 in Cleft Lip and Palate Patients

INTRODUCTION A resorbable collagen matrix with recombinant human bone morphogenetic protein (rhBMP-2) was compared with traditional iliac crest bone graft for the closure of alveolar defects during secondary dental eruption. METHODS Sixteen patients with unilateral cleft lip and palate, aged 8 to 12 years, were selected and randomly assigned to group 1 (rhBMP-2) or group 2 (iliac crest bone graft). Computed tomography was performed to assess both groups preoperatively and at months 6 and 12 postoperatively. Bone height and defect volume were calculated through Osirix Dicom Viewer (Pixmeo, Apple Inc.). Overall morbidity was recorded. RESULTS Preoperative and follow-up examinations revealed progressive alveolar bone union in all patients. For group 1, final completion of the defect with a 65.0% mean bone height was detected 12 months postoperatively. For group 2, final completion of the defect with an 83.8% mean bone height was detected 6 months postoperatively. Dental eruption routinely occurred in both groups. Clinical complications included significant swelling in three group 1 patients (37.5%) and significant donor-site pain in seven group 2 patients (87.5%). CONCLUSIONS For this select group of patients with immature skeleton, rhBMP-2 therapy resulted in satisfactory bone healing and reduced morbidity compared with traditional iliac crest bone grafting.
Transcriptional activation by artificial recruitment in mammalian cells.

We show that the typical "nonclassical" activator, which comprises a fusion protein bearing a component of the transcriptional machinery fused to a DNA-binding domain, activates transcription in mammalian cells only weakly when tested with an array of promoters. However, as found in analogous "artificial recruitment" experiments performed in yeast, these activators work synergistically with "classical" activators. The effect of the classical activator in such experiments requires that it be tethered to DNA, a requirement that cannot be overcome by expression of that classical activator at high levels. The effect of the one nonclassical activator that does elicit significant levels of transcription when working alone (i.e., that bearing TATA box-binding protein) is strongly influenced by promoter architecture. The results, consistent with those of analogous experiments in yeast [see the accompanying paper: Gaudreau, L. , Keaveney, M. , Nevado, J., Zaman, Z. , Bryant, G. O. , Struhl, K. & Ptashne, M. (1999) Proc. Natl. Acad. Sci. USA 96, 2668-2673], suggest that classical activators, presumably by virtue of their abilities to interact with multiple targets, have a functional flexibility that nonclassical activators lack.
Over-parameterized method on variational surface for point-based reconstruction

This article tackles the problem of using varitional method for reconstructing 3D surface. We give an overview of over-parameterized method on variational surface when the 3D surface is represented by a point-based surface and a triangular mesh-based surface, and we detail the variational surface which embody used on surface reconstruction. In particular, we show how to rigorously account for efficiency in the surface reconstructing process. The key idea is to consider utilizing variational surface from a finite number of normals for surface reconstruction. We investigate the properties of the regularization functional and illustrate our technique by applying it to converge to the input shape as the number of measurements increases. In contrast to previous works our method can be considered on point-based surface and allows the use of over-parameterized scheme for 3D surface reconstruction. Experimental results show the proposed method is efficient.
Region-of-Interest Extraction Based on Saliency Analysis of Co-Occurrence Histogram in High Spatial Resolution Remote Sensing Images

The extraction of a region of interest is an important component of remote sensing image analyses. Driven by practical applications, a good region of interest (ROI) needs to have three properties: uniformly highlighting entire ROIs, well-defined boundaries, and good stability against noisy data. Motivated by these requirements, we propose a ROI extraction model based on saliency analysis of co-occurrence histogram (SACH) in high spatial resolution remote sensing images. First, a co-occurrence histogram is utilized to capture the global and local distribution of intensity values. Secondly, our model estimates the saliency of the co-occurrence histogram by utilizing a logarithm function. Thirdly, a saliency-enhanced method based on moving K-means aggregation is utilized to establish well-defined boundary for ROIs and improve immunity to noise. Finally, ROIs are segmented from the saliency maps of original images, which are acquired from the saliency of the co-occurrence histogram. In the experimental part, we compare our model with nine other extraction models by applying the models to clean images and to images corrupted by noises. The experimental results show that compared to the nine competing models, SACH model better defines the boundaries of target ROIs and gets more entire ROIs. Furthermore, SACH model is also robust against images corrupted by Gaussian and Salt and Pepper noises.
Preoperative radiotherapy with or without concurrent fluorouracil and leucovorin in T3-4 rectal cancers: results of FFCD 9203.

PURPOSE In 1992, preoperative radiotherapy was considered in France as the standard treatment for T3-4 rectal cancers. The present randomized trial compares preoperative radiotherapy with chemoradiotherapy. PATIENTS AND METHODS Patients were eligible if they presented a resectable T3-4, Nx, M0 rectal adenocarcinoma accessible to digital rectal examination. Preoperative radiotherapy with 45 Gy in 25 fractions during 5 weeks was delivered. Concurrent chemotherapy with fluorouracil 350 mg/m2/d during 5 days, together with leucovorin, was administered during the first and fifth week in the experimental arm. Surgery was planned 3 to 10 weeks after the end of radiotherapy. All patients should receive adjuvant chemotherapy with the same fluorouracil/leucovorin regimen. The primary end point of the trial was overall survival. RESULTS A total of 733 patients were eligible. Grade 3 or 4 acute toxicity was more frequent with chemoradiotherapy (14.6% v 2.7%; P < .05). There was no difference in sphincter preservation. Complete sterilization of the operative specimen was more frequent with chemoradiotherapy (11.4% v 3.6%; P < .05). The 5-year incidence of local recurrence was lower with chemoradiotherapy (8.1% v 16.5%; P < .05). Overall 5-year survival in the two groups did not differ. CONCLUSION Preoperative chemoradiotherapy despite a moderate increase in acute toxicity and no impact on overall survival significantly improves local control and is recommended for T3-4, N0-2, M0 adenocarcinoma of the middle and distal rectum.
RAD5A, RECQ4A, and MUS81 Have Specific Functions in Homologous Recombination and Define Different Pathways of DNA Repair in Arabidopsis thaliana[W]

The processing of complex DNA intermediates in replication and repair is essential. This work defines the role of two ATPases, RAD5A and RECQ4A, and the endonuclease MUS81 in DNA repair and recombination in Arabidopsis. It shows that all three proteins are involved in different pathways of DNA repair and have specific roles in double-strand break–induced homologous recombination. Complex DNA structures, such as double Holliday junctions and stalled replication forks, arise during DNA replication and DNA repair. Factors processing these intermediates include the endonuclease MUS81, helicases of the RecQ family, and the yeast SNF2 ATPase RAD5 and its Arabidopsis thaliana homolog RAD5A. By testing sensitivity of mutant plants to DNA-damaging agents, we defined the roles of these factors in Arabidopsis. rad5A recq4A and rad5A mus81 double mutants are more sensitive to cross-linking and methylating agents, showing that RAD5A is required for damage-induced DNA repair, independent of MUS81 and RECQ4A. The lethality of the recq4A mus81 double mutant indicates that MUS81 and RECQ4A also define parallel DNA repair pathways. The recq4A/mus81 lethality is suppressed by blocking homologous recombination (HR) through disruption of RAD51C, showing that RECQ4A and MUS81 are required for processing recombination-induced aberrant intermediates during replication. Thus, plants possess at least three different pathways to process DNA repair intermediates. We also examined HR-mediated double-strand break (DSB) repair using recombination substrates with inducible site-specific DSBs: MUS81 and RECQ4A are required for efficient synthesis-dependent strand annealing (SDSA) but only to a small extent for single-strand annealing (SSA). Interestingly, RAD5A plays a significant role in SDSA but not in SSA.
Indigestible carbohydrates alter the intestinal microbiota but do not influence the performance of broiler chickens

Aims: Prebiotics are a potential alternative to in‐feed antimicrobials to improve performance of chickens. We investigated the effects of mannanoligosaccharide (MOS) and fructooligosaccharide (FOS) on growth, performance and the intestinal microbiota.
Terbutaline Accumulates in Blood and Urine after Daily Therapeutic Inhalation

Purpose This study investigated pharmacokinetics of terbutaline after single and seven consecutive days of inhalation in exercising trained men. Methods Twelve healthy trained men underwent two pharmacokinetic trials comparing single dose (2 mg) and seven consecutive days (2 mg·d−1) of inhaled terbutaline. After inhalation of terbutaline at each trial, subjects performed 90 min of bike ergometer exercise at 55%–65% of maximal oxygen consumption after which they stayed inactive. Blood and urine samples were collected before and after inhalation of terbutaline. Samples were analyzed by high-performance liquid chromatography–tandem mass spectrometry. Results Maximum serum concentration of terbutaline (Cmax) (6.4 ± 1.2 vs 4.9 ± 1.2 ng·mL−1, P = 0.01) (mean ± 95% confidence interval) and area under serum concentration–time curve from 0 to 4 h after inhalation (AUC0–4) (16 ± 3 vs 13 ± 2 ng·mL−1·h−1, P ⩽ 0.005) were higher after 7 d of inhalation compared with the first day. Seven days of terbutaline inhalation resulted in accumulation of terbutaline in urine, in which total urine excretion of terbutaline was higher after 7 d of inhalation compared with the first day (274 ± 43 vs 194 ± 33 &mgr;g, P ⩽ 0.001). These differences were partly attributed to systemic accumulation of terbutaline after consecutive days of inhalation, in that baseline serum and urine samples revealed incomplete elimination of terbutaline. Conclusion Terbutaline accumulates in serum and urine after consecutive days of inhalation. For doping control purposes, these observations are of relevance if a urine threshold and decision limit is to be introduced for terbutaline on the World Anti-Doping Agency's list of prohibited substances because asthmatic athletes may use their bronchorelievers for consecutive days.
LUMO Energies and hydrophobicity as determinants of mutagenicity by nitroaromatic compounds in Salmonella typhimurium

Quantitative structure‐activity relationships have been derived for the mutagenic activity of 47 nitroaromatic compounds acting on Salmonella typhimurium (TA100) and 66 acting on TA98. The mutagenicity is linearly dependent on the energy of the lowest occupied molecular orbital and bilinearly dependent on the hydrophobicity (octanol/water log P) of the mutagens. The mechanism of action is considered in the light of these findings.
Screening for Depression in Women with Metastatic Breast Cancer: A Comparison of the Beck Depression Inventory Short form and the Hospital Anxiety and Depression Scale

Objective: To compare two self-report questionnaires for identifying possible depression in women with metastatic breast cancer. Method: We conducted structured psychiatric interviews and administered the Beck Depression Inventory Short Form (BDI-SF) and Hospital Anxiety and Depression Scale (HADS) to 227 women with stage IV breast cancer. The accuracy for identifying DSM-IVdefined major and minor depression was examined. Sensitivity, specificity, positive (PPV) and negative (NPV) predictive values were calculated and receiver operating characteristic curves plotted. Results: Seventy-four (32.6%) patients satisfied DSM-IV criteria for a depressive disorder. With a cut-off of 4, the BDI-SF had a sensitivity of 0.84, specificity of 0.63, and PPV of 0.52. A cut-off of 11 on the HADS-Depression scale (HADS-D) resulted in sensitivity, specificity, and PPV of 0.16, 0.97, and 0.75, respectively. For major depression alone, the BDI-SF with a cut-off of 5 had excellent sensitivity but poor PPV; the HADS, with a cut-off of 7, had weak sensitivity and PPV. Conclusions: Overall, the two scales perform similarly in identifying major depression, while the BDI-SF is the more useful in screening for DSM-IV major or minor depression categories in this clinical group.
Muscle ultrasonography and computed tomography in elderly trained and untrained women

Ultrasonography (US) and computed tomography (CT) were compared in studying the associations between long‐term physical training and quadriceps muscle mass and structure in female athletes and controls, aged 66–85 years. Muscle cross‐sectional area (CSA) measured using US correlated highly with that measured using CT, but the latter technique yielded 30% higher values on average. The echo intensity of the fasciae and bone measured by US correlated positively with the mean radiological density and negatively with the relative proportion of fat obtained from CT. Low intramuscular echo intensity was accompanied by high muscle density and low relative proportion of fat. The athletes had larger quadriceps CSA and more discerned fasciae and connective tissue septa but less fat than the controls. The results indicate that US and CT both are useful methods in comparing muscle mass and structure in elderly trained and untrained women. © 1993 John Wiley & Sons, Inc.
Exploring API Embedding for API Usages and Applications

Word2Vec is a class of neural network models that as being trainedfrom a large corpus of texts, they can produce for each unique word acorresponding vector in a continuous space in which linguisticcontexts of words can be observed. In this work, we study thecharacteristics of Word2Vec vectors, called API2VEC or API embeddings, for the API elements within the API sequences in source code. Ourempirical study shows that the close proximity of the API2VEC vectorsfor API elements reflects the similar usage contexts containing thesurrounding APIs of those API elements. Moreover, API2VEC can captureseveral similar semantic relations between API elements in API usagesvia vector offsets. We demonstrate the usefulness of API2VEC vectorsfor API elements in three applications. First, we build a tool thatmines the pairs of API elements that share the same usage relationsamong them. The other applications are in the code migrationdomain. We develop API2API, a tool to automatically learn the APImappings between Java and C# using a characteristic of the API2VECvectors for API elements in the two languages: semantic relationsamong API elements in their usages are observed in the two vectorspaces for the two languages as similar geometric arrangements amongtheir API2VEC vectors. Our empirical evaluation shows that API2APIrelatively improves 22.6% and 40.1% top-1 and top-5 accuracy over astate-of-the-art mining approach for API mappings. Finally, as anotherapplication in code migration, we are able to migrate equivalent APIusages from Java to C# with up to 90.6% recall and 87.2% precision.
Earthquake - A Natural Disaster, Prediction, Mitigation, Laws and Government Policies, Impact on Biogeochemistry of Earth Crust, Role of Remote Sensing and GIS in Management in India - An Overview

The whole world from time to time is exposed to the unpredictable disaster called Earthquake which causes immense damage to the infrastructure, life and injury to the people. The present manuscript tries to discuss different aspects of the Earthquake in the present scenario in India and the role of government and its policies, society, schools and technology for the prevention and mitigation measures and impact on biogeochemistry of the earth crust. Due to location of India in tropics and happening of plate tectonic activities under and around the Indian plates has made India prone to the different types of disaster of which one of them is the Earthquake. The prediction of Earthquake is still not possible accurately. In India, during the 10th Five year plan, there has been paradigm shift in the laws and policies related to the disaster management. A separate act called Disaster Management Act-2005, has been passed by the Parliament of India. This act provides institutional, legal, financial and coordination mechanisms at the national, state, district and local levels for management of all types of disaster happening in India. This law made the role of government from relief oriented measures to the prevention and preparedness. During the Earthquake, there occurs a different type of impacts on the Biogeochemistry of the earth crust. Among them, there are the impacts on biodiversity of living organisms, variation in the water levels, folding and faulting in the crust of the Earth and generation of sea waves called Tsunami etc. Technology in the form of remote sensing and GIS can play important role and can be used before and after the occurrence of Earthquake for proper management. The Earthquake is a disaster which is unpredictable, untimely and we lack of mechanism and technology to predict its time of happening precisely. With regard to Earthquake disaster, we can only prepare our self, take preventive and preparedness measures, so that there is less damage to infrastructure and loss of life. This can be achieved by investing more in research and development of tools for prediction, proper understanding of Earthquake phenomenon, along with it there is need to concentrate more on prevention, preparedness and mitigation before and quick relief to the people after the occurrence of Earthquake.
Non-linear model predictive control for constrained mobile robots

An application of Non-Linear Model Predictive Control (NLMPC) to the stabilisation of a kinematic model of a two wheel mobile robot with input and (non-holonomic) state constraints is studied. Since linear (and even successively linearised or time-variant) MPC is not feasible for this mechanical benchmark problem (as the linearisation around any fixed point is not controllable and the assumptions for guaranteed stability with stability constraints fail), the potential of non-linear predictive control techniques is investigated. The NLMPC implementation is discussed and results are presented for several configurations. The expense and reliability of the non-convex optimisation causes problems. Tuning of the controller parameters appears to be decisive. In general, terminal state constraints are required to guarantee asymptotical stability. In this paper, these constraints are, analogous to the linear case, replaced by time-varying (exponential) weightings which are easier to handle. The results for the newly proposed non-linear control scheme are very promising, including improved convergence rates. The advantages of predictive control (constraint handling) are fully exploited. Still, the excessive computational demands make real-time implementation almost impossible and stability and robustness issues need to be further investigated.