Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclophosphamide Dose Intensification during Induction Therapy for Intermediate-Risk Pediatric Rhabdomyosarcoma Is Feasible but Does Not Improve Outcome

Purpose: More than half of pediatric rhabdomyosarcoma cases have intermediate-risk features and suboptimal outcome (3-year failure-free survival estimates, 55 to 76%). Dose intensification of known active agents may improve outcome. Experimental Design: This pilot study evaluated the feasibility of dose intensification of cyclophosphamide in previously untreated patients ages < 21 years with intermediate-risk rhabdomyosarcoma. Induction therapy comprised four 3-week cycles of VAC: vincristine (V) 1.5 mg/m2 on days 0, 7, and 14; actinomycin D (A) 1.35 mg/m2 on day 0; and dose-intensified cyclophosphamide (C) on days 0, 1, and 2. The three cyclophosphamide dose levels tested were as follows: (a) 1.2 g/m2/dose; (b) 1.5 g/m2/dose; and (c) 1.8 g/m2/dose. Continuation therapy comprised nine additional cycles of VAC with 2.2 g/m2/cycle of C. Radiotherapy was administered at week 0 (parameningeal tumors with intracranial extension) or week 12 or 15 (all others). Results: Between October 1996 and August 1999, 115 eligible patients were enrolled. Three of 15 patients treated at dose level 2 experienced life-threatening dose-limiting toxicity (typhlitis ± other severe toxicity). Dose level 1 was the maximum-tolerated dose, and 91 evaluable patients were treated at this level. The 3-year failure-free and overall survival estimates for patients treated at the maximum-tolerated dose were 52% (95% confidence interval, 41–64%) and 67% (95% confidence interval, 56–77%), respectively, at a median follow-up of 3 years. Conclusions: A 64% increase in the standard cyclophosphamide dosage during induction (to 3.6 g/m2/cycle) was tolerated. However, outcomes were similar to those observed at lower dosages, suggesting that alkylator dose intensification does not benefit patients with intermediate-risk rhabdomyosarcoma.
Sinr , Rsrp , Rssi and Rsrq Measurements in Long Term Evolution

The four basic Radio Resource Management (RRM) measurements in Long Term Evolution (LTE) system are Channel Quality Indicator (CQI), Reference Signal Received Power (RSRP), Reference Signal Received Quality (RSRQ), and Carrier Received Signal Strength Indicator (RSSI). A measurement of channel quality represented by Signal to Interference plus Noise Ratio (SINR) is used for link adaptation along with packet scheduling, whereas RSRP and RSRQ are needed for making handover decision during intra-eUTRAN (evolved Universal Terrestrial Random Access Network) handover in LTE. In this paper, some practical measurement results recorded from a live LTE network of Australia using a commercial measurement tool namely NEMO Handy are analysed to verify the possible relationships among SINR, RSRP, RSSI and RSRQ as well as to evaluate the effects of SNR on throughput. In addition, the intra- eUTRAN handover events occurred during the test period within the test area are studied. The analysis yields some useful information such as: if the SINR is good for a measurement slot, higher throughput is achieved; RSRP and SNR are proportional to each other on average; and lesser is the difference between RSSI and RSRP, better is the RSRQ - each of which is consistent with theory. All the measurement results are evaluated using computer programs built on MATLAB platform.
Walking Versus Running for Hypertension, Cholesterol, and Diabetes Mellitus Risk Reduction

Objective—To test whether equivalent energy expenditure by moderate-intensity (eg, walking) and vigorous-intensity exercise (eg, running) provides equivalent health benefits. Approach and Results—We used the National Runners’ (n=33 060) and Walkers’ (n=15 945) Health Study cohorts to examine the effect of differences in exercise mode and thereby exercise intensity on coronary heart disease (CHD) risk factors. Baseline expenditure (metabolic equivant hours per day [METh/d]) was compared with self-reported, physician-diagnosed incident hypertension, hypercholesterolemia, diabetes mellitus, and CHD during 6.2 years follow-up. Running significantly decreased the risks for incident hypertension by 4.2% (P<10−7), hypercholesterolemia by 4.3% (P<10−14), diabetes mellitus by 12.1% (P<10−5), and CHD by 4.5% per METh/d (P=0.05). The corresponding reductions for walking were 7.2% (P<10−6), 7.0% (P<10−8), 12.3% (P<10−4), and 9.3% (P=0.01). Relative to <1.8 METh/d, the risk reductions for 1.8 to 3.6, 3.6 to 5.4, 5.4 to 7.2, and ≥7.2 METh/d were as follows: (1) 10.1%, 17.7%, 25.1%, and 34.9% from running and 14.0%, 23.8%, 21.8%, and 38.3% from walking for hypercholesterolemia; (2) 19.7%, 19.4%, 26.8%, and 39.8% from running and 14.7%, 19.1%, 23.6%, and 13.3% from walking for hypertension; and (3) 43.5%, 44.1%, 47.7%, and 68.2% from running, and 34.1%, 44.2% and 23.6% from walking for diabetes mellitus (walking >5.4 METh/d excluded for too few cases). The risk reductions were not significantly different for running than walking for diabetes mellitus (P=0.94), hypertension (P=0.06), or CHD (P=0.26), and only marginally greater for walking than running for hypercholesterolemia (P=0.04). Conclusions—Equivalent energy expenditures by moderate (walking) and vigorous (running) exercise produced similar risk reductions for hypertension, hypercholesterolemia, diabetes mellitus, and possibly CHD.
Competition Studies Confirm Two Major Barriers That Can Preclude the Spread of Resistance to Quorum-Sensing Inhibitors in Bacteria

The growing threat of antibiotic resistance necessitates the development of novel antimicrobial therapies. Antivirulence agents that target group-beneficial traits in microorganisms (i.e., phenotypes that help the cells surrounding the producer cell instead of selfishly benefiting only the producer cell) represent a new antimicrobial approach that may be robust against the spread of resistant mutants. One prominent group-beneficial antivirulence target in bacteria is quorum sensing (QS). While scientists are producing new QS inhibitors (QSIs) at an increasing pace for use as research tools and potential therapeutic leads, substantial work remains in empirically demonstrating a robustness against resistance. Herein we report the results of in vitro competition studies in Pseudomonas aeruginosa that explicitly confirm that two separate barriers can impede the spread of resistance to QSIs: (1) insufficient native QS signal levels prevent rare QSI-resistant bacteria from expressing their QS regulon, and (2) group-beneficial QS-regulated phenotypes produced by resistant bacteria are susceptible to cheating by QSI-sensitive neighbors, even when grown on a solid substrate with limited mixing to mimic infected tissue. These results underscore the promise of QSIs and other antivirulence molecules that target group beneficial traits as resistance-robust antimicrobial treatments and provide support for their further development.
Gadd45a and Gadd45b modulate innate immune functions of granulocytes and macrophages by differential regulation of p38 and JNK signaling

Gadd45 proteins function as stress sensors in response to various physiological and environmental stressors, interacting with other cellular proteins implicated in cellular stress responses, including p38 and JNK. This study shows that mice lacking either Gadd45a or Gadd45b are defective in the recruitment of granulocytes and macrophages to the intra‐peritoneal cavity following intra‐peritoneal administration of the bacterial cell wall pathogen‐associated molecular pattern lipopolysaccharide (LPS). Bone marrow derived granulocytes and macrophages lacking either Gadd45a or Gadd45b are shown to be impaired in their chemotactic response to LPS, as well as other inflammatory stimuli such as N‐formyl‐methionine–leucine–phenylalanine and IL‐8. Evidence was obtained also implicating Gadd45a and Gadd45b in other myeloid innate immune functions, including reactive oxygen species production, phagocytosis, and adhesion. Gadd45a and Gadd45b activation of p38 kinase was implicated in the response of granulocytes to LPS mediated chemotaxis, whereas Gadd45a and Gadd45b curtailment of JNK activation was linked to chemotaxis of macrophages in response to LPS. Collectively, these data highlight a novel role for both Gadd45a and Gadd45b in myeloid innate immune functions by differential modulation of p38 and JNK signaling in granulocytes compared to macrophages. J. Cell. Physiol. 227: 3613–3620, 2012. © 2012 Wiley Periodicals, Inc.
A constructive algorithm for the Lovász Local Lemma on permutations

While there has been significant progress on algorithmic aspects of the Lovasz Local Lemma (LLL) in recent years, a noteworthy exception is when the LLL is used in the context of random permutations: the "lopsided" version of the LLL is usually at play here, and we do not yet have subexponential-time algorithms. We resolve this by developing a randomized polynomial-time algorithm for such applications. A noteworthy application is for Latin Transversals: the best-known general result here (Bissacot et al., improving on Erdos and Spencer), states that any n x n matrix in which each entry appears at most (27/256)n times, has a Latin transversal. We present the first polynomial-time algorithm to construct such a transversal. Our approach also yields RNC algorithms: for Latin transversals, as well as the first efficient ones for the strong chromatic number and (special cases of) acyclic edge-coloring.
Using simple page placement policies to reduce the cost of cache fills in coherent shared-memory systems

The cost of a cache miss depends heavily on the location of the main memory that backs the missing line. For certain applications, this cost is a major factor in overall performance. We report on the utility of OS-based page placement as a mechanism to increase the frequency with which cache fills access local memory in distributed shared memory multiprocessors. Even with the very simple policy of first-use placement, we find significant improvements over round-robin placement for many applications on both hardware- and software-coherent systems. For most of our applications, first-use placement allows 35 to 75 percent of cache fills to be performed locally, resulting in performance improvements of up to 40 percent with respect to round-robin placement. We were surprised to find no performance advantage in more sophisticated policies, including page migration and page replication. In fact, in many cases the performance of our applications suffered under these policies. <<ETX>>
Monaural detection of a phase difference between clicks.

Pairs of very brief pulses can be arranged to produce transient signals having spectra that differ only in power, only in phase, or in both power and phase. Conventional intensity discrimination for such click pairs is obtained by using the signals that differ only in their power spectra. Some of the corresponding signals that differ only in their phase spectra are also readily discriminable. An attempt is made to assess the relative saliency of the power and phase variables by adding the phase cue as a distracting feature to the power‐discrimination task. The presence of such an uncorrelated phase cue can lower the detectability of power differences.
Multimodality Data Integration in Epilepsy

An important goal of software development in the medical field is the design of methods which are able to integrate information obtained from various imaging and nonimaging modalities into a cohesive framework in order to understand the results of qualitatively different measurements in a larger context. Moreover, it is essential to assess the various features of the data quantitatively so that relationships in anatomical and functional domains between complementing modalities can be expressed mathematically. This paper presents a clinically feasible software environment for the quantitative assessment of the relationship among biochemical functions as assessed by PET imaging and electrophysiological parameters derived from intracranial EEG. Based on the developed software tools, quantitative results obtained from individual modalities can be merged into a data structure allowing a consistent framework for advanced data mining techniques and 3D visualization. Moreover, an effort was made to derive quantitative variables (such as the spatial proximity index, SPI) characterizing the relationship between complementing modalities on a more generic level as a prerequisite for efficient data mining strategies. We describe the implementation of this software environment in twelve children (mean age 5.2 ± 4.3 years) with medically intractable partial epilepsy who underwent both high-resolution structural MR and functional PET imaging. Our experiments demonstrate that our approach will lead to a better understanding of the mechanisms of epileptogenesis and might ultimately have an impact on treatment. Moreover, our software environment holds promise to be useful in many other neurological disorders, where integration of multimodality data is crucial for a better understanding of the underlying disease mechanisms.
The Potential of Mycofoam as a Biocomposite Material with Various Substrate and Mushroom Compositions

Mycofoam is a biocomposite composed of mycelial filaments that bind to the host substrate, which can replace polystyrene. This research aims to determine the most appropriate formulation of the growing medium and mushroom to be used in mycofoam products based on some parameters. Composition is one of the main factors for selecting the most appropriate mycofoam to replace polystyrene. On the other hand, the quality of mycofoam can be assessed through its strength and water resistance. The mushroom mycelium used in this study came from Pleurotus ostreatus and Lentinula edodes. Besides, the growing medium formulation comprises five different compositions, each containing different proportions of sawdust and bagasse. This research was composed of preparation of growing medium, spawn inoculation, molding, heating, testing, and data analysis. Based on the results, the combination of 100 percent sawdust and L. edodes was the most appropriate choice compared to other formulations based on strength and appearance. The results of the water absorption test showed that all mycofoam formulations were not resistant to water, bio-based coating can be used to overcome this problem.
Deep Feature Learning for EEG Recordings

We introduce and compare several strategies for learning discriminative features from electroencephalography (EEG) recordings using deep learning techniques. EEG data are generally only available in small quantities, they are high-dimensional with a poor signal-to-noise ratio, and there is considerable variability between individual subjects and recording sessions. Our proposed techniques specifically address these challenges for feature learning. Cross-trial encoding forces auto-encoders to focus on features that are stable across trials. Similarity-constraint encoders learn features that allow to distinguish between classes by demanding that two trials from the same class are more similar to each other than to trials from other classes. This tuple-based training approach is especially suitable for small datasets. Hydra-nets allow for separate processing pathways adapting to subsets of a dataset and thus combine the advantages of individual feature learning (better adaptation of early, low-level processing) with group model training (better generalization of higher-level processing in deeper layers). This way, models can, for instance, adapt to each subject individually to compensate for differences in spatial patterns due to anatomical differences or variance in electrode positions. The different techniques are evaluated using the publicly available OpenMIIR dataset of EEG recordings taken while participants listened to and imagined music.
Effects of Short-Term Exercise Interventions on Behavioral and Psychological Symptoms in Patients with Dementia: A Systematic Review.

Observational and interventional studies indicate a direct link between the patients' physical activity and the extent of behavioral and psychological symptoms of dementia (BPSD). At present, there are no evidence-based recommendations for physical exercise in the acute dementia care settings. Hence, this systematic review investigates the effects of short-term exercise trials on BPSD. Trials with a length up to three months investigating the effects of structured exercise interventions on BPSD in acute dementia care settings were included. Five trials, referring to a total of N = 206 patients, met the inclusion criteria. The trial durations ranged from three up to twelve weeks. All trials conducted three sessions per week of 30 to 45 minutes. Three trials reported significant reductions of BPSD and differences in comparison to the pre-test and control groups. Out of the three trials investigating the effects of exercise interventions on depressive symptoms, one reported significant reduction and two reported no differences in pre-post analysis. Exercise represents a potentially worthwhile approach for the treatment of patients suffering from BPSD. Given the scarcity of available studies, more randomized controlled short-term exercise trials in acute dementia care settings are needed to define appropriate exercise recommendations for clinicians treating these patients.
Exploring Semantic Concept Using Local Invariant Features

This paper studies the role and performance of local invariant features arisen from interest points in describing and sketching semantic concepts. Both the local description and spatial location of interest points are exploited, separately and jointly, for concept-based retrieval. In concept description, a visual dictionary is generated with each keyframe being depicted as a vector of keywords. Semantic concepts are learnt and then spotted in this vector space model. In concept sketching, the location distribution of interest points, which outlines the basic shape of concepts, is novelly modelled with embedded Earth Mover's Distance. Experimental results with TRECVID-2005 corpus show that by incorporating both properties of interest points with baseline features, an improvement of 70% (over color) and 26% (over color and texture) in concept retrieval is reported.
Meta-Analysis of the Prognostic Value of Circulating Tumor Cells in Breast Cancer

Purpose: The prognostic value of circulating tumor cells (CTC) detected in breast cancer patients is currently under debate. Different time points of blood collections and various CTC assays have been used in the past decades. Here, we conducted the first comprehensive meta-analysis of published literature on the prognostic relevance of CTC, including patients with early and advanced disease. Experimental Design: A comprehensive search for articles published between January 1990 and January 2012 was conducted; reviews of each study were conducted and data were extracted. The main outcomes analyzed were overall survival (OS) and disease-free survival (DFS) in early-stage breast cancer patients, as well as progression-free survival (PFS) and OS in metastatic breast cancer patients. Pooled hazard ratio (HR) and 95% confidence intervals (CIs) were calculated using the random and the fixed-effects models. Subgroup and sensitivity analyses were also conducted. Results: Forty-nine eligible studies enrolling 6,825 patients were identified. The presence of CTC was significantly associated with shorter survival in the total population. The prognostic value of CTC was significant in both early (DFS: HR, 2.86; 95% CI, 2.19–3.75; OS: HR, 2.78; 95% CI, 2.22–3.48) and metastatic breast cancer (PFS: HR, 1.78; 95% CI, 1.52–2.09; OS: HR, 2.33; 95% CI, 2.09–2.60). Further subgroup analyses showed that our results were stable irrespective of the CTC detection method and time point of blood withdrawal. Conclusion: Our present meta-analysis indicates that the detection of CTC is a stable prognosticator in patients with early-stage and metastatic breast cancer. Further studies are required to explore the clinical utility of CTC in breast cancer. Clin Cancer Res; 18(20); 5701–10. ©2012 AACR.
HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection

Nucleoside analogs (NAs) are used to treat numerous viral infections and cancer. They compete with endogenous nucleotides (dNTP/NTP) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension. To date, an integrated mathematical model that could allow the analysis of their mechanism of action, of the various resistance mechanisms, and their effect on viral fitness is still lacking. We present the first mechanistic mathematical model of polymerase inhibition by NAs that takes into account the reversibility of polymerase inhibition. Analytical solutions for the model point out the cellular- and kinetic aspects of inhibition. Our model correctly predicts for HIV-1 that resistance against nucleoside analog reverse transcriptase inhibitors (NRTIs) can be conferred by decreasing their incorporation rate, increasing their excision rate, or decreasing their affinity for the polymerase enzyme. For all analyzed NRTIs and their combinations, model-predicted macroscopic parameters (efficacy, fitness and toxicity) were consistent with observations. NRTI efficacy was found to greatly vary between distinct target cells. Surprisingly, target cells with low dNTP/NTP levels may not confer hyper-susceptibility to inhibition, whereas cells with high dNTP/NTP contents are likely to confer natural resistance. Our model also allows quantification of the selective advantage of mutations by integrating their effects on viral fitness and drug susceptibility. For zidovudine triphosphate (AZT-TP), we predict that this selective advantage, as well as the minimal concentration required to select thymidine-associated mutations (TAMs) are highly cell-dependent. The developed model allows studying various resistance mechanisms, inherent fitness effects, selection forces and epistasis based on microscopic kinetic data. It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment.
A chromosomal translocation in cyclin D1-negative/cyclin D2-positive mantle cell lymphoma fuses the CCND2 gene to the IGK locus.

Mantle cell lymphoma (MCL) is a lymphoproliferative disorder with distinct pathologic and clinical features. Genetically, the vast majority of MCLs carry the t(11;14)(q13;q32). This characteristic chromosomal abnormality leads to deregulation of the CCND1 gene encoding cyclin D1 at 11q13 through