Miracle-dz/UniFAR-FTUs huggingface dataset:
Oblimersen combined with docetaxel, adriamycin and cyclophosphamide as neo-adjuvant systemic treatment in primary breast cancer: final results of a multicentric phase I study.

BACKGROUND Combining the Bcl-2 down-regulator oblimersen with cytotoxic treatment leads to synergistic antitumor effects in preclinical trials. This multicentric phase I study was carried out to evaluate maximum tolerated dose (MTD), safety and preliminary efficacy of oblimersen in combination with docetaxel, adriamycin and cyclophosphamide as neo-adjuvant systemic treatment (NST) in primary breast cancer (PBC). METHODS Previously untreated patients with PBC T2-4a-c N0-3 M0 received one cycle of docetaxel 75 mg/m(2), adriamycin 50 mg/m(2) and cyclophosphamide 500 mg/m(2) administered on day 5 combined with escalating doses of oblimersen as a 24-h continuous infusion on days 1-7 followed by five cycles of combination of docetaxel, adriamycin and cyclophosphamide (TAC) without oblimersen every 3 weeks. Prophylactic antibiotic therapy and granulocyte colony-stimulating factor administration were used in all six cycles. Blood serum samples were taken throughout the treatment period for pharmacokinetic analysis. RESULTS Twenty-eight patients were enrolled (median age, 50 years; ductal-invasive histology, 68%; tumorsize 2-5 cm, 61%; grade 3, 43%; hormone receptor negative, 36%; Her2 positive 18%) and received oblimersen in a dose of 3 mg/kg/day (cohort I, nine patients), 5 mg/kg/day (cohort II, nine patients) and 7 mg/kg/day (cohort III, 10 patients) respectively. No dose-limiting toxicity occurred. Following oblimersen combined with TAC, the most severe toxicity was neutropenia [National Cancer Institute-Common Toxicity Criteria (NCI-CTC) grades 1-2/3/4] which developed in 0/0/56% of patients (cohort I), 11/0/56% of patients (cohort II) and 20/20/50% of patients (cohort III). No febrile neutropenia occurred. Most common adverse events (all NCI-CTC grade < or = 2) were fatigue, nausea, alopecia, headache and flue-like symptoms observed in 78% (cohort I), 89% (cohort II) and 90% (cohort III) of patients. With increasing dose of oblimersen, a higher incidence of grade IV leukopenia and neutropenia was noted. At the MTD of 7 mg/kg/day of oblimersen, serious adverse events occurred in 40% of the patients. CONCLUSION Oblimersen up to a dose of 7 mg/kg/day administered as a 24-h infusion on days 1-7 can be safely administered in combination with standard TAC on day 5 as NST in patients with PBC. The safety and preliminary efficacy warrants further evaluation of oblimersen in combination with every cycle of the TAC regimen in a randomized trial.
Kinetic cooperativity in Escherichia coli 30S ribosomal subunit reconstitution reveals additional complexity in the assembly landscape

The Escherichia coli 30S ribosomal subunit self-assembles in vitro in a hierarchical manner, with the RNA binding by proteins enabled by the prior binding of others under equilibrium conditions. Early 16S rRNA binding proteins also bind faster than late-binding proteins, but the specific causes for the slow binding of late proteins remain unclear. Previously, a pulse-chase monitored by quantitative mass spectrometry method was developed for monitoring 30S subunit assembly kinetics, and here a modified experimental scheme was used to probe kinetic cooperativity by including a step where subsets of ribosomal proteins bind and initiate assembly prior to the pulse-chase kinetics. In this work, 30S ribosomal subunit kinetic reconstitution experiments revealed that thermodynamic dependency does not always correlate with kinetic cooperativity. Some folding transitions that cause subsequent protein binding to be more energetically favorable do not result in faster protein binding. Although 3′ domain primary protein S7 is required for RNA binding by both proteins S9 and S19, prior binding of S7 accelerates the binding of S9, but not S19, indicating there is an additional mechanistic step required for S19 to bind. Such data on kinetic cooperativity and the presence of multiphasic assembly kinetics reveal complexity in the assembly landscape that was previously hidden.
Particle Algorithms for Optimization on Binary Spaces

We discuss a unified approach to stochastic optimization of pseudo-Boolean objective functions based on particle methods, including the cross-entropy method and simulated annealing as special cases. We point out the need for auxiliary sampling distributions, meaning parametric families on binary spaces, which are able to reproduce complex dependency structures, and illustrate their usefulness in our numerical experiments. We provide numerical evidence that particle-driven optimization algorithms based on parametric families yield superior results on strongly multimodal optimization problems while local search heuristics outperform them on easier problems.
Hybrid Concept of NoSQL and Relational Database for GIS Operation

Relational Database Management Systems (RDBMS) have a strong point at handling data with clear-defined structures. Consequently, RDBMS are generally not suitable for the data management without pre-defined schema in which the schema flexibility is a requirement to cope with data variations and inconsistencies. The term of NoSQL (Not only SQL) databases have been raised as a potential alternative solution which is growing rapidly to provide persistence for free schema application. They combine the capability of data sharding in a non-relational structure. This type of databases can potentially accommodate variety of information from Volunteered Geographic Information (VGI) with different structures and schemas into one single geodatabase. For instance, MongoDB introduces an open source NoSQL document-based storage with a replication using data partitioning approach. This approach supports a robust specific query task by using geospatial index of simple point feature. In specific, JSON format in MongoDB is used as a data model on a basis of a document-based rather than on a tuple basis. This situation provides lightweight query and data transfer to support efficient operation especially for Geographical Information System (GIS). However, GIS is a mature system that is already extensively developed using RDBMS approach on the production lines. Therefore in this paper, we propose a hybrid concept between NoSQL and relational database to perform complete necessary task i.e. Create, Read, Update, and Delete (CRUD) operations by using GIS desktop platform. It shows a reliable performance for handling big data from Open Street Map (OSM) datasets.
Performance of Fly Ash Concretes in Accelerated and Natural Chloride Exposure Regimes

The purpose of this research was to study the penetrating characteristics of chloride ions into fly ash concrete and the corrosion of steel reinforcement in concrete, where some parts of fine and coarse aggregates were replaced by fly ash. Several tests such as compressive strength tests, chloride penetration test and corrosion diagnosis of steel reinforcement in concrete were performed. Through these tests, the physical properties and durability of fly ash concrete against aggressive environments have been studied.
A Bayesian Network View on Acoustic Model-Based Techniques for Robust Speech Recognition

This article provides a unifying Bayesian network view on various approaches for acoustic model adaptation, missing feature, and uncertainty decoding that are well-known in the literature of robust automatic speech recognition. The representatives of these classes can often be deduced from a Bayesian network that extends the conventional hidden Markov models used in speech recognition. These extensions, in turn, can in many cases be motivated from an underlying observation model that relates clean and distorted feature vectors. By converting the observation models into a Bayesian network representation, we formulate the corresponding compensation rules leading to a unified view on known derivations as well as to new formulations for certain approaches. The generic Bayesian perspective provided in this contribution thus highlights structural differences and similarities between the analyzed approaches.
Accentuate the positive, eliminate the negative? The variable value dynamics of non-suicidal self-hurting

Medical accounts mostly frame non-suicidal self-hurting as an adverse event, the frequency of which has supposedly increased to a current ‘epidemic’ level, and which can be predicted probabilistically in terms of risk factors. This set of presuppositions gives rise to the common stigmatisation of those who present to Accident and Emergency services as a result of self-hurting. It is now being challenged in a small but growing body of social science literature which emphasises the diversity of self-hurting, and its range of socially situated meanings for those who self-hurt, family and health professionals. The present paper contributes to this research strand by discussing the accounts of their self-hurting given by a sample of 25 UK adults who had not been in contact with health or other services for this reason. The analysis focused on three value issues: the positive gains which motivated research participants to self-hurt; their own active efforts to mitigate associated risks; and the longer-term downsides which some respondents identified.
Growth hormone and mild exercise in combination markedly enhance cortical bone formation and strength in old rats.

The effects of a combination of mild exercise and GH injections on bone were studied in old female rats. Biosynthetic human GH, 2.7 mg/kg/day, was injected s.c. for 73 days. Exercised rats ran 8 m/min on a treadmill for 1 h/day. All rats (age 21 months old) were labeled with a tetracycline injection 56 days and a calcein injection 11 days before killing. The GH injections resulted in an 11-fold increase in femoral middiaphyseal bone formation rate and a 12% increase in cross-sectional area compared with the saline-injected group. The mild exercise doubled the mineralizing surface but did not influence the bone formation rate significantly. The combination of GH injections plus exercise, however, resulted in a further increase of 39% in bone formation rate, primarily at the anterolateral aspects, and an increase of 5% in cross-sectional area compared with the group injected with GH only. The femur ultimate breaking load was increased by 37% and the stiffness by 42% in the group injected with GH compared with the saline-injected group. Exercise alone did not influence the femur mechanical properties. The combination of GH injections plus exercise induced a 4% further increase in ultimate breaking load and 7% further increase in stiffness compared with the group injected with GH alone. The GH injections induced a 117% increase in serum insulin-like growth factor I. The GH-insulin-like growth factor I axis stimulates recruitment of osteoblast precursor cells, resulting in increased bone formation at the periosteal surface. GH injections and mild excercise in combination modulate and increase further the formation and strength of cortical bone in old female rats.
Title Eigen-based Clutter Filter Design for Ultrasound Color Flow Imaging: a Review Rights Creative Commons: Attribution 3.0 Hong Kong License

—Proper suppression of tissue clutter is a prerequisite for visualizing flow accurately in ultrasound color flow imaging. Among various clutter suppression methods, the ei-gen-based filter has shown potential because it can theoretically adapt its stopband to the actual clutter characteristics even when tissue motion is present. This paper presents a formative review on how eigen-based filters should be designed to improve their practical efficacy in adaptively suppressing clutter without affecting the blood flow echoes. Our review is centered around a comparative assessment of two eigen-filter design considerations: 1) eigen-component estimation approach (single-ensemble vs. multi-ensemble formulations), and 2) filter order selection mechanism (eigenvalue-based vs. frequency-based algorithms). To evaluate the practical efficacy of existing eigen-filter designs, we analyzed their clutter suppression level in two in vivo scenarios with substantial tissue motion (intra-operative coronary imaging and thyroid imaging). Our analysis shows that, as compared with polynomial regression filters (with or without instantaneous clutter downmixing), eigen-filters that use a frequency-based algorithm for filter order selection generally give Doppler power images with better contrast between blood and tissue regions. Results also suggest that both multi-ensemble and single-ensemble eigen-estimation approaches have their own advantages and weaknesses in different imaging scenarios. It may be beneficial to develop an algorithmic way of defining the eigen-filter formulation so that its performance advantages can be better realized.
Contour extraction based on improved GVF snake model in ASAR images

This paper proposes an improved GVF Snake-based method which is applied to Envisat ASAR images to determine the interested object's boundaries. ASAR images have a lot of noise and speckle. But different from other low SNR images, they are also full of texture. While using GVF snake model, the result of the gradient vector field in ASAR images becomes even worse. How to reduce the influence of the unimportant texture and the noise level while to preserve the image features is the key problem. To solve this, log Gabor wavelets that have the ability to preserve the phase data is introduced into the new scheme to correct the gradient vector flow. Results show that the new method can detect the contour of the interested object more accurately and false edges are removed.
Biometric User Authentication on Smartphone Accelerometer Sensor Data

— This study attempts to build a statistical model to identify a user, based on how the user picks up the phone and how he/she holds the phone to the ear. Phone-pickup and phone-holding methods are quantified using accelerometer readings on the three axes. This study is based on the theory that every person has a unique way of handling the phone during a phone call. The minute variations in the angle of tilt and the micro movements made during the phone call can be quite different between two individuals. The Accelerometer gives a convenient method of quantifying the phone movements and the change in orientation of the phone on a three dimensional space. This study involves data gathered from seven participants who made five test phone calls each lasting for a little over 5 seconds. The study produced a model that can predict the user with high accuracy using a smartphone accelerometer.
Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue

Background and Methods Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform is lacking. To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material. Methodology and Principal Findings We show that after proper normalization, all FFPE and FF pairs exhibit a high level of similarity (Pearson correlation >0.7), significantly larger than the similarity between non-paired samples. Interestingly, the probes showing the highest correlation had a higher percentage G/C content and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene signature) showed a high level of concordance between FFPE and FF matched pairs. Interestingly, predictions based on a 60 gene DASL list (best match with the 70 gene signature) showed very high concordance with the MammaPrint® results. Conclusions and Significance We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. Specifically, gene expression profiles for a known set of prognostic genes for a specific disease are highly comparable between two conditions. This opens up the possibility of using both FFPE and FF material in gene expressions analyses, leading to a vast increase in the potential resources available for cancer research.
Link correlation aware opportunistic routing

By exploiting reception diversity of wireless network links, researchers have shown that opportunistic routing can improve network performance significantly over traditional routing schemes. However, recently empirical studies indicate that we are too optimistic, i.e. diversity gain can be overestimated if we continue to assume that packet receptions of wireless links are independent events. For the first time, this paper formally analyzes the opportunistic routing gain under the presence of link correlation considering the loss of DATA and ACK packets. Based on the model, we introduce a new link-correlation-aware opportunistic routing scheme, which improves the performance by exploiting the diverse uncorrelated forwarding links. Our design is evaluated using simulation where we show (i) link correlation leads to less diversity gain, (ii) and with our link-correlation-aware design; improvement can be gained. We also provide a unique model to generate strings of randomly correlated receptions.
Reconstructing Graphs from Neighborhood Data

Consider a social network and suppose that we are given the number of common friends between each pair of users. Can we reconstruct the underlying network? Similarly, consider a set of documents and the words that appear in them. If we know the number of common words for every pair of documents, as well as the number of common documents for every pair of words, can we infer which words appear in which documents? In this paper, we develop a general methodology for answering questions like the ones above. We formalize these questions in what we call the Reconstruct problem: Given information about the common neighbors of nodes in a network, our goal is to reconstruct the hidden binary matrix that indicates the presence or absence of relationships between individual nodes. We propose an effective and practical heuristic, which exploits properties of the singular value decomposition of the hidden binary matrix. More specifically, we show that using the available neighborhood information, we can reconstruct the hidden matrix by finding the components of its singular value decomposition and then combining them appropriately. Our extensive experimental study suggests that our methods are able to reconstruct binary matrices of different characteristics with up to 100% accuracy.
Taking a walk on the wild side: teaching cloud computing on distributed research testbeds

Distributed platforms are now a de facto standard in modern software and application development. Although the ACM/IEEE Curriculum 2013 introduces Parallel and Distributed Computing as a first class knowledge area for the first time, the right level of abstraction to teach these concepts is still an important question that needs to be explored. This work presents our findings in teaching cloud computing by exposing upper-level students to testbeds in use by the distributed systems research community. The possibility of giving students practical and relevant experience was explored in the context of new course assignment objectives. Furthermore, students were able to significantly contribute to a pilot class project with medium-scale computation based on satellite data. However, the software engineering challenges in these environments proved to be daunting. In particular, these challenges were exacerbated by a lack of debugging support relative to the environments students were more familiar with---requiring development practices that out-stripped typical course experiences. Our proposed set of experiments and project provide a basis for an evaluation of the trade-offs of teaching cloud and distributed systems on the wild side. We hope that these findings provide insight into some of the possibilities to consider when preparing the next generation of computer scientists to engage with software practices and paradigms that are already fundamental in today's highly distributed systems.
Morphosyntactic Parser for Brazilian Portuguese: Methodology for Development and Assessment

– In text-to-speech (TTS) systems, an effective morphosyntactic classification is important to improve the prosody of synthesized speech as well as the pronunciation of words subject to vocalic alternation. This research work presents a methodology used for developing and assessing an ad hoc morphosyntactic parser to a TTS system for Brazilian Portuguese. The developed parser is composed of a dictionary and a set of rules structured in four levels. The methodology used for development consisted firstly in the creation of a large annotated dataset and an incremental development of rules for morphosyntactic classification. By using this approach, the achieved accuracy rate of the classification process is of 98.59% for words and 80.66% for sentences in a specific dataset.
Myocardial Protection Against Pressure Overload in Mice Lacking Bach1, a Transcriptional Repressor of Heme Oxygenase-1

Bach1 is a stress-responsive transcriptional factor that is thought to control the expression levels of cytoprotective factors, including heme-oxygenase (HO)-1. In the present study, we investigated the roles of Bach1 in the development of left ventricular (LV) hypertrophy and remodeling induced by transverse aortic constriction (TAC) in vivo using Bach1 gene-deficient (Bach1−/−) mice. TAC for 3 weeks in wild-type control (Bach1+/+) mice produced LV hypertrophy and remodeling manifested by increased heart weight, histological findings showing increased myocyte cross-sectional area (CSA) and interstitial fibrosis (picro Sirius red staining), reexpressions of ANP, BNP, and &bgr;MHC genes, and echocardiographic findings showing wall thickening, LV dilatation, and reduced LV contraction. Deletion of Bach1 caused significant reductions in heart weight (by 16%), CSA (by 36%), tissue collagen content (by 38%), and gene expression levels of ANP (by 75%), BNP (by 45%), and &bgr;MHC (by 74%). Echocardiography revealed reduced LV dimension and ameliorated LV contractile function. Deletion of Bach1 in the LV caused marked upregulation of HO-1 protein accompanied by elevated HO activity in both basal or TAC-stimulated conditions. Treatment of Bach1−/− mice with tin-protoporphyrin, an inhibitor of HO, abolished the antihypertrophic and antiremodeling effects of Bach1 gene ablation. These results suggest that deletion of Bach1 caused upregulation of cytoprotective HO-1, thereby inhibiting TAC-induced LV hypertrophy and remodeling, at least in part, through activation of HO. Bach1 repressively controls myocardial HO-1 expression both in basal and stressed conditions, inhibition of Bach1 may be a novel therapeutic strategy to protect the myocardium from pressure overload.