Miracle-dz/UniFAR-FTUs huggingface dataset:
The hOGG1 Ser326Cys Polymorphism and Lung Cancer Risk: A Meta-analysis

The potentially functional polymorphism Ser326Cys in the human 8-oxoguanine DNA glycosylase (hOGG1) gene has been implicated in lung cancer risk, but published studies have mixed findings. To summarize published data, we did a comprehensive meta-analysis. Two investigators extracted data independently from 17 case control studies published in the PubMed using the search phrases “hOGG1/OGG1/OGG and polymorphism/genetic variation and lung cancer. ” The meta-analysis included 6,375 cancer cases and 6,406 control subjects. The results showed that individuals carrying the hOGG1 Cys/Cys genotype did not have significantly increased risk of lung cancer [odds ratios (OR), 1.15; 95% (confidence interval) CI, 0.94-1.41] compared with those with the Ser/Ser genotype; similarly, no significant association with lung cancer risk was found either in the recessive (OR, 1.09; 95% CI, 0.90-1.32 for Cys/Cys versus Ser/Cys+Ser/Ser) or dominant model of the Ser326 allele (OR, 1.06; 95% CI, 0.93-1.21 for Cys/Cys+Ser/Cys versus Ser/Ser). However, significantly increased risks were found among Asian subjects (OR, 1.18; 95% CI, 1.01-1.38 for Cys/Cys+Ser/Cys versus Ser/Ser) in a dominant model. In stratified analyses by control source, compared with the Ser/Ser genotype, lung cancer risk associated with the hOGG1 Cys/Cys genotype was significantly increased in population-based studies (OR, 1.32; 95% CI, 1.04-1.67) but not in hospital-based studies (OR, 1.18; 95% CI, 0.98-1.42); in stratified analyses by the smoking status, however, the increased risk was observed only among nonsmokers in a dominant model (OR, 1.32; 95% CI, 1.04-1.67). The meta-analysis suggested that a careful matching should be considered in future larger genetic association studies including multiple ethnic groups. (Cancer Epidemiol Biomarkers Prev 2008;17(7):1739–45)
DnaSP, DNA polymorphism analyses by the coalescent and other methods

SUMMARY DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. AVAILABILITY The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub. es/dnasp
Generalized Rewriting in Type Theory

While type theories such as Nuprl are expressive logics for theorem proving, they present diiculties for designers of term rewriting systems. The two most serious diiculties are: 1) They do not provide a global equality. Instead users rewrite over arbitrary user-deened relations. 2) Each rewrite step must be proved valid. In general, these proofs cannot be recursively generated. We have overcome these diiculties and designed a package for the Nuprl system that works well in practice. Our solution is an extensible set of functions for directing and validating relational inferences. The heart of our package is a set of operators that use a user-supplied lemma database to create new rewrites from old ones. These routines place no restrictions on relations; a rewrite's success depends on the strength of the database. Overall, the package allows rewrites to be pieced together in numerous ways, providing the user with a tool to construct sophisticated rewrite strategies.
A bivalent recombinant immunotoxin with high potency against tumors with EGFR and EGFRvIII expression

EGFR and EGFRvIII are overexpressed in various types of cancer, serving as optimal targets for cancer therapy. Capitalizing on the high specificity of humanized antibody 806 (mAb806) to the EGFR and EGFRvIII overexpressed in cancer, we designed and generated a bivalent recombinant immunotoxin (RIT, DT390-BiscFv806) by fusing the mAb806-derived bivalent single-chain variable fragment with a diphtheria toxin fragment, DT390. In vitro, DT390-BiscFv806 efficiently internalized into the cells and exhibited high cytotoxicity against the U87 glioblastoma cells and the EGFRvIII-transfected U87 (U87-EGFRvIII) cells with a half maximal inhibition concentration (IC50) of 1.47 nM and 2.26 × 10−4 nM, respectively. Notably, DT390-BiscFv806 was 4 orders of magnitude more potent against the U87-EGFRvIII cells than against the parent U87 cells. The cytotoxicity against a group of 6 head and neck squamous cell carcinoma cell lines were further analyzed, showing an IC50 ranging from 0.24 nM to 156 nM, depending on the expression level of EGFR/EGFRvIII. In animals, the U87-EGFRvIII tumor xenografts grew extremely faster than the parental U87, and systemic administration of DT390-BiscFv806 significantly inhibited the growth of established U87-EGFRvIII and U87 tumor xenografts, showing a growth inhibition rate of 76.3% (59.82–96.2%) and 59.4% (31.5–76.0%), respectively. In pathology, the RIT-treated tumors exhibited a low mitotic activity and a large number of degenerative tumor cells, compared with the control tumors. The results indicate that DT390-BiscFv806 is promising for treatment of various types of cancer, especially for those with high EGFR expression or with EGFR and EGFRvIII co-expression.
The Age of Information: Real-Time Status Updating by Multiple Sources

We examine multiple independent sources providing status updates to a monitor through simple queues. We formulate an age of information (AoI) timeliness metric and derive a general result for the AoI that is applicable to a wide variety of multiple source service systems. For first-come first-served and two types of last-come first-served systems with Poisson arrivals and exponential service times, we find the region of feasible average status ages for multiple updating sources. We then use these results to characterize how a service facility can be shared among multiple updating sources. A new simplified technique for evaluating the AoI in finite-state continuous-time queuing systems is also derived. Based on stochastic hybrid systems, this method makes AoI evaluation to be comparable in complexity to finding the stationary distribution of a finite-state Markov chain.
A study of anthropometric measures before and after external septoplasty in children: a preliminary study.

OBJECTIVE To test the hypothesis that surgery on the growing nasal septum does not adversely affect nasal and midfacial dimensions. DESIGN Paired study. SETTING Tertiary care center. PARTICIPANTS Children treated consecutively during a 4-year period; all had significant nasal obstruction and cosmetic disfigurement secondary to skeletal septal deformities. INTERVENTION Nasal septal surgery (using an external approach), in which the quadrilateral cartilage was removed, remodeled, and reinserted as a free graft. OUTCOME MEASURES Anthropometric linear measurements and indexes of the face and nose preoperatively and postoperatively; nasal dorsum length, nasal height, nasal dorsum index, nasal tip protrusion, columellar length, facial height, face width, upper face height, facial index, nose-upper face height index, and columellar length-nasal tip protrusion index. Continuous measurements were transformed into ordered categories with reference to normative data. Data were analyzed using Wilcoxon signed rank sum test (alpha level of.05) and by applying the Bonferroni adjustment for multiple testing. RESULTS Twenty-six children were studied (12 females and 14 males); age at surgery ranged from 4.5 to 15.5 years (mean age, 9.5 years); average age at postoperative measurement, 12.5 years; mean follow-up, 3.1 years. Only nasal dorsum length (P =.007) and nasal tip protrusion (P =.04) were decreased by a statistically significant level before the Bonferroni adjustment. The change was not considered clinically significant. Thus, relative to age-appropriate norms, the dimensions of the nose and midface and their proportionality did not change after surgery. CONCLUSIONS Appropriate nasal septal surgery involving excision and subsequent reinsertion of a remodeled segment of the quadrilateral cartilage has no deleterious effects on development of the nose and midface. We question the absolute dogma that nasal surgery in children must always be avoided.
Towards an Architecture of Electronic Service Market System - requirements analysis and evaluation

The last decade was a time of a very successful growth of Electronic Markets (EMs). EM is an electronicallysupported system which is rather focused on selling physical goods. Electronic Service Market (ESM) is a special case of EM, focused on selling services. The raising business of running ESM seems to be the next possible evolution of the classic EM, and in last few years, several ESM projects were started by various organizations. This paper presents the essential Functional and Architectural Requirements needed in ESM system. The way of their transformation into the architecture of real-life application based on STCMBER meta-architecture was presented. The proposed architecture was validated in the series of pilot implementations performed in compliance with Consortium Research method.
Detection of Microcalcification Clusters in Mammograms using Neural Network

This paper presents a new classification approach for detection of microcalcification clusters in digital mammograms. The proposed microcalcification detection method is done in two stages. In the first stage, features are extracted to discriminate between textures representing clusters of microcalcifications and texture representing normal tissue. The original mammogram image is decomposed using wavelet decomposition and gabor features are extracted from the original image Region of Interest (ROI). With these features individual microcalcification clusters is detected. In the second stage, the ability of these features in detecting microcalcification is done using Backpropagation Neural Network (BPNN). The proposed classification approach is applied to a database of 322 dense mammographic images, originating from the MIAS database. Results shows that the proposed BPNN approach gives a satisfactory detection performance.
Classification improvement of P300 response based auditory spatial speller brain-computer interface paradigm

The aim of the presented study is to provide a comprehensive test of the EEG evoked response potential (ERP) feature selection techniques for the spatial auditory BCI-speller paradigm, which creates a novel communication option for paralyzed subjects or body-able individuals requiring a direct brain-computer interfacing application. For rigor, the study is conducted with 16 BCI-naive healthy subjects in an experimental setup based on five Japanese hiragana characters in an offline processing mode. In our previous studies the spatial auditory stimuli related P300 responses resulted with encouragingly separable target vs. non-target latencies in averaged responses, yet that finding was not well reproduced in the online BCI single trial based settings. We present the case study indicating that the auditory spatial unimodal paradigm classification accuracy can be enhanced with an AUC based feature selection approach, as far as BCI-naive healthy subjects are concerned.
Time-motion studies of internal medicine residents’ duty hours: a systematic review and meta-analysis

Background Since the mid-1980s, medical residents’ long duty hours have been under scrutiny as a factor affecting patient safety and the work environment for the residents. After several mandated changes in duty hours, it is important to understand how residents spend their time before proposing and implementing future changes. Time-motion methodology may provide reliable information on what residents do while on duty. Purpose The purpose of this study is to review all available literature pertaining to time-motion studies of internal medicine residents while on a medicine service and to understand how much of their time is apportioned to various categories of tasks, and also to determine the effects of the Accreditation Council for Graduate Medical Education (ACGME)-mandated duty hour changes on resident workflow in North America. Methods Electronic bibliographic databases were searched for articles in English between 1941 and April 2013 reporting time-motion studies of internal medicine residents rotating through a general medicine service. Results Eight articles were included. Residents spent 41.8% of time in patient care activities, 18.1% communicating, 13.8% in educational activities, 19.7% in personal/other, and 6.6% in transit. North American data showed the following changes after the implementation of the ACGME 2003 duty hours standard: patient care activities from 41.8% to 40.8%, communication activities from 19.0% to 22.3%, educational activities from 17.7% to 11.6%, and personal/other activities from 21.5% to 17.1%. Conclusion There was a paucity of time-motion data. There was great variability in the operational definitions of task categories reported in the studies. Implementation of the ACGME duty hour standards did not have a significant effect on the percentage of time spent in particular tasks. There are conflicting reports on how duty hour changes have affected patient safety. A low proportion of time spent in educational activities deserves further study and may point to a review of the educational models used.
Water-based Tai Chi: theoretical benefits in musculoskeletal diseases. Current evidence

Tai Chi is a low-impact and moderate intensity exercise that has shown positive effects in patients with musculoskeletal disorders. Recently have been developed clinical studies on the benefits of Tai Chi techniques combined with hydrotherapy. Both types of treatment include physical training of balance, mobility, strength, coordination and sensory input that could complement each other. This report aims to present the current evidence about the benefits of the combination of water based Tai Chi in musculoskeletal diseases in order to establish whether the combined intervention is better than Tai Chi or hydrotherapy alone.
Datapoints: use of restraint before and after implementation of the new HCFA rules.

138 T use of physical restraint in psychiatric settings is highly controversial, and the issue is all the more contentious for the lack of systematic data collection and careful evaluation of indications, methods, outcomes, and adverse events. In July 1999 the Health Care Financing Administration (HCFA), now the Centers for Medicare and Medicaid Services, issued rules on restraint and seclusion for general and psychiatric hospitals that participate in Medicare and Medicaid (1). The rules require that a physician or a licensed independent practitioner make a face-to-face assessment of a patient within one hour of the initiation of restraint or seclusion. The “one-hour rule” has provoked tremendous debate as smaller and rural facilities struggle to comply with this “unfunded mandate. ” The rules also shorten the interval between mandatory renewal orders, codify requirements for staff training, and create more stringent requirements for documentation. No data on the use of restraints on inpatient psychiatric wards have been published since these rules were put into effect. We report information about restraint episodes on four psychiatric units with a total of 80 beds at the University of Rochester Medical Center during the three months before Use of Restraint Before and After Implementation of the New HCFA Rules
Superimposed or time-division multiplexed pilots in time-varying channels: an informative consideration

Two major techniques are used to embed pilots into data, time-division multiplexed (TDM) and superimposed (SIP). In this paper, we compare these two techniques in an informative consideration under time varying fading channels. Besides the ordinary SIP without dealing with the interference, we also study two different kinds of performance improved iterative SIP: interference subtraction (IS) and interference exploitation (IE). Using Wiener filtering and accounting estimation error, the capacity lower bounds and BER expressions are derived. Numerical results show that great potential benefits are brought by SIP if the interference is utilized properly. With this potential exploited, SIP shows great superior to PSAM, especially in high speed environments.
Translating GPU Binaries to Tiered SIMD Architectures with Ocelot

Parallel Thread Execution ISA (PTX) is a virtual instruction set used by NVIDIA GPUs that explicitly expresses hierarchical MIMD and SIMD style parallelism in an application. In such a programming model, the programmer and compiler are left with the not trivial, but not impossible, task of composing applications from parallel algorithms and data structures. Once this has been accomplished, even simple architectures with low hardware complexity can easily exploit the parallelism in an application. With these applications in mind, this paper presents Ocelot, a binary translation framework designed to allow architectures other than NVIDIA GPUs to leverage the parallelism in PTX programs. Specifically, we show how (i) the PTX thread hierarchy can be mapped to many-core architectures, (ii) translation techniques can be used to hide memory latency, and (iii) GPU data structures can be efficiently emulated or mapped to native equivalents. We describe the low level implementation of our translator, ending with a case study detailing the complete translation process from PTX to SPU assembly used by the IBM Cell Processor.
Comparing the Learning Effectiveness of REDEEM and CBT

The REDEEM authoring tool creates simple ITSs from existing computer-based training (CBT). In this study, learning outcomes of 33 adult volunteers, who studied ‘ Introduction to Personal Computing and Networking’ courses with CBT and with REDEEM, were compared. Performance of all students improved from pre-test to post-test and was significantly better on the course students had learnt with REDEEM. Analysis of students’ performance suggested that this REDEEM enhancement was due to the increased interaction that REDEEM promotes. Those students who learnt most from REDEEM tended to be those who experienced REDEEM first and who required less attempts to answer REDEEM’s questions correctly. This study showed how simple improvements to educational software can significantly increase students’ learning.
Optimizing the induction of Bayesian Networks using PC and Variable Ordering Genetic Algorithms

Variable Ordering (VO) plays an important role when inducing Bayesian Networks (BN). Previous works in the literature suggest that it is worth pursuing the use of genetic algorithms for identifying a suitable VO, when learning a BN structure from data. However, these algorithms may be computationally costly. This paper proposes a hybrid adaptive algorithm named PC-VOGA where initially the PC algorithm is performed to provide a previous VO before the genetic algorithm begins. Such previous ordering is produced by CGSort algorithm, which is also proposed in this work from BN structure induced by PC. Initial experiments revealed that the PC-VOGA approach is promising having the assistance of CGSort algorithm.
Subcellular proteomics and global analysis of posttranslational modifications to study functional roles of Trypanosoma cruzi molecules

One century after the discovery of Chagas disease, the treatment for this illness is still based only on two drugs with limited efficacy and severe side effects. In this mini-review, we discuss the application of mass spectrometry (MS)- based proteomic approaches to study the biochemistry and cell biology of etiologic agent of Chagas disease, Trypanosoma cruzi. We focus the discussion in the analysis of subcellular proteomics and posttranslational modifications (PTMs). In re- cent years, subcellular proteomics has brought new insights into the localization of proteins and possible functions of or- ganelles. Thus far, proteomic analysis of reservosomes, ribosomes, detergent-solubilized membranes, and a preparation of an organelle mixture have been performed. In addition, a number of analyses of PTMs of T. cruzi proteins (i.e., histone modifications, phosphorylation, glycosylation, glycosylphosphatidylinositol (GPI)-anchoring, and nitrosylation) have been successfully carried out. The identification of those and other PTMs combined with cutting-edge biochemical, im- munological and cell biology approaches, have allowed a more in-depth understanding of biological and pathophysiologi- cal processes resulting from host cell-parasite interactions.
Metoclopramide versus metoclopramide and lorazepam. Superiority of combined therapy in the control of cisplatin‐induced emesis

Sixty‐four patients treated with cisplatin‐containing regimens were entered into a randomized, double‐blinded study examining the antiemetic efficacy of metoclopramide with and without lorazepam for control of cisplatin‐induced emesis. Metoclopramide was administered to all patients at 2 mg/kg, intravenously, 30 minutes before chemotherapy and 1.5, 3.5, and 5.5 hours posttreatment. Patients randomized to receive combined antiemetic therapy were administered lorazepam at 2 mg/m2 (maximum, 4 mg dose) intravenously, 30 minutes before chemotherapy. Those patients not receiving lorazepam were given normal saline placebo. Degree of nausea and number of vomiting episodes were recorded on a data flow sheet with a visual analogue scale. Drug toxicities were evaluated before each administered dose. Patients receiving both metoclopramide and lorazepam experienced significantly less vomiting episodes (P < 0.05) and nausea (P < 0.01) when compared to patients given metoclopramide alone. Forty‐four percent of those receiving the combined therapy reported no nausea or vomiting episodes compared to only 22% receiving metoclopramide alone. Sedation was significantly more common in patients receiving lorazepam (88%) as opposed to patients receiving only metoclopramide (43%), P < 0.01. Amnesia was seen in 25% receiving lorazepam. No significant difference in diarrhea, dystonia, or disinhibition was observed between the two arms. The authors conclude that the combination of lorazepam and metoclopramide was superior to metoclopramide alone in the prevention of cisplatin‐induced nausea and vomiting, with sedation and amnesia more commonly observed in the combined regimen.
A New Algorithm for Estimating the Effective Dimension-Reduction Subspace

The statistical problem of estimating the effective dimension-reduction (EDR) subspace in the multi-index regression model with deterministic design and additive noise is considered. A new procedure for recovering the directions of the EDR subspace is proposed. Many methods for estimating the EDR subspace perform principal component analysis on a family of vectors, say β1,. ,βL, nearly lying in the EDR subspace. This is in particular the case for the structure-adaptive approach proposed by Hristache et al. (2001a). In the present work, we propose to estimate the projector onto the EDR subspace by the solution to the optimization problem minimize maxl=1,. ,L βlT (I-A)βl subject to A ∈ Am where Am is the set of all symmetric matrices with eigenvalues in [0,1] and trace less than or equal to m, with m being the true structural dimension. Under mild assumptions, √n-consistency of the proposed procedure is proved (up to a logarithmic factor) in the case when the structural dimension is not larger than 4. Moreover, the stochastic error of the estimator of the projector onto the EDR subspace is shown to depend on L logarithmically. This enables us to use a large number of vectors βl for estimating the EDR subspace. The empirical behavior of the algorithm is studied through numerical simulations.