Miracle-dz/UniFAR-FTUs huggingface dataset:
Do Genetic Polymorphisms Modulate Response Rate and Toxicity of Cisplatin Associated With Radiotherapy in Laryngeal Squamous Cell Carcinoma?

AbstractCisplatin (CDDP) plus radiotherapy (RT) has been used to treat advanced laryngeal squamous cell carcinoma (LSCC) patients. Single nucleotide polymorphisms (SNPs) may be responsible for differences in chemo/radiosensitivity and side effects in those patients. We reported an advanced LSCC patient, who obtained durable complete response and unexpected pronounced toxicity during CDDP and RT, possibly due to SNPs in genes that modulate the effects of this therapeutic modality. Case presentation: A 30-year-old man with advanced LSCC obtained durable complete response and severe alopecia and pancytopenia after standard and reduced doses of CDDP and RT. Analyses of SNPs revealed that the patient presented GSTT1 deletion, variant MSH3 1045ThrThr, wild GSTP1 105IleIle, and wild BAX -248GG genotypes, which were previously described in association with abnormal detoxification, DNA repair, and damaged cell apoptosis, respectively. Seven other advanced LSCC patients with GSTT1 gene, MSH3 AlaAla or AlaThr, GSTP1 IleVal or ValVal, and BAX GA or AA genotypes served as controls of the study. Only 1 control presented complete response; the other 6 controls obtained partial response of short duration. Four and 3 controls presented grade 1 or 2 and grade 3 anemia or leukopenia during treatment, respectively. The CDDP level in urine collected after CDDP infusion in the reported patient was lower than the median value obtained in controls, suggesting a higher amount of intracellular CDDP in the reported case.The data suggest, for the first time, that inherited abnormalities in intracellular detoxification of CDDP, DNA repair of lesions induced by CDDP and RT, and damaged cell apoptosis may alter treatment response and toxicity in LSCC, but should be confirmed by large pharmacogenomic studies.
Genome Scale Identification of Treponema pallidum Antigens

ABSTRACT Antibody responses for 882 of the 1,039 proteins in the proteome of Treponema pallidum were examined. Sera collected from infected rabbits were used to systematically identify 106 antigenic proteins, including 22 previously identified antigens and 84 novel antigens. Additionally, sera collected from rabbits throughout the course of infection demonstrated a progression in the breadth and intensity of humoral immunoreactivity against a representative panel of T. pallidum antigens.
Does animation help users build mental maps of spatial information?

We examine how animating a viewpoint change in a spatial information system affects a user's ability to build a mental map of the information in the space. We found that animation improves users' ability to reconstruct the information space, with no penalty on task performance time. We believe that this study provides strong evidence for adding animated transitions in many applications with fixed spatial data where the user navigates around the data space.
Unsupervised parallel image classification using a hierarchical Markovian model

The paper deals with the problem of unsupervised classification of images modeled by Markov random fields (MRF). If the model parameters are known then we have various methods to solve the segmentation problem (simulated annealing, ICM, etc.). However, when they are not known, the problem becomes more difficult. One has to estimate the hidden label field parameters from the only observable image. Our approach consists of extending a recent iterative method of estimation, called iterative conditional estimation (ICE) to a hierarchical Markovian model. The idea resembles the estimation-maximization (EM) algorithm as we recursively look at the maximum a posteriori (MAP) estimate of the label field given the estimated parameters then we look at the maximum likelihood (ML) estimate of the parameters given a tentative labeling obtained at the previous step. We propose unsupervised image classification algorithms using a hierarchical model. The only parameter supposed to be known is the number of regions, all the other parameters are estimated. The presented algorithms have been implemented on a Connection Machine CM200. Comparative tests have been done on noisy synthetic and real images (remote sensing). <<ETX>>
Optimization of Contemporary Telecommunications Networks: Generalized Spanning Trees and WDM Optical Networks

Title of dissertation: OPTIMIZATION OF CONTEMPORARY TELECOMMUNICATIONS NETWORKS: GENERALIZED SPANNING TREES AND WDM OPTICAL NETWORKS Daliborka Stanojević, Doctor of Philosophy, 2005 Dissertation directed by: Associate Professor Subramanian Raghavan Department of Decision and Information Technologies We present a study of two NP-hard telecommunications network design problems the prize-collecting generalized minimum spanning tree problem (PCGMST) and the design of optical networks with wavelength division multiplexing. The first problem, the PCGMST problem, involves the design of regional backbone networks, where a set of local area networks (LANs) need to be connected by a minimum cost tree network using exactly one gateway site from each LAN. We present several polynomial time heuristics for the PCGMST problem and show that these algorithms, at best, provide only modest quality solutions. We also present two metaheuristics a local search procedure and a genetic algorithm, and show that these procedures provide compelling high-quality results on a large set of test problems. Our study of the PCGMST problem is concluded by a presentation of two exact solution procedures that can be used to find optimal solutions in networks of moderate size. The second problem studied in this dissertation is a more complex network design problem that involves optical networks with wavelength division multiplexing (WDM). These networks provide an abundance of transmission bandwidth, but require the use of expensive equipment, which, in turn, mandates careful use of the resources available for their design. The novel aspect of WDM optical networks is that they require simultaneous design of two network layers. The first layer is the virtual topology that requires routing of logical paths over the physical layer of optical fibers. The second layer involves routing and grooming of traffic requests over the logical paths established in the virtual topology. This problem has been extensively studied in the last 10 years, but due to its notoriously hard nature, only few exact solution procedures for relaxed versions of this problem were developed so far. We propose one exact and two approximate branch-and-price algorithms for two versions of the WDM optical network design problem and present results of the computational study involving two different design objectives. Finally, we propose two classes of valid inequalities for our branch-and-price algorithms, and discuss applicability of our algorithms to different versions of the WDM optical network design problem. OPTIMIZATION OF CONTEMPORARY TELECOMMUNICATIONS NETWORKS: GENERALIZED SPANNING TREES AND WDM OPTICAL NETWORKS
Obese Black Women as “Social Dead Weight”: Reinventing the “Diseased Black Woman”

A flurry of recent articles in the medical and popular press have decried black women’s “alarmingly high” rates of obesity. The number of high-profile publications lamenting the “epidemic” among black women has grown, even as mounting evidence indicates that obesity (defined as a body mass index ≥ 30) does not necessarily lead to poor health outcomes. Indeed, given its functional limitations in explaining or predicting health status, a number of medical researchers are now issuing calls to revise the standard definition of obesity. In this article, I examine the curious nature of the discourse decrying the obesity epidemic among black women. I argue that rather than being a novel concern about black women’s health or public health, the medical and popular discourse about obesity and black women is largely a reproduction of the trope of the diseased black woman that has been used throughout American history. This trope reifies the purported sensualism of black women. Moreover, the newest incarnation of this discursive device is distinct in that it renders black women as triply signified “social dead weight. ”
Is Accurate Mapping of EMG Signals on Kinematics Needed for Precise Online Myoelectric Control?

In this paper, we present a systematic analysis of the relationship between the accuracy of the mapping between EMG and hand kinematics and the control performance in goal-oriented tasks of three simultaneous and proportional myoelectric control algorithms: nonnegative matrix factorization (NMF), linear regression (LR), and artificial neural networks (ANN). The purpose was to investigate the impact of the precision of the kinematics estimation by a myoelectric controller for accurately complete goal-directed tasks. Nine naïve subjects performed a series of goal-directed myoelectric control tasks using the three algorithms, and their online performance was characterized by 6 indexes. The results showed that, although the three algorithms' mapping accuracies were significantly different, their online performance was similar. Moreover, for LR and ANN, the offline performance was not correlated to any of the online performance indexes, and only a weak correlation was found with three of them for NMF . We conclude that for reliable simultaneous and proportional myoelectric control, it is not necessary to achieve high accuracy in the mapping between EMG and kinematics. Rather, good online myoelectric control is achieved by the continuous interaction and adaptation of the user with the myoelectric controller through feedback (visual in the current study). Control signals generated by EMG with rather poor association with kinematic variables can still be fully exploited by the user for precise control. This conclusion explains the possibility of accurate simultaneous and proportional control over multiple degrees of freedom when using unsupervised algorithms, such as NMF.
A MODEL FOR ESTIMATING THREE-DIMENSIONAL BOUNDARY LAYERS IN ROTATING DUCT FLOW AT HIGH ROTATION RATES

Numerical simulations of flow in a rotating square duct at high rotation rates are presented. Computation and analysis of the different terms of the averaged momentum budget near the sidewalls have shown the dominant mechanisms of momentum transfer in these regions. A model for the velocities has been developed by analytically solving simplified versions of these budgets within the lateral three-dimensional boundary layers. The resulting predictions of the velocity profiles and the boundary layer quantities are in good agreement with present numerical results.
Wide-Coverage Deep Statistical Parsing Using Automatic Dependency Structure Annotation

A number of researchers have recently conducted experiments comparing deep hand-crafted wide-coverage with shallow treebank- and machine-learning-based parsers at the level of dependencies, using simple and automatic methods to convert tree output generated by the shallow parsers into dependencies. In this article, we revisit such experiments, this time using sophisticated automatic LFG f-structure annotation methodologies with surprising results. We compare various PCFG and history-based parsers to find a baseline parsing system that fits best into our automatic dependency structure annotation technique. This combined system of syntactic parser and dependency structure annotation is compared to two hand-crafted, deep constraint-based parsers, RASP and XLE. We evaluate using dependency-based gold standards and use the Approximate Randomization Test to test the statistical significance of the results. Our experiments show that machine-learning-based shallow grammars augmented with sophisticated automatic dependency annotation technology outperform hand-crafted, deep, wide-coverage constraint grammars. Currently our best system achieves an f-score of 82.73% against the PARC 700 Dependency Bank, a statistically significant improvement of 2.18% over the most recent results of 80.55% for the hand-crafted LFG grammar and XLE parsing system and an f-score of 80.23% against the CBS 500 Dependency Bank, a statistically significant 3.66% improvement over the 76.57% achieved by the hand-crafted RASP grammar and parsing system.
Intracoronary Radiation Therapy Improves the Clinical and Angiographic Outcomes of Diffuse In-Stent Restenotic Lesions: Results of the Washington Radiation for In-Stent Restenosis Trial for Long Lesions (Long WRIST) Studies

Background—The Washington Radiation for In-Stent Restenosis Trial for long lesions (Long WRIST) was designed to determine the safety and efficacy of vascular brachytherapy for the treatment of diffuse in-stent restenosis. Methods and Results—A total of 120 patients with diffuse in-stent restenosis in native coronary arteries (lesion length, 36 to 80 mm) were randomized for either radiation with 192Ir with 15 Gy at 2 mm from the source axis or placebo. After enrollment, 120 additional patients with the same inclusion criteria were treated with 192Ir with 18 Gy and included in the Long WRIST High Dose registry. Antiplatelet therapy was initially prescribed for 1 month and was extended to 6 months in the last 60 patients of the Long WRIST High Dose registry. At 6 months, the binary angiographic restenosis rate was 73%, 45%, and 38% in the placebo, 15 Gy, and 18 Gy radiated groups, respectively (P <0.05). At 1 year, the primary clinical end point of major cardiac events was 63% in the placebo group and 42% in the radiated group with 15 Gy (P <0.05). The major cardiac event rate was further reduced with 18 Gy (22%;P <0.05 versus 15 Gy). Late thrombosis was 12%, 15%, and 9% in the placebo group, 15 Gy group with 1 month of antiplatelet therapy, and 18 Gy group with 6 months of antiplatelet therapy, respectively. Conclusions—Vascular brachytherapy with 192Ir is safe and reduces the rate of recurrent restenosis in diffuse in-stent restenosis. The efficacy of vascular brachytherapy on angiographic and clinical outcomes is enhanced with a radiation dose of 18 Gy and prolonged antiplatelet therapy.
Effectiveness of the social-emotional prevention program as a function of children's baseline risk status

ABSTRACT We report here findings from a community-based multifaceted prevention program which was implemented concomitantly as a universal and indicated intervention. Screening of social competence development was used to select preschool children targeted by the indicated intervention (high risk), and by the universal intervention (moderate and low risk). The intervention's effectiveness on children's behaviors at home increased as a function of higher baseline risk status and higher parental attendance rates. The results also suggest that short, four session parent training is sustainable, generating attendance rates up to 60%. The intervention's effectiveness on parent behaviors was only partially sustained by significant within intervention group trends. The results indicate that the use of parent training in community-based interventions sustain skills transfer from the classroom to parent–child interactions. Furthermore, the most consistent effects were found for moderate risk children, suggesting that universal interventions might be efficient for this marginally at risk category.
Influence of Cognitive Impairment on Mobility Recovery of Patients With Hip Fracture

Objective The aims of this study were to study the mobility recovery in hip fracture patients and determine the influence of cognitive impairment on mobility within the first 3 months after surgery. Design This prospective cohort study was carried out in an acute public hospital in southern Spain and included 275 patients, 65 years or older, with a hip fracture. Mobility and Cognitive status were measured by Tinetti Performance-Oriented Mobility Assessment and Pfeiffers’ Scale (Short Portable Mental State Questionnaire), respectively. Multiple linear regression was used to examine the influence of cognitive impairment on mobility. Results The median Performance-Oriented Mobility Assessment score changed from 4 (3–4) points at discharge to 17 (7–22) at 3 months. All degrees of cognitive impairment were negatively associated with gait and balance at 1 and 3 months after surgery (P < 0.01). Age, weight bearing, length of hospital stay, and postsurgical complications were also identified as independent predictors of mobility outcome at 3 months. Conclusions Cognitive impairment is a negative prognostic factor for the recovery of mobility in elderly patients with a hip fracture. New treatment strategies are needed for hip fracture patients with cognitive impairment.
A mathematical model for the age distribution of cancer in man

Incidence data that have been collected by cancer registries in different parts of the world provide an opportunity for examining the relationship between cancer incidence and age on a wider scale and more accurately than has been possible before. In the present paper the relationship has been examined in a large group of cancers whose incidence increases progressively from young adult life into old age.
A 90-nm low-power 32-kB embedded SRAM with gate leakage suppression circuit for mobile applications

In sub-100-nm generation, gate-tunneling leakage current increases and dominates the total standby leakage current of LSIs based on decreasing gate-oxide thickness. Showing that the gate leakage current is effectively reduced by lowering the gate voltage, we propose a local dc level control (LDLC) for SRAM cell arrays and an automatic gate leakage suppression driver (AGLSD) for peripheral circuits. We designed and fabricated a 32-kB 1-port SRAM using 90-nm CMOS technology. The six-transistor SRAM cell size is 1.25 /spl mu/m/sup 2/. Evaluation shows that the standby current of 32-kB SRAM is 1.2 /spl mu/A at 1.2 V and room temperature. It is reduced to 7.5% of conventional SRAM.
Crafting GBD-Net for Object Detection

The visual cues from multiple support regions of different sizes and resolutions are complementary in classifying a candidate box in object detection. Effective integration of local and contextual visual cues from these regions has become a fundamental problem in object detection. In this paper, we propose a gated bi-directional CNN (GBD-Net) to pass messages among features from different support regions during both feature learning and feature extraction. Such message passing can be implemented through convolution between neighboring support regions in two directions and can be conducted in various layers. Therefore, local and contextual visual patterns can validate the existence of each other by learning their nonlinear relationships and their close interactions are modeled in a more complex way. It is also shown that message passing is not always helpful but dependent on individual samples. Gated functions are therefore needed to control message transmission, whose on-or-offs are controlled by extra visual evidence from the input sample. The effectiveness of GBD-Net is shown through experiments on three object detection datasets, ImageNet, Pascal VOC2007 and Microsoft COCO. Besides the GBD-Net, this paper also shows the details of our approach in winning the ImageNet object detection challenge of 2016, with source code provided on https://github.com/craftGBD/craftGBD. In this winning system, the modified GBD-Net, new pretraining scheme and better region proposal designs are provided. We also show the effectiveness of different network structures and existing techniques for object detection, such as multi-scale testing, left-right flip, bounding box voting, NMS, and context.
Impact of Maternal Melatonin Suppression on Amount and Functionality of Brown Adipose Tissue (BAT) in the Newborn Sheep

In human and sheep newborns, brown adipose tissue (BAT) accrued during fetal development is used for newborn thermogenesis. Here, we explored the role of maternal melatonin during gestation on the amount and functionality of BAT in the neonate. We studied BAT from six lambs gestated by ewes exposed to constant light from 63% gestation until delivery to suppress melatonin (LL), six lambs gestated by ewes exposed to LL but receiving daily oral melatonin (12 mg at 1700 h, LL + Mel) and another six control lambs gestated by ewes maintained in 12 h light:12 h dark (LD). Lambs were instrumented at 2 days of age. At 4–6 days of age, they were exposed to 24°C (thermal neutrality conditions) for 1 h, 4°C for 1 h, and 24°C for 1 h. Afterward, lambs were euthanized and BAT was dissected for mRNA measurement, histology, and ex vivo experiments. LL newborns had lower central BAT and skin temperature under thermal neutrality and at 4°C, and higher plasma norepinephrine concentration than LD newborns. In response to 4°C, they had a pronounced decrease in skin temperature and did not increase plasma glycerol. BAT weight in LL newborns was about half of that of LD newborns. Ex vivo, BAT from LL newborns showed increased basal lipolysis and did not respond to NE. In addition, expression of adipogenic/thermogenic genes (UCP1, ADBR3, PPARγ, PPARα, PGC1α, C/EBPβ, and perilipin) and of the clock genes Bmal1, Clock, and Per2 was increased. Remarkably, the effects observed in LL newborns were absent in LL + Mel newborns. Thus, our results support that maternal melatonin during gestation is important in determining amount and normal functionality of BAT in the neonate.
An Immunofluorescence-Assisted Microfluidic Single Cell Quantitative Reverse Transcription Polymerase Chain Reaction Analysis of Tumour Cells Separated from Blood

Circulating tumour cells (CTCs) are important indicators of metastatic cancer and may provide critical information for individualized treatment. As CTCs are usually very rare, the techniques to obtain information from very small numbers of cells are crucial. Here, we propose a method to perform a single cell quantitative reverse transcription polymerase chain reaction (qPCR) analysis of rare tumour cells. We utilized a microfluidic immunomagnetic assay to separate cancer cells from blood. A combination of detailed immunofluorescence and laser microdissection enabled the precise selection of individual cells. Cancer cells that were spiked into blood were successfully separated and picked up for a single cell PCR analysis. The breast cancer cell lines MCF7, SKBR3 and MDAMB231 were tested with 10 different genes. The result of the single cell analysis matched the results from a few thousand cells. Some markers (e.g., ER, HER2) that are commonly used for cancer identification showed relatively large deviations in expression levels. However, others (e.g., GRB7) showed deviations that are small enough to supplement single cell disease profiling.