Miracle-dz/UniFAR-FTUs huggingface dataset:
A cache memory with unit tile and line accessibility

Ineffective data access of cache memory has become a bottleneck for efficient 2-dimensional (2-D) data processing, such as image processing and matrix multiplication. To solve this problem, a cache memory with both unit tile and unit line accessibility, based on a 4-level Z-order tiling layout is proposed. Conventional raster scan order access to this layout is enabled via a hardware-based address translation, which can eliminate the overhead of address calculation. The proposed cache can access data in parallel in the column (unit tile) and row (unit line) directions by using the 4-level Z-order tiling layout and multi-bank cache organization. Unit tile access corresponding to parallel data access in the column direction can exploit the 2-D locality. Simulation results show that the 4-level Z-order tiling layout provides less TLB and L1 data cache misses compared to the raster scan order and Morton order layouts in matrix multiplication, especially for the larger matrix size, LU decomposition, successive over relaxation, and matrix transposition benchmarks. An LSI chip of the proposed cache combined with an SIMD-based datapath was designed in a 2.5×5 mm2 area by using 0.18 μm CMOS technology. Under the 3.8 ns clock period, the read latency was suppressed to 3 clock cycles, the same as the conventional cache memory of an Intel or ARM high-performance processor.
Individualized adjustments to reference phantom internal organ dosimetry—scaling factors given knowledge of patient external anatomy

Internal radiation dose estimates for diagnostic nuclear medicine procedures are typically calculated for a reference individual. Resultantly, there is uncertainty when determining the organ doses to patients who are not at 50th percentile on either height or weight. This study aims to better personalize internal radiation dose estimates for individual patients by modifying the dose estimates calculated for reference individuals based on easily obtainable morphometric characteristics of the patient. Phantoms of different sitting heights and waist circumferences were constructed based on computational reference phantoms for the newborn, 10 year-old, and adult. Monoenergetic photons and electrons were then simulated separately at 15 energies. Photon and electron specific absorbed fractions (SAFs) were computed for the newly constructed non-reference phantoms and compared to SAFs previously generated for the age-matched reference phantoms. Differences in SAFs were correlated to changes in sitting height and waist circumference to develop scaling factors that could be applied to reference SAFs as morphometry corrections. A further set of arbitrary non-reference phantoms were then constructed and used in validation studies for the SAF scaling factors. Both photon and electron dose scaling methods were found to increase average accuracy when sitting height was used as the scaling parameter (~11%). Photon waist circumference-based scaling factors showed modest increases in average accuracy (~7%) for underweight individuals, but not for overweight individuals. Electron waist circumference-based scaling factors did not show increases in average accuracy. When sitting height and waist circumference scaling factors were combined, modest average gains in accuracy were observed for photons (~6%), but not for electrons. Both photon and electron absorbed doses are more reliably scaled using scaling factors computed in this study. They can be effectively scaled using sitting height alone as patient-specific morphometric parameter.
A stability-based algorithm to validate hierarchical clusters of genes

Stability-based methods have been successfully applied in functional genomics to the analysis of the reliability of clusterings characterised by a relatively low number of examples and clusters. The application of these methods to the validation of gene clusters discovered in biomolecular data may lead to computational problems due to the large amount of possible clusters involved. To address this problem, we present a stability-based algorithm to discover significant clusters in hierarchical clusterings with a large number of examples and clusters. The reliability of clusters of genes discovered in gene expression data of patients affected by human myeloid leukaemia is analysed through the proposed algorithm, and their relationships with specific biological processes are tested by means of Gene Ontology-based functional enrichment methods.
Hybrid Integration of Magnetoresistive Sensors with MEMS as a Strategy to Detect Ultra-Low Magnetic Fields

In this paper, we describe how magnetoresistive sensors can be integrated with microelectromechanical systems (MEMS) devices enabling the mechanical modulation of DC or low frequency external magnetic fields to high frequencies using MEMS structures incorporating magnetic flux guides. In such a hybrid architecture, lower detectivities are expected when compared with those obtained for individual sensors. This particularity results from the change of sensor’s operating point to frequencies above the 1/f noise knee.
Perceptual Quality Assessment for Multi-Exposure Image Fusion

Multi-exposure image fusion (MEF) is considered an effective quality enhancement technique widely adopted in consumer electronics, but little work has been dedicated to the perceptual quality assessment of multi-exposure fused images. In this paper, we first build an MEF database and carry out a subjective user study to evaluate the quality of images generated by different MEF algorithms. There are several useful findings. First, considerable agreement has been observed among human subjects on the quality of MEF images. Second, no single state-of-the-art MEF algorithm produces the best quality for all test images. Third, the existing objective quality models for general image fusion are very limited in predicting perceived quality of MEF images. Motivated by the lack of appropriate objective models, we propose a novel objective image quality assessment (IQA) algorithm for MEF images based on the principle of the structural similarity approach and a novel measure of patch structural consistency. Our experimental results on the subjective database show that the proposed model well correlates with subjective judgments and significantly outperforms the existing IQA models for general image fusion. Finally, we demonstrate the potential application of the proposed model by automatically tuning the parameters of MEF algorithms.1
Australian biodiversity via its plants and marine organisms. A high-throughput screening approach to drug discovery

Abstract High-throughput screening (HTS) of extracts of Australian plants and marine organisms commenced in our laboratory in 1994. The biota collections commenced in late 1993. The collection has in excess of 30 000 biota samples including over 16 000 biota samples of vascular plants, algae, and macro fungi from Queensland, and over 4000 marine invertebrates from Australian waters. The plant collection represents ∼9 % of the world species diversity of higher plants, with representation from 73 % of the world's plant families. The marine collection contains ∼10 % of the world diversity of sponges, ∼10 % of the world diversity of ascidians, and ∼5 % of the world diversity of soft corals and gorgonians. The lecture will highlight some of the advances to knowledge about Australian biodiversity as a result of the HTS project, discuss drug discovery using HTS, and give some examples of the chemistry arising from the screening of the extracts.
Lyme disease: diagnostic issues and controversies

The diagnosis of Lyme disease is a controversial topic. Most practitioners and scientists recognize that Lyme disease is associated with certain objective clinical manifestations supported by laboratory evidence of infection with Borrelia burgdorferi sensu lato (the etiologic agent). There are others, however, who believe that patients with Lyme disease may have a wide variety of entirely nonspecific symptoms without any objective clinical manifestation and that laboratory evidence of infection by B. burgdorferi is not required to support the diagnosis. In reality, this perspective is not evidence based and would inevitably lead to innumerable misdiagnoses, given the high frequency of medically unexplained symptoms, such as fatigue and musculoskeletal pains, in the general population. Although those espousing this viewpoint do not believe that a positive laboratory test is required, nevertheless, they often seek out and promote alternative, unapproved testing methods that frequently provide false-positive results to justify their diagnosis. Herein, we provide a brief overview of Lyme disease testing, emphasizing current usage and limitations. We also discuss the use of nonvalidated procedures and the prospects for a reduction in such testing practices in the future.
Resistance to action potential depression of a rat axon terminal in vivo

Significance During high-frequency firing, the shape of a presynaptic action potential (AP) can alter, thereby changing neurotransmitter release. In this paper, we describe how a giant terminal in the brainstem of newborn rats called the calyx of Held can fire in vivo at high frequencies without substantial AP depression. The underlying mechanism was found to be the presence of sodium channels that can recover rapidly from depression in combination with a close match between the potential that is attained following an AP with the potential that maximizes AP stability. Surprisingly, this match was already there shortly after formation of the calyx of Held. We speculate that these mechanisms help synapses to maximize timing precision during high-frequency firing. The shape of the presynaptic action potential (AP) has a strong impact on neurotransmitter release. Because of the small size of most terminals in the central nervous system, little is known about the regulation of their AP shape during natural firing patterns in vivo. The calyx of Held is a giant axosomatic terminal in the auditory brainstem, whose biophysical properties have been well studied in slices. Here, we made whole-cell recordings from calyceal terminals in newborn rat pups. The calyx showed a characteristic burst firing pattern, which has previously been shown to originate from the cochlea. Surprisingly, even for frequencies over 200 Hz, the AP showed little or no depression. Current injections showed that the rate of rise of the AP depended strongly on its onset potential, and that the membrane potential after the AP (Vafter) was close to the value at which no depression would occur during high-frequency activity. Immunolabeling revealed that Nav1.6 is already present at the calyx shortly after its formation, which was in line with the fast recovery from AP depression that we observed in slice recordings. Our findings thus indicate that fast recovery from depression and an inter-AP membrane potential that minimizes changes on the next AP in vivo, together enable high timing precision of the calyx of Held already shortly after its formation.
Non-parametric estimation of proportion of cured patients and survival probabilities

In the usual survival analysis setup, it is assumed that all individuals are susceptible to the event of interest. However, there are some clinical trials in which a group of patients responds favorably to the treatment. Those patients are usually followed up for a long time and can be regarded as cured. Survival models that consider a cured fraction, known as cure rate models, are becoming more popular to deal with data from cancer clinical trials. When a cure rate model is assumed, it is often of interest to estimate the proportion of cured patients. A simple non-parametric estimator for the proportion of cured patients was proposed by Maller & Zhou (1992). Parametric regression models have been proposed by Ghitany, Maller & Zhou (1994), Farewell (1982) and Gamel & Vogel (1997) and some authors have considered a semiparametric approach (Peng 2003). Also, in the context of cure rate estimation, the problem of sufficient follow-up arises naturally and it has been addressed by Maller & Zhou (1995) and Klebanova & Yakovlev (2007). In this work, we consider the problem of non-parametric estimation of the proportion of cured patients and of the survival distribution of the uncured ones. We propose estimators based on the IPW (Inverse Probability Weighting) technique (Robins, Rotnitzky & Zhao 1995) and some properties are obtained.
Genetic Relationships Among Continental Cotton Species Based On ITS1 Gene Region Aligned With Different Alignment Tools

The molecular systematic studies that reveal the biodiversity have been rapidly evolving in the last 20 years. In this developing process sequence analysis and methods of phylogenetic analysis of molecular systematics have also started to contribute the phylogenetic studies In terms of phylogenetic information, morphological characters are insufficient for phylogenetic studies. In that situation DNA sequence analysis is very useful for phylogenetic studies. In this study, sequences of “Internal transcribed spacer1” (ITS1) rDNA regions were aligned with three different alignment tools (ClustalW, T-COFFEE, MAFFT) to infer the genetic relationship between forty-four woody, bushy and herbaceous cotton species originated from Africa, America, Australia. In the study maximum likelihood (ML), maximum parsimony (MP), and Bayesian-MCMC methods were utilized. Results revealed that MAFFT presented the best alignments while parsimony and Bayesian methods provided better tree topologies.
Bench-To-Bedside Oximetry for Real-Time Monitoring of Tumor Po 2 : A Critical Parameter Which Influences Radiotherapeutic Outcome

Tumor hypoxia (pO2; partial pressure of oxygen < 10 – 15 mmHg) plays a critical role in radio-resistance and promotes the development of aggressive tumor phenotypes. Furthermore, tumor hypoxia is dynamic and varies with tumor type, stage and as a consequence of ionizing radiation and other therapies. In spite of its profound effect on treatment outcome, tumor pO2 has been sub-optimally exploited in radiation oncology. Current radiotherapy plans do not take into account specific temporal changes in individual tumor pO2 levels due to lack of appropriate oximetry techniques, and therefore potentially may be suboptimal. In particular, hypofractionated treatments are increasingly used with large doses (4 20 Gy) of ionizing radiation that may have different effects on the levels of oxygen in individual tumors during the course of treatment. Real-time monitoring of tumor pO2 might make it feasible to improve the outcome by scheduling fractions at times of increased tumor pO2. Such tumor oxygen guided treatment protocols can only be accomplished by oximetry techniques that can provide accurate serial measurements of tumor pO2 throughout the course of therapy. We have pioneered in vivo EPR oximetry using micro-particulate oxygen-sensing probes for real-time monitoring of tissue pO2 in superficial (<10 mm) as well as deep-sited tumors, repeatedly and accurately, for clinical applications. Our goal is to improve treatment outcome by providing the information about dynamic tumor oxygen levels so that irradiations can be scheduled when the tumors are better oxygenated either with or without oxygen enhancing interventions e. g. pre-irradiation, carbogen (2 5% CO2 balance O2) inhalation, hyperthermia, and anti-angiogenic treatment. Temporal changes in tumor pO2 can also be used as a prognostic marker to predict efficacy, identify responders and non-responders, and individualize therapy. An overview of in vivo EPR oximetry, pre-clinical results and the current status of clinical oximetry are briefly described to highlight the potential advantages of EPR oximetry in radiation oncology. Minireview Bench-To-Bedside Oximetry for Real-Time Monitoring of Tumor Po2: A Critical Parameter Which Influences Radiotherapeutic Outcome Nadeem Khan1,4, Huagang Hou1,4, Eunice Y. Chen2, Lesley A. Jarvis3,4, Philip E. Schaner3,4, Benjamin B. Williams1,4, Harold M. Swartz1,4 and Periannan Kuppusamy1,4* 1EPR Center for the Study of Viable Systems, Department of Radiology, USA 2Department of Surgery Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA 3Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA 4Norris Cotton Cancer Center, One Medical Center Drive, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
Tissue Distribution of Heavy Metals (Cd, Cu, Pb and Zn) in the Green- lipped Mussel Perna viridis from Nenasi and Kuala Pontian, East Coast of Peninsular Malaysia

Previous studies reported that the green-lipped mussel Perna viridis were widely found on the west coast of Peninsular Malaysia but not on the east coast of the Peninsula. In this study, surveys and sampling were conductedfrom Tumpat to Mersingin April 2004, but the mussels were only found at Nenasi and Kuala Pontian in Pahang coastal waters. Therejare, from this study, we confirm that the mussels on the east coast were not as widely found as on the west coast of Peninsular Malaysia. The mussel samples collected were analysed far cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) and the metal concentrations (J.lg/g dry weight) were 1.89­ 2.13, 3.84-10.34, 7.95-8.84 and 93.1-119.6 far Cd, Cu, Pb and Zn, respectively. These results indicate that Kuala Pontian samples accumulated higher concentrations of Cu (in remaining soft tissue and mantle) and Zn (in remaining soft tissue, mantle and muscle) compared to those in Nenasi while Cd and Pb showed no significant difference (P> 0.05) between the two sample sites. Since there were no observable anthropogenicinputs ar activities at the two sampling sites, the variation of metal concentrations accumulated in the soft tissues could be mostly attributable to the significant difference in size (shell length, and shell width) and salinity of the two sites. The other environmentalfactars could also cause differences in the metal bioavailabilities in the coastal waters that were reflected in different concentrations accumulated in the different soft tissues of the mussels.
The decade of the dendritic NMDA spike

In the field of cortical cellular physiology, much effort has been invested in understanding thick apical dendrites of pyramidal neurons and the regenerative sodium and calcium spikes that take place in the apical trunk. Here we focus on thin dendrites of pyramidal cells (basal, oblique, and tuft dendrites), and we discuss one relatively novel form of an electrical signal (“NMDA spike”) that is specific for these branches. Basal, oblique, and apical tuft dendrites receive a high density of glutamatergic synaptic contacts. Synchronous activation of 10–50 neighboring glutamatergic synapses triggers a local dendritic regenerative potential, NMDA spike/plateau, which is characterized by significant local amplitude (40–50 mV) and an extraordinary duration (up to several hundred milliseconds). The NMDA plateau potential, when it is initiated in an apical tuft dendrite, is able to maintain a good portion of that tuft in a sustained depolarized state. However, if NMDA‐dominated plateau potentials originate in proximal segments of basal dendrites, they regularly bring the neuronal cell body into a sustained depolarized state, which resembles a cortical Up state. At each dendritic initiation site (basal, oblique, and tuft) an NMDA spike creates favorable conditions for causal interactions of active synaptic inputs, including the spatial or temporal binding of information, as well as processes of short‐term and long‐term synaptic modifications (e.g., long‐term potentiation or long‐term depression). Because of their strong amplitudes and durations, local dendritic NMDA spikes make up the cellular substrate for multisite independent subunit computations that enrich the computational power and repertoire of cortical pyramidal cells. We propose that NMDA spikes are likely to play significant roles in cortical information processing in awake animals (spatiotemporal binding, working memory) and during slow‐wave sleep (neuronal Up states, consolidation of memories). © 2010 Wiley‐Liss, Inc.
Depressive symptoms, health behaviors, and risk of cardiovascular events in patients with coronary heart disease.

CONTEXT Depressive symptoms predict adverse cardiovascular outcomes in patients with coronary heart disease, but the mechanisms responsible for this association are unknown. OBJECTIVE To determine why depressive symptoms are associated with an increased risk of cardiovascular events. DESIGN AND PARTICIPANTS The Heart and Soul Study is a prospective cohort study of 1017 outpatients with stable coronary heart disease followed up for a mean (SD) of 4.8 (1.4) years. SETTING Participants were recruited between September 11, 2000, and December 20, 2002, from 12 outpatient clinics in the San Francisco Bay Area and were followed up to January 12, 2008. MAIN OUTCOME MEASURES Baseline depressive symptoms were assessed using the Patient Health Questionnaire (PHQ). We used proportional hazards models to evaluate the extent to which the association of depressive symptoms with subsequent cardiovascular events (heart failure, myocardial infarction, stroke, transient ischemic attack, or death) was explained by baseline disease severity and potential biological or behavioral mediators. RESULTS A total of 341 cardiovascular events occurred during 4876 person-years of follow-up. The age-adjusted annual rate of cardiovascular events was 10.0% among the 199 participants with depressive symptoms (PHQ score > or = 10) and 6.7% among the 818 participants without depressive symptoms (hazard ratio [HR], 1.50; 95% confidence interval, [CI], 1.16-1.95; P = .002). After adjustment for comorbid conditions and disease severity, depressive symptoms were associated with a 31% higher rate of cardiovascular events (HR, 1.31; 95% CI, 1.00-1.71; P = .04). Additional adjustment for potential biological mediators attenuated this association (HR, 1.24; 95% CI, 0.94-1.63; P = .12). After further adjustment for potential behavioral mediators, including physical inactivity, there was no significant association (HR, 1.05; 95% CI, 0.79-1.40; P = .75). CONCLUSION In this sample of outpatients with coronary heart disease, the association between depressive symptoms and adverse cardiovascular events was largely explained by behavioral factors, particularly physical inactivity.
Bivariate Weibull Distributions Derived From Copula Functions In The Presence Of Cure Fraction And Censored Data

In this paper we introduce bivariate Weibull distributions derived from copula functions in presence of cure fraction, censored data and covariates. Two copula functions are explored: the FGM (Farlie- Gumbel Morgenstern) copula and the Gumbel copula. Inferences for the proposed models are obtained under the Bayesian approach, using standard MCMC (Markov Chain Monte Carlo) methods. An illustration of the proposed methodology is given considering a medical data set.