Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigations of dipole localization accuracy in MEG using the bootstrap

We describe the use of the nonparametric bootstrap to investigate the accuracy of current dipole localization from magnetoencephalography (MEG) studies of event related neural activity. The bootstrap is well suited to analysis of event-related MEG data since the experiments are often repeated 100 or more times and averaged to achieve acceptable SNRs. The set of repetitions or "epochs" can be viewed as a set of i.i. d. realizations of the brain's response to the experiment. Sampling from these epochs and averaging can generate bootstrap resamples. In this study we applied the bootstrap resampling technique to MEG data from a somatotopic experiment. Four fingers of the right and left hand of a healthy subject were electrically stimulated, and about 400 trials per stimulation were recorded and averaged in order to measure the somatotopic mapping of the fingers in the SI area of the brain. Based on the single trial recordings for each finger, we performed 5000 bootstrap resamples. We reconstructed dipoles from these resampled averages, using the RAP-MUSIC source localization algorithm. To find the correspondences between multiple sources in each resample dipoles with similar time-series and forward fields were assumed to represent the same source. These dipoles were then clustered using a GMM (Gaussian mixture model) clustering algorithm, using their combined normalized time-series and topography as feature vectors. The mean and standard deviation of the dipole position and the dipole time-series in each cluster were computed to provide estimates of the accuracy of the reconstructed source locations and time-series.
Growth Factor Receptor Surface by Transactivation of the Epidermal Innate Immunity at the Airway Epithelial The Antimicrobial Peptide LL-37 Activates

Antimicrobial peptides produced by epithelial cells and neutrophils represent essential elements of innate immunity, and include the defensin and cathelicidin family of antimicrobial polypeptides. The human cathelicidin cationic antimicrobial protein-18 is an antimicrobial peptide precursor predominantly expressed in neutrophils, and its active peptide LL-37 is released from the precursor through the action of neutrophil serine proteinases. LL-37 has been shown to display antimicrobial activity against a broad spectrum of microorganisms, to neutralize LPS bioactivity, and to chemoattract neutrophils, monocytes, mast cells, and T cells. In this study we show that LL-37 activates airway epithelial cells as demonstrated by activation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) and increased release of IL-8. Epithelial cell activation was inhibited by the MAPK/ERK kinase (MEK) inhibitors PD98059 and U0126, by the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor AG1478, by blocking anti-EGFR and anti-EGFR-ligand Abs, and by the metalloproteinase inhibitor GM6001. These data suggest that LL-37 transactivates the EGFR via metalloproteinase-mediated cleavage of membrane-anchored EGFR-ligands. LL-37 may thus constitute one of the mediators by which neutrophils regulate epithelial cell activity in the lung. The Journal of Immunology, 2003, 171: 6690–6696.
Simple Cystatin C Formula Compared to Sophisticated CKD‐EPI Formulas for Estimation of Glomerular Filtration Rate in the Elderly

Despite the fact that the serum creatinine level is notoriously unreliable for the estimation of glomerular filtration rate (GFR) in the elderly, the serum creatinine concentration and serum creatinine‐based formulas, such as the Modification of Diet in Renal Disease study equation (MDRD) are the most commonly used markers to estimate GFR. Recently, serum cystatin C‐based formulas, the newer creatinine formula (the Chronic Kidney Disease Epidemiology Collaboration formula (CKD‐EPI creatinine formula), and an equation that uses both serum creatinine and cystatin C (CKD‐EPI creatinine and cystatin formula) were proposed as new GFR markers. The aim of our study was to compare the MDRD formula, CKD‐EPI creatinine formula, CKD‐EPI creatinine and cystatin formula, and simple cystatin C formula (100/serum cystatin C) against 51Cr‐EDTA clearance in the elderly. A total of 317 adult Caucasian patients aged >65 years were enrolled. In each patient, 51Cr‐EDTA clearance, serum creatinine, and serum cystatin C were determined, and the GFR was calculated using the MDRD formula, CKD‐EPI formulas, and simple cystatin C formula. Statistically significant correlations between 51Cr‐EDTA clearance and all formulas were found. In the receiver operating characteristic (ROC) curve analysis with a cut‐off of GFR 45 mL/min/1.73 m2, a higher diagnostic accuracy was achieved with the equation that uses both serum creatinine and cystatin C (CKD‐EPI creatinine and cystatin formula) than the MDRD formula (P < 0.013) or CKD‐EPI creatinine formula (P < 0.01), but it was not higher than that achieved for the simple cystatin C formula (P = 0.335). Bland and Altman analysis for the same cut‐off value showed that the creatinine formulas underestimated and the simple cystatin C formula overestimated measured GFR. All equations lacked precision. The accuracy within 30% of estimated 51Cr‐EDTA clearance values differ according to the stage of CKD. Analysis of the ability to correctly predict GFR below and above 45 mL/min/1.73 m2 showed a high prediction for all formulas. Our results indicate that the simple cystatin C formula, which requires just one variable (serum cystatin C concentration), is a reliable marker of GFR in the elderly and comparable to the creatinine formulas, including the CKD‐EPI formulas.
2006-2015 Research Summary of Demand Response Potential in California Industry, Agriculture, and Water Sectors:

Author(s): Aghajanzadeh, Arian; McKane, Aimee; Wray, Craig; Therkelsen, Peter | Abstract: In 2006, the Industrial Demand Response Team of the Demand Response Research Center (DRRC) started its research into the potential for Demand Response (DR) and Automated Demand Response (Auto-DR) in the Industrial, Agricultural, and Water (IAW) sectors. DR involves electricity end-use customers reducing their electricity usage over a given time period (shed), or shifting that usage to another time period (shift), in response to a price signal, a financial incentive, an environmental condition, or a reliability signal. Two approaches to DR are manual DR programs and Auto-DR programs. California industry currently participates primarily in manual DR programs (e.g., demand bidding, base interruptible programs). However, Auto DR, in which loads are shed automatically in response to grid control signals (unless the customer opts-out), has the potential to be used for ancillary services, which are growing in importance due to the load uncertainty and variability caused by the integration of large shares of renewables. The California Independent System Operator (CAISO) is interested in “hardening” demand response across participating sectors through the use of Auto DR. While there have been notable exceptions in some industrial subsectors (e.g., industrial gases, refrigerated warehouses), only a small number of industrial sites are participating in Auto-DR. The industrial sector provides opportunities for large sheds or shifts from relatively few facilities. Through years of industrial DR studies, Lawrence Berkeley National Laboratory (LBNL) conducted research about wastewater treatment, agricultural irrigation, refrigerated warehouse, data center, cement, and dairy processing industries. This research identified several opportunities and barriers for achieving Auto-DR in the industries of interest. The outcomes of the past decade of industrial DR research are summarized in this report.
Intermittent Bolus Feeding Has a Greater Stimulatory Effect on Protein Synthesis in Skeletal Muscle than Continuous Feeding in Neonatal Pigs

Feeding by orogastric tube, using either continuous or intermittent bolus delivery, is common for infants for whom normal feeding is contraindicated. To determine the impact of different feeding modalities on muscle protein anabolism, neonatal pigs (5–7 day old) received a balanced enteral formula either by intermittent bolus (B, n=7) every four hours or were continuously fed (C, n=5). Fractional protein synthesis rates and translational control mechanisms in skeletal muscle were examined at 0, 24 and 25.5 hours. Plasma amino acid and insulin levels were modestly increased in the continuously fed group and in the bolus group mimicked the pulsatile pattern of meal feeding. Feeding increased protein synthesis by 53% in the continuous group, by 63% in the bolus group before a meal, and by 126 % after a bolus feed. The activation of eukaryotic initiation factor (eIF) 4E binding protein (4EBP1), rp S6 kinase 1 (S6K1), protein kinase B (PKB), dissociation of 4EBP1‐eIF4E complex, and formation of the active eIF4E‐eIF4G complex were unaffected by continuous feeding but were increased more than 10 fold after a bolus meal. These results suggest that intermittent bolus feeding increases muscle protein synthesis to a greater extent than continuous feeding by stimulating translation initiation. (Supported by NIH grants AR‐44474 and AR‐51563 and USDA/ARS 6250510000‐33).
Paleomagnetic evidence for the emplacement mechanism of an enigmatic boulder accumulation on a coastal cliff top in New South Wales: implications for the Australian Megatsunami Hypothesis

ABSTRACT Paleomagnetic sampling and measurement of a boulder accumulation on Little Beecroft Head on the Illawarra coastline of New South Wales was undertaken to evaluate potential emplacement mechanisms. This deposit is of central importance in the Australian Megatsunami Hypothesis (AMH) debate, but to date, there has been no unequivocal determination of its provenance. The most likely emplacement mechanisms are by slow collapse during denudation of overlying strata, storm wave overwash or a combination of these. Characteristic Remanent Magnetisation (ChRM) directions were obtained from 15 individual boulders and the in situ bedrock platform on which they currently rest. The in situ Permian bedrock has a normal polarity mean ChRM direction of D/I = 1.6°/–66.7° (α95 = 5.2°; k = 33.9) that is statistically indistinguishable from the Present Earth Field direction at the site. The magnetisation is most likely due to Cenozoic/recent weathering, which is common in surficial rocks throughout the Sydney Basin. ChRM directions for the boulders are stable but scattered, although not random, and the mean boulder direction is indistinguishable in geographic (i.e. current in situ) coordinates, at the 5% significance level, from the mean direction of the in situ bedrock. Further statistical tests confirm that the scatter in the mean directions of the boulders and the in situ bedrock is different, at the 5% significance level, with the boulder mean being more scattered. At an individual boulder level, some blocks have mean ChRM directions that are statistically indistinguishable from the mean in situ rock ChRM direction, whereas others are distinguishable at the 5% significance level. These results indicate that the boulders were magnetised prior to emplacement but were not moved far from their original positions during emplacement. The emplacement age is constrained to the last ca 780 000 years. These observations strongly support the hypothesis that the Little Beecroft Head boulder deposit was emplaced by a non-catastrophic mechanism, namely slow collapse during denudation of pre-existing cliff material or overtopping from severe storms, which occur regularly on the east coast of New South Wales. Even if a catastrophic wave were responsible, the results constrain the age of that event to be older than 780 000 years. Therefore, the results presented here are not supportive of the AMH as it currently stands. Further paleomagnetic work, on similar deposits along the Illawarra coastline and from elsewhere in Australia, is needed to evaluate the interpretations presented here.
Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana

Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations.
Brain Activity Investigation by EEG Processing: Wavelet Analysis, Kurtosis and Renyi's Entropy for Artifact Detection

Electroencephalographic (EEG) recordings are employed in order to investigate the brain activity in neuro pathological subjects. Unfortunately EEG are often contaminated by the artifacts, signals that have non-cerebral origin and that might mimic cognitive or pathologic activity and therefore distort the analysis of EEG. In this paper we propose a multiresolution analysis, based on EEG wavelet processing, to extract the cerebral EEG rhythms. We also present a method based on Renyi's entropy and kurtosis to automatically identify the Wavelet components affected by artifacts. Finally, we discuss as the joint use of wavelet analysis, kurtosis and Renyi's entropy allows for a deeper investigation of the brain activity and we discuss the capability of this technique to become an efficient preprocessing step to optimize artifact rejection from EEG. This is the first technique that exploits the peculiarities of EEG to optimize EEG artifact detection.
Predictive Approach for User Long-Term Needs in Content-Based Image Suggestion

In this paper, we formalize content-based image suggestion (CBIS) as a Bayesian prediction problem. In CBIS, users provide the rating of images according to both their long-term needs and the contextual situation, such as time and place, to which they belong. Therefore, a CBIS model is defined to fit the distribution of the data in order to predict relevant images for a given user. Generally, CBIS becomes challenging when only a small amount of data is available such as in the case of “new users” and “new images. ” The Bayesian predictive approach is an effective solution to such a problem. In addition, this approach offers efficient means to select highly rated and diversified suggestions in conformance with theories in consumer psychology. Experiments on a real data set show the merits of our approach in terms of image suggestion accuracy and efficiency.
Anuria, Omphalocele, and Perinatal Lethality in Mice Lacking the Cd34-Related Protein Podocalyxin

Podocalyxin is a CD34-related sialomucin that is expressed at high levels by podocytes, and also by mesothelial cells, vascular endothelia, platelets, and hematopoietic stem cells. To elucidate the function of podocalyxin, we generated podocalyxin-deficient (podxl −/−) mice by homologous recombination. Null mice exhibit profound defects in kidney development and die within 24 hours of birth with anuric renal failure. Although podocytes are present in the glomeruli of the podxl −/− mice, they fail to form foot processes and slit diaphragms and instead exhibit cell–cell junctional complexes (tight and adherens junctions). The corresponding reduction in permeable, glomerular filtration surface area presumably leads to the observed block in urine production. In addition, podxl −/− mice frequently display herniation of the gut (omphalocele), suggesting that podocalyxin may be required for retraction of the gut from the umbilical cord during development. Hematopoietic and vascular endothelial cells develop normally in the podocalyxin-deficient mice, possibly through functional compensation by other sialomucins (such as CD34). Our results provide the first example of an essential role for a sialomucin in development and suggest that defects in podocalyxin could play a role in podocyte dysfunction in renal failure and omphalocele in humans.
Enhanced SDRSAC Algorithm for Robust Registration on Non-Cooperative Targets

Efficiently registering point clouds of spatial targets or defunct debris is a formidable challenge. SDRSAC is a robust point cloud registration method based on correspondence-free approaches. In this paper, we propose an enhanced SDRSAC algorithm for rigid alignment of non-cooperative space targets. Our improvements to SDRSAC are twofold. First, we incorporate the difference in surface normal angles into the penalty matrix, allowing it to account for both distance and angle invariance under rigid transformations. This significantly reduces the possibility of ambiguous registrations in spatial targets. Second, we compute the planarity of local surfaces using eigenvalues from the neighborhood covariance matrix, focusing random sampling on flatter surface points. This approach lessens the impact of noise and outliers in real point clouds. Experimental results demonstrate that our method outperforms others in terms of registration accuracy and speed on non-cooperative space targets.
Collaborative Coalescing of Redundant Memory Access for GPU System

GPU-based computing serves as the primary solution driving the performance of HPC systems. However, modern GPU systems encounter performance bottlenecks resulting from heavy memory access traffic and insufficient NoC bandwidth. In this work, we propose a collaborative coalescing mechanism aimed at eliminating redundant memory access and boosting GPU system performance. To achieve this, we design a coalescing unit for each memory partition, effectively merging requests from both inter-cluster and intra-cluster SMs. Additionally, we introduce a hierarchical multicast module to replicate and distribute the coalesced reply messages to multiple destination SMs. Experimental results show that our method achieves 20.6% improvement on performance and 27.1% reduction on NoC traffic over the baseline.
Epistasis between mutations is host-dependent for an RNA virus

How, and to what extent, does the environment influence the way mutations interact? Do environmental changes affect both the sign and the magnitude of epistasis? Are there any correlations between environments in the variability, sign or magnitude of epistasis? Very few studies have tackled these questions. Here, we addressed them in the context of viral emergence. Most emerging viruses are RNA viruses with small genomes, overlapping reading frames and multifunctional proteins for which epistasis is abundant. Understanding the effect of host species in the sign and magnitude of epistasis will provide insights into the evolutionary ecology of infectious diseases and the predictability of viral emergence.
PRESS: Persistence Relaxation for Efficient and Secure Data Sanitization on Zoned Namespace Storage : (Invited Paper)

Recently, secure data deletion or data sanitization has been identified as a key technology of storage devices to securely delete obsolete sensitive data that are no longer used. However, secure data deletion requires extra management efforts on flash memory storage devices, due to the deferred reclamation of flash blocks in many flash translation layer schemes. The emerging zoned namespace storage further exacerbates the design complexity of secure data deletion, due to the much larger size of a zone than that of a flash block. Concerning the very long latency to reset an entire zone, once some data have been written into a zone, it is very difficult to securely delete them from the zone. To achieve efficient and secure data deletion on zoned namespace storage, we propose persistence relaxation for efficient and secure sanitization (PRESS), which considers the working principle of zones of zoned namespace storage and allows the fine-grained control of deferred data persistence. As a result, applications can efficiently delete their recently written data or make the data persistent for long-term storage. Our proposal, PRESS, is evaluated through a series of experimental studies, where the results are quite encouraging.
How Sharp Is the Cratonic Lithosphere‐Asthenosphere Transition?

Earth's cratonic mantle lithosphere is distinguished by high seismic wave velocities that extend to depths greater than 200 km, but recent studies disagree on the magnitude and depth extent of the velocity gradient at their lower boundary. Here we analyze and model the frequency dependence of Sp waves to constrain the lithosphere‐asthenosphere velocity gradient at long‐lived stations on cratons in North America, Africa, Australia, and Eurasia. Beneath 33 of 44 stations, negative velocity gradients at depths greater than 150 km are less than a 2–3% velocity drop distributed over more than 80 km. In these regions the base of the typical cratonic lithosphere is gradual enough to be explained by a thermal transition. Vertically sharper lithosphere‐asthenosphere transitions are permitted beneath 11 stations, but these zones are spatially intermittent. These results demonstrate that lithosphere‐asthenosphere viscosity contrasts and coupling fundamentally differ between cratons and younger continents.
National Prevalence and Trends of HIV Transmitted Drug Resistance in Mexico

Background Transmitted drug resistance (TDR) remains an important concern for the management of HIV infection, especially in countries that have recently scaled-up antiretroviral treatment (ART) access. Methodology/Principal Findings We designed a study to assess HIV diversity and transmitted drug resistance (TDR) prevalence and trends in Mexico. 1655 ART-naïve patients from 12 Mexican states were enrolled from 2005 to 2010. TDR was assessed from plasma HIV pol sequences using Stanford scores and the WHO TDR surveillance mutation list. TDR prevalence fluctuations over back-projected dates of infection were tested. HIV subtype B was highly prevalent in Mexico (99.9%). TDR prevalence (Stanford score>15) in the country for the study period was 7.4% (95% CI, 6.2∶8.8) and 6.8% (95% CI, 5.7∶8.2) based on the WHO TDR surveillance mutation list. NRTI TDR was the highest (4.2%), followed by NNRTI (2.5%) and PI (1.7%) TDR. Increasing trends for NNRTI (p = 0.0456) and PI (p = 0.0061) major TDR mutations were observed at the national level. Clustering of viruses containing minor TDR mutations was observed with some apparent transmission pairs and geographical effects. Conclusions TDR prevalence in Mexico remains at the intermediate level and is slightly lower than that observed in industrialized countries. Whether regional variations in TDR trends are associated with differences in antiretroviral drug usage/ART efficacy or with local features of viral evolution remains to be further addressed.