Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of insulin infusion on glucose homeostasis and glucose metabolism in rainbow trout fed a high-carbohydrate diet

SUMMARY The origin for the poor glucose utilization in carnivorous fish species fed high carbohydrate diets remains under debate. In the present study, we have fed rainbow trout a diet containing 30% carbohydrate for 1 or 5 days. In both cases, fish were implanted with mini-osmotic pumps releasing 0.7 i.u. kg–1 day–1 bovine insulin, and mRNA transcripts and the protein phosphorylation status of proteins controlling glycemia and glucose-related metabolism were studied in fish killed 6 h after the last meal. We demonstrate that when the exposure occurs over a short term (30 h), insulin exerts beneficial actions on trout glucose homeostasis, including a lowered glycemia and increased hepatic lipogenic and glycogenic potentials. However, when trout were fed for 5 days, these beneficial actions of insulin infusion were no longer observed. Thus, the increased lipogenic potential observed after one single meal was not present, and this together with the increased glycogenesis and the decreased glucose exported to the blood from the liver explains the lack of hypoglycemic action of insulin. The fact that insulin improved glucose homeostasis when administrated over a short time period implies that endogenous insulin secretion is inadequate in trout to deal with this amount of dietary carbohydrates. Moreover, the fact that a longer exposure to insulin resulted in a reduced response indicates that the rainbow trout is sensitive to insulin, re-enforcing the hypothesis that the hyperglycemia observed following a high carbohydrate meal is an insulin secretion issue rather an insulin action issue.
Evaluating Probabilistic Matrix Factorization on Netflix Dataset

Collaborative Filtering attempts to make automatic taste recommendations by examing a large number of taste information. Methods for achieving Collaborative Filtering can be broadly categorized into model based, and memory based techniques. In this project, we review and implement three variants of Probabilistic Matrix Factorization, a model based Collaborative Filtering algorithm. We compare the performance of Probabilistic Matrix Factorization to a memory based Collaborative Filtering algorithm, the K nearest neighbor algorithm. The model performance is compared using three datasets derived from the full NetFlix movie dataset, each with varying data sparsity. Specifically, the root mean square error measure (RMSE) is used as the metric to compare the relative performance between the different CF algorithms. In our performance evaluation, we discovered when the data sparsity is sufficiently low, Probabilistic Matrix Factorization out performs K nearest neighbor, achieving RMSE of as low as 0.83. However, when the data sparsity is high, KNN yields marginally better performance, obtaining RMSE score of 1.0453 on the most sparse dataset, while the regular Probabilistic Matrix Factorization scored a 1.0771 on the same dataset
An Unsupervised Model of Orthographic Variation for Historical Document Transcription

Historical documents frequently exhibit extensive orthographic variation, including ar-chaic spellings and obsolete shorthand. OCR tools typically seek to produce so-called diplo-matic transcriptions that preserve these variants, but many end tasks require transcriptions with normalized orthography. In this paper, we present a novel joint transcription model that learns, unsupervised, a probabilistic mapping between modern orthography and that used in the document. Our system thus produces dual diplomatic and normalized transcriptions simultaneously, and achieves a 35% relative error reduction over a state-of-the-art OCR model on diplomatic transcription, and a 46% reduction on normalized transcription.
Glycosylation catalyzed by lysyl hydroxylase 3 is essential for basement membranes

Lysyl hydroxylase 3 (LH3) is a multifunctional enzyme possessing lysyl hydroxylase (LH), hydroxylysyl galactosyltransferase (GT) and galactosylhydroxylysyl glucosyltransferase (GGT) activities in vitro. To investigate the in vivo importance of LH3-catalyzed lysine hydroxylation and hydroxylysine-linked glycosylations, three different LH3-manipulated mouse lines were generated. Mice with a mutation that blocked only the LH activity of LH3 developed normally, but showed defects in the structure of the basement membrane and in collagen fibril organization in newborn skin and lung. Analysis of a hypomorphic LH3 mouse line with the same mutation, however, demonstrated that the reduction of the GGT activity of LH3 disrupts the localization of type IV collagen, and thus the formation of basement membranes during mouse embryogenesis leading to lethality at embryonic day (E) 9.5-14.5. Strikingly, survival of hypomorphic embryos and the formation of the basement membrane were directly correlated with the level of GGT activity. In addition, an LH3-knockout mouse lacked GGT activity leading to lethality at E9.5. The results confirm that LH3 has LH and GGT activities in vivo, LH3 is the main molecule responsible for GGT activity and that the GGT activity, not the LH activity of LH3, is essential for the formation of the basement membrane. Together our results demonstrate for the first time the importance of hydroxylysine-linked glycosylation for collagens.
Inducible and neuron‐specific gene expression in the adult mouse brain with the rtTA2S‐M2 system

To achieve inducible and reversible gene expression in the adult mouse brain, we exploited an improved version of the tetracycline‐controlled transactivator‐based system (rtTA2S‐M2, rtTA2 hereafter) and combined it with the forebrain‐specific CaMKIIα promoter. Several independent lines of transgenic mice carrying the CaMKIIα promoter‐rtTA2 gene were generated and examined for anatomical profile, doxycycline (dox)‐dependence, time course, and reversibility of gene expression using several lacZ reporter lines. In two independent rtTA2‐expressing lines, dox‐treatment in the diet induced lacZ reporter expression in neurons of several forebrain structures including cortex, striatum, hippocampus, amygdala, and olfactory bulb. Gene expression was dose‐dependent and was fully reversible. Further, a similar pattern of expression was obtained in three independent reporter lines, indicating the consistency of gene expression. Transgene expression could also be activated in the developing brain (P0) by dox‐treatment of gestating females. These new rtTA2‐expressing mice allowing inducible and reversible gene expression in the adult or developing forebrain represent useful models for future genetic studies of brain functions. genesis 43:205–212, 2005. © 2005 Wiley‐Liss, Inc.
Planetary Radii across Five Orders of Magnitude in Mass and Stellar Insolation: Application to Transits

To aid in the physical interpretation of planetary radii constrained through observations of transiting planets, or eventually direct detections, we compute model radii of pure hydrogen-helium, water, rock, and iron planets, along with various mixtures. Masses ranging from 0.01 Earth masses to 10 Jupiter masses at orbital distances of 0.02-10 AU are considered. For hydrogen-helium rich planets, our models are the first to couple planetary evolution to stellar irradiation over a wide range of orbital separations (0.02-10 AU) through a nongray radiative-convective equilibrium atmosphere model. Stellar irradiation retards the contraction of giant planets, but its effect is not a simple function of the irradiation level: a planet at 1 AU contracts as slowly as a planet at 0.1 AU. We confirm the assertion of Guillot that very old giant planets under modest stellar irradiation (like that received by Jupiter and Saturn) develop isothermal atmospheric radiative zones once the planet's intrinsic flux drops to a small fraction of the incident flux. For hydrogen-helium planets, we consider cores up to 90% of the total planet mass, comparable to those of Uranus and Neptune. If "hot Neptunes" have maintained their original masses and are not remnants of more massive planets, radii of ~0.30-0.45 RJ are expected. Water planets are ~40%-50% larger than rocky planets, independent of mass. Finally, we provide tables of planetary radii at various ages and compositions, and for ice-rock-iron planets we fit our results to analytic functions, which will allow for quick composition estimates, given masses and radii, or mass estimates, given only planetary radii. These results will assist in the interpretation of observations for both the current transiting planet surveys as well as upcoming space missions, including COROT and Kepler.
IGF-1 Reduces Inflammatory Responses, Suppresses Oxidative Stress, and Decreases Atherosclerosis Progression in ApoE-Deficient Mice

Objective—Whereas growth factors, via their ability to stimulate vascular smooth muscle cell (VSMC) proliferation and migration, have been thought to play a permissive role in atherosclerosis initiation and progression, the role of insulin-like growth factor-1 (IGF-1) is unknown. Here we report for the first time that IGF-1 infusion decreased atherosclerotic plaque progression in ApoE-deficient mice on a Western diet. Methods and Results—ApoE-null mice (8 weeks) were infused with vehicle or recombinant human IGF-1 and fed a high-fat diet for 12 weeks. Analysis of aortic sinuses revealed that IGF-1 infusion decreased atherosclerotic plaque progression and macrophage infiltration into lesions. Furthermore, IGF-1 decreased vascular expression of the proinflammatory cytokines interleukin-6 and tumor necrosis factor-α, reduced aortic superoxide formation and urinary 8-isoprostane levels, and increased aortic pAkt and eNOS expression and circulating endothelial progenitor cells, consistent with an antiinflammatory, antioxidant, and prorepair effect on the vasculature. Conclusions—Our data indicate that an increase in circulating IGF-1 reduces vascular inflammatory responses, systemic and vascular oxidant stress and decreases atherosclerotic plaque progression. These findings have major implications for the treatment of atherosclerosis.
Assessing the Contribution of the Oscillatory Potentials to the Genesis of the Photopic ERG with the Discrete Wavelet Transform

The electroretinogram (ERG) is composed of slow (i.e., a-, b-waves) and fast (i.e., oscillatory potentials: OPs) components. OPs have been shown to be preferably affected in some diseases (such as diabetic retinopathy), while the a- and b-waves remain relatively intact. The purpose of this study was to determine the contribution of OPs to the building of the ERG and to examine whether a signal mostly composed of OPs could also exist. DWT analyses were performed on photopic ERGs (flash intensities: −2.23 to 2.64 log cd·s·m−2 in 21 steps) obtained from normal subjects (n = 40) and patients (n = 21) affected with a retinopathy. In controls, the %OP value (i.e., OPs energy/ERG energy) is stimulus- and amplitude-independent (range: 56.6–61.6%; CV = 6.3%). In contrast, the %OPs measured from the ERGs of our patients varied significantly more (range: 35.4%–89.2%; p < 0.05) depending on the pathology, some presenting with ERGs that are almost solely composed of OPs. In conclusion, patients may present with a wide range of %OP values. Findings herein also support the hypothesis that, in certain conditions, the photopic ERG can be mostly composed of high-frequency components.
Parameter optimization for a grating-based phase contrast x-ray system

Differential Phase Contrast Imaging (DPCI) has the potential to vastly increase soft tissue contrast. DPCI requires spatial and temporal coherence as generated by a synchrotron or a micro-focus X-ray source; however, recent research demonstrates DPCI can be implemented using a conventional X-ray source with three transmission gratings (Pfeiffer et al., Nature 2006). This paper describes the optimization of the essential system parameters (system size, delivered dose, spatial resolution) of this implementation from a theoretical perspective. The optimization of these parameters is an essential step in practical application of DPCI. We conclude that the minimum size of the system is approximately 700 mm, the minimum resolution is 100 um, and the dose is 1/1000 that of conventional absorption CT.
On-line automatic detection of driver drowsiness using a single electroencephalographic channel

In this paper, an on-line drowsiness detection algorithm using a single electroencephalographic (EEG) channel is presented. This algorithm is based on a means comparison test to detect changes of the alpha relative power ([8–12]Hz band). The main advantage of the method proposed is that the detection threshold is completely independent of drivers and does not need to be tuned for each person. This algorithm, which works on-line, has been tested on a huge dataset representing 60 hours of driving and give good results with nearly 85% of good detections and 20% of false alarms.
Discriminating the early stages of Sirex noctilio infestation using classification tree ensembles and shortwave infrared bands

The woodwasp Sirex noctilio is causing extensive damage to Pinus patula trees in the summer rainfall areas of South Africa. The ability to remotely detect S. noctilio infestation remains crucial for monitoring purposes and for the effective deployment of suppression activities. In this study, we evaluated whether random forest and boosting trees can accurately discriminate between healthy trees and the early stages of S. noctilio infestation using reflectance measurements in the shortwave infrared (SWIR). Three variable selection methods, namely, a filter, the random forest out-of-bag samples and a wrapper algorithm, were used to select the smallest subset of SWIR bands. The results show that random forest produces better classification results than the competing boosting trees for all three variable selection methods, even when noise is introduced into the SWIR bands and class labels. The ability of the bands centred at 1990, 2009, 2028, 2047 and 2065 nm to discriminate between healthy trees and the early stages of infestation could be explained due to the rapid physiological changes that occur as a result of the toxic mucus and a fungus that S. noctilio injects into the tree. Overall, the results are encouraging and show that there is a link between the selected SWIR bands and existing physiological knowledge, thereby improving the chances of detecting the early stages of S. noctilio infestation at a canopy or landscape level.
Dynamic analysis of an ultra-lightweight sandwich structure for multiple applications

The paper presents the most important features of damping in the case of an ultra-lightweight sandwich structure starting from the dampings-, dynamic Young moduli- and Poisson ratio determination for every lamina. The structure's architecture is based on two twill weave carbon fabric/epoxy resin skins and an expanded polystyrene (EPS) core. At the dynamic analysis of fiber reinforced composite materials, a so called concept of complex moduli will be used in which the elastic constants will be replaced through their viscoelastic correspondences. The mechanical modeling is based on the correspondence principle of linear viscoelasticity theory. Testing scheme allows specimens to be put in one side fixed connection and subjected at bending oscillations in normal conditions: 23°C, 50% relative air humidity. Dampings, rigidities and compliances of the sandwich structure are computed.
Diabetic ketoacidosis Predictors of outcome in a pediatric intensive care unit of a developing country*

Objectives: To study the outcome and predictors of mortality in children with diabetic ketoacidosis. Design: Retrospective case series. Setting: Pediatric intensive care unit of an urban multiple-specialty teaching and referral hospital in north India. Patients: Sixty-eight patients with diabetic ketoacidosis treated between 1993 and 2000. Interventions: Data were retrieved from case records with respect to patients’ age; clinical features; osmolality at admission; blood glucose, serum potassium, and arterial pH at admission, 6 hrs, and 24 hrs; complications during the course of hospital stay; treatment; and outcome in terms of survival or death. Survivors and nonsurvivors were compared to determine the predictors of mortality. Measurements and Main Results: The mean (sd) age of the study population was 6.9 (3.5) yrs (range, 0.5–12 yrs). Impaired consciousness (n = 45; 66%), rapid breathing (n = 41; 60%), and vomiting (n = 35; 51.4%) were common presenting symptoms. Thirty-two (50%) patients had clinically evident dehydration. Precipitating events identified were new-onset diabetes with sepsis (37%), new-onset diabetes alone (31%), insulin omission (15%), and infection with insulin omission (7%). The mean (sd) blood glucose, osmolality, and pH at admission were 473 (sd 184) mg/dL, 305 (sd 24) mOsm/L, and 7.08 (sd 0.1), respectively. Complications noted during treatment were hypokalemia (n = 28; 41%), hypoglycemia (n = 10; 15%), cerebral edema (n = 9; 13.2%), and pulmonary edema (n = 2; 3%). Nine (13.2%) patient died, with the causes of death being septic shock (n = 4), cerebral edema (n = 2), cerebral edema with pulmonary edema (n = 2), and hypokalemia with ventricular tachycardia (n = 1). Those who died were older, had higher osmolality and severe acidosis at admission, and had persistent hyperglycemia and acidosis at 6–12 hrs. On multiple logistic regression analysis, osmolality at admission was the most significant predictor of death. Conclusions: Two thirds of children with diabetic ketoacidosis in our series had new-onset diabetes, and 13.2% died. Serum osmolality at admission was the most important predictor of death.
An Efficient VMIMO Scheduling Scheme for Wireless Sensor Networks

This paper gives an efficient VMIMO scheduling scheme for wireless sensor networks(WSNs) with a node selection algorithm. Scheduling communication scheme with feedback channel is proposed in this paper. Using the feedback channel, channel state information (CSI) could be return to transmitting cluster. Then the “better” node could be selected to participate in cooperation. Simulation results show the efficient of the proposed Scheme in energy saving.
A Reduction from DLP to PDL

We present a reduction from a new logic extending van der Meyden's dynamic logic of permission (DLP) into propositional dynamic logic (PDL), providing a 2EXPTIME decision procedure and showing that all the machinery for PDL can be reused for reasoning about dynamic policies. As a side-effect, we establish that DLP is EXPTIME-complete. The logic we introduce extends the logic DLP so that the policy set can be updated depending on its current value and such an update corresponds to add/delete transitions in the model, showing similarities with van Benthem's sabotage modal logic.
Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease

Microbial community structure on coral reefs is strongly influenced by coral–algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease.
Insights from the Inside: A View of Botnet Management from Infiltration

Recent work has leveraged botnet infiltration techniques to track the activities of bots over time, particularly with regard to spam campaigns. Building on our previous success in reverse-engineering C&C protocols, we have conducted a 4-month infiltration of the MegaD botnet, beginning in October 2009. Our infiltration provides us with constant feeds on MegaD's complex and evolving C&C architecture as well as its spam operations, and provides an opportunity to analyze the botmasters' operations. In particular, we collect significant evidence on the MegaD infrastructure being managed by multiple botmasters. Further, FireEye's attempt to shutdown MegaD on Nov. 6, 2009, which occurred during our infiltration, allows us to gain an inside view on the takedown and how MegaD not only survived it but bounced back with significantly greater vigor. In addition, we present new techniques for mining information about botnet C&C architecture: "Google hacking" to dig out MegaD C&C servers and "milking" C&C servers to extract not only the spectrum of commands sent to bots but the C&C's overall structure. The resulting overall picture then gives us insight into MegaD's management structure, its complex and evolving C&C architecture, and its ability to withstand takedown.
Run-Time Thermal Management of Three-Dimensional Chip-Multiprocessors

Three-dimensional (3D) integration has the potential to improve the communication latency and integration density of chip-level multiprocessors (CMPs). However, the stacked high power density layers of 3D CMPs increase the importance and difficulty of thermal management. In this paper, we investigate the 3D CMP run-time thermal management problem and describe efficient management techniques. This work makes the following main contributions: (1) it identifies and describes the critical concepts required for optimal thermal management, namely the methods by which heterogeneity in both workload power characteristics and processor core thermal characteristics should be exploited and (2) it proposes an efficient, proactive, continuously-engaged hardware and operating system thermal management technique governed by optimal thermal management polices. The proposed technique is evaluated using multiprogrammed and multithreaded benchmarks in an integrated power, performance, and temperature full-system simulation environment. We find that proactive power–thermal budgeting allows a 30% improvement in instruction throughput compared to a state-of-the-art proactive thermal management approach that bases decisions only upon local information. The software components of the proposed thermal management technique have been implemented in the Linux 2.6. 8 kernel. This source code will be publicly released. The analysis and technique developed in this work provide a general solution for future 3D and 2D CMPs.