Miracle-dz/UniFAR-FTUs huggingface dataset:
Quasar Absorption Lines as a Function of Quasar Orientation Measures

We present high-resolution radio data at 3.5 and 20 cm from the VLA in the A configuration for 144 quasars with known C IV absorption-line properties. Using these measurements, we compare and contrast a number of quasar orientation indicators. These quantities are used to study the velocity distribution of C IV absorption lines as a function of quasar orientation measures. That there is an excess of narrow, high-velocity C IV absorbers in flat spectrum quasars as compared to steep spectrum quasars is confirmed. Orientation indicators that are not based upon spectral indices (e.g., RV and the core-to-lobe ratio) do not show the same effect. These seemingly contradictory results may be reconciled if the absorber distribution is not strictly a function of orientation, but rather a function of intrinsic radio properties that may or may not be good orientation indicators.
Targeting Matrilysin and Its Impact on Tumor Growth In vivo: The Potential Implications in Breast Cancer Therapy

Introduction: Matrilysin (MMP-7) is a metalloproteinase that is involved in the degradation of extracellular matrix, invasion, and tumor progression. The current study examined if targeting matrilysin using retroviral ribozyme transgenes may have an impact on breast cancer cells and may have clinical implications. Experimental Design: Retroviral hammerhead ribozyme transgenes were designed to specifically target human matrilysin mRNA. The breast cancer cell MDA-MB-231 was transfected with either a retroviral matrilysin transgene or a control retroviral transgene. Stably transfected cells were tested for their invasiveness and migratory properties in vitro. The cells were also used in creating a tumor model in athymic nude mice in which the growth of tumors and levels of matrilysin were assessed. In addition, levels of both protein and mRNA of matrilysin were investigated in a cohort of human breast tumors. Results: Expression of matrilysin in MDA-MB-231 was successfully eliminated by the retroviral hammerhead ribozyme transgene for matrilysin as revealed by reverse transcription-PCR. Matrilysin transgene–transduced cancer cells (MDA-MB-231ΔMatrilysin) exhibited a significantly lower degree of invasion (number of invading cells 16.0 ± 2.5) compared with wild type (MDA-MB-231WT; 26.2 ± 6.2, P < 0.05) or control transgene-transduced cancer cells (MDA-MB-231pRevTRE; 25.3 ± 4.2, P < 0.01). However, the rate of growth of the cells in vitro was not significantly affected. In the in vivo tumor model, MDA-MB-231ΔMatrilysin tumors, which had very low levels of immunoreactive matrilysin, grew at a significantly lower rate (0.24 ± 0.03 cm3, 4 weeks after inoculation) compared with the wild-type MDA-MB-231WT (1.46 ± 0.04 cm3) and MDA-MB-231pRevTRE (1.12 ± 1.0 cm3) tumors. In human breast tumors, breast cancer cells stained matrilysin at a significantly higher density, compared with normal mammary epithelium. The highest level of matrilysin was seen in high-grade tumors and that from patients with moderate and poor prognosis. Finally, high levels of matrilysin were significantly linked with a poor long-term survival (P = 0.0143). Conclusion: Matrilysin, which is aberrantly expressed in human breast tumors, can be effectively eliminated from breast cancer cells by way of hammerhead ribozyme transgene. Elimination of matrilysin is associated with low invasiveness and slow tumor growth. Taken together, the study suggests that targeting matrilysin may have important therapeutic implications.
Pharmacokinetics of oleandomycin administered alone and after oral ascorbic acid in three bird species.

The influence of ascorbic acid administration via drinking water at a dose of 15 mg/l over a period of 7 days on the pharmacokinetics of oleandomycin in chickens, musk ducks and Japanese quails was investigated. After ascorbic acid oleandomycin elimination, half-life was longer. Oleandomycin bioavailability in chickens and quails after per os application was increased with ascorbic acid. Interspecies differences in oleandomycin body disposition were observed. Lower elimination rate constants were obtained in the musk ducks in comparison with two other species. The volume of distribution (Vss) was larger in quails. In conclusion, ascorbic acid did not change oleandomycin disposition significantly in the treated birds.
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

Significance Tardigrades, also known as moss piglets or water bears, are renowned for their ability to withstand extreme environmental challenges. A recently published analysis of the genome of the tardigrade Hypsibius dujardini by Boothby et al. concluded that horizontal acquisition of genes from bacterial and other sources might be key to cryptobiosis in tardigrades. We independently sequenced the genome of H. dujardini and detected a low level of horizontal gene transfer. We show that the extensive horizontal transfer proposed by Boothby et al. was an artifact of a failure to eliminate contaminants from sequence data before assembly. Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976–15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1–2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
On improving trust-region variable projection algorithms for separable nonlinear least squares learning

In numerical linear algebra, the variable projection (VP) algorithm has been a standard approach to separable “mixed” linear and nonlinear least squares problems since early 1970s. Such a separable case often arises in diverse contexts of machine learning (e.g., with generalized linear discriminant functions); yet VP is not fully investigated in the literature. We thus describe in detail its implementation issues, highlighting an economical trust-region implementation of VP in the framework of a so-called block-arrow least squares (BA) algorithm for a general multiple-response nonlinear model. We then present numerical results using an exponential-mixture benchmark, seven-bit parity, and color reproduction problems; in some situations, VP enjoys quick convergence and attains high classification rates, while in some others VP works poorly. This observation motivates us to investigate original VP's strengths and weaknesses compared with other (full-functional) approaches. To overcome the limitation of VP, we suggests how VP can be modified to be a Hessian matrix-based approach that exploits negative curvature when it arises. For this purpose, our economical BA algorithm is very useful in implementing such a modified VP especially when a given model is expressed in a multi-layer (neural) network for efficient Hessian evaluation by the so-called second-order stagewise backpropagation.
A Wavelet‐Based Test for Stationarity

We develop a test for stationarity of a time series against the alternative of a time‐varying covariance structure. Using localized versions of the periodogram, we obtain empirical versions of a reasonable notion of a time‐varying spectral density. Coefficients with respect to a Haar wavelet series expansion of such a time‐varying periodogram are an indicator of whether there is some deviation from covariance stationarity. We propose a test based on the limit distribution of these empirical coefficients.
Two-Phase EA/k-NN for Feature Selection and Classification in Cancer Microarray Datasets

Efficient and reliable methods that can find a small sample of informative genes amongst thousands are of great importance. In this area, much research is investigating the combination of advanced search strategies (to find subsets of features), and classification methods. We investigate a simple evolutionary algorithm/classifier combination on two microarray cancer datasets, where this combination is applied twice – once for feature selection, and once for further selection and classification. Our contribution are: (further) demonstration that a simple EA/classifier combination is capable of good feature discovery and classification performance with no initial dimensionality reduction; demonstration that a simple repeated EA/k-NN approach is capable of competitive or better performance than methods using more sophisticated preprocessing and classifer methods; new and challenging results on two public datasets with clear explanation of experimental setup; review material on the EA/kNN area; and specific identification of genes that our work suggests are significant regarding colon cancer and prostate cancer.
Explicit coupled thermo‐mechanical finite element model of steel solidification

The explicit finite element method is applied in this work to simulate the coupled and highly non‐linear thermo‐mechanical phenomena that occur during steel solidification in continuous casting processes. Variable mass scaling is used to efficiently model these processes in their natural time scale using a Lagrangian formulation. An efficient and robust local–global viscoplastic integration scheme (Int. J. Numer. Meth. Engng 2006; 66:1955–1989) to solve the highly temperature‐ and rate‐dependent elastic–viscoplastic constitutive equations of solidifying steel has been implemented into the commercial software ABAQUS/Explicit (ABAQUS User Manuals v6.7. Simulia Inc., 2007) using a VUMAT subroutine. The model is first verified with a known semi‐analytical solution from Weiner and Boley (J. Mech. Phys. Solids 1963; 11:145–154). It is then applied to simulate temperature and stress development in solidifying shell sections in continuous casting molds using realistic temperature‐dependent properties and including the effects of ferrostatic pressure, narrow face taper, and mechanical contact. Example simulations include a fully coupled thermo‐mechanical analysis of a billet‐casting and thin‐slab casting in a funnel mold. Explicit temperature and stress results are compared with the results of an implicit formulation and computing times are benchmarked for different problem sizes and different numbers of processor cores. The explicit formulation exhibits significant advantages for this class of contact‐solidification problems, especially with large domains on the latest parallel computing platforms. Copyright © 2008 John Wiley & Sons, Ltd.
High‐resolution images from compressed low‐resolution video: Motion estimation and observable pixels

In this article, we address the problem of obtaining a high‐resolution (HR) image from a compressed low‐resolution (LR) video sequence. Motion information plays a critical role in solving this problem, and we determine which pixels in the sequence provide useful information for calculating the high‐resolution image. The bit stream of hybrid motion compensated video compression methods includes low‐resolution motion‐compensated images; we therefore also study which pixels in these images should be used to increase the quality of the reconstructed image. Once the useful (observable) pixels in the low‐resolution and motion‐compensated sequences have been detected, we modify the acquisition model to only account for these observations. The proposed approach is tested on real compressed video sequences and the improved performance is reported. © 2004 Wiley Periodicals, Inc. Int J Imaging Syst Technol 14, 58–66, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.20008
Doubly Robust Estimation in Missing Data and Causal Inference Models

Summary The goal of this article is to construct doubly robust (DR) estimators in ignorable missing data and causal inference models. In a missing data model, an estimator is DR if it remains consistent when either (but not necessarily both) a model for the missingness mechanism or a model for the distribution of the complete data is correctly specified. Because with observational data one can never be sure that either a missingness model or a complete data model is correct, perhaps the best that can be hoped for is to find a DR estimator. DR estimators, in contrast to standard likelihood‐based or (nonaugmented) inverse probability‐weighted estimators, give the analyst two chances, instead of only one, to make a valid inference. In a causal inference model, an estimator is DR if it remains consistent when either a model for the treatment assignment mechanism or a model for the distribution of the counterfactual data is correctly specified. Because with observational data one can never be sure that a model for the treatment assignment mechanism or a model for the counterfactual data is correct, inference based on DR estimators should improve upon previous approaches. Indeed, we present the results of simulation studies which demonstrate that the finite sample performance of DR estimators is as impressive as theory would predict. The proposed method is applied to a cardiovascular clinical trial.
A Potential Role of the Inferior Frontal Gyrus and Anterior Insula in Cognitive Control, Brain Rhythms, and Event-Related Potentials

In the present paper, we review evidence for of a model in which the inferior frontal gyrus/anterior insula (IFG/AI) area is involved in elaborate attentional and working memory processing and we present the hypothesis that this processing may take different forms and may have different effects, depending on the task at hand: (1) it may facilitate fast and accurate responding, or (2) it may cause slow responding when prolonged elaborate processing is required to increase accuracy of responding, or (3) it may interfere with accuracy and speed of next-trial (for instance, post-error) performance when prolonged elaborate processing interferes with processing of the next stimulus. We present our viewpoint that ventrolateral corticolimbic control pathways, including the IFG/AI, and mediodorsal corticolimbic control pathways, including dorsal anterior cingulate cortex areas, play partly separable, but interacting roles in adaptive behavior in environmental conditions that differ in the level of predictability: compared to dorsal feed-forward control, the ventral corticolimbic control pathways implement control over actions through higher responsiveness to momentary environmental stimuli. This latter control mode is associated with an attentional focus on stimuli that are urgent or close in time and space, while the former control mode is associated with a broader, more global focus in time and space. Both control pathways have developed extensively through evolution, and both developed their own “cognitive controls,” such that neither one can be properly described as purely “cognitive” or “emotional. ” We discuss literature that suggests that the role of IFG/AI in top-down control is reflected in cortical rhythms and event-related potentials. Together, the literature suggests that the IFG/AI is an important node in brain networks that control cognitive and emotional processing and behavior.
The Role of Heart Rate Variability in Risk Stratification for Adverse Postoperative Cardiac Events

There is growing evidence of a strong association between the compromised autonomic nervous system and sudden cardiac death. Heart rate variability (HRV) measures are widely used to measure alterations in the autonomic nervous system. Several studies with cardiac patients show that decreased HRV as well as baroreceptor dysfunction are more powerful predictors for sudden cardiac death than established clinical predictors such as left ventricular ejection fraction. One-third of all postoperative complications and more than half of the deaths are due to cardiac complications. Several risk indices are useful for immediate perioperative short-term, but not for long-term outcome risk stratification of an individual patient. Currently, there are no clinically assimilated methods for long-term postoperative risk assessment. Recently, few studies have shown that preoperatively decreased HRV can independently predict postoperative long-term mortality. Further studies with surgical patients are needed to establish a possible predictive value of preoperative baroreceptor dysfunction, alone and combined with HRV, for short- and long-term postoperative outcome.
Proton transfer in solution: Molecular dynamics with quantum transitions

We apply ‘‘molecular dynamics with quantum transitions’’ (MDQT), a surface‐hopping method previously used only for electronic transitions, to proton transfer in solution, where the quantum particle is an atom. We use full classical mechanical molecular dynamics for the heavy atom degrees of freedom, including the solvent molecules, and treat the hydrogen motion quantum mechanically. We identify new obstacles that arise in this application of MDQT and present methods for overcoming them. We implement these new methods to demonstrate that application of MDQT to proton transfer in solution is computationally feasible and appears capable of accurately incorporating quantum mechanical phenomena such as tunneling and isotope effects. As an initial application of the method, we employ a model used previously by Azzouz and Borgis to represent the proton transfer reaction AH–B■A−–H+B in liquid methyl chloride, where the AH–B complex corresponds to a typical phenol–amine complex. We have chosen this model, in part,.
SqueezeNet: AlexNet-level accuracy with 50x fewer parameters and <1MB model size

Recent research on deep neural networks has focused primarily on improving accuracy. For a given accuracy level, it is typically possible to identify multiple DNN architectures that achieve that accuracy level. With equivalent accuracy, smaller DNN architectures offer at least three advantages: (1) Smaller DNNs require less communication across servers during distributed training. (2) Smaller DNNs require less bandwidth to export a new model from the cloud to an autonomous car. (3) Smaller DNNs are more feasible to deploy on FPGAs and other hardware with limited memory. To provide all of these advantages, we propose a small DNN architecture called SqueezeNet. SqueezeNet achieves AlexNet-level accuracy on ImageNet with 50x fewer parameters. Additionally, with model compression techniques we are able to compress SqueezeNet to less than 0.5MB (510x smaller than AlexNet). The SqueezeNet architecture is available for download here: this https URL
Transfer Learning by Borrowing Examples for Multiclass Object Detection

Despite the recent trend of increasingly large datasets for object detection, there still exist many classes with few training examples. To overcome this lack of training data for certain classes, we propose a novel way of augmenting the training data for each class by borrowing and transforming examples from other classes. Our model learns which training instances from other classes to borrow and how to transform the borrowed examples so that they become more similar to instances from the target class. Our experimental results demonstrate that our new object detector, with borrowed and transformed examples, improves upon the current state-of-the-art detector on the challenging SUN09 object detection dataset.
The power spectrum of the flux distribution in the Lyman α forest of a large sample of UVES QSO absorption spectra (LUQAS)

The flux power spectra of the Lyman a forest from a sample of 27 quasi-stellar objects (QSOs) taken with the high-resolution Ultraviolet Echelle Spectrograph (UVES) on the Very Large Telescope (VLT) are presented. We find a similar fluctuation amplitude at the peak of the '3D' flux power spectrum at k ∼ 0.03 s km -1 as the study by Croft et al. (2002), in the same redshift range. The amplitude of the flux power spectrum increases with decreasing redshift if corrected for the increase in the mean flux level as expected if the evolution of the flux power spectrum is sensitive to the gravitational growth of matter density fluctuations. This is in agreement with the findings of McDonald et al. (2000) at larger redshift. The logarithmic slope of the '3D' flux power spectrum, P F (k), at large scales k < 0.03 s km -1 , is 1.4 ± 0.3, i.e. 0.3 shallower than that found by Croft et al. but consistent within the errors.
Correlation between emotional status and pupils size in normal people

Objective To analyze the correlation between emotional status,age,gender and the size and alteration of pupils in normal people.Methods A toatl of 60 volunteers(60 eyes) waiting for taxis in the ground transportation waiting zone of BCIA(Beijing Capital International Airport) were interviewed.Emotional status,gender,age,the size and alteration of volunteers' pupils were recorded.Emotional status included happiness,calmness,anxiety and impatience.People were divided into low-aged group(younger than 40years old) and high-aged group(older than 40 years old). Comparison of the size and alteration of pupils in different gender,age,and emotional status group were analyzed by the means of ANOVA,difference between two groups was analyzed by LSD test.Results The size of pupils in cases with emotional status of happiness,calmness,anxiety and impatience were(5.34±1.41) mm,(3.50±1.25) mm,(3.17±0.86) mm and(4.91±1.81)mm,respectively,and the alteration were(3.24±1.99) mm,(1.62±1.25) mm,(1.01±0.89) mm and(2.86±1.93) mm,respectively,the difference of the size and alteration of pupils under different emotional status were statistically significance(F=10.86,9.87; All P=0.00). There were statistical differences in the size and alteration of pupils between happiness group and calmness group,anxiety group(P=0.001,0.007; P=0.000,0.000),but no statistical difference between happiness group and impatience group(P=0.375,0.467). There were statistical differences in the size and alteration of pupils between impatience group and calmness group,anxiety group(P=0.027,0.042; P=0.001,0.001),but there was no statistical difference between calmness group and anxiety group(P=0.560,0.297). The size of pupils in male and female group were(4.61±1.64) mm and(2.95±1.58) mm,respectively,the alteration were(3.01±1.52) mm and(1.86±1.04) mm,respectively,there were statistical differences(F=9.58,10.34; All P=0.00). The size of pupils in young and elder group were(5.10±1.62) mm and(3.84±1.47) mm,respectively,the alteration were(2.97±1.45) mm and(1.23±0.69) mm,there were statistical differences(F=8.29,11.47; All P=0.00). The size of pupil were bigger and changes faster in young group than elder group.Conclusion In normal people,pupillary size and reaction capacity is related to their emotional status.The size of pupil is bigger and changes faster under happiness status,while it is smaller and slower under anxiety status.Men and young people have bigger pupil and faster response than female and older people.