Miracle-dz/UniFAR-FTUs huggingface dataset:
Effective fragment potential method in Q‐CHEM: A guide for users and developers

A detailed description of the implementation of the effective fragment potential (EFP) method in the Q‐CHEM electronic structure package is presented. The Q‐CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as Hartree–Fock, density functional theory, perturbation theory, and coupled‐cluster methods, as well as with methods for electronically excited and open‐shell species, for example, configuration interaction, time‐dependent density functional theory, and equation‐of‐motion coupled‐cluster models. In addition to the QM/EFP functionality, a “fragment‐only” feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the C++ classes and EFP module's workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q‐CHEM's auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user‐defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described. © 2013 Wiley Periodicals, Inc.
A baseline spectroscopic study of the infrared auroras of Jupiter

Abstract We present the results of a spectroscopic study of the H + 3 infrared emissions of Jupiter, obtained using the United Kingdom Infrared Telescope (UKIRT) on Mauna Kea, Hawaii, during May 3–5, 1993. Although we have obtained data from the whole of the planet, in this paper we concentrate on the auroral regions. Derived H + 3 temperatures for these vary between 700 and 1000 K, and column densities are of the order of 10 12 cm −2 . There is a strong (anti-)correlation between these parameters, however, that requires the introduction of new variables to characterize the jovian auroras fully. The total H + 3 auroral emission is presented as a function of central meridian longitude. A simple geometric model of this emission does not describe the data adequately. The integrated infrared auroral emission in each hemisphere is of the order of a few × 10 12 W, making it comparable to auroral output in the ultraviolet.
Regulation of vascular endothelial growth factor ( VEGF ) gene transcription by estrogen receptors a and b

Vascular endothelial growth factor (VEGF) mediates angiogenic activity in a variety of estrogen target tissues. To determine whether estrogen has a direct transcriptional effect on VEGF gene expression, we developed a model system by transiently transfecting human VEGF promoter-luciferase reporter constructs into primary human endometrial cells and into Ishikawa cells, derived from a well-differentiated human endometrial adenocarcinoma. In primary endometrial epithelial cells, treatment with 17b-estradiol (E2) resulted in a 3.8-fold increase in luciferase activity, whereas a 3.2-fold induction was demonstrated for stromal cells. Our Ishikawa cells had less than 100 functional estrogen receptors (ER)y cell and were therefore cotransfected with expression vectors encoding either the aor the b-form of the human ER. In cells cotransfected with ERa, E2 induced 3.2-fold induction in VEGFpromoter luciferase activity. A 2.3-fold increase was observed in cells cotransfected with ERb. Through specific deletions, the E2 response was restricted to a single 385-bp PvuII-SstI fragment in the 5* flanking DNA. Cotransfection of this upstream region with a DNA binding domain ER mutant, or site-directed mutagenesis of a variant ERE within this fragment, resulted in the loss of the E2 response. Electromobility shift assays demonstrated that this same ERE sequence specifically binds estradiol-ER complexes. These studies demonstrate that E2-regulated VEGF gene transcription requires a variant ERE located 1.5 kb upstream from the transcriptional start site. Site-directed mutagenesis of this ERE abrogated E2-induced VEGF gene expression.
PCA on a Data Frame

Principal components analysis (PCA) is a well-known technique for constructing a low rank model of a data matrix. Here, we propose a new method which performs an analogue of PCA on a data frame, i.e., an arbitrary data set consisting of numerical, Boolean, categorical, ordinal, and other data types. We illustrate our method by fitting a low rank model to the 2013 American Community Survey (ACS), a demographic survey covering 1% of the population of the United States.
Crowd Access Path Optimization: Diversity Matters

Quality assurance is one the most important challenges in crowdsourcing. Assigning tasks to several workers to increase quality through redundant answers can be expensive if asking homogeneous sources. This limitation has been overlooked by current crowdsourcing platforms resulting therefore in costly solutions. In order to achieve desirable cost-quality tradeoffs it is essential to apply efficient crowd access optimization techniques. Our work argues that optimization needs to be aware of diversity and correlation of information within groups of individuals so that crowdsourcing redundancy can be adequately planned beforehand. Based on this intuitive idea, we introduce the Access Path Model (APM), a novel crowd model that leverages the notion of access paths as an alternative way of retrieving information. APM aggregates answers ensuring high quality and meaningful confidence. Moreover, we devise a greedy optimization algorithm for this model that finds a provably good approximate plan to access the crowd. We evaluate our approach on three crowdsourced datasets that illustrate various aspects of the problem. Our results show that the Access Path Model combined with greedy optimization is cost-efficient and practical to overcome common difficulties in large-scale crowdsourcing like data sparsity and anonymity.
Can Ultrasound of the Tibial Nerve Detect Diabetic Peripheral Neuropathy?

OBJECTIVE Peripheral nerve imaging by portable ultrasound (US) may serve as a noninvasive and lower-cost alternative to nerve conduction studies (NCS) for diagnosis and staging of diabetic sensorimotor polyneuropathy (DSP). We aimed to examine the association between the size of the posterior tibial nerve (PTN) and the presence and severity of DSP. RESEARCH DESIGN AND METHODS We performed a cross-sectional study of 98 consecutive diabetic patients classified by NCS as subjects with DSP or control subjects. Severity was determined using the Toronto Clinical Neuropathy Score. A masked expert sonographer measured the cross-sectional area (CSA) of the PTN at 1, 3, and 5 cm proximal to the medial malleolus. RESULTS Fifty-five patients had DSP. The mean CSA of the PTN in DSP compared with control subjects at distances of 1 (23.03 vs. 17.72 mm2; P = 0.004), 3 (22.59 vs. 17.69 mm2; P < 0.0001), and 5 cm (22.05 vs. 17.25 mm2; P = 0.0005) proximal to the medial malleolus was significantly larger. Although the area under the curve (AUC) for CSA measurements at all three anatomical levels was similar, the CSA measured at 3 cm above the medial malleolus had an optimal threshold value for identification of DSP (19.01 mm2) with a sensitivity of 0.69 and a specificity of 0.77 by AUC analysis. CONCLUSIONS This large study of diabetic patients confirms that the CSA of the PTN is larger in patients with DSP than in control subjects, and US is a promising point-of-care screening tool for DSP.
Evaluating ‘ Throw Away ’ Prototyping for Requirements Capture

This paper demonstrates the advantages of extending the scope of prototyping to the requirements captur e phase of a project. Prototyping has long been used to elicit users’ responses to ready-formed designs (Boehm, 1988), but only recently has the use of concept demonstrators (Sanderson, 1997) and early throw-away prototypes (Smith et al., 1990) been suggested as a means to capture response to alterna tiv design options, before any design has been agreed, and with the intention that some of them will never be developed. We show that this is not only practicab le, but actually cost-effective.
Specific reaction of 9-cis-retinoyl fluoride with bovine opsin.

Opsin readily undergoes Schiff base formation between an active site lysine and 9-cis- or 11-cis-retinaldehyde to form the visual pigments isorhodopsin (lambda max = 487 nm) and rhodopsin (lambda max = 500 nm), respectively (Dratz, 1977). It would be predicted that 9-cis-retinoyl fluoride (1), an isostere of 9-cis-retinal, should be an active site directed, mechanism-based labeling agent of opsin, since a stable peptide bond should be formed instead of a Schiff base. It is shown here that 9-cis-retinoyl fluoride (1) reacts with opsin in a time-dependent fashion (t1/2 = 9 min at 25 microM 1) to form a new, nonbleachable pigment with a lambda max of approximately 365 nm. beta-Ionone competitively slows down the rate of the reaction. The absorbance of the new pigment at approximately 365 nm is similar to that of model amide compounds. This result is consistent in a general and qualitative way with the Nakanishi-Honig point-charge model for visual pigments which requires that the chromophore be charged, a situation not possible when the retinoid is linked to opsin via a peptide bond rather than a protonated Schiff base [Honig, B. , Dinur, U. , Nakanishi, K. , Balogh-Nair, V. , Gawinowicz, M.A., Arnabaldi, M. , & Motto, M.G. (1979) J. Am. Chem. Soc. 101, 7084-7086]. 9-cis-Retinoyl fluoride (1) is approximately 4-fold more potent than all-trans-retinoyl fluoride (2) as an inactivator of bovine opsin. Importantly, 13-cis-retinoyl fluoride (3) is inactive, and no new absorption band at 365 nm is observed. (ABSTRACT TRUNCATED AT 250 WORDS)
Evaluating cost-sensitive Unsolicited Bulk Email categorization

In the recent years, Unsolicited Bulk Email has became an increasingly important problem, with a big economic impact. In this paper, we discuss cost-sensitive Text Categorization methods for UBE filtering. In concrete, we have evaluated a range of Machine Learning methods for the task (C4.5, Naive Bayes, PART, Support Vector Machines and Rocchio), made cost sensitive through several methods (Threshold Optimization, Instance Weighting, and Meta-Cost). We have used the Receiver Operating Characteristic Convex Hull method for the evaluation, that best suits classification problems in which target conditions are not known, as it is the case. Our results do not show a dominant algorithm nor method for making algorithms cost-sensitive, but are the best reported on the test collection used, and approach real-world hand-crafted classifiers accuracy.
Strengthening DoD Cyber Security with the Vulnerability Market

Abstract : In the past decade, the DoD and defense contractors have witnessed an immense theft of intellectual property which originated inside and outside our borders. So how do these thefts occur when the DoD has one of the most secure and defended networks in the world? Every year, the DoD upgrades their IT systems, allows new applications to connect to the network, and reconfigures the enterprise to gain efficiencies. While these actions are often in support of the warfighter and securing national security interests, they also introduce new system vulnerabilities that lie in wait to be exploited. Often, these vulnerabilities are discovered when the system is already deployed and too late to stop a leak of sensitive information. A proactive approach is needed to identify possible system vulnerabilities prior to fielding when the costs to fix a bug are much less. This paper recommends that the DoD adopt an Information and Software Assurance tactic that has recently grown in popularity; the vulnerability market. Through use of the vulnerability market, DoD can ensure that information security is built into the application layer, minimize the number of patches distributed, and optimize the investment in defense programs.
Research and implementation of a safe file system based on the Mandatory Hardware Confirming Control technology

With the demand of guaranteeing the safety of the files, which contain enterprise core information resource, this paper presents the Mandatory Hardware Confirming Control technology and a safe file system based on it. The system captures the operations on sensitive files by various processes, and then examines if the corresponding hardware signals exist. Optionally, operations are performed on these files. The system ensures trusted operations on files and puts an end to any malicious manipulations.
Mouse Hepatic Oval Cells Require Met-Dependent PI3K to Impair TGF-β-Induced Oxidative Stress and Apoptosis

We have previously shown that oval cells harboring a genetically inactivated Met tyrosine kinase (Met−/− oval cells) are more sensitive to TGF-β-induced apoptosis than cells expressing a functional Met (Metflx/flx), demonstrating that the HGF/Met axis plays a pivotal role in oval cell survival. Here, we have examined the mechanism behind this effect and have found that TGF-β induced a mitochondria-dependent apoptotic cell death in Metflx/flx and Met−/− oval cells, associated with a marked increase in levels of the BH3-only proteins Bim and Bmf. Bmf plays a key role during TGF-β-mediated apoptosis since knocking down of BMF significantly diminished the apoptotic response in Met−/− oval cells. TGF-β also induced oxidative stress accompanied by NADPH oxidase 4 (Nox4) mRNA up-regulation and decreased protein levels of antioxidant enzymes. Antioxidants inhibit both TGF-β-induced caspase 3 activity and Bmf up-regulation, revealing an oxidative stress-dependent Bmf regulation by TGF-β. Notably, oxidative stress-related events were strongly amplified in Met−/− oval cells, emphasizing the critical role of Met in promoting survival. Pharmacological inhibition of PI3K did impair HGF-driven protection from TGF-β-induced apoptosis and increased sensitivity of Metflx/flx oval cells to TGF-ß by enhancing oxidative stress, reaching apoptotic indices similar to those obtained in Met−/− oval cells. Interestingly, both PI3K inhibition and/or knockdown itself resulted in caspase-3 activation and loss of viability in Metflx/flx oval cells, whereas no effect was observed in Met−/− oval cells. Altogether, results presented here provide solid evidences that both paracrine and autocrine HGF/Met signaling requires PI3K to promote mouse hepatic oval cell survival against TGF-β-induced oxidative stress and apoptosis.
Use of ontology-to-text relation for creating semantic annotation

The paper is focused on the problem of creating new semantic annotations of multimedia objects stored in a digital library. In most cases creating such annotations is a time-consuming and expensive process when it is carried out manually by domain experts. This cumbersome process could be facilitated if a part of the information used for annotating is available in form of natural language texts. In such cases it is possible to apply some Natural Language Processing techniques for extracting needed information and then convert it into desired semantic annotations. The paper describes an approach for solving the task of ontological terms recognition within Bulgarian texts by application of a Natural Language Processing technique called "Ontology-to-Text Relation". All preliminary steps to prepare needed resources for implementation of this technique are discussed.
Integrating Local and Global Error Statistics for Multi-Scale RBF Network Training: An Assessment on Remote Sensing Data

Background This study discusses the theoretical underpinnings of a novel multi-scale radial basis function (MSRBF) neural network along with its application to classification and regression tasks in remote sensing. The novelty of the proposed MSRBF network relies on the integration of both local and global error statistics in the node selection process. Methodology and Principal Findings The method was tested on a binary classification task, detection of impervious surfaces using a Landsat satellite image, and a regression problem, simulation of waveform LiDAR data. In the classification scenario, results indicate that the MSRBF is superior to existing radial basis function and back propagation neural networks in terms of obtained classification accuracy and training-testing consistency, especially for smaller datasets. The latter is especially important as reference data acquisition is always an issue in remote sensing applications. In the regression case, MSRBF provided improved accuracy and consistency when contrasted with a multi kernel RBF network. Conclusion and Significance Results highlight the potential of a novel training methodology that is not restricted to a specific algorithmic type, therefore significantly advancing machine learning algorithms for classification and regression tasks. The MSRBF is expected to find numerous applications within and outside the remote sensing field.
Mechanical Properties of TiN Coatings

It is difficult to measure the mechanical properties of physical vapor deposition coatings owing to their small layer thickness. This report c describes a special four-point bending device that makes it possible to determine quantitative critical tensile or compressive failure stresses and shear stresses in thin coatings. The bending test was also used to carry out measurements of hardness and critical loads (scratch test) under stress, excluding other influences such as microstructure changes. The material parameters determined form the basis of a finite element model of the indentation process, and this offers new possibilities for mechanical characterization of coated materials.
Blind motion deblurring from a single image using sparse approximation

Restoring a clear image from a single motion-blurred image due to camera shake has long been a challenging problem in digital imaging. Existing blind deblurring techniques either only remove simple motion blurring, or need user interactions to work on more complex cases. In this paper, we present an approach to remove motion blurring from a single image by formulating the blind blurring as a new joint optimization problem, which simultaneously maximizes the sparsity of the blur kernel and the sparsity of the clear image under certain suitable redundant tight frame systems (curvelet system for kernels and framelet system for images). Without requiring any prior information of the blur kernel as the input, our proposed approach is able to recover high-quality images from given blurred images. Furthermore, the new sparsity constraints under tight frame systems enable the application of a fast algorithm called linearized Bregman iteration to efficiently solve the proposed minimization problem. The experiments on both simulated images and real images showed that our algorithm can effectively removing complex motion blurring from nature images.
Performance metrics as drivers of quality: getting to second gear.

For simplicity’s sake, the history of US health care performance improvement can be divided into the eras before and after the 1999 publication of To Err is Human by the Institute of Medicine.1 Before publication of that report, the conventional wisdom was that the quality of health care was generally excellent, and, in any case, impossible to measure. Guidelines had been developed for some issues, but the preservation of physicians’ autonomy to do what they judged best for patients was often invoked as the first principle of high quality health care. Article see p 980 In truth, most health care providers knew well before 1999 that the real story was more complex – that, despite the hard work of good people, health care often fell short of what it could and should be. Then, To Err is Human and its 2001 successor, Crossing the Quality Chasm ,2 drew national attention to startling gaps in safety, reliability, efficiency, and the overall experience of care. It was at this point that hospital Boards of Trustees throughout the country began to ask management about quality, and quality became a routine part of the Board and management meetings. At many institutions, the work of improving health care was deconstructed – leading to several new roles and an abundance of new metrics. New titles included Chief Quality Officer, Chief Safety Officer, Chief Patient Experience Officer, Chief Population Management Officer, and Chief Value Officer. Sometimes these roles were combined, sometimes not. To manage these different domains of quality, internally-derived and externally-imposed measures proliferated, and hospitals hired a dozen or more personnel simply to collect and track the data. Inevitably, complaints about measurement fatigue and skepticism about performance measurement emerged.3 A commonly-voiced complaint from many clinicians was “Just tell me what you want me …
Preservation of General Intelligence following Traumatic Brain Injury: Contributions of the Met66 Brain-Derived Neurotrophic Factor

Brain-derived neurotrophic factor (BDNF) promotes survival and synaptic plasticity in the human brain. The Val66Met polymorphism of the BDNF gene interferes with intracellular trafficking, packaging, and regulated secretion of this neurotrophin. The human prefrontal cortex (PFC) shows lifelong neuroplastic adaption implicating the Val66Met BDNF polymorphism in the recovery of higher-order executive functions after traumatic brain injury (TBI). In this study, we examined the effect of this BDNF polymorphism on the preservation of general intelligence following TBI. We genotyped a sample of male Vietnam combat veterans (n = 156) consisting of a frontal lobe lesion group with focal penetrating head injuries for the Val66Met BDNF polymorphism. Val/Met did not differ from Val/Val genotypes in general cognitive ability before TBI. However, we found substantial average differences between these groups in general intelligence (≈ half a standard deviation or 8 IQ points), verbal comprehension (6 IQ points), perceptual organization (6 IQ points), working memory (8 IQ points), and processing speed (8 IQ points) after TBI. These results support the conclusion that Val/Met genotypes preserve general cognitive functioning, whereas Val/Val genotypes are largely susceptible to TBI.
On Data-Driven Delay Estimation for Media Cloud

It is well known that delay announcement is an economical and efficient way to improve the user satisfaction since the waiting time (delay) is an important performance metric for media cloud. However, how to accurately estimate the delay in an online-implementation manner is still an open and challenging problem. In this study, we study the data-driven delay estimation in a practical cloud media with heavy traffic, and propose an accurate estimation strategy only with a small amount of dataset. Importantly, we explicitly model the subjective announcement-dependent user response via an objective response function through the elaborate data analysis and model. On the theoretical end, the user response in terms of the estimated delay is characterized by the time window data-cleaning, where an appropriate dataset is set up through the window function analysis. On the technical end, we analyze the conditions for data-driven delay estimation, and prove that the proposed method is able to obtain a near-optimal solution within a finite time period. Extensive simulation results demonstrate the efficiency of the proposed delay estimation method.