Miracle-dz/UniFAR-FTUs huggingface dataset:
Poly[trans-diaquabis[μ-3-(3-pyridyl)propionato-κ2 N,O]cadmium(II)]

The title compound [Cd(L)2(H2O)2]n (L = 3-pyridinepropionic acid, C8H8NO2), is a two-dimensional coordination polymer in which the CdII ion lies on an inversion center and is coordinated in a slightly distorted octahedral environment. The aqua H atoms are involved in intermolecular O–H⋯O hydrogen bonds, which extend the two-dimensional structure to a three-dimensional architecture. The Cd⋯Cd separation within a layer is 9.0031 (1) Å.
PERSIVAL demo: categorizing hidden-web resources

The information available in electronic form continues to grow at an exponential rate and this trend is expected to continue. Although traditional search engines like AltaVista can address common information needs, they ignore the often valuable information that is “hidden” behind search interfaces, the so-called “hidden web. ” Automating the classification of “hidden web” resources is challenging, since the contents of these collections are available only by querying, not by traditional crawling. For example, consider the PubMed medical database from the National Library of Medicine, which stores medical bibliographic information and links to full-text journals accessible through the web. This database is accessible through a query interface. A query to PubMed with keyword “cancer” returns 1,313,266 matches, which are high-quality citations to medical articles, stored locally at the PubMed site. The contents of PubMed are not “crawlable” by traditional search engines. Thus, a query on AltaVista for all the pages in the PubMed site with keyword “cancer” returns only 16,380 matches. Hence, techniques that need to have the documents available for inspection are not applicable to analyze and classify the “hidden web” resources. The ability to access these resources and organize them for subsequent use is a central component of the Digital Libraries Initiative – Phase 2 (DLI2) project at Columbia University. The project is named PERSIVAL and its main goal is to provide personalized access to a distributed patient care digital library with all kinds of collections. The manual inspection and classification of these resources is a non-scalable solution, so we developed a novel technique to automate this task.
Investigating the Intrinsic Differences in Flank Regions of Exon-Intron Junction Sites

The flank regions of exon-intron junction sites (EIJSs) are closely related to gene structure; and their sequence context is the determinants for the spliceosome to recognize the authentic EIJSs. Although some efforts had been devoted to mining sequence information in the flank regions of EIJSs, significant breakthroughs are still awaiting. In this paper, a hypothesis on EIJSs' flank regions was proposed, it stated that the sequence context of intron flank is more flexible than the conjoined exon flank for a specific EIJS; it means that the exon flanks are more conservative than the intron flanks. For investigating the proposed hypothesis, a frameshift strategy was used to explore the sequence context; and a codon-based measurement, frameshift oscillation (FO), was devised to estimate the sensitivity of being disturbed by frame shifting; according to the hypothesis, the exon flanks will be more sensitive to frameshift than their conjoined intron flanks. After investigating all EIJSs in complete human genome with various lengths of flank regions by FO, the results reveal there do exist intrinsic differences in the flank regions of EIJSs. Therefore, the proposed hypothesis has great implications in predicting gene structure; furthermore, it is believed that the devised estimator FO really catches a key feature of authentic EIJSs and it is of great potential in identifying authentic EIJSs.
Tibial Bone Geometry in Chronic Stroke Patients: Influence of Sex, Cardiovascular Health, and Muscle Mass

This study aimed to examine the geometry of the tibia in chronic stroke survivors. Fifty‐five ambulatory individuals with chronic stroke were included in the study. pQCT was used to obtain a cross‐sectional scan of the tibia at the 30% site on both the paretic and nonparetic sides. Leg lean mass was derived from a total body scan using DXA. Each subject was also evaluated for peak oxygen consumption rate, spasticity, and functional mobility. Paired t‐tests were used to compare the pQCT parameters between the two sides. Multiple linear regression analysis was used to identify the significant determinants of tibial bone strength index (BSI). In men, marrow cavity area on the paretic side was significantly greater than the nonparetic side (p = 0.011), whereas the total bone area showed no significant side‐to‐side difference (p = 0.252). In women, total bone area on the paretic side was significantly smaller than the nonparetic side (p = 0.003), whereas the marrow cavity area had no side‐to‐side difference (p = 0.367). Peak oxygen consumption (r2 = 0.739, F5,49 = 22.693, p < 0.001) and paretic leg lean mass (r2 = 0.802, F6,48 = 32.475, p < 0.001) remained independently associated with tibial BSI, after controlling for age, sex, body mass index, years since stroke onset, and physical activity level. The geometry of the tibia in stroke patients showed sex‐specific side‐to‐side differences. The results suggested that, whereas endosteal resorption was apparent in men, periosteal resorption was more predominant in women. The results also highlight the potential importance of promoting cardiovascular health and leg muscle mass in enhancing bone geometry in chronic stroke survivors.
Mad2 Checkpoint Gene Silencing Using Epidermal Growth Factor Receptor-Targeted Chitosan Nanoparticles in Non-Small Cell Lung Cancer Model

RNA interference has emerged as a powerful strategy in cancer therapy because it allows silencing of specific genes associated with tumor progression and resistance. Mad2 is an essential mitotic checkpoint component required for accurate chromosome segregation during mitosis, and its complete abolition leads to cell death. We have developed an epidermal growth factor receptor (EGFR)-targeted chitosan system for silencing the Mad2 gene as a strategy to efficiently induce cell death in EGFR overexpressing human A549 non-small cell lung cancer cells. Control and EGFR-targeted chitosan nanoparticles loaded with small interfering RNAs (siRNAs) against Mad2 were formulated and characterized for size, charge, morphology, and encapsulation efficiency. Qualitative and quantitative intracellular uptake studies by confocal imaging and flow cytometry, respectively, showed time-dependent enhanced and selective intracellular internalization of EGFR-targeted nanoparticles compared to nontargeted system. Targeted nanoparticles showed nearly complete depletion of Mad2 expression in A549 cells contrasting with the partial depletion in the nontargeted system. Accordingly, Mad2-silencing-induced apoptotic cell death was confirmed by cytotoxicity assay and flow cytometry. Our results demonstrate that EGFR-targeted chitosan loaded with Mad2 siRNAs is a potent delivery system for selective killing of cancer cells.
The nucleoid occlusion protein SlmA is a direct transcriptional activator of chitobiose utilization in Vibrio cholerae

Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon. SlmA has not previously been implicated in gene regulation. Also, SlmA is a member of the TetR family of proteins, which are generally transcriptional repressors. In vitro, we find that SlmA binds directly to the chb operon promoter, and in vivo, we show that this interaction is, surprisingly, required for transcriptional activation of this locus and for chitobiose utilization. Using point mutations that disrupt distinct functions of SlmA, we find that DNA-binding, but not nucleoid occlusion, is critical for transcriptional activation. This study identifies a novel role for SlmA as a transcriptional regulator in V. cholerae in addition to its established role as a cell division licensing factor. AUTHOR SUMMARY The cholera pathogen Vibrio cholerae is a natural resident of the aquatic environment and causes disease when ingested in the form of contaminated food or drinking water. In the aquatic environment, the shells of marine zooplankton, which are primarily composed of chitin, serve as an important food source for this pathogen. The genes required for the utilization of chitin are tightly regulated in V. cholerae, however, the exact mechanism underlying this regulation is currently unclear. Here, we uncover that a protein involved in regulating cell division is also important for regulating the genes involved in chitin utilization. This is a newly identified property for this cell division protein and the significance of a common regulator for these two disparate activities remains to be understood.
Effects of plant diversity on simulated climate-vegetation interaction towards the end of the African Humid Period

This thesis explores the role of plant diversity in simulated climate–vegetation interaction towards the end of the “African Humid Period” (AHP) in models of different complexity, from the conceptual model by Claussen et al. (2013) to the Dynamic Global Vegetation Model JSBACH, the land component of the Max Planck Earth System Model MPIESM1. In the light of recently published pollen data and the current state of ecological literature, the conceptual model by Claussen et al. (2013) reproduces the main features of different plant types interacting together with climate, but it does not capture the reconstructed AHP plant diversity. With a new model version adjusted to AHP vegetation, I can simulate a diverse mosaic-like environment as reconstructed from pollen, and I observe a stabilizing effect of high plant diversity on vegetation cover and precipitation. Plant composition ultimately determines the stability of the climate–vegetation system. The assessment of plant diversity in JSBACH illustrates that the “Plant Functional Type” (PFT) concept is not capable to capture AHP plant diversity and cannot depict mosaic-like environments as reconstructed from pollen. However, offline simulations with different PFT compositions confirm that high PFT diversity can smooth the vegetation response to a – here prescribed linear – precipitation decline. Eventually, the steepness of vegetation decline depends on the composition rather than on the number of PFTs. In coupled ECHAM6/JSBACH simulations, PFT diversity significantly affects land surface parameters, water cycling, surface energy budget, and atmospheric circulation patterns during the AHP as well as the rate and timing of the transition from a wet “green” state to a dry “desert” state. Higher precipitation is not necessarily associated with a higher vegetation cover fraction and a higher stability of the climate–vegetation system, but determined by the properties of prevailing PFTs, thus PFT composition. Despite different underlying assumptions, all considered levels of model complexity lead to the same conclusions: high plant diversity could stabilize a climate–vegetation system, but plant composition is the decisive factor for the climate–vegetation feedback strength and consequently for the system response to changes in orbital forcing. This highlights that the choice of plant types/PFTs and their representation in models significantly affect simulated climate–vegetation interaction during the AHP, the extent of the “green” Sahara, and the timing and rate of transition to the “desert” state. From this I conclude that accounting for plant diversity in future studies – not only on palaeoclimates – could significantly improve the understanding of climate–vegetation interaction and the simulation of the vegetation response to changing climate.
Visual sameness: a choice time analysis of pattern recognition processes.

Ss judged the "sameness" of pairs of matrixes, each having several cells blackened at random. One group (Similarity search) classified matrix pairs as "same" if they had even one pair of blackened cells in corresponding locations. A second group (Identity search) classified pairs as "same" that were identical with respect to all blackened cell locations. Decision times of the Similarity-search group were much longer than those of the Identity-search group. While the performance of the Similarity-search Ss indicated they were engaged in a serial processing of the stimulus array that of the Identity-search Ss in some conditions closely approximated gestalt processing.
Denoising and Completion of 3D Data via Multidimensional Dictionary Learning

In this paper a new dictionary learning algorithm for multidimensional data is proposed. Unlike most conventional dictionary learning methods which are derived for dealing with vectors or matrices, our algorithm, named KTSVD, learns a multidimensional dictionary directly via a novel algebraic approach for tensor factorization as proposed in [3, 12, 13]. Using this approach one can define a tensor-SVD and we propose to extend K-SVD algorithm used for 1-D data to a K-TSVD algorithm for handling 2-D and 3-D data. Our algorithm, based on the idea of sparse coding (using group-sparsity over multidimensional coefficient vectors), alternates between estimating a compact representation and dictionary learning. We analyze our KTSVD algorithm and demonstrate its result on video completion and multispectral image denoising.
Angular dose dependency of MatriXX TM and its calibration

One of the applications of MatriXX (IBA Dosimetry) is experimental verification of dose for IMRT, VMAT, and tomotherapy. For cumulative plan verification, dose is delivered for all the treatment gantry angles to a stationary detector. Experimental calibration of MatriXX detector recommended by the manufacturer involves only AP calibration fields and does not address angular dependency of MatriXX. Angular dependency may introduce dose bias in cumulative plan verification if not corrected. For this reason, we characterized angular dependency of MatriXX and developed a method for its calibration. We found relatively large discrepancies in responses to posterior vs. anterior fields for four MatriXX (Evolution series) detectors (up to 11%), and relatively large variability of responses as a function of gantry angle in the gantry angle ranges of 91°–110° and 269°–260°. With our calibration method, the bias due to angular dependency is effectively removed in experimental verification of IMRT and VMAT plans. PACS number: 87.56Fc
Lexical Reading in Dysfluent Readers of German

ABSTRACT Dyslexia in consistent orthographies like German is characterized by dysfluent reading, which is often assumed to result from failure to build up an orthographic lexicon and overreliance on decoding. However, earlier evidence indicates effects of lexical processing at least in some German dyslexic readers. We investigated variations in reading style in an eye-tracking paradigm with German dysfluent 3rd and 4th graders. Twenty-six TypFix-readers (fixation counts within the range of 47 age-matched typical readers) were compared with 42 HighFix-readers (increased fixation counts). Both groups showed lexical access: Words were read more efficiently than nonwords and pseudohomophones. TypFix-readers showed stronger reliance on lexical reading than HighFix-readers (smaller length effects for number of fixations and total reading time, stronger lexicality effects for gaze duration, stronger word-pseudohomophone effects for mean saccade amplitude). We conclude that in both groups, sublexical and lexical reading processes were impaired due to inefficient visual-verbal integration.
Blind broadband source localization and separation in miniature sensor arrays

We study the ability of a sensor array to blindly separate and localize broadband traveling waves impinging on the array, with additive sensor noise. We consider arrays smaller than the shortest wavelength in the sources, such as MEMS acoustic arrays or VLSI arrays of RF receivers. A series expansion about the center of the array of the time-delayed signals emanating from the sources reduces the problem of separating and localizing the delayed sources to that of separating instantaneous signal mixtures using conventional tools of Independent Component Analysis. The covariance of the noise in the estimated sources is expressed in terms of the covariance of the sensor noise and the angular direction of the sources. Physical simulations demonstrate separation and localization of three non-coplanar speech sources using a planar array of four sensors within a 1 mm radius.
Authentication in Insecure Environments - Using Visual Cryptography and Non-Transferable Credentials in Practise

Sebastian Pape discusses two different scenarios for authentication. On the one hand, users cannot trust their devices and nevertheless want to be able to do secure authentication. On the other hand, users may not want to be tracked while their service provider does not want them to share their credentials. Many users may not be able to determine whether their device is trustworthy, i.e. it might contain malware. One solution is to use visual cryptography for authentication. The author generalizes this concept to human decipherable encryption schemes and establishes a relationship to CAPTCHAS. He proposes a new security model and presents the first visual encryption scheme which makes use of noise to complicate the adversary's task. To prevent service providers from keeping their users under surveillance, anonymous credentials may be used. However, sometimes it is desirable to prevent the users from sharing their credentials. The author compares existing approaches based on non-transferable anonymous credentials and proposes an approach which combines biometrics and smartcards.
Implementing statically typed object-oriented programming languages

Object-oriented programming represents an original implementation issue due to its philosophy of making the program behavior depend on the dynamic type of objects. This is expressed by the late binding mechanism, aka message sending. The underlying principle is that the address of the actually called procedure is not statically determined at compile-time, but depends on the dynamic type of a distinguished parameter known as the receiver. A similar issue arises with attributes, because their position in the object layout may also depend on the object's dynamic type. Furthermore, subtyping introduces another original feature (i.e., runtime subtype checks). All three mechanisms need specific implementations and data structures. In static typing, late binding is generally implemented with so-called virtual function tables. These tables reduce method calls to pointers to functions via a small fixed number of extra indirections. It follows that object-oriented programming yields some overhead, as compared to the usual procedural languages. The different techniques and their resulting overhead depend on several parameters. First, inheritance and subtyping may be single or multiple, and even a mixing is possible, as in Java and ˙NET which present single inheritance for classes and multiple subtyping for interfaces. Multiple inheritance is a well-known complication. Second, the production of executable programs may involve various schemes, from global compilation, which implies the closed-world assumption (CWA), as the whole program is known at compile time, to separate compilation and dynamic loading, where each program unit is compiled and loaded independently of any usage, hence under the open-world assumption (OWA). Global compilation is well-known to facilitate optimization. This article reviews the various implementation techniques available in static typing and in the three cases of single inheritance, multiple inheritance, and multiple subtyping. This language-independent survey focuses on separate compilation and dynamic loading, as they represent the most commonly used and the most demanding framework. However, many works have been undertaken in the global compilation framework, mostly for dynamically typed languages, but also applied to the EIFFEL language. Hence, we also examine global techniques and how they can improve implementation efficiency. Finally, mixed frameworks that combine open and closed world assumptions are considered. For instance, just-in-time (JIT) compilers work under provisional CWA, at the expense of possible recompilations. In contrast, we present an experimental compiler-linker, where separate compilation implies the OWA, whereas the whole program is finally linked under the CWA.
Cardiovascular Antioxidant Therapy: A Review of Supplements, Pharmacotherapies, and Mechanisms

Oxidant stress plays an important role in the pathogenesis of atherosclerosis. In the late 1980s, biological studies demonstrated that oxygen-free radicals oxidize low-density lipoprotein-cholesterol, resulting in the creation of foam cells and inciting the cascade of biological events that ultimately result in the formation of atherosclerosis. In vitro studies showed the ability of antioxidant vitamins to scavenge free radicals and block the oxidation of low-density lipoprotein. This data was supported in vivo by early observational studies suggesting the benefit of antioxidants, particularly vitamin E, in the prevention of coronary artery disease. On the basis of these studies, the use of antioxidant supplements by the general population increased substantially and became a multibillion dollar industry. Despite strong biological evidence and promising observational data, more rigorous scientific evaluation did not support a causational relationship between vitamin supplements and lowering coronary artery disease risk. Several prospective, double-blind, placebo-controlled trials showed no benefit and possibly harmful effects. Therapies such as angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and statins, which are known to have benefit in preventing and treating atherosclerosis by reducing blood pressure and cholesterol, also have a “pleiotropic” effect in reducing the formation of reactive oxygen species (ROS). Advances in molecular biology and the study of ROS led to a better understanding of the mechanisms that govern their production and role in atherogenesis. This progress identified unforeseen pathways by which these drugs favorably alter the balance in ROS production, and have raised possibilities for future targeted therapies in the prevention of atherosclerosis.