Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Characterization of a New Porin Gene of Klebsiella pneumoniae: Its Role in β-Lactam Antibiotic Resistance

ABSTRACT Klebsiella pneumoniae porin genes were analyzed to detect mutations accounting for the porin deficiency observed in many β-lactam-resistant strains. PCR and Southern blot analysis revealed the existence of a third porin gene in addition to the OmpK36 and OmpK35 porin genes previously described. This new porin gene was designated ompK37 and is present in all of the clinical isolates tested. The OmpK37 porin gene was cloned, sequenced, and overexpressed in Escherichia coli. In contrast to that of the major porins, OmpK37 porin expression was only detectable by Western blot analysis in porin-deficient β-lactam-resistant strains, suggesting strong down regulation under standard laboratory conditions. Functional characterization suggested a narrower pore for the OmpK37 porin than for K. pneumoniae porins OmpK36 and OmpK35. This correlated with the susceptibility to certain β-lactam antibiotics, since a K. pneumoniae strain expressing porin OmpK37, but not porin OmpK36 or OmpK35, was less susceptible to β-lactam antibiotics than the same strain expressing either porin OmpK36 or OmpK35.
Well-being of adolescents in context of Culture and Gender: An Empirical Analysis

The aim of the present research is to study the effect of Culture and Gender on well-being of adolescents. Well-being is one of the most important aspects of human being and the state of well-being can be attained in terms of healthy body with healthy mind. Well-being has been defined as encompassing people's cognitive and affective evaluations of their lives. Well- being has been interchangeably used with health and quality of life. According to the WHO, the main determinants of health include the Social, Economic and the physical environment and the person's individual characteristics and behaviors. WHO lists other factors that can influence the well-being of a person such as the gender, culture, education, social, support networks and health services. The main objective of the present investigation is to know the effect of Culture and Gender on well-being of adolescents. The sample of 180 adolescents belonging to Vernacular and Convent Culture were selected randomly from Vernacular and Convent culture schools of Ahmedabad City of Gujarat (India). General Well-being Scale by Dr. Ashok Kalia and Ms. Anita Deswal was administered to measure the Physical. Emotional, Social and school well-being, the result shows that the significant difference found between Culture and Well-being in adolescents. Gender is also affect significantly to the well-being of adolescents.
IDEAL: a dyslexic-friendly ebook reader

We present an ebook reader for Android which displays ebooks in a more accessible manner for users with dyslexia. The ebook reader combines features that other related tools already have, such as text-to-speech technology, and new features, such as displaying the text with an adapted text layout based on the results of a user study with participants with dyslexia. Since there is no universal profile of a user with dyslexia, the layout settings are customizable and users can override the special layout setting according to their reading preferences.
Effects of Weight-Shift Training on Balance Control and Weight Distribution in Chronic Stroke: A Pilot Study

Abstract Purpose: The objective was to evaluate the effect of weight-shift training on functional balance, weight distribution, and postural control measures during standing and forward reach tasks in subjects with chronic stroke. Methods: Nine male subjects (mean age, 66 years; range, 60–75 years) who experienced a stroke 3 to 13 years previously participated in a 4-week training program consisting of static and dynamic balance exercises with visual feedback and gait training with wall support. Balance control was assessed before and after the intervention with clinical measures (Berg Balance Scale) and with a pressure platform for registering the center of pressure (CoP) during quiet stance (weight distribution, CoP sway area, and velocity), and during a forward reach task at shoulder and knee levels. Intervention effects were evaluated with the Wilcoxon matched-pairs test. Results: After training, the group improved their Berg Balance Scale median score from 42 (range, 14–54) to 46 (20–55) (P = .01), CoP sway area [10.6 (5.0–31.4) to 3.0 (1.8–10.8) cm2; P = . 01], and mean velocity [3.5 (2.4–8.0) to 1.7 (0.9–3.7) mm/s; P = . 01] during quiet standing but not weight distribution (P = .59). During the forward reach tasks, most of the postural control measures such as movement time, CoP displacement, and CoP velocity were significantly (P < .05) improved after the training period for both the affected and nonaffected sides as compared to before the training period. Conclusion: A weight-shift training program improved balance control but not weight distribution in a group of chronic stroke subjects. Larger, randomized, and controlled studies are necessary.
Towards Quality Advancement of Underwater Machine Vision with Generative Adversarial Networks

Underwater machine vision has attracted significant attention, but its low quality has prevented it from a wide range of applications. Although many different algorithms have been developed to solve this problem, real-time adaptive methods are frequently deficient. In this paper, based on filtering and the use of generative adversarial networks (GANs), two approaches are proposed for the aforementioned issue, i.e., a filtering-based restoration scheme (FRS) and a GAN-based restoration scheme (GAN-RS). Distinct from previous methods, FRS restores underwater images in the Fourier domain, which is composed of a parameter search, filtering, and enhancement. Aiming to further improve the image quality, GAN-RS can adaptively restore underwater machine vision in real time without the need for pretreatment. In particular, information in the Lab color space and the dark channel is developed as loss functions, namely, underwater index loss and dark channel prior loss, respectively. More specifically, learning from the underwater index, the discriminator is equipped with a carefully crafted underwater branch to predict the underwater probability of an image. A multi-stage loss strategy is then developed to guarantee the effective training of GANs. Through extensive comparisons on the image quality and applications, the superiority of the proposed approaches is confirmed. Consequently, the GAN-RS is considerably faster and achieves a state-of-the-art performance in terms of the color correction, contrast stretch, dehazing, and feature restoration of various underwater scenes. The source code will be made available.
DOMAC: an accurate, hybrid protein domain prediction server

Protein domain prediction is important for protein structure prediction, structure determination, function annotation, mutagenesis analysis and protein engineering. Here we describe an accurate protein domain prediction server (DOMAC) combining both template-based and ab initio methods. The preliminary version of the server was ranked among the top domain prediction servers in the seventh edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006. DOMAC server and datasets are available at: http://www.bioinfotool. org/domac.html
A Visual Language Approach to the Transformation of Web Pages for Mobile Presentation

With the fast growth of mobile devices, it is desirable to browse Web pages, typically designed to render on desktops, efficiently on the small screens of mobile devices. Graph grammar offers a visual means for specifying and extracting the hierarchical structure of information within a Web page with the help of a parsing algorithm. The extracted hierarchical structure provides useful information for partitioning the original Web page into several small pages, each of which fits both spatially and semantically on small screens. However, a parsing process used to extract the hierarchical structure is time-consuming. This paper presents an optimized parsing algorithm which improves the time complexity.
Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer

Gene expression signatures that are predictive of therapeutic response or prognosis are increasingly useful in clinical care; however, mechanistic (and intuitive) interpretation of expression arrays remains an unmet challenge. Additionally, there is surprisingly little gene overlap among distinct clinically validated expression signatures. These “causality challenges” hinder the adoption of signatures as compared to functionally well-characterized single gene biomarkers. To increase the utility of multi-gene signatures in survival studies, we developed a novel approach to generate “personal mechanism signatures” of molecular pathways and functions from gene expression arrays. FAIME, the Functional Analysis of Individual Microarray Expression, computes mechanism scores using rank-weighted gene expression of an individual sample. By comparing head and neck squamous cell carcinoma (HNSCC) samples with non-tumor control tissues, the precision and recall of deregulated FAIME-derived mechanisms of pathways and molecular functions are comparable to those produced by conventional cohort-wide methods (e.g. GSEA). The overlap of “Oncogenic FAIME Features of HNSCC” (statistically significant and differentially regulated FAIME-derived genesets representing GO functions or KEGG pathways derived from HNSCC tissue) among three distinct HNSCC datasets (pathways:46%, p<0.001) is more significant than the gene overlap (genes:4%). These Oncogenic FAIME Features of HNSCC can accurately discriminate tumors from control tissues in two additional HNSCC datasets (n = 35 and 91, F-accuracy = 100% and 97%, empirical p<0.001, area under the receiver operating characteristic curves = 99% and 92%), and stratify recurrence-free survival in patients from two independent studies (p = 0.0018 and p = 0.032, log-rank). Previous approaches depending on group assignment of individual samples before selecting features or learning a classifier are limited by design to discrete-class prediction. In contrast, FAIME calculates mechanism profiles for individual patients without requiring group assignment in validation sets. FAIME is more amenable for clinical deployment since it translates the gene-level measurements of each given sample into pathways and molecular function profiles that can be applied to analyze continuous phenotypes in clinical outcome studies (e.g. survival time, tumor volume).
Two Forces in the Development of Relational Similarity

Analogy commands the attention of developmental psychologists, first, because like grammar and mathematics, analogy is a supremely elegant form of thought ; and, second, because of its importance in cognitive development . An appreciation of relational similarity is fundamental to learning beyond the basic level-to grasping theory-laden concepts that must be defined relationally, such as predator in biology and limiting case in mathematics . In this chapter, we explore two forces that promote the development of relational similarity . Our goal is to illuminate both the nature of the similarity mechanism and its role in experiential learning . Despite the attention given to how and when children acquire the ability to process relational similarity=to carry out analogies-a number of important issues remain unresolved . Most researchers agree that there is a relational shift from early reliance on either holistic or object-level similarities to the possibility of purely relational similarities (Gentner, 1988; Gentner & Rattermann, 1991) . However, there is disagreement as to the nature of the shift . Is it governed by cognitive stage or by degree of domain knowledge ; is it maturational or the product of learning ; is it an all-or-none shift from object similarity to relational similarity ; and finally, when does
Resourcing Change: A Grounded Theory Explaining the Process by Which Managers Address Challenges in Their Initiation of Change as Learning at Work

This grounded theory study conceptualises an abstract social process of ‘resourcing change’, explaining challenges managers face during the initiation of change as their learning in organisations and their responses to them. Both management challenges and their resolutions are theoretically organised on the global-local continuum, reflecting the inter-connected and mutually influencing nature of the social reality. The abstract social process of ‘resourcing change’ has general implications beyond the temporal and spatial boundaries of the study – managers in one UK subsidiary within each of two multinational corporations – Cooper Standard (UK) and Ricoh (UK), respectively, at the time when this study was conducted. The grounded theory of ‘resourcing change’ has made several significant theoretical and methodological contributions. First, the study of learning has been extended to the management population, given their strategic importance in organisations (Easterby-Smith et al., 1998). Second, management learning in organisations is conceptualised as ‘initiation of change’ – a seldom recognised, individual-to-organisation process of change (Quinn, 1996). Learning, as in this study, has been re-connected to accounts of organisational change (Hendry, 1996). A particular emphasis is placed on the initiation stage of change, not on any other stages (e.g. implementation). Third, from a process-relational perspective of organising and managing (Watson, 2002), this grounded theory study of ‘resourcing change’ has identified the contradictions in many processual-oriented research studies, highlighting the absence of the temporal and spatial dimensions in the on-going evolution of social processes. The methodological contributions that this grounded theory study makes are, first and foremost, the conceptualisation of the emerged concepts that are used to explain the process of initiating change in management learning. Research problems and questions are then formulated by abstractly conceptualising the concerns and resolutions of research participants, as opposed to the researcher’s own. This study begins with no focus, however uncomfortable that may make some researchers, recognising the key fact that the focus of the researcher, prior to his or her exposure to the research participants, has no relevance whatsoever to them. The focus is only established at the end of the study, following a set of rigorous and transparent methodological procedures. The adherence to the orthodox grounded theory (Glaser & Strauss, 1967) confirms that grounded theory is a fully-fledged research methodology in its own right, not a set of methods for data analysis (McCallin, 2003).
Selective targeting of gene transfer to vascular endothelial cells by use of peptides isolated by phage display.

BACKGROUND Gene transfer to vascular cells is a highly inefficient and nonselective process, defined by the lack of specific cell-surface receptors for both nonviral and viral gene delivery vectors. METHODS AND RESULTS We used filamentous phage display to isolate a panel of peptides that have the ability to bind selectively and efficiently to quiescent human umbilical vein endothelial cells (HUVECs) with reduced or negligible binding to nonendothelial cells, including vascular smooth muscle cells and hepatocytes. By direct biopanning on HUVECs and a second approach involving preclearing steps before panning on HUVECs, we isolated and sequenced 140 individual phages and identified 59 peptides. We selected 7 candidates for further investigation by secondary screening of homogeneous phages on a panel of cell types. Using adenovirus-mediated gene transfer as a model gene delivery system, we cloned the peptide SIGYPLP and the positive control peptide KKKKKKK upstream of the S11e single-chain Fv ("adenobody") directed against the knob domain of the adenovirus to create fusion proteins. Adenovirus-mediated gene transfer via fiber-dependent infection was blocked with S11e, whereas inclusion of the KKKKKKK peptide retargeted gene transfer. The peptide SIGYPLP, however, retargeted gene delivery specifically to endothelial cells with a significantly enhanced efficiency over nontargeted adenovirus and without transduction of nontarget cells. CONCLUSIONS Our study demonstrates the feasibility of using small, novel peptides isolated via phage display to target gene delivery specifically and efficiently to HUVECs and highlights their use for retargeting both viral and nonviral gene transfer to vascular endothelial cells for future clinical applications.
Content scalability in multiple description image and video coding

High compression ratio, scalability and reliability are the main issues for transmitting multimedia content over best effort networks. Scalable image and video coding meets the user requirements by truncating the scalable bitstream at different quality, resolution and frame rate. However, the performance of scalable coding deteriorates rapidly over packet networks if the base layer packets are lost during transmission. Multiple description coding (MDC) has emerged as an effective source coding technique for robust image and video transmission over lossy networks. In this research problem of incorporating scalability in MDC for robust image and video transmission over best effort network is addressed. The first contribution of this thesis is to propose a strategy for generating more than two descriptions using multiple description scalar quantizer (MDSQ) with an objective to jointly decoded any number of descriptions in balanced and unbalanced manner. The distortion constraints and design conditions for multichannel unbalanced description coding (MUDC) using several MDSQs for improving quality as the number of description is increased are formulated. Secondly, the design of MDSQ is extended to incorporate the quality scalability in each de- scription by using the concept of successive refinement in the side quantizers of multiple description scalar quantizer called MDSQ-SR. The design conditions of the MDSQ-SR are formulated with the objective to improve the quality of side and joint decoding for any combination of quality refinement layers. The joint decoding of different spatial resolution descriptions having different quality re- finement layers is demonstrated for images by combining MUDC and MDSQ-SR schemes respectively. Finally, a fully scalable multiple description video coding (SMDVC) scheme is proposed by integrating MUDC and MDSQ-SR schemes in a motion compensated temporal filtering based video coding framework. The pro- posed SMDVC scheme is capable of generating and joint decoding any number of descriptions in balanced and unbalanced manner at any quality, resolution and frame rate. According to the experimental results the unbalanced joint decoding results into 1.1 dB better peak to signal noise ratio (PSNR) than the balanced joint decod- ing at the same data rate. Furthermore, the joint decoding of MDSQ-SR based scheme gives an average of 1.35 dB and 0.3 dB better PSNR performance with re- spect to the state-of-the-art embedded-MDSQ for images and video respectively. The PSNR performance of the MDSQ-SR based video scheme is improved by 0.2-0.6 dB by controlling inter description and motion vector redundancies. In addition to superior rate-distortion performance than embedded-MDSQ, MDSQ- SR has reduced the computational complexity by 83%.
The Impact of Reflections From Stratified Building Materials on the Wave Propagation in Future Indoor Terahertz Communication Systems

In order to derive reliable propagation models for future terahertz indoor pico-cellular communication systems, accurate reflectivity data of building materials is necessary. Here we present reflection terahertz time domain spectroscopy (THz-TDS) measurements and matching transfer matrix simulations of the frequency dependent reflection coefficient of multi layer building materials in the frequency range from 100 to 500 GHz for a set of angles, both in TE- and TM-polarization. Two prominent stratified structures, a double pane window and white paint on plaster are investigated as they usually account for large areas in indoor environments. Communication systems located above 100 GHz are expected to be strongly affected by the variations of the reflectivity over the frequency and incident angle of such stratified materials as they will rely both on line of sight (LOS) and non line of sight (NLOS) propagation. We discuss this impact on the power distribution in a sample scenario employing the ray-tracing method.
A New Approach for the FDTD Modeling of Antennas Over Periodic Structures

A new approach is proposed for the time-domain modeling of antennas over periodic substrates. This class of problems would typically require a time-consuming simulation of the antenna structure with a finite number of unit cells of the periodic substrate, chosen to be large enough to achieve convergence. On the contrary, the present work employs periodic boundary conditions applied at the substrate, to dramatically reduce the computational domain and hence, the cost of such simulations. Emphasis is given on radiation pattern calculation, and the consequences of the truncated computational domain of the proposed method on the computation of the electric and magnetic surface currents invoked in the near-to-far field transformation. The theoretical aspects of the proposed methodology are complemented by numerical examples of a wire and an integrated patch antenna over electromagnetic band-gap substrates.
A popularity-aware buffer management to improve buffer hit ratio and sequentiality for Solid State Drive

Random writes significantly limit the application of flash memory in enterprise environment due to its poor latency, shorten lifetime and high garbage collection overhead. Solid State Drive (SSD) uses a small part of memory as buffer to reduce random write and extend lifetime. Existing block-based buffer management schemes exploit spatial locality to improve the write sequentiality at a cost of low buffer hit ratio. In this paper, we propose a novel buffer management scheme referred to as PAB, which adopts both buffer hit ratio and write sequentiality as design objectives. Leveraging block popularity, PAB makes full use of both temporal and spatial localities at block level. When replacement happens, PAB selects victim block based on block popularity, page counter and block dirty flag. As universal buffer, PAB serves both read and write requests to increase the possibility to form sequential write. PAB has been extensively evaluated under real enterprise workloads. Our benchmark results conclusively demonstrate that PAB can achieve up to 72% performance improvement and 78% garbage collection overhead reduction compared to existing buffer management schemes.