Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of an “alternate water supply system” in enzymatic hydrolysis in the processive endocellulase Cel7A from Rasamsonia emersonii by molecular dynamics simulation

Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation. In addition, four strong hydrophobic interactions are also determined. The domain cross‐correlation map analysis shows movement correlation of protein including autocorrelation between residues. The root mean square fluctuations analysis represents the various flexibilities of different fragment in the two conformations. Comparing the two conformations reveals the water‐supply mechanism of selective hydrolysis of cellulose in Cel7A. The mechanism can be described as follow. When the reducing end of substrate slides from the unhydrolyzing site (sliding conformation) to the hydrolyzing site (hydrolyzing conformation), His225 is pushed down and rotated, the rotation leads to the movement of Glu209 with the interstrand hydrogen bonding in β‐sheet. It further makes Asp211 close to the hydrolysis center and provides a water molecule bounding on its carboxyl in the previous unhydrolyzing site. After the hydrolysis takes place and the product is excluded from the enzyme, the Asp211 comes back to its initial position. In summary, Asp211 acts as an elevator to transport outer water molecules into the hydrolysis site for every other glycosidic bond.
Scalable privacy-preserving participant selection in mobile crowd sensing

Auction based participant selection has been widely used for mobile crowd sensing (MCS) to achieve user incentive and assignment optimization. However, mobile crowd sensing problems solved with auction-based approaches usually involve participants' privacy concerns because a participant's bids may contain her private information (such as location visiting patterns), and disclosure participants' bids may disclose their private information as well. In this paper, we study how to protect such bid privacy in a temporally and spatially dynamic MCS system. We assume that both sensing tasks and mobile participants have dynamic characteristics over spatial and temporal domains. Following the classical VCG auction, we carefully design a scalable grouping based privacy-preserving participant selection scheme, which leverages Lagrange polynomial interpolation to perturb participants' bids within groups. The proposed solution does not affect the operation of current MCS platform. Both theoretical analysis and real-life tracing data simulations verify the efficiency and security of the proposed solution.
Effects on Housing Prices of Urban Attraction and Labor-Market Accessibility

Through a hedonic approach the authors focus primarily on how house prices vary systematically with respect to some general spatial structure characteristics in a Norwegian region. The introduction of a gravity-based labor-market accessibility measure contributes significantly to explain variation in housing prices, and is used in a model formulation where the distance from the city center is accounted for. Based on these results we suggest a distinction between an urban-attraction effect and a labor-market accessibility effect. Quantitatively, the two distinct effects are found to contribute about equally to intraregional variation in housing prices.
Theory and Practice of Non-Binary Graph-Based Codes: A Combinatorial View

We are undergoing a revolution in data. The ever-growing amount of information in our world has created an unprecedented demand for ultra-reliable, affordable, and resource-efficient data storage systems. Error-correcting codes, as a critical component of any memory device, will play a crucial role in the future of data storage.One particular class of error-correcting codes, known as graph-based codes, has drawn significant attention in both academia and in industry. Graph-based codes offer superior performance compared to traditional algebraic codes. Recently, it has been shown that non-binary graph-based codes, which operate over finite fields rather than binary alphabets, outperform their binary counterparts and exhibit outstanding overall performance. For this reason, these codes are particularly suitable for emerging data storage systems.In this dissertation, we present a comprehensive combinatorial analysis of non-binary graph-based codes. We perform both finite-length and asymptotic analyses for these codes, providing a systematic framework to evaluate and optimize various families of non-binary graph-based codes.In the finite-length case, we provide a mathematical characterization of the error floor problem, including a general definition of absorbing sets over non-binary alphabets. We consider several structured low-density parity-check (LDPC) codes, including quasi-cyclic and spatially-coupled codes, as well as unstructured LDPC codes. We offer design guidelines for non-binary LDPC codes with outstanding performance in extremely low error-rate regimes; making them excellent candidates for data storage applications.In the asymptotic case, we provide a novel toolbox for the evaluation of families of non-binary graph-based codes. By utilizing insights from graph theory and combinatorics, we establish enumerators for a general family of graph-based codes which are constructed based on protographs. We provide asymptotic distributions of codewords and trapping sets for the family of protograph-based codes. Furthermore, we present an asymptotic enumeration of binary and non-binary elementary absorbing sets for regular code ensembles.The contributions of this dissertation can potentially impact a broad range of data storage and communication technologies that require excellent performance in high-reliability regimes.
Practical Disk Diffusion Test for Detecting Group B Streptococcus with Reduced Penicillin Susceptibility

ABSTRACT Although group B streptococcus (GBS) has been considered to be uniformly susceptible to β-lactams, the presence of GBS with reduced penicillin susceptibility (PRGBS) was recently confirmed genetically. We developed a feasible and reliable method for screening PRGBS in clinical microbiology laboratories using a combination of ceftibuten, oxacillin, and ceftizoxime disks.
An intra-visibility matrix based environment pre-processing for efficient Ray tracing

This paper presents a new approach to compute the image tree of given order of ray interaction for ray-tracing. The intra-visibility of walls and vertical edges along with their angular position in the visibility region is computed. The image tree is readily created as the angular information is used to determine if a wall or vertical edge lies within an image illumination zone. Validation results show a considerable reduction in run times for image tree computations. The elimination of a recursive visibility algorithm for image tree creation is a first step towards efficient ray-tracing in mobile transmitter scenarios such as in vehicular networks.
Interference-aware resource allocation for device-to-device communications as an underlay using sequential second price auction

An innovative resource allocation scheme is proposed to improve the performance of device-to-device (D2D) communications as an underlay in the downlink (DL) cellular networks. To optimize the system sum rate over the resource sharing of both D2D and cellular modes, we introduce a sequential second price auction as the allocation mechanism. In the auction, all the spectrum resources are considered as a set of resource units, which are auctioned off by groups of D2D pairs in sequence. We first formulate the value of each resource unit for each D2D pair, as a basis of the proposed auction. And then a detailed auction algorithm is explained using a N-ary tree. The equilibrium path of a sequential second price auction is obtained in the auction process, and the state value of the leaf node in the end of the path represents the final allocation. The simulation results show that the proposed auction algorithm leads to a good performance on the system sum rate, efficiency and fairness.
A simple and robust algorithm for the detection of QRS complexes

The objective of this paper is to develop an easy, efficient and robust algorithm for the analysis of electrocardiogram signals. The technique used in this algorithm is based on the use of Moving Average Filters and Adaptive Thresholding for QRS complex detection. Several established ECG databases published on PhysioNet with sampling frequency ranging from 128Hz-1KHz, were used for analyzing the technique. The accuracy of the algorithm is determined on the basis of two statistical parameters: sensitivity (SE) and Positive Predictivity (+P).
Surveillance or Self-Surveillance? Behavioral Cues Can Increase the Rate of Drivers’ Pro-Environmental Behavior at a Long Wait Stop

By leaving their engines idling for long periods, drivers contribute unnecessarily to air pollution, waste fuel, and produce noise and fumes that harm the environment. Railway level crossings are sites where many cars idle, many times a day. In this research, testing two psychological theories of influence, we examine the potential to encourage drivers to switch off their ignition while waiting at rail crossings. Two field studies presented different signs at a busy rail crossing site with a 2-min average wait. Inducing public self-focus (via a “Watching Eyes” stimulus) was not effective, even when accompanied by a written behavioral instruction. Instead, cueing a private-self focus (“think of yourself”) was more effective, doubling the level of behavioral compliance. These findings confirm the need to engage the self when trying to instigate self-regulatory action, but that cues evoking self-surveillance may sometimes be more effective than cues that imply external surveillance.
Secondary choriocapillaritis in infectious chorioretinitis

Purpose: To analyse the indocyanine green angiography (ICGA) patterns of hypofluorescence that are compatible with choriocapillaritis that occur secondarily to toxoplasmic retinochoroiditis (ToRC), ocular tuberculosis (including tuberculous choroiditis, TuCR and multifocal serpiginoid choroiditis, TMSC) and syphilitic chorioretinitis (SyCR).
Comments on “A Convolution and Product Theorem for the Linear Canonical Transform”

A recent letter proposed a new convolution structure for the linear canonical transform , and claimed that theirs was clearly easier to implement in the designing of filters than the one suggested earlier in . However, we find that the two kinds of filtering methods are essentially the same through the theoretic deduction. That is to say, the two kinds of filtering methods can obtain the same effect through the same filtering steps. Taking digital signal processing into account, we analyze further the computation complexity according to the steps of multiplicative filter.
Cloning and high-level expression of the glutathione-independent formaldehyde dehydrogenase gene from Pseudomonas putida

A DNA fragment of 485 bp was specifically amplified by PCR with primers based on the N-terminal sequence of the purified formaldehyde dehydrogenase (EC 1.2.1.46) from Pseudomonas putida and on that of a cyanogen bromide-derived peptide. With this product as a probe, a gene coding for formaldehyde dehydrogenase (fdhA) in P. putida chromosomal DNA was cloned in Escherichia coli DH5 alpha. Sequencing analysis revealed that the fdhA gene contained 1,197-bp open reading frame, encoding a protein composed of 399 amino acid residues whose calculated molecular weight was 42,082. The transformant of E. coli DH5 alpha harboring the hybrid plasmid, pFDHK3DN71, showed about 50-fold-higher formaldehyde dehydrogenase activity than P. putida. The predicted amino acid sequence contained several features characteristic of the zinc-containing medium-chain alcohol dehydrogenase (ADH) family. Most of the glycine residues strictly conserved within the family, including a Gly-Xaa-Gly-Xaa-Xaa-Gly pattern in the coenzyme binding domain, were well conserved in this enzyme. Regions around both the catalytic and the structural zinc atoms were also conserved. Analyses of structural and enzymatic characteristics indicated that P. putida FDH belongs to the medium-chain ADH family, with mixed properties of mammalian class I and III ADHs.
An on-chip blood serum separator using self-assembled silica microsphere filter

In this paper, we report a disposable on-chip blood serum separator using self-assembled silica microsphere filter, which can passively separate serum from human blood. A self-assembly packing method was developed for packing silica microspheres through a microfluidic channel on cyclic olefin copolymer (COC) substrate. Using the self-assembled microsphere filter, serum has been successfully separated from diluted human blood. The filters realized in this work are suitable for incorporating into a disposable polymer lab-on-a-chip, which can perform point-of-care testing (POTC) for clinical diagnostics using human blood.
The influence of tumor- and treatment-related factors on the development of local recurrence in osteosarcoma after adequate surgery. An analysis of 1355 patients treated on neoadjuvant Cooperative Osteosarcoma Study Group protocols.

BACKGROUND Local recurrence (LR) in osteosarcoma is associated with very poor prognosis. We sought to evaluate which factors correlate with LR in patients who achieved complete surgical remission with adequate margins. PATIENTS AND METHODS We analyzed 1355 patients with previously untreated high-grade central osteosarcoma of the extremities, the shoulder and the pelvis registered in neoadjuvant Cooperative Osteosarcoma Study Group trials between 1986 and 2005. Seventy-six patients developed LR. RESULTS Median follow-up was 5.56 years. No participation in a study, pelvic tumor site, limb-sparing surgery, soft tissue infiltration beyond the periosteum, poor response to neoadjuvant chemotherapy, failure to complete the planned chemotherapy protocol and biopsy at a center other than the one performing the tumor resection were significantly associated with a higher LR rate. No differences were found for varying surgical margin widths. Surgical treatment at centers with small patient volume and additional surgery in the primary tumor area, other than biopsy and tumor resection, were significantly associated with a higher rate of ablative surgery. CONCLUSIONS Patient enrollment in clinical trials and performing the biopsy at experienced institutions capable of undertaking the tumor resection without compromising the oncological and functional outcome should be pursued in the future.
Lytic Activity of LysH 5 Endolysin Secreted by Lactococcus lactis Using the Secretion Signal Sequence of Bacteriocin Lcn 972

Bacteriophage endolysins have an interesting potential as antimicrobials. The endolysin LysH5, encoded by Staphylococcus aureus phage vB_SauS-phi-IPLA88, was expressed and secreted in Lactococcus lactis using the signal peptide of bacteriocin lactococcin 972 and lactococcal constitutive and inducible promoters. Up to 80 U/mg of extracellular active endolysin was detected in culture supernatants, but most of the protein (up to 323 U/mg) remained in the cell extracts.
Web Engineering for Workflow-based Applications: Models, Systems and Methodologies

This dissertation presents novel solutions for the construction of Workflow-based Web applications: The Web Engineering DSL Framework, a stakeholder-oriented Web Engineering methodology based on Domain-Specific Languages; the Workflow DSL for the efficient engineering of Web-based Workflows with strong stakeholder involvement; the Dialog DSL for the usability-oriented development of advanced Web-based dialogs; the Web Engineering Reuse Sphere enabling holistic, stakeholder-oriented reuse.
Case Report : Contagious Ecthyma-Deviations in the Anatomical Appearance of Lesions in an Outbreak in Lambs in Israel

Bouznach, A. 246 INTRODUCTION Contagious ecthyma (orf, contagious pustular dermatitis) is a viral disease of sheep, goats and many species of wild ruminants (1, 2). Orf is also a zoonotic disease affecting humans, usually those working with small ruminants (1, 2, 3) and rarely other species like dogs and rabbits (1, 2). Orf is distributed worldwide and is endemic in the Mediterranean region and primarily affects young sheep and goats but can be present at any age (4). Contagious ecthyma is caused by orf virus of the genus parapoxvirus – epitheliotropic parapoxvirus (2, 3) of the family poxviridae. The orf lesions appear 6-7 days after infection of abrasions and wounds. The disease is characterized by the formation of crusty vesiculo-proliferative lesions, papules, pustules, scabs covering ulceration, and granulation tissue (1, 2). In lambs, lesions are usually located around the mouth on lips and nostrils. Lesions can also be found within the buccal cavity and occasionally in the osphagus and abomasum (5). Rarely lesions can be seen in the rumen mucosa (1, 3, 6). The infection initiates in scar tissue and the virus can first be detected in newly formed epidermis (1). Swelling and vacuolization of the keratinocytes and eosinophilic cytoplasmic inclusion bodies occasionally can be seen in histological section of squamous epithelial cells (7). Diagnostic confirmation of the disease is made by virus identification using PCR. This unusual case report describes the rare appearance of orf lesions in the in gingival and rumen mucosa of lambs.
Attitudes to food differ between adolescent dieters and non-dieters from Otago, New Zealand, but overall food intake does not

Abstract Objective There is increasing pressure for adolescents to be thin and this may not always be acted upon in healthy ways; for example, certain foods or food groups may be restricted or meals skipped. As foods are not eaten in isolation it is useful to examine dietary patterns and associated psychosocial factors to better understand eating behaviour. The aim of the present study was to identify correlates of ‘dieting’ in adolescents from Otago, New Zealand. Design A web-based survey was conducted in 2009, collecting information on food consumption and factors potentially associated with food consumption. Principal components analysis was used to investigate dietary patterns. Correlates were examined in 1329 students using multiple logistic regression analysis. Setting Nineteen secondary schools in the province of Otago, New Zealand. Subjects Students from school years 9 and 10 (mean age 14·1 (sd 0·7) years). Results There was no relationship between dieting and dietary patterns. Those not dieting were 17 % (95 % CI 7, 26 %) more likely to eat lunch and 22 % (95 % CI 3, 37 %) more likely to eat an evening meal on one more weekday than those who were dieting. Those who reported dieting were more likely to report healthiness (OR = 2·18, 95 % CI 1·11, 4·26) as an important factor when choosing food and that eating fruit and vegetables makes you better looking. No sex by dieting interaction was found. Conclusions In this cohort, while there was no difference in actual food consumption between dieters and non-dieters, there were significant differences in attitudes to food.
Possible superconductivity in nearly antiferromagnetic itinerant fermion systems.

Strong spin fluctuations arising in itinerant fermion systems close to a magnetic instability may induce or inhibit superconductivity depending on the nesting wave vector q/sub 0/ for which the instability occurs. If chemically bondq/sub 0/chemically bond is small but finite, triplet pairing is favored and singlet pairing is suppressed as efficiently as in nearly ferromagnetic systems (q/sub 0/ = 0). If chemically bondq/sub 0/chemically bond is large, there is a repulsive contribution from backward scattering by which triplet as well as singlet pairings are strongly depressed. The cases of UPt/sub 3/, CePb/sub 3/, and some organic compounds are considered.
Development of a Vital Fluorescent Staining Method for Monitoring Bacterial Transport in Subsurface Environments

ABSTRACT Previous bacterial transport studies have utilized fluorophores which have been shown to adversely affect the physiology of stained cells. This research was undertaken to identify alternative fluorescent stains that do not adversely affect the transport or viability of bacteria. Initial work was performed with a groundwater isolate,Comamonas sp. strain DA001. Potential compounds were first screened to determine staining efficiencies and adverse side effects. 5-(And 6-)-carboxyfluorescein diacetate, succinimidyl ester (CFDA/SE) efficiently stained DA001 without causing undesirable effects on cell adhesion or viability. Members of many other gram-negative and gram-positive bacterial genera were also effectively stained with CFDA/SE. More than 95% of CFDA/SE-stained Comamonas sp. strain DA001 cells incubated in artificial groundwater (under no-growth conditions) remained fluorescent for at least 28 days as determined by epifluorescent microscopy and flow cytometry. No differences in the survival and culturability of CFDA/SE-stained and unstained DA001 cells in groundwater or saturated sediment microcosms were detected. The bright, yellow-green cells were readily distinguished from autofluorescing sediment particles by epifluorescence microscopy. A high throughput method using microplate spectrofluorometry was developed, which had a detection limit of mid-105CFDA-stained cells/ml; the detection limit for flow cytometry was on the order of 1,000 cells/ml. The results of laboratory-scale bacterial transport experiments performed with intact sediment cores and nondividing DA001 cells revealed good agreement between the aqueous cell concentrations determined by the microplate assay and those determined by other enumeration methods. This research indicates that CFDA/SE is very efficient for labeling cells for bacterial transport experiments and that it may be useful for other microbial ecology research as well.