Miracle-dz/UniFAR-FTUs huggingface dataset:
Replacement of endogenous cholesteryl esters of low density lipoprotein with exogenous cholesteryl linoleate. Reconstitution of a biologically active lipoprotein particle.

The cholesteryl esters of human plasma low density lipoprotein (LDL) reside in a neutral lipid core sur- rounded by a polar shell consisting of phospholipids, unesterified cholesterol, and apoprotein B. In the cur- rent paper, we describe a procedure by which more than 99% of the core cholesteryl esters can be removed from the LDL particle by heptane extraction and re- placed with an equal amount of exogenous cholesteryl linoleate. The reconstituted water-soluble LDL particle resembled native LDL with regard to the following physical and chemical properties: The of the reconstituted was slightly greater determined by sucrose density centrifugation.
Users’ computer human interface capabilities in information system development life cycle: An organizational perspective

Computer Human interaction (CHI) capabilities are critical for successful systems development life cycle (SDLC) in order to manage information systems (IS) effectively. CHI capabilities play crucial roles in interfacing information technology (IT) deployment with organisational goals. It is said that success of IT deployment is dependent on a successful process, usability, usefulness of IS products and services which are CHI centric. End-users in the organisation contribute the most towards CHI issues and their capabilities influence success of IT deployment projects. However, modern SDLC models are based more on organizational needs than understanding CHI capability needs. This incapability shows up in the form of poor reflection of user-intentions to use the services in post implementation stages. Insensitivities of IT acquirers towards end-users contribute to the gap between satisfying organizational needs, end-user deliveries and supporting organisational goals in the process. This problem can be addressed by carefully integrating end-user capabilities issues in the SDLC process to achieve a truly human-centered IS development. In this paper a framework is suggested to capture CHI capabilities in an acquiring organisation. The framework is tested for its fitness through structural equation modeling (SEM) with active participation from thirteen organizations. A case is discussed to appreciate application of the framework.
Specific Labeling of the Bovine Heart Mitochondrial Phosphate Carrier with Fluorescein 5-Isothiocyanate

The amine/SH-modifying fluorescein 5-isothiocyanate (FITC) specifically labeled Lys185in the putative membrane-spanning region of the phosphate carrier from both the cytosolic and matrix sides of bovine heart mitochondria at 0 °C and pH 7.2, and the labeling inhibited the phosphate transport. Nonmodifying fluorescein derivatives having similar structural features to those of ADP and ATP (Majima, E., Yamaguchi, N., Chuman, H., Shinohara, Y., Ishida, M., Goto, S., and Terada, H. (1998)Biochemistry 37, 424–432) inhibited the specific FITC labeling and phosphate transport, but the nonfluorescein phenylisothiocyanate did not inhibit FITC labeling, suggesting that there is a region recognizing the adenine nucleotides in the phosphate carrier and that this region is closely associated with the transport activity. The phosphate transport inhibitor pyridoxal 5′-phosphate inhibited the specific FITC labeling, possibly due to competitive modification of Lys185. In addition, FITC inhibited the ADP transport and specific labeling of the ADP/ATP carrier with the fluorescein SH reagent eosin 5-maleimide. Based on these results, we discuss the structural features of the phosphate carrier in relation to its transport activity.
The impact of HIV tropism on decreases in CD4 cell count, clinical progression, and subsequent response to a first antiretroviral therapy regimen.

BACKGROUND Human immunodeficiency virus (HIV) uses 2 distinct chemokine receptors, CCR5 (R5) or CXCR4 (X4), during entry. Viruses may be R5 tropic, X4 tropic, or dual/mixed (D/M) tropic. R5-tropic virus predominates at high CD4 cell counts, with the number of X4-tropic strains increasing as CD4 cell count decreases. METHODS We investigated the relationship between tropism and decreases in CD4 cell count before antiretroviral therapy initiation, the frequency of clinical events, and responses to antiretroviral therapy in a cohort of treatment-naive patients. RESULTS Four hundred two treatment-naive patients underwent tropism determination; 326 harbored R5-tropic virus, and 76 harbored X4- or D/M-tropic virus. After adjustment for baseline characteristics, the rate of decrease in CD4 cell count was significantly greater in patients infected with X4- or D/M-tropic virus at 12 months (P=.026). Two hundred twenty-nine individuals infected with R5-tropic virus and 60 individuals infected with X4- or D/M-tropic virus commenced antiretroviral therapy between tropism testing and the time of data analysis. Time to viral suppression and the proportion of patients achieving viral suppression were similar at 6, 12, and 24 months. CD4 cell count increases were similar. Clinical events were significantly more common in the group infected with X4- or D/M-tropic virus. Multivariate analysis demonstrated a relative risk of experiencing a clinical event of 2.56 (95% confidence interval, 1.37-4.76; P=.003) among patients infected with X4- or D/M-tropic virus. CONCLUSIONS The presence of D/M- or X4-tropic virus has a deleterious effect on CD4 cell count decrease and risk of clinical disease. Response to standard antiretroviral therapy is not affected by viral tropism.
Broadside Dual-Channel Orthogonal-Polarization Radiation Using a Double-Asymmetric Periodic Leaky-Wave Antenna

This paper demonstrates that double unit-cell asymmetry in periodic leaky-wave antennas (P-LWAs), i.e., asymmetry with respect to both the longitudinal and transversal axes of the structure—longitudinal asymmetry (LA) and transversal asymmetry (TA)—allows for the simultaneous broadside radiation of two orthogonal modes excited at the two ports of the antenna. This means that the antenna may simultaneously support two orthogonal channels, which represents interesting polarization diversity characteristics for wireless communications. The double asymmetric (DA) unit cell combines a circularly polarized LA unit cell and a coupled mode TA unit cell, where the former provides equal radiation in the series and shunt modes while the latter separates these two modes in terms of their excitation ports. It is also shown that the degree of TA in the DA unit cell controls the cross-polarization discrimination level. The DA P-LWA concept is illustrated by two examples, a series-fed line-connected patch (SF-LCP) P-LWA and a series-fed capacitively coupled patch (SF-CCP) P-LWA, via full-wave simulation and also experiment for the SF-LCP P-LWA case.
Personalized Multi-Objective Approach for Refactoring Recommendations

Refactoring is an extremely important solution to reduce and manage the growing complexity of software systems. However, maintaining a high-level code quality can be expensive since time and monetary pressures force developers to neglect to improve the quality of their source code. Thus, programmers are “opportunistic” when they apply refactorings since most of them are interested in improving the quality of the code fragments that they frequently update or those related to the planned activities for the next release (fixing bugs, adding new functionalities, etc.). In this work, we describe a search based approach to recommend refactorings based on the analysis of the history of changes to maximize the recommended refactorings for 1) recently modified classes, 2) classes containing incomplete refactorings detected in previous releases, and 3) buggy classes identified based on bug reports. The obtained results on 2 industrial projects shows significant improvements of the relevance of recommended refactorings, as evaluated by the original developers of the systems, and much lower execution time comparing to existing search-based refactoring techniques. Keywords— Search-based software engineering, multi-objective simulated annealing, refactoring, history of changes.
A cell-autonomous, ubiquitous marker for the analysis of Drosophila genetic mosaics.

Mosaic analysis, the study of animals containing cells of two different genotypes, has been used to address a wealth of questions in developmental biology. Up to now, the cell markers used to distinguish cells of the two genotypes have only been applicable to specific experimental situations (e.g., only in adult wings). We have designed a general purpose cell marker for mosaic analysis. It consists of the bacterial LacZ gene expressed under the control of the constitutive promoter of the Drosophila armadillo gene. Transformants carrying this fusion gene express beta-galactosidase in all tissue and at all stages analyzed. Zygotic expression is detectable as early as gastrulation. In mosaics obtained by nuclear transplantation, cells carrying the transgene are easily distinguished from beta-galactosidase-negative host cells. The marker should also be useful for mosaics generated with the "Flp technique. "
Teller II and Cardiff Acuity Testing in a School-Age Deafblind Population

Purpose. To compare Teller Acuity Cards II (TAC II) and Cardiff Acuity Test (CAT) acuities, test-retest reliability and testability in children with visual, auditory, motor and cognitive impairments. Methods. Twenty-one children designated as “Deafblind” were tested under binocular conditions. Visual acuity was measured with both the TAC II and CAT in two sessions, with test order randomized and counterbalanced between sessions. Visual acuity, examiner confidence in the acuity result (3 point scale), testing time, and level of motor impairment (3 point scale) were recorded. Information about visual and auditory function and ocular and medical diagnoses were obtained by record review. Results. The success rate was high (95%) and test time similar (p = 0.267) for both tests (TAC II, 204 ± 111 s; CAT, 222 ± 111 s). Mean LogMAR acuities were not significantly different (TAC II, 0.82 ± 0.47; CAT, 0.72 ± 0.47; p = 0.068). The 95% limits of agreement for LogMAR test-retest differences were ±0.60 for TAC II and ±0.70 for the CAT and there was a trend for increased variability with poorer acuity for the CAT test only. Conclusions. The TAC II and CAT give similar estimates of acuity, test-retest reliability, and testing time in this small population of “Deafblind” children. Future studies should be designed to explore whether these results are consistent in subpopulations, such as Deafblind children with very poor vision and/or significant motor impairment. Moreover, additional study is necessary to evaluate the effect of patient characteristics on the examiner’s ability to make threshold acuity judgements.
Retrieval Processes in Adults With ADHD: A RAVLT Study

Attention-deficit hyperactivity disorder (ADHD) is associated with memory deficiencies. In the current study we compared different aspects of verbal memory using standard and constructed measures of the Rey auditory verbal learning test (RAVLT). Performance on learning and recognition measures of RAVLT was similar in both ADHD and control groups. In contrast, adults with ADHD committed more double recalls and intrusion errors, indicating inaccurate recall processes. These findings suggest that memory problems in adults with ADHD may be caused by deficient executive processes that support retrieval from memory.
A diplexer design method using an augmented channel filter approach

A new method of microwave diplexer design is presented. The new technique does not require a final diplexer tuning. The method is a modification of the technique based on accurate channel filters synthesis using surrogate models of coupling coefficients in order to obtain initial structure dimensions [1]. Here the structure optimized during channel synthesis is modified to assure correct loading of the junction. By doing so, the diplexer response after channels synthesis agrees with design specification and diplexer tuning is not needed.
Convex optimization approach to identify fusion for multisensor target tracking

We consider the problem of identity fusion for a multisensor target tracking system whereby the sensors generate reports on the target identities. Since sensor reports are typically fuzzy, incomplete, or inconsistent, the fusion of such sensor reports becomes a major challenge. In this paper, we introduce a new identity fusion method based on the minimization of inconsistencies among the sensor reports by using a convex quadratic programming formulation. In contrast to Dempster-Shafer's evidential reasoning approach which suffers from exponentially growing complexity, our approach is highly efficient (polynomial time solvable). Moreover, our approach can fuse sensor reports of the form more general than that allowed by the evidential reasoning theory. Simulation results show that our method generates reasonable fusion results which are similar to that obtained via the evidential reasoning theory.
Solution structure and backbone dynamics of an antigen‐free heavy chain variable domain (VHH) from Llama

Camelids, (dromedaries, camels, and llamas) produce heavy‐chains antibodies, with their antigen recognition sites composed of a single VH‐like domain, referred to as VHH. The solution structure of one of these VHHs domains (VHH‐H14), raised against the α subunit of the human chorionic gonadotropin hormone (hCG), has been determined by 15N heteronuclear three‐dimensional NMR spectroscopy. The framework is well resolved within the set of 20 best‐calculated NMR structures and is close to that of classical VH domains from vertebrate antibodies, consisting of two antiparallel β‐sheets organized in a β‐barrel. Loops display a lower precision, especially the Complementarity Determining Regions (CDRs), involved in antigen recognition. Comparison of the three‐dimensional VHH‐H14 solution structure with its previously solved crystal structure (Spinelli et al., Nature Struct. Biol. 1996;3:752–757) reveals a high similarity to the framework, whereas significant conformational differences occur on CDRs, leading to the assumption that the antigen recognition site is a more mobile part. In order to deepen our insights into the dynamics of VHH‐H14 in solution, 15N relaxation was measured with longitudinal R1 and transverse R2 self‐relaxation rates, and 15N steady‐state heteronuclear nuclear Overhauser enhancements (NOE), making it possible to probe picosecond‐to‐millisecond internal motions. Determination of dynamic parameters (S2, τe, and Rex) through the Lipari‐Szabo Model‐free approach enables the identification of several regions with enhanced dynamics. Especially, the mobility measurements from NMR confirm that the antigen recognition site is the most mobile part of the VHH‐H14 domain on picosecond‐to‐nanosecond fast time scales. Several residues belonging to the three CDRs are submitted to chemical exchange processes occurring on slow microsecond‐to‐millisecond time scales, suggesting that the formation of the VHH/antigen complex should be accompanied by structural changes. Proteins 2002;47:546–555. © 2002 Wiley‐Liss, Inc.
Geomagnetic Surface Navigation Using Adaptive EKF

In need of accurate and covert positioning, a geomagnetic surface navigation system is investigated in the paper. The Earth anomaly magnetic field intensity is selected as the reference to bound the INS (inertial navigation system) errors. Using stochastic linearization technique, we have proposed an EKF (extended Kalman filtering) algorithm which is adaptive in two aspects: linearization region size determination and linearization noise variance estimation. Simulation results show that the proposed algorithm can achieve high positioning accuracy with moderate initial position errors and has great robustness with respect to the velocity errors, attitude errors and the geomagnetic map quality. The geomagnetic navigation system can be extended to air and underwater applications.
Protease activity and host cell binding of the 42-kDa rhoptry protein from Toxoplasma gondii after secretion.

Three proteases were identified in the excretory/secretory proteins (ESP) from Toxoplasma gondii by the gelatin acrylamide gel electrophoresis (GAGE), of which the molecular masses were 80, 70, and 42 kDa. One of the proteases with 42 kDa was reactive to a monoclonal antibody (mAb), Tg786 clone, which was localized in the rhoptry of T. gondii by immunohistochemistry. The protease was maximally active at the pH range between 7.5 and 8.5, and was sensitive to inhibition by TPCK and EGTA. The gelatinolytic activity of the protease was dependent on the concentration of calcium ion. The protease was active only in the millimolar ranges of calcium but not in micromolar ranges, implicating that the secretion is critical event for the activation of the protease. The secreted protease was shown to bind to the host cells upon Western blot and immunofluorescence analysis. It is suggested that the protease may target to the plasma membrane of the host cells, which provides appropriate environment for the entry of the parasite into host cells. The mAb (Tg786) of T. gondii also reacted with a protein of the same size and equivalent locality of rhoptry in Neospora caninum, a similar Apicomplexan protozoa, suggesting that secreted protease mediates a common function in the mechanism of entry into host cells.
Near Optimal Jointly Private Packing Algorithms via Dual Multiplicative Weight Update

We present an improved (e, Δ)-jointly differentially private algorithm for packing problems. Our algorithm gives a feasible output that is approximately optimal up to an an additive factor as long as the supply of each resource is at least [Equation], where m is the number of resources. This improves the previous result by Hsu et al. (SODA '16), which requires the total supply to be at least O(m2/αe), and only guarantees approximate feasibility in terms of total violation. Further, we complement our algorithm with an almost matching hardness result, showing that [Equation] supply is necessary for any (e, Δ)-jointly differentially private algorithm to compute an approximately optimal packing solution. Finally, we introduce an alternative approach that runs in linear time, is exactly truthful, can be implemented online, and can be e-jointly differentially private, but requires a larger supply of each resource.
Development of neuromuscular organization in the ctenophore Pleurobrachia bachei

The phylogenetic position of the phylum Ctenophora and the nature of ctenphore nervous systems are highly debated topics in modern evolutionary biology. However, very little is known about the organization of ctenophore neural and muscular systems, and virtually nothing has been reported about their embryogenesis. Here we have characterized the neural and muscular development of the sea gooseberry, Pleurobrachia bachei, starting from the cleavage stages to posthatching larvae. Scanning electron microscopy and immunochemistry were used to describe the formation of the embryonic mouth, tentacles, combs, aboral organ, and putative sensory cells. The muscles started their specification at the end of the first day of Pleurobrachia development. In contrast, neurons appeared 2 days after myogenesis, just before the hatching of fully formed cydippid larvae. The first tubulin‐immunoreactive neurons, a small group of four to six cells with neuronal processes, was initially recognized at the aboral pole during the third day of development. Surprisingly, this observed neurogenesis occurred after the emergence of distinct behavioral patterns in the embryos. Thus, the embryonic behavior associated with comb cilia beatings and initial muscle organization does not require morphologically defined neurons and their elongated neurites. This study provides the first description of neuromuscular development in the enigmatic ctenophores and establishes the foundation for future research using emerging genomic tools and resources. J. Comp. Neurol. 524:136–151, 2016. © 2015 Wiley Periodicals, Inc.
Diversity of the cadherin‐related neuronal receptor/protocadherin family and possible DNA rearrangement in the brain

Both the brain and the immune systems are complex. The complexity is generated by enormously diversified single cells. In the immune system, extensive cell death, gene regulation of immunoglobulin (Ig) and T‐cell receptor (TCR) gene expression, and somatic rearrangement and mutations are known to generate an enormous diversity of lymphocytes. In this process, double‐strand DNA breaks (DSBs) and DSB repair play significant roles. These processes at a DNA level are also physiologically significant in the nervous system during neurogenesis, and chromosomal variations have been detected in the nucleus of differentiated neurones. In another parallel with the immune system, cadherin‐related neuronal receptors (CNRs) are diversified synaptic proteins. The CNR genes belong to protocadherin (Pcdh) gene clusters. Genomic organizations of CNR/Pcdh genes are similar to that of the Ig and TCR genes. Somatic mutations in and combinatorial gene regulation of CNR/Pcdh transcripts during neurogenesis have been reported. This review focuses on the diversity of the CNR/Pcdh genes and possible DNA diversification in the nervous system.
Ammonia-Oxidizing Bacteria along Meadow-to-Forest Transects in the Oregon Cascade Mountains

ABSTRACT Although nitrification has been well studied in coniferous forests of Western North America, communities of NH3-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization and nitrification potential rates changed significantly between vegetation zones. Nonetheless, terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR-amplified NH3 monooxygenase subunit A gene (amoA) showed the same DNA fragments (TaqI [283 bp], CfoI [66 bp], and AluI [392 bp]) to dominate ≥45 of 47 soil samples recovered from both sites. Two fragments (491-bp AluI [AluI491] and CfoI135) were found more frequently in meadow and transition zone soil samples than in forest samples at both sites. At the Lookout site the combination AluI491-CfoI135 was found primarily in meadow samples expressing the highest N mineralization rates. Four unique amoA sequences were identified among 15 isolates recovered into pure culture from various transect locations. Six isolates possessed the most common T-RFLP amoA fingerprint of the soil samples (TaqI283-AluI392-CfoI66), and their amoA sequences shared 99.8% similarity with a cultured species, Nitrosospira sp. strain Ka4 (cluster 4). The other three amoA sequences were most similar to sequences of Nitrosospira sp. strain Nsp1 and Nitrosospira briensis (cluster 3). 16S ribosomal DNA sequence analysis confirmed the affiliation of these isolates with Nitrosospira clusters 3 and 4. Two amoA clone sequences matched T-RFLP fingerprints found in soil, but they were not found among the isolates.
A statistical study of defect maps of large area VLSI IC's

Defect maps of 57 wafers containing large area VLSI IC's were analyzed in order to find a good match between the empirical distribution of defects and a theoretical model. Our main result is that the commonly employed models, most notably, the large area clustering negative binomial distribution, do not provide a sufficiently good match for these large area IC's. Only the recently proposed medium size clustering model is close enough to the empirical distribution. An even better match can be obtained either by combining two theoretical distributions or by a "censoring" procedure in which the worst chips are ignored. Another goal of the study was to find out whether certain portions of either the chip or the wafer had more defects than the others. >