Miracle-dz/UniFAR-FTUs huggingface dataset:
Border Control—A Membrane-Linked Interactome of Arabidopsis

Degrees of Separation Proteins embedded in membranes represent an interesting point of communication between the cell and its environment, but their localization to membranes can make them difficult to study. Jones et al. (p. 711) found an approach to catalog thousands of interactions involving membrane proteins and membrane-associated signaling machinery—including many previously uncharacterized proteins. With a focus on the model plant Arabidopsis, several of the identified interactions fill gaps in important signal transduction chains, while others point to functions for enigmatic unknown proteins. Amembrane and signaling protein interaction network for gene discovery and hypothesis generation is identified in Arabidopsis. Cellular membranes act as signaling platforms and control solute transport. Membrane receptors, transporters, and enzymes communicate with intracellular processes through protein-protein interactions. Using a split-ubiquitin yeast two-hybrid screen that covers a test-space of 6.4 × 106 pairs, we identified 12,102 membrane/signaling protein interactions from Arabidopsis. Besides confirmation of expected interactions such as heterotrimeric G protein subunit interactions and aquaporin oligomerization, >99% of the interactions were previously unknown. Interactions were confirmed at a rate of 32% in orthogonal in planta split–green fluorescent protein interaction assays, which was statistically indistinguishable from the confirmation rate for known interactions collected from literature (38%). Regulatory associations in membrane protein trafficking, turnover, and phosphorylation include regulation of potassium channel activity through abscisic acid signaling, transporter activity by a WNK kinase, and a brassinolide receptor kinase by trafficking-related proteins. These examples underscore the utility of the membrane/signaling protein interaction network for gene discovery and hypothesis generation in plants and other organisms.
Effect of treatments for depression on quality of life: a meta-analysis*

Abstract Cognitive-behavioral therapy (CBT) and selective serotonin reuptake inhibitors (SSRIs) are the two first-line treatments for depression, but little is known about their effects on quality of life (QOL). A meta-analysis was conducted to examine changes in QOL in adults with major depressive disorder who received CBT (24 studies examining 1969 patients) or SSRI treatment (13 studies examining 4286 patients) for their depression. Moderate improvements in QOL from pre to post-treatment were observed in both CBT (Hedges’ g = .63) and SSRI (Hedges’ g = .79) treatments. The effect size remained stable over the course of the follow-up period for CBT. No data were available to examine follow-ups in the SSRI group. QOL effect sizes decreased linearly with publication year, and greater improvements in depression were significantly associated with greater improvements in QOL for CBT, but not for SSRIs. CBT and SSRIs for depression were both associated with moderate improvements in QOL, but are possibly caused by different mechanisms.
Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing

Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.
Microsatellite Genotyping Clarified Conspicuous Accumulation of Candida parapsilosis at a Cardiothoracic Surgery Intensive Care Unit

ABSTRACT Candida parapsilosis has become a significant cause of invasive fungal infections in seriously ill patients. Nosocomial outbreaks through direct and indirect contact have been described. The aim of this study was the molecular characterization of what appeared to be an ongoing C. parapsilosis outbreak at the cardiothoracic intensive care unit of the University Hospital of Vienna between January 2007 and December 2008. Using two different molecular typing methods—automated repetitive sequence-based PCR (DiversiLab; bioMérieux) and microsatellite genotyping—we investigated the genetic relationship of 99 C. parapsilosis isolates. Eighty-three isolates originated from the cardiothoracic intensive care unit, while 16 isolates were random control isolates from other intensive care units and a different Austrian hospital. The 99 C. parapsilosis isolates analyzed by repetitive-element PCR all showed identical genotypes, suggesting an ongoing outbreak. In contrast, microsatellite genotyping showed a total of 56 different genotypes. Two major genotypes were observed in 10 and 15 isolates, respectively, whereas another 13 genotypes were observed in 2 to 4 isolates each. Forty-one genotypes were observed only once. Closely related genotypes that differed in only a single microsatellite marker were grouped into clonal complexes. When it comes to C. parapsilosis, microsatellite genotyping is a more discriminative method than repetitive-element PCR genotyping to investigate outbreaks.
Ideal body size beliefs and weight concerns of fourth-grade children.

OBJECTIVE The purpose of this study was to assess racial and gender differences in perceptions of ideal body size among White and Black fourth-grade children. METHOD A random sample of 817 children (51.4% female, 51.8% White, and mean age 9 years) participated in a body image and weight concern survey. RESULTS Using socioeconomic status (SES), race, and gender as independent variables, Black children selected significantly heavier ideal sizes than White children for self, male child, female child, adult male, and adult female. Although almost one half (46%) of Black females wanted to be thinner than their current size, their body size selections were significantly larger than those of White females. Black and White males differed only in the selections of ideal-female child and adult sizes. Cross-gender comparisons indicated females and Whites experience more body dissatisfaction and weight concern than males and Blacks. DISCUSSION Our study indicates that early in the sociocultural development of children, gender, race, and SES are influential factors in selecting ideal body size and determining body satisfaction.
Relationship between HIV-1 Env subtypes A and D and disease progression in a rural Ugandan cohort

ObjectiveTo investigate the role of HIV-1 envelope subtypes on disease progression in a rural cohort of Ugandan adults where two major HIV-1 subtypes (A and D) exist. MethodsParticipants of a clinical cohort seen between December 1995 and December 1998 had blood collected for HIV-1 subtyping. These included prevalent cases (people already infected with HIV at the start of the study in 1990) and incident cases (those who seroconverted between 1990 and December 1998). HIV-1 subtyping was carried out by heteroduplex mobility assay and DNA sequencing in the V3 env region. Disease progression was measured by the rate of CD4 lymphocyte count decline, clinical progression for the incident cases as time from seroconversion to AIDS or death, to first CD4 lymphocyte count < 200 × 106/l and to the World Health Organization clinical stage 3. All analyses were adjusted for age and sex. ResultsOne hundred and sixty-four individuals, including 47 prevalent and 117 incident cases, had V3 env subtype data of which 65 (40%) were subtyped as A and 99 as D. In the incident cases, 44 (38%) were subtyped as A and 73 as D. There was a suggestion that for most end-points A had a slower progression than D. The cumulative probability of remaining free from AIDS or death at 6 years post-seroconversion was 0.72 [95% confidence interval (CI), 0.50 to 0.85] for A and 0.58 (95% CI, 0.42 to 0.71) for D, and the adjusted hazard ratio of subtype D compared to A was estimated to be 1.39 (95% CI, 0.66 to 2.94;P = 0.39). The estimated difference in rates of decline in square root CD4 lymphocyte counts was −0.41 per year (95% CI, −0.98 to 0.15;P = 0.15). ConclusionThis study suggests that although subtype A may have a slower progression than D, HIV-1 envelope subtype is not a major factor in determining the progression of HIV-1 disease in a rural population in Uganda.
Machine Translation without Words through Substring Alignment

In this paper, we demonstrate that accurate machine translation is possible without the concept of "words," treating MT as a problem of transformation between character strings. We achieve this result by applying phrasal inversion transduction grammar alignment techniques to character strings to train a character-based translation model, and using this in the phrase-based MT framework. We also propose a look-ahead parsing algorithm and substring-informed prior probabilities to achieve more effective and efficient alignment. In an evaluation, we demonstrate that character-based translation can achieve results that compare to word-based systems while effectively translating unknown and uncommon words over several language pairs.
Protein glycosylation and diseases: blood and urinary oligosaccharides as markers for diagnosis and therapeutic monitoring.

BACKGROUND N- and O-oligosaccharide variants on glycoproteins (glycoforms) can lead to alterations in protein activity or function that may manifest themselves as overt disease. APPROACH This review summarizes those diseases that are known to be the result of an inherited or acquired glycoprotein oligosaccharide structural alteration and that are diagnosed in blood or urine by chemical characterization of that oligosaccharide alteration. CONTENT The biochemical synthesis steps and catabolic pathways important in determining glycoprotein function are outlined with emphasis on alterations that lead to modified function. Clinical and biochemical aspects of the diagnosis are described for inherited diseases such as I-cell disease, congenital disorders of glycosylation, leukocyte adhesion deficiency type II, hereditary erythroblastic multinuclearity with a positive acidified serum test, and Wiskott-Aldrich syndrome. We also review the laboratory use of measurements of glycoforms related to acquired diseases such as alcoholism and cancer. CONCLUSIONS Identification of glycoprotein glycoforms is becoming an increasingly important laboratory contribution to the diagnosis and management of human diseases as more diseases are found to result from glycan structural alterations.
Transmembrane Topology of Glucose-6-Phosphatase*

Deficiency of microsomal glucose-6-phosphatase (G6Pase), the key enzyme in glucose homeostasis, causes glycogen storage disease type 1a, an autosomal recessive disorder. Characterization of the transmembrane topology of G6Pase should facilitate the identification of amino acid residues contributing to the active site and broaden our understanding of the effects of mutations that cause glycogen storage disease type 1a. Using N- and C-terminal tagged G6Pase, we show that in intact microsomes, the N terminus is resistant to protease digestion, whereas the C terminus is sensitive to such treatment. Our results demonstrate that G6Pase possesses an odd number of transmembrane helices, with its N and C termini facing the endoplasmic reticulum lumen and the cytoplasm, respectively. During catalysis, a phosphoryl-enzyme intermediate is formed, and the phosphoryl acceptor in G6Pase is a His residue. Sequence alignment suggests that mammalian G6Pases, lipid phosphatases, acid phosphatases, and a vanadium-containing chloroperoxidase (whose tertiary structure is known) share a conserved phosphatase motif. Active-site alignment of the vanadium-containing chloroperoxidase and G6Pases predicts that Arg-83, His-119, and His-176 in G6Pase contribute to the active site and that His-176 is the residue that covalently binds the phosphoryl moiety during catalysis. This alignment also predicts that Arg-83, His-119, and His-176 reside on the same side of the endoplasmic reticulum membrane, which is supported by the recently predicted nine-transmembrane helical model for G6Pase. We have previously shown that Arg-83 is involved in positioning the phosphate during catalysis and that His-119 is essential for G6Pase activity. Here we demonstrate that substitution of His-176 with structurally similar or dissimilar amino acids inactivates the enzyme, suggesting that His-176 could be the phosphoryl acceptor in G6Pase during catalysis.
A Method for Hand Gesture Recognition

Ongoing efforts at our laboratory have been aimed at developing techniques to reduce the complexity of interaction between humans and modern computer systems. As an example of these efforts, we have investigated the use of gesture recognition to allow more natural user interaction while still providing rich information content. In this paper, we present a real-time gesture recognition system which can track hand movement, orientation, and recognize the number of fingers being held up. This modularized system utilizes single-image processing techniques for noise reduction, hand segmentation, arm removal, hand movement calculations, orientation calculation, and a heuristic approach to finger-counting. With these capabilities in place, it is straight forward to utilize hand gestures to, for example, control a user interface. By supporting a more natural interface modality and utilizing only common hardware and software components, human-computer interaction can be simplified while also enriched. Sample images, results, and benchmark tests are presented. 2 Methods The system was developed using the Visual C++ compiler with the Image Processing Libraries (IPL) and Open Computer Vision (OpenCV) library from Intel. These libraries contain special image-processing functions which utilize nuances of Pentium chip architectures to ensure efficient computational performance.
Interactions in Nanoscale Arrays of Soft Magnetic Bi-Layers

Magnetic bi-layers are becoming increasingly popular as a medium for perpendicular patterned media. In order to understand the net interactions between the layers and between adjacent magnetic elements in an array, we use a coupled Preisach model to model the hysteresis loops we measured for a sample consisting two magnetically soft layers of FeCoTaZr, separated by an 0.8-nm Ru spacer layer. The model reproduces the major hysteresis loop to decent agreement. The model was then decoupled to reveal the reversal behavior of the individual layers. This paper demonstrates that coupled Preisach modeling of the hysteresis loop is an effective tool to analyze such interacting material systems.
A randomized behavioural trial targeting glycaemic index improves dietary, weight and metabolic outcomes in patients with type 2 diabetes

Abstract Objective Glycaemic index (GI) reflects the postprandial glucose response of carbohydrate-containing foods. A diet with lower GI may improve glycaemic control in people with diabetes. The purpose of the present study was to evaluate the change in outcomes following a behavioural intervention which promoted lower-GI foods among adults with diabetes. Design A pre-test–post-test control group design was used with participants randomly assigned to an immediate (experimental) or delayed (control) treatment group. The intervention included a 9-week, group-based intervention about carbohydrate and the glycaemic index. Dietary, anthropometric and metabolic measures were obtained pre/post-intervention in both groups and at 18-week follow-up for the immediate group. Setting The study was conducted in a rural community in the north-eastern USA. Subjects Adults having type 2 diabetes mellitus for ≥1 year, aged 40–70 years and not requiring insulin therapy (n 109) were recruited. Results Following the intervention, mean dietary GI (P < 0·001), percentage of energy from total fat (P < 0·01) and total dietary fibre (P < 0·01) improved in the immediate compared with the delayed group. Mean BMI (P < 0·0001), fasting plasma glucose (P = 0·03), postprandial glucose (P = 0·02), fructosamine (P = 0·02) and insulin sensitivity factor (P = 0·04) also improved in the immediate group compared with the delayed group. Mean waist circumference among males (P < 0·01) and body weight among males and females (P < 0·01) were significantly different between treatment groups. Conclusions Educating clients about carbohydrate and the glycaemic index can improve dietary intake and health outcomes among adults with type 2 diabetes.
Performance of various commercial TiO2 in photocatalytic degradation of a mixture of indoor air pollutants: Effect of photocatalyst and operating parameters

Photocatalytic oxidation (PCO) air cleaners can be installed in air handling units to reduce occupants’ exposure to hazardous gases, boost indoor air quality, and concomitantly lower HVAC energy consumption by lowering the required ventilation rate. In this work, photocatalytic activity of four commercialized titanium dioxide photocatalysts (P25, PC500, UV100, and S5-300A) for treating a mixture of seven prevalent volatile organic compounds (VOCs) were assessed in a continuous flow reactor. The impacts of major experimental factors, namely concentration (15–100 ppb), relative humidity level (0–60% at 23°C), and residence time (0.012–0.05 s), on the removal efficiency and by-products generation were examined. Photocatalysts were characterized by X-ray diffraction (XRD), nitrogen adsorption–desorption, Fourier transform infrared (FTIR), and scanning electron microscopy (SEM). UV100 possessed the highest values for total VOC removal efficiency, which could be attributed to its large surface area, high porosity, good crystallinity, and large population of surface hydroxyls. Regarding relative humidity, two dominant trends were found: i) increasing the humidity resulted in lower removal efficiencies or ii) existence of an optimum humidity level in some cases. The treatment efficiency followed the order: alcohols > ketones > aromatics > alkanes. The main by-products in the gas phase were formaldehyde, acetaldehyde, acetone, and propionaldehyde.
A Novel Headway-Based Vehicle-to-Vehicle Multi-Mode Broadcasting Protocol

We propose a novel application adaptive (multi-mode) headway-based broadcasting protocol that is most appropriate for public-safety applications in VANETs. Being headway-based, the proposed protocol possesses unique robustness at different speeds and traffic volumes. Moreover, it addresses application differences with a new multi-mode feature. The logic behind the new concepts/approaches adopted in the protocol and their merits are highlighted, supported with analysis and simulation.
Using Quaternions for Parametrizing 3-D Rotations in Unconstrained Nonlinear Optimization

In this paper we address the problem of using quaternions in unconstrained nonlinear optimization of 3-D rotations. Quaternions representing rotations have four elements but only three degrees of freedom, since they must be of norm one. This constraint has to be taken into account when applying e. g. the Levenberg-Marquardt algorithm, a method for unconstrained nonlinear optimization widely used in computer vision. We propose an easy to use method for achieving this. Experiments using our parametrization in photogrammetric bundle-adjustment are presented at the end of the paper.
Additional role for the ccd operon of F-plasmid as a transmissible persistence factor

Toxin-antitoxin (TA) systems are found on both bacterial plasmids and chromosomes, but in most cases their functional role is unclear. Gene knockouts often yield limited insights into functions of individual TA systems because of their redundancy. The well-characterized F-plasmid–based CcdAB TA system is important for F-plasmid maintenance. We have isolated several point mutants of the toxin CcdB that fail to bind to its cellular target, DNA gyrase, but retain binding to the antitoxin, CcdA. Expression of such mutants is shown to result in release of the WT toxin from a functional preexisting TA complex as well as derepression of the TA operon. One such inactive, active-site mutant of CcdB was used to demonstrate the contribution of CcdB to antibiotic persistence. Transient activation of WT CcdB either by coexpression of the mutant or by antibiotic/heat stress was shown to enhance the generation of drug-tolerant persisters in a process dependent on Lon protease and RecA. An F-plasmid containing a ccd locus can, therefore, function as a transmissible persistence factor.
Identification of Bacillus subtilis genes for septum placement and shape determination

The Bacillus subtilis divIVB1 mutation causes aberrant positioning of the septum during cell division, resulting in the formation of small, anucleate cells known as minicells. We report the cloning of the wild-type allele of divIVB1 and show that the mutation lies within a stretch of DNA containing two open reading frames whose predicted products are in part homologous to the products of the Escherichia coli minicell genes minC and minD. Just upstream of minC and minD, and in the same orientation, are three genes whose products are homologous to the products of the E. coli shape-determining genes mreB, mreC, and mreD. The B. subtilis mreB, mreC, and mreD genes are the site of a conditional mutation (rodB1) that causes the production of aberrantly shaped cells under restrictive conditions. Northern (RNA) hybridization experiments and disruption experiments based on the use of integrational plasmids indicate that the mre and min genes constitute a five-cistron operon. The possible involvement of min gene products in the switch from medial to polar placement of the septum during sporulation is discussed.
Multi-Part SIFT feature based particle filter for rotating object tracking

This paper presents an effective rotating object tracking algorithm based on Multi-Part SIFT (MPS) with particle filter. SIFT describes the characteristics of feature points that are invariant to changes in illumination, image noise, rotation, scaling and view direction. In order to use proper effect of SIFT feature for target tracking, single region based object representation is not enough. Therefore, the reference and target object are divided into some sub-regions in order to extract the potential SIFT features for measurement the similarity. This solution introduces spatial information in the representation, without compromising the benefits of SIFT features. In this propose algorithm, for smooth tracking we include the rotation information into the MPS based particle filter since the object rotation directly affects the tracking performance. Additionally, for the illumination changes as well as occlusions, it is required that reference model is adaptively updated. Within the particle filtering framework, we propose to address this adaptation problem using rapidly updated the reference model. We obtained a robust result with the proposed system in particle filter framework. Experimental results show that our system is robust against false target tracking, partial occlusion problem, rotation and scaling without extra computational cost.