Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence-independent Control of Peptide Conformation in Liposomal Vaccines for Targeting Protein Misfolding Diseases*

Synthetic peptide immunogens that mimic the conformation of a target epitope of pathological relevance offer the possibility to precisely control the immune response specificity. Here, we performed conformational analyses using a panel of peptides in order to investigate the key parameters controlling their conformation upon integration into liposomal bilayers. These revealed that the peptide lipidation pattern, the lipid anchor chain length, and the liposome surface charge all significantly alter peptide conformation. Peptide aggregation could also be modulated post-liposome assembly by the addition of distinct small molecule β-sheet breakers. Immunization of both mice and monkeys with a model liposomal vaccine containing β-sheet aggregated lipopeptide (Palm1–15) induced polyclonal IgG antibodies that specifically recognized β-sheet multimers over monomer or non-pathological native protein. The rational design of liposome-bound peptide immunogens with defined conformation opens up the possibility to generate vaccines against a range of protein misfolding diseases, such as Alzheimer disease.
Antioxidant Capacity and the Correlation with Major Phenolic Compounds, Anthocyanin, and Tocopherol Content in Various Extracts from the Wild Edible Boletus edulis Mushroom

Boletus edulis is a wild edible mushroom habitually consumed by rural populations. Ethanolic and methanolic extracts was obtained in cold and hot water from dried fruit bodies. The antioxidant activity of freeze-dried extracts from B. edulis were investigated using free radicals scavenging activity, reducing power, metal chelating effect, inhibition of lipid peroxidation, and the identification of antioxidant compounds. The levels of different compounds with antioxidant properties were higher in alcoholic extracts compared with aqueous extracts. Rosmarinic acid was the major phenolic compound, it being identified in a concentration between 7 ± 0.23 and 56 ± 0.15 mg/100 g extract. A positive correlation between the content of total phenols, flavonoids, anthocyanins, and tocopherols, and the antioxidant capacity of the extracts was determined. The results showed that the ethanolic extract of Romanian wild mushroom B. edulis represents a natural source of functional compounds.
IN THE NAME OF LOVE - THEME IN U2 SONGS

This research aim was to find out the most frequent Themes in the songs of the Irish pop music band U2, as well how such Themes reflect the overall message in the lyrics, as perceived by Brazilian listeners. We hypothesized that the social messages presumably present in their songs would be encoded in the Themes. Thematic analysis was conducted with the aim of finding the most recurrent Themes. We analyzed Themes in 83 U2 songs. Subsequently, the lyrics were submitted to commentary by undergraduate students majoring in English. They were asked to read the song lyrics and categorize them in five main message topics: socio-political, love (man/woman), religion, existentialism (philosophical issues) and homage. The students' comments were then compared to the Thematic analysis in order to see to what extent the Themes reflected the main message topics identified by the students.
A Randomized Clinical Trial of an Inactivated Avian Influenza A (H7N7) Vaccine

Background Concern for a pandemic caused by a newly emerged avian influenza A virus has led to clinical trials with candidate vaccines as preparation for such an event. Most trials have involved vaccines for influenza A (H5N1), A (H7N7) or A (H9N2). Objective To evaluate dosage-related safety and immunogenicity of an inactivated influenza A (H7N7) vaccine in humans. Design One hundred twenty-five healthy young adults were randomized to receive two doses intramuscularly of placebo or 7.5, 15, 45 or 90 µg of HA of an inactivated subunit influenza A (H7N7) vaccine (25 per group), four weeks apart. Reactogenicity was evaluated closely for one week and for any adverse effect for six months after each dose. Serum hemagglutination-inhibiting and neutralizing antibody responses were determined four weeks after each dose and at six months. Results Reactogenicity evaluations indicated the vaccinations were well tolerated. Only one subject developed a ≥4-fold serum hemagglutination-inhibition (HAI) antibody response and a final titer of ≥1∶40 four weeks after dose two and only five subjects developed a neutralizing antibody rise and a final titer of ≥1∶40 in tests performed at a central laboratory. Four of the five were given the 45 or 90 µg HA dosage. A more sensitive HAI assay at the study site revealed a dose-response with increasing HA dosage but only 36% in the 90 µg HA group developed a ≥4-fold rise in antibody in this test and only one of these achieved a titer of ≥1∶32. Conclusion This inactivated subunit influenza A (H7N7) vaccine was safe but poorly immunogenic in humans. Trials Registration ClinicalTrials.gov NCT00546585
The use of whole food animal studies in the safety assessment of genetically modified crops: Limitations and recommendations

Abstract There is disagreement internationally across major regulatory jurisdictions on the relevance and utility of whole food (WF) toxicity studies on GM crops, with no harmonization of data or regulatory requirements. The scientific value, and therefore animal ethics, of WF studies on GM crops is a matter addressable from the wealth of data available on commercialized GM crops and WF studies on irradiated foods. We reviewed available GM crop WF studies and considered the extent to which they add to the information from agronomic and compositional analyses. No WF toxicity study was identified that convincingly demonstrated toxicological concern or that called into question the adequacy, sufficiency, and reliability of safety assessments based on crop molecular characterization, transgene source, agronomic characteristics, and/or compositional analysis of the GM crop and its near-isogenic line. Predictions of safety based on crop genetics and compositional analyses have provided complete concordance with the results of well-conducted animal testing. However, this concordance is primarily due to the improbability of de novo generation of toxic substances in crop plants using genetic engineering practices and due to the weakness of WF toxicity studies in general. Thus, based on the comparative robustness and reliability of compositional and agronomic considerations and on the absence of any scientific basis for a significant potential for de novo generation of toxicologically significant compositional alterations as a sole result of transgene insertion, the conclusion of this review is that WF animal toxicity studies are unnecessary and scientifically unjustifiable.
Sub-scene generation: A step towards complex scene understanding

This paper proposes a new method for generating sub-scenes from images of natural scenes. It is based on over-segmented image patches initially and uses rules derived from human psychology to merge the patches into reasonable sub-scenes. This merging process focuses on covering semantic gaps by exploring semantic connections among the patches, such as the influence area of each patch where the potential interaction with other patches may exist; and applying visual organization rules of proximity property and color harmony property. The proposed method is simple yet efficient computationally. It does not have any limitation on the input image class and does not include a training process. Our experiments indicate that it handles complex scenes with clutters and occlusions very well, and outperforms general segmentation methods by its meaningful semantic grouping and self determined stop criteria.
Correlated and Individual Multi-Modal Deep Learning for RGB-D Object Recognition

In this paper, we propose a new correlated and individual multi-modal deep learning (CIMDL) method for RGB-D object recognition. Unlike most conventional RGB-D object recognition methods which extract features from the RGB and depth channels individually, our CIMDL jointly learns feature representations from raw RGB-D data with a pair of deep neural networks, so that the sharable and modal-specific information can be simultaneously exploited. Specifically, we construct a pair of deep convolutional neural networks (CNNs) for the RGB and depth data, and concatenate them at the top layer of the network with a loss function which learns a new feature space where both correlated part and the individual part of the RGB-D information are well modelled. The parameters of the whole networks are updated by using the back-propagation criterion. Experimental results on two widely used RGB-D object image benchmark datasets clearly show that our method outperforms state-of-the-arts.
Contrast-Enhanced Magnetic Resonance Angiography for Preoperative Imaging of Deep Inferior Epigastric Artery Perforator Flaps: Advantages and Disadvantages Compared With Computed Tomography Angiography A United Kingdom Perspective

The anatomy of the anterior abdominal wall is highly variable and leads to uncertainty when harvesting a deep inferior epigastric artery perforator flap. Presurgical imaging has been shown to reduce the operating time, as well as reduce the rates of flap and donor site complications. The importance of imaging of the venous system has also been recognized for reducing the risk of venous congestion. The modalities currently available for presurgical imaging include handheld Doppler ultrasound, duplex ultrasound, computed tomographic angiography (CTA), and contrast-enhanced magnetic resonance angiography (CE-MRA). Of these, the most promising are CTA and CE-MRA, and advantages and disadvantages exist for both modalities. In this article, we review the use of CE-MRA for preoperative flap imaging and report our experience with its use in deep inferior epigastric artery perforator flap harvest, as well as compare it with CTA. We also explore the future directions for presurgical flap imaging.
Iterative per-Frame Gain and SNR Estimation for DVB-S 2 receivers

In future 2nd-generation digital video broadcasting (DVB-S2) receivers working in ACM (Adaptive Coded Modulation) mode, an unknown residual gain must be estimated before the low-density parity-check (LDPC) decoding stage. Moreover, the signal-to-noise ratio (SNR) has to be estimated also, since the iterative decoding algorithms, such as those employed to decode LDPC codes, require its knowledge. Due to the presence of a time-varying phase, classical coherent algorithms for gain and SNR estimation cannot be carried out. We propose a novel gain and SNR estimator which works in conjunction with a recently proposed detection algorithm for channels with phase noise, known as CBC algorithm. In this way, implicit phase estimates by the CBC algorithm are employed to perform a partially coherent estimation of gain and SNR, which is iteratively refined.
Estimating precipitation errors using spaceborne surface soil moisture retrievals

Limitations in the availability of ground‐based rain gauge data currently hamper our ability to quantify errors in global precipitation products over data‐poor areas of the world. Over land, these limitations may be eased by approaches based on interpreting the degree of dynamic consistency existing between precipitation estimates and remotely‐sensed surface soil moisture retrievals. This paper demonstrates how such an approach can be implemented using a Kalman filter tuning procedure to reliably estimate daily rainfall errors in global precipitation products without reliance on ground‐based rainfall observations.
The Role of Language Processing in Language Acquisition

Language processing research is changing in two ways that should make it more relevant to the study of grammatical learning. First, grammatical phenomena are re-entering the psycholinguistic fray, and we have learned a lot in recent years about the real-time deployment of grammatical knowledge. Second, psycholinguistics is reaching more diverse populations, leading to much research on language processing in child and adult learners. We discuss three ways that language processing can be used to understand language acquisition. Level 1 approaches (“Processing in learners”) explore well-known phenomena from the adult psycholinguistic literature and document how they play out in learner populations (child learners, adult learners, bilinguals). Level 2 approaches (“Learning effects as processing effects”) use insights from adult psycholinguistics to understand the language proficiency of learners. We argue that a rich body of findings that have been attributed to the grammatical development of anaphora should instead be attributed to limitations in the learner’s language processing system. Level 3 approaches (“Explaining learning via processing”) use language processing to understand what it takes to successfully master the grammar of a language, and why different learner groups are more or less successful. We examine whether language processing may explain why some grammatical phenomena are mastered late in children but not in adult learners. We discuss the idea that children’s language learning prowess is directly caused by their processing limitations (‘less is more’: Newport, 1990). We conclude that the idea is unlikely to be correct in its original form, but that a variant of the idea has some promise (‘less is eventually more’). We lay out key research questions that need to be addressed in order to resolve the issues addressed in the paper.
Heterogeneous Nuclear Ribonucleoprotein A3 Is the Liver Nuclear Protein Binding to Age Related Increase Element RNA of the Factor IX Gene

Background In the ASE/AIE-mediated genetic mechanism for age-related gene regulation, a recently identified age-related homeostasis mechanism, two genetic elements, ASE (age-related stability element) and AIE (age-related increase element as a stem-loop forming RNA), play critical roles in producing specific age-related expression patterns of genes. Principal Finding We successfully identified heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) as a major mouse liver nuclear protein binding to the AIE-derived RNAs of human factor IX (hFIX) as well as mouse factor IX (mFIX) genes. HnRNP A3 bound to the AIE RNA was not phosphorylated at its Ser359, while hnRNP A3 in the mouse liver nuclear extracts was a mixture of phosphorylated and unphosphorylated Ser359. HepG2 cells engineered to express recombinant hFIX transduced with adenoviral vectors harboring an effective siRNA against hnRNP A3 resulted in a substantial reduction in hFIX expression only in the cells carrying a hFIX expression vector with AIE, but not in the cells carrying a hFIX expression vector without AIE. The nuclear hnRNP A3 protein level in the mouse liver gradually increased with age, while its mRNA level stayed age-stable. Conclusions We identified hnRNP A3 as a major liver nuclear protein binding to FIX-AIE RNA. This protein plays a critical role in age-related gene expression, likely through an as yet unidentified epigenetic mechanism. The present study assigned a novel functional role to hnRNP A3 in age-related regulation of gene expression, opening up a new avenue for studying age-related homeostasis and underlying molecular mechanisms.
A hybrid IP lookup architecture with fast updates

As network link rates are being pushed beyond 40 Gbps, IP lookup in high-speed routers is moving to hardware. The TCAM (Ternary Content Addressable Memory)-based IP lookup engine and the SRAM (Static Random Access Memory)-based IP lookup pipeline are the two most common ways to achieve high throughput. However, route updates in both engines degrade lookup performance and may lead to packet drops. Moreover, there is a growing interest in virtual IP routers where more frequent updates happen. Finding solutions that achieve both fast lookup and low update overhead becomes critical. In this paper, we propose a hybrid IP lookup architecture to address this challenge. The architecture is based on an efficient trie partitioning scheme that divides the Forwarding Information Base (FIB) into two prefix sets: a large disjoint leaf prefix set mapped into an external TCAM-based lookup engine and a small overlapping prefix set mapped into an on-chip SRAM-based lookup pipeline. Critical optimizations are developed on both IP lookup engines to reduce the update overhead. We show how to extend the proposed hybrid architecture to support virtual routers. Our implementation shows a throughput of 250 million lookups per second (MLPS). The update overhead is significantly lower than that of previous work and the utilization ratio of most external TCAMs is up to 100%.
A Reliability-Enhanced TCAM Architecture with Associated Embedded DRAM and ECC

This paper describes a novel TCAM architecture designed for enhancing the soft-error immunity. An associated embedded DRAM and ECC circuits are placed next to TCAM macro to implement a unique methodology of recovering upset bits due to soft errors. The proposed configuration allows an improvement of soft-error immunity by 6 orders of magnitude compared with the conventional TCAM. We also propose a novel testing methodology of the soft-error rate with a fast parallel multi-bit test. In addition, the proposed architecture resolves the critical problem of the look-up table maintenance of TCAM. The design techniques reported in this paper are especially attractive for realizing soft-error immune, high-performance TCAM chips.
Critical Interpretive Inquiry: A Qualitative Study of Five Contemporary Artists' Ways of Seeing

Contemporary art practice is a complex coalition of conditions that influence artistic production and frame the way interpretations are constructed. The renewed interest in the practice of discipline-experts as models of learning requires a deep understanding of what they do. This study used computer assisted qualitative analysis to inquire into the practice of five artists who responded to an exhibition challenge posed within the constituency of the artworld. Four themes emerged which focused on influence and collaboration; co-constructing meaning by thinking in a setting; achieving an insider's perspective; and the concept of agreeable difference. Findings suggest the complexity of contemporary art practice offers a rich range of models of art learning and can be seen as a site for reconciling the cognitive character of artistic practice and postmodern interpretive stances.
Root isolation for bivariate polynomial systems with local generic position method

A local generic position method is proposed to isolate the real roots of a bivariate polynomial system ∑={<i>f</i>(<i>x,y</i>),<i>g</i>(<i>x,y</i>)}. In this method, the roots of the system are represented as linear combinations of the roots of two univariate polynomial equations <i>t</i>(<i>x</i>)=0 and <i>T</i>(<i>X</i>)=0: {<i>x</i> = α, <i>y</i> = β -- α/<i>s</i> | α ε <i>V</i>(<i>t</i>(<i>x</i>)), β ε <i>V</i>(<i>T</i>(<i>X</i>)), ||β -- α| < <i>S</i>}, where <i>s</i>, <i>S</i> are constants satisfying certain conditions. The multiplicities of the roots of Σ=0 are the same as that of the corresponding roots of <i>T</i>(<i>X</i>)=0. This representation leads to an efficient and stable algorithm to isolate the real roots of Σ.
Characterization of the quantitatively major collagen in the mantle of oyster Crassostrea gigas

A quantitatively major collagen was isolated from the pepsin-solubilized collagen preparation of the mantle by differential salt precipitation and phosphocellulose column chromatography, and its constituent α components (α1 and α2) were purified by phosphocellulose column chromatography. The subunits were demonstrated to be genetically distinct from each other by peptide mapping and amino acid analysis. The amino acid composition calculated from those of the α1 and α2 components in 2∶1 ratio coincided well with that of the major collagen from the mantle. These results suggest that the major collagen in the mantle of the oyster may have a heterotrimer structure (α1)2 α2.
The Specificity of General Human Capital: Evidence from College Major Choice

College graduates do not always pursue careers related to their major. Science majors working in jobs unrelated to their field of study earn approximately 30% lower wages than those working in related jobs. We develop a structural model of major choice and labor market outcomes that allows for skill uncertainty and differential accumulation of human capital across major. Our findings confirm that the average return to obtaining a science degree and working in a related job remains close to 30%. We also find that individuals are uncertain about their future productivity at the time of the college major decision.
Phylogenetic tree shapes resolve disease transmission patterns

Background and Objectives Whole genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterised infectious periods, epidemiological and clinical meta-data which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. Methodology We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks. Results We show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny’s structure and find that computational classifiers based on these are capable of predicting an outbreak’s transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. Conclusions and implications There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission, and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.
Molecular cloning and characterization of an rRNA operon in Streptomyces lividans TK21

The number of rRNA genes in Streptomyces lividans was examined by Southern hybridization. Randomly labeled 23 and 16S rRNAs were hybridized with BamHI, BglII, PstI, SalI, or XhoI digests of S. lividans TK21 DNA. BamHi, BglII, SalI and XhoI digests yielded six radioactive bands each for the 23 and 16S rRNAs, whereas PstI digests gave one band for the 23S rRNA and one high-intensity band and six low-density bands for the 16S rRNA. The 7.4-kilobase-pair BamHI fragment containing one of the rRNA gene clusters was cloned into plasmid pBR322. The hybrid plasmid, pSLTK1, was characterized by physical mapping, Southern hybridization, and electron microscopic analysis of the R loops formed between pSLTK1 and the 23 and 16S rRNAs. There were at least six rRNA genes in S. lividans TK21. The 16 and 23S rRNA genes were estimated to be about 1.40 and 3.17 kilobase pairs, respectively. The genes for the rRNAs were aligned in the sequence 16S-23S-5S. tRNA genes were not found in the spacer region or in the context of the rRNA genes. The G + C content of the spacer region was calculated to be approximately 58%, in contrast to 73% for the chromosome as a whole.