Miracle-dz/UniFAR-FTUs huggingface dataset:
A Tyr Residue in the Reverse Transcriptase Domain Can Mimic the Protein-Priming Tyr Residue in the Terminal Protein Domain of a Hepadnavirus P Protein

ABSTRACT Hepadnaviruses are the only known viruses that replicate by protein-primed reverse transcription. Beyond the conserved reverse transcriptase (RT) and RNase H domains, their polymerases (P proteins) carry a unique terminal protein (TP) domain that provides a specific Tyr residue, Tyr96 in duck hepatitis B virus (DHBV), to which the first nucleotide of minus-strand DNA is autocatalytically attached and extended by three more nucleotides. In vitro reconstitution of this priming reaction with DHBV P protein and cellular chaperones had revealed strict requirements for the Dε RNA stem-loop as a template and for catalytic activity of the RT domain plus RNA-binding competence of the TP domain. Chaperone dependence can be obviated by using a truncated P protein (miniP). Here, we found that miniP with a tobacco etch virus (TEV) protease cleavage site between TP and RT (miniPTEV) displayed authentic priming activity when supplied with α-32P-labeled deoxynucleoside triphosphates; however, protease cleavage revealed, surprisingly, that the RT domain was also labeled. RT labeling had identical requirements as priming at Tyr96 and originated from dNMP transfer to a unique Tyr residue identified as Tyr561 in the presumed RT primer grip motif. Mutating Tyr561 did not affect Tyr96 priming in vitro and only modestly reduced replication competence of an intact DHBV genome; hence, deoxynucleotidylated Tyr561 is not an obligate intermediate in TP priming. However, as a first alternative substrate for the exquisitely complex protein-priming reaction, dNMP transfer to Tyr561 is a novel tool to further clarify the mechanism of hepadnaviral replication initiation and suggests that specific priming inhibitors can be found.
Inactivation of VEGF in mammary gland epithelium severely compromises mammary gland development and function

To investigate the role of the angiogenic cytokine vascular endothelial growth factor (VEGF) during pregnancy and lactation, we used mice in which VEGF had been inactivated in mammary gland epithelial cells. Pups born to mutant mothers failed to thrive, displaying little milk in their stomachs. However, when they were transferred to control mothers they developed normally. Investigation of the mammary gland morphology revealed that lobulo‐alveolar expansion into the fat pad was not complete in lactating mutant glands, and an accumulation of fat globules was evident in their secretory epithelium. In contrast to control glands, lactating mutant glands failed to up‐regulate mRNAs for genes involved in milk secretion. Blood vessel density was comparable in pregnant mice of both groups but was only half that of controls in lactating mutant mice. FITC‐labeled albumin injected intrave‐nously(i.v.) into lactating mice extravasated rapidlyand accumulated in the mammary gland epithelial cells in control animals, but was almost completely retained within the vessels in the mutants. Injection of recombi‐nant VEGF i.v. reversed this effect. These findings demonstrate that mammary epithelium‐derived VEGF is partially dispensable for angiogenesis during pregnancy and lactation, and by regulating vascular function during lactation, this factor is crucial to mammary gland differentiation and milk production. — Rossiter, H. , Barresi, C. , Ghannadan, M. , Gruber, F. , Mildner, M. , Fodinger, D. , Tschachler, E. Inactivation of VEGF in mammary gland epithelium severely compromises mammary gland development and function. FASEB J. 21, 3994–4004 (2007)
Research on group methods of second-use Li-ion batteries based on k-means clustering model

Aiming at the fact that the weeded out car batteries are with bad consistency of capacity and internal resistance, screening and grouping must be adopted to second-use them. This paper determines the characteristic indexes for screening and grouping by analyzing the inconsistency of the second-use batteries and figures out the weighted value of each characteristic index. By grouping the second-use batteries based on the k-means clustering model, batteries are with preferable consistency and also, they have high capacity utilization ratio.
Design of Absorptive/Transmissive Frequency-Selective Surface Based on Parallel Resonance

This communication presents a novel frequency-selective surface (FSS) with high in-band transmission at high frequency and wideband absorption at low frequency. It consists of a resistive sheet and a metallic bandpass FSS separated by a foam spacer. The resistive element is realized by inserting a strip-type parallel $LC$ (PLC) structure into the center of a lumped-resistor-loaded metallic dipole. The PLC resonates at the passband of the bandpass FSS and exhibits an infinite impedance, which splits the resistive dipole into two short sections per the surface current; this setup allows for high in-band transmission at high frequency. Below the resonance frequency, the PLC becomes finite inductive and the entire FSS performs as an absorber with the metallic FSS as a ground plane. The surface current distribution on the resistive element can be controlled at various frequencies via the PLC structure. The wideband absorption and high in-band transmission of the proposed design are verified by both numerical simulation and experimental measurements. The potential extension to polarization-insensitive designs is also discussed.
Twitch and tetanic force responses and longitudinal propagation of action potentials in skinned skeletal muscle fibres of the rat

1 Transverse electrical field stimulation (50 V cm−1, 2 ms duration) of mechanically skinned skeletal muscle fibres of the rat elicited twitch and tetanic force responses (36 ± 4 and 83 ± 4 % of maximum Ca2+‐activated force, respectively; n= 23) closely resembling those in intact fibres. The responses were steeply dependent on the field strength and were eliminated by inclusion of 10 μm tetrodotoxin (TTX) in the (sealed) transverse tubular (T‐) system of the skinned fibres and by chronic depolarisation of the T‐system. 2 Spontaneous twitch‐like activity occurred sporadically in many fibres, producing near maximal force in some instances (mean time to peak: 190 ± 40 ms; n= 4). Such responses propagated as a wave of contraction longitudinally along the fibre at a velocity of 13 ± 3 mm s−1 (n= 7). These spontaneous contractions were also inhibited by inclusion of TTX in the T‐system and by chronic depolarisation. 3 We examined whether the T‐tubular network was interconnected longitudinally using fibre segments that were skinned for only ∼2/3 of their length, leaving the remainder of each segment intact with its T‐system open to the bathing solution. After such fibres were exposed to TTX (60 μm), the adjacent skinned region (with its T‐system not open to the solution) became unresponsive to subsequent electrical stimulation in ∼50 % of cases (7/15), indicating that TTX was able to diffuse longitudinally inside the fibre via the tubular network over hundreds of sarcomeres. 4 These experiments show that excitation–contraction coupling in mammalian muscle fibres involves action potential propagation both transversally and longitudinally within the tubular system. Longitudinal propagation of action potentials inside skeletal muscle fibres is likely to be an important safety mechanism for reducing conduction failure during fatigue and explains why, in developing skeletal muscle, the T‐system first develops as an internal longitudinal network.
Convolutional Dictionary Learning via Local Processing

Convolutional sparse coding is an increasingly popular model in the signal and image processing communities, tackling some of the limitations of traditional patch-based sparse representations. Although several works have addressed the dictionary learning problem under this model, these relied on an ADMM formulation in the Fourier domain, losing the sense of locality and the relation to the traditional patch-based sparse pursuit. A recent work suggested a novel theoretical analysis of this global model, providing guarantees that rely on a localized sparsity measure. Herein, we extend this local-global relation by showing how one can efficiently solve the convolutional sparse pursuit problem and train the filters involved, while operating locally on image patches. Our approach provides an intuitive algorithm that can leverage standard techniques from the sparse representations field. The proposed method is fast to train, simple to implement, and flexible enough that it can be easily deployed in a variety of applications. We demonstrate the proposed training scheme for image inpainting and image separation, achieving state-of-the-art results.
The Simpson–Golabi–Behmel gene, GPC3, is not involved in sporadic Wilms tumorigenesis

Many genes have been implicated in Wilms tumor; however, only one gene, WT1, has a proven role in the development of this embryonal tumor. Wilms tumor occurs in a number of congenital syndromes including the Simpson–Golabi–Behmel syndrome (SGBS) which has phenotypic overlap with another Wilms tumor‐predisposing syndrome Wiedemann–Beckwith syndrome. The putative function and expression pattern of the SGBS gene, glypican 3 (GPC3), makes it an attractive candidate Wilms tumor gene. We, therefore, hypothesized that Wilms tumors from non‐SGBS patients may harbor somatic mutations of GPC3. Mutation analysis of 64 Wilms tumors was performed. One case of a tumor‐specific deletion of the entire GPC3 gene and several polymorphisms were identified. GPC3 expression was evaluated in 36 Wilms tumors and 29/36 expressed GPC3. Surprisingly, we did not find evidence of functional mutations of GPC3 in sporadic Wilms tumor suggesting that GPC3 is not often directly involved in Wilms tumorigenesis. © 2003 Wiley‐Liss, Inc.
Effects of patriline on gustatory responsiveness and olfactory learning in honey bees

Associative proboscis extension learning differs widely among bees of a colony. This variety of performances is often related to differences in sucrose responsiveness, which determines learning performance. Sucrose responsiveness is partly determined genetically. We studied for the first time effects of paternal genes on associative learning independent of sucrose responsiveness. To do this, we used wild-type workers stemming from five unrelated patrilines. Bees of the patrilines were first tested for sucrose responsiveness. Only bees with equal sucrose responsiveness were analysed for associative olfactory learning, memory and discrimination. The bees of different patrilines did not differ in their acquisition, memory or discrimination of odours when they had similar sucrose responsiveness. But patrilines differed significantly in their sucrose responsiveness. This shows genetic effects on sensory responsiveness but no independent effects on associative learning.ZusammenfassungArbeiterinnen einer Honigbienenkolonie unterscheiden sich oft sehr stark in ihrem Rüsselreflex-Lernen. Diese Vielfalt im Lernverhalten hängt dabei häufig mit der individuellen Empfindlichkeit für den Belohnungsreiz Zuckerwasser zusammen. Die Zuckerwasserempfindlichkeit ist zumindest teilweise genetisch programmiert.Wir haben zum ersten Mal untersucht, inwieweit väterliche Gene das assoziative Lernverhalten unabhängig von der Zuckerwasserempfindlichkeit beeinflussen. Dazu haben wir Arbeiterinnen untersucht, die von fünf nicht miteinander verwandten Patrilinien stammten. Von jeder Arbeiterin wurde zunächst die Zuckerwasserempfindlichkeit bestimmt. Anschließend wurden Bienen mit ähnlicher Empfindlichkeit auf ihr Duftlernen, ihr Gedächtnis und ihre Duftdiskriminierung getestet.Bienen gleicher Zuckerwasserempfindlichkeit haben sich weder im Lernverlauf noch im Gedächtnis oder in der Diskriminierung unterschieden. Aber Bienen verschiedener Patrilinien unterschieden sich in ihrer Zuckerwasserempfindlichkeit. Unsere Ergebnisse zeigen daher keinen von der Zuckerwasserempfindlichkeit unabhängigen Effekt väterlicher Gene auf das Lernverhalten bei Bienen.
Ambient Mass Spectrometry

A recent innovation in mass spectrometry is the ability to record mass spectra on ordinary samples, in their native environment, without sample preparation or preseparation by creating ions outside the instrument. In desorption electrospray ionization (DESI), the principal method described here, electrically charged droplets are directed at the ambient object of interest; they release ions from the surface, which are then vacuumed through the air into a conventional mass spectrometer. Extremely rapid analysis is coupled with high sensitivity and high chemical specificity. These characteristics are advantageously applied to high-throughput metabolomics, explosives detection, natural products discovery, and biological tissue imaging, among other applications. Future possible uses of DESI for in vivo clinical analysis and its adaptation to portable mass spectrometers are described.
Emergency decision making: a theoretical analysis of responses to disaster warnings.

This article presents a theoretical model of emergency decision making that focuses on the decision maker's answers to basic questions evoked by warnings or signs of danger. Effective emergency decisions are most likely to be made, according to the theory, when a vigilant coping pattern is dominant, which requires that the following four mediating conditions are met: 1) awareness of serious risks if no protective action is taken; 2) awareness of serious risks if any of the salient protective actions is taken; 3) moderate or high degree of hope that a search for information and advice will lead to a better (i.e., less risky) solution; and 4) belief that there is sufficient time to search and deliberate before any serious threat will materialize. When one or another of these conditions is not met, a defective coping pattern, such as defensive avoidance or hypervigilance, will be dominant, which generally leads to maladaptive actions. In addition to suggesting new interventions for facilitating adaptive behavior in emergencies, the theoretical model provides a basis for integrating disparate findings from psychological research on the effects of warnings and confrontations with danger.
External reinforcement of varicose veins with PTFE prosthesis in infrainguinal bypass surgery -- clinical results.

OBJECTIVE Segmental varicose degeneration of the autogenous greater saphenous vein may limit its use in infrainguinal bypass surgery. Wrapping a PTFE prosthesis around dilated veins has emerged as an option to create externally reinforced vein bypasses. Results regarding graft patency and limb salvage were analyzed. METHODS Between September 1995 and January 2001, 35 infrainguinal bypass operations in 33 patients were performed with greater saphenous veins exhibiting segmental varicose dilatation. Grafts were followed by duplex scan and retrospective analysis of graft patency and limb salvage was performed. RESULTS One bypass prompted successful revision for early occlusion. Four bypasses required additional reintervention during follow-up. 48 months primary, primary assisted and secondary patency rates were 66%, 82% and 82%, respectively, with a limb salvage rate of 97%. Duplex scan failed to demonstrate stenosis of the reinforced vein segments or aneurysmal degeneration of the residual vein. CONCLUSION External reinforcement with a PTFE prosthesis allows the use of autogenous greater saphenous veins with varicose dilatation and enables the construction of all autogenous bypasses with promising graft patency and limb salvage.
Learning Morphological Normalization for Translation from and into Morphologically Rich Languages

Abstract When translating between a morphologically rich language (MRL) and English, word forms in the MRL often encode grammatical information that is irrelevant with respect to English, leading to data sparsity issues. This problem can be mitigated by removing from the MRL irrelevant information through normalization. Such preprocessing is usually performed in a deterministic fashion, using hand-crafted rules and yielding suboptimal representations. We introduce here a simple way to automatically compute an appropriate normalization of the MRL and show that it can improve machine translation in both directions.
Effect of metabolic syndrome on coronary artery stenosis and plaque characteristics as assessed with 64-detector row cardiac CT.

PURPOSE To investigate the prevalence and severity of subclinical coronary atherosclerosis and plaque characteristics in asymptomatic subjects according to the presence or absence of metabolic syndrome (MS) with multidetector computed tomography (CT). MATERIALS AND METHODS This study was approved and the requirement for informed patient consent was waived by the local institutional review board. Degree of coronary artery stenosis, multivessel involvement, and plaque characteristics, as well as coronary artery calcium score (CACS), were assessed with 64-detector row CT in 3000 age- and sex-matched asymptomatic individuals (mean age, 50.2 years ± 8.9 [standard deviation]; age range, 30-79 years). Anthropometric and metabolic profiles were also measured. Multivariate logistic regression analyses were performed to identify variables related to coronary atherosclerosis and plaque types. RESULTS Subjects with MS had significant coronary artery stenosis (>50% stenosis), multivessel involvement, more positive remodeling, more atherosclerotic coronary segments, and higher CACS than subjects without MS (P < .01 for all). Mixed and noncalcified plaques were also more prominent in subjects with MS than in those without MS (14.2% ± 4.4 vs 7.6% ± 3.1 and 13.1% ± 4.3 vs 7.3% ± 2.8, respectively; P < .01 for both). After adjustment for confounding factors, MS was strongly associated with significant coronary artery stenosis, multivessel involvement, and mixed plaque. CONCLUSION Multidetector CT is useful in the early diagnosis and evaluation of subclinical coronary atherosclerosis in asymptomatic patients with MS; however, future prospective studies are needed to address the clinical implications of these findings.
New insights in synthetic fiber rope elongation and its detection for ultra lightweight tendon driven series elastic robots

Selecting transmission components for tendon driven actuation systems can be challenging because of the variety of available solutions. Synthetic fiber ropes have great potential for these systems, but the typically provided characteristics are not always suitable to decide whether a rope should be used in the specific system or not. In this paper, a comparative evaluation of the elongation characteristic regarding different rope materials, manufacturers and temperatures is presented. Further, the influence of guiding pulleys is investigated concerning the application at ultra lightweight tendon driven series elastic robots. The knowledge gained from the performed new rope analysis supports the design process of tendon driven robots. Since tendon elongation influences the control performance and joint torque estimation of the regarded class of robots, a novel observer-based approach for tendon elongation detection is presented and evaluated, which enables to monitor wear for quality assurance and to avoid failures.
Complement Activation on B Lymphocytes Opsonized with Rituximab or Ofatumumab Produces Substantial Changes in Membrane Structure Preceding Cell Lysis1

Binding of the CD20 mAb rituximab (RTX) to B lymphocytes in normal human serum (NHS) activates complement (C) and promotes C3b deposition on or in close proximity to cell-bound RTX. Based on spinning disk confocal microscopy analyses, we report the first real-time visualization of C3b deposition and C-mediated killing of RTX-opsonized B cells. C activation by RTX-opsonized Daudi B cells induces rapid membrane blebbing and generation of long, thin structures protruding from cell surfaces, which we call streamers. Ofatumumab, a unique mAb that targets a distinct binding site (the small loop epitope) of the CD20 Ag, induces more rapid killing and streaming on Daudi cells than RTX. In contrast to RTX, ofatumumab promotes streamer formation and killing of ARH77 cells and primary B cells from patients with chronic lymphocytic leukemia. Generation of streamers requires C activation; no streaming occurs in media, NHS-EDTA, or in sera depleted of C5 or C9. Streamers can be visualized in bright field by phase imaging, and fluorescence-staining patterns indicate they contain membrane lipids and polymerized actin. Streaming also occurs if cells are reacted in medium with bee venom melittin, which penetrates cells and forms membrane pores in a manner similar to the membrane-attack complex of C. Structures similar to streamers are demonstrable when Ab-opsonized sheep erythrocytes (non-nucleated cells) are reacted with NHS. Taken together, our findings indicate that the membrane-attack complex is a key mediator of streaming. Streamer formation may, thus, represent a membrane structural change that can occur shortly before complement-induced cell death.
Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila

In this study, Kang et al. investigate how PcG complexes form repressive chromatin domains. The findings show that Scm, a transcriptional repressor, is an important regulator of PRC1, PRC2, and transcriptional silencing and suggest that Scm coordinates PcG complexes and polymerizes, resulting in PcG silencing.
Specific proteins mediate enhanced osteoblast adhesion on nanophase ceramics.

Osteoblast, fibroblast, and endothelial cell adhesion on nanophase (that is, materials with grain sizes less than 100 nm) alumina, titania, and hydroxyapatite (HA) was investigated using in vitro cellular models. Osteoblast adhesion was significantly (p < 0.01) greater after 4 h on nanophase alumina, titania, and HA than it was on conventional formulations of the same ceramics. In contrast, compared to conventional alumina, titania, and HA, after 4 h fibroblast adhesion was significantly (p < 0.01) less on nanophase ceramics. Examination of the underlying mechanism(s) of cell adhesion on nanophase ceramics revealed that these ceramics adsorbed significantly (p < 0.01) greater quantities of vitronectin, which, subsequently, may have contributed to the observed select enhanced adhesion of osteoblasts. Select enhanced osteoblast adhesion was independent of surface chemistry and material phase but was dependent on the surface topography (specifically on grain and pore size) of nanophase ceramics. The capability of synthesizing and processing nanomaterials with tailored (through, for example, specific grain and pore size) structures and topographies to control select subsequent cell functions provides the possibility of designing the novel proactive biomaterials (that is, materials that elicit specific, timely, and desirable responses from surrounding cells and tissues) necessary for improved implant efficacy.
Deep Learning Interior Tomography for Region-of-Interest Reconstruction

Interior tomography for the region-of-interest (ROI) imaging has advantages of using a small detector and reducing X-ray radiation dose. However, standard analytic reconstruction suffers from severe cupping artifacts due to existence of null space in the truncated Radon transform. Existing penalized reconstruction methods may address this problem but they require extensive computations due to the iterative reconstruction. Inspired by the recent deep learning approaches to low-dose and sparse view CT, here we propose a deep learning architecture that removes null space signals from the FBP reconstruction. Experimental results have shown that the proposed method provides near-perfect reconstruction with about 7-10 dB improvement in PSNR over existing methods in spite of significantly reduced run-time complexity.