Miracle-dz/UniFAR-FTUs huggingface dataset:
snRNA 3′ End Formation Requires Heterodimeric Association of Integrator Subunits

ABSTRACT The Integrator Complex is a group of proteins responsible for the endonucleolytic cleavage of primary small nuclear RNA (snRNA) transcripts within the nucleus. Integrator subunits 9 and 11 (IntS9/11) are thought to contain the catalytic activity based on their high sequence similarity to CPSF100 and CPSF73, which have been shown to be components of both the poly(A)+ and histone pre-mRNA cleavage complex. Here we demonstrate that the specific heterodimeric interaction between IntS9 and IntS11 is mediated by a discrete domain present at the extreme C terminus of IntS9 and within the C terminus of IntS11, adjacent to the predicted active site of this endonuclease. This domain is highly conserved within IntS11 but conspicuously absent in CPSF73. Using a cell-based complementation assay that measures Integrator activity, we determined that the IntS9 interaction domain within IntS11 is required for its ability to restore snRNA 3′ end processing after RNA interference (RNAi)-mediated depletion of IntS11. Moreover, overexpression of these interaction domains alone elicits snRNA misprocessing through a dominant-negative titration of endogenous Integrator subunits. These data collectively explain the mechanism by which the IntS11/9 and, by analogy, the CPSF73/100 heterodimeric cleavage factors distinguish themselves from each other and demonstrate that the heterodimeric interaction is functionally required for snRNA 3′ end formation.
Recurrent Cutaneous Herpes Simplex in Hairless Mice

Passively immunized hairless mice were inoculated cutaneously with herpes simplex virus. Thirty-nine days later, when the primary cutaneous lesions had completely healed, the mice were treated subcutaneously with prednisone. Within 12 to 30 days after starting prednisone treatment, herpesvirus was recovered by skin swabs from 12 of 71 (17%) of the treated mice. This new model has potential application for understanding and treating recurrent cutaneous herpes infections.
A Scale Factor-Based Interpolated DFT for Chatter Frequency Estimation

In this paper, a scale factor-based interpolated discrete Fourier transform (IpDFT) algorithm is proposed to estimate the dominant chatter frequency. In practical measurement systems of machining processes, the number of acquired sine-wave cycles (NASCs) is small. Therefore, the significant spectral interference from the negative frequency leads to the degradation of conventional IpDFTs that neglect such interference. The proposed IpDFT algorithm overcomes this problem by completely removing the long-range leakage of the negative frequency of the investigated component. We establish statistical properties of the approach contaminated with white noise, including upper and lower bounds of the theoretical variance. The simulation results demonstrate that our IpDFT algorithm outperforms existing IpDFT algorithms, especially when the NASC approaches zero. The proposed IpDFT algorithm has better antinoise capability and computational efficiency than the optimization-based algorithm by Radil. Furthermore, it is illustrated that the simulation results agree well with upper and lower bounds of the theoretical variance. Cutting force signals are collected to evaluate the algorithm experimentally.
On calmness conditions in convex bilevel programming

In this article, we compare two different calmness conditions which are widely used in the literature on bilevel programming and on mathematical programs with equilibrium constraints. In order to do so, we consider convex bilevel programming as a kind of intersection between both research areas. The so-called partial calmness concept is based on the function value approach for describing the lower level solution set. Alternatively, calmness in the sense of multifunctions may be considered for perturbations of the generalized equation representing the same lower level solution set. Both concepts allow to derive first-order necessary optimality conditions via tools of generalized differentiation introduced by Mordukhovich. They are very different, however, concerning their range of applicability and the form of optimality conditions obtained. The results of this article seem to suggest that partial calmness is considerably more restrictive than calmness of the perturbed generalized equation. This fact is also illustrated by means of a dicretized obstacle control problem.
Development and evaluation of efficient recombinant Escherichia coli strains for the production of 3‐hydroxypropionic acid from glycerol

3‐Hydroxypropionic acid (3‐HP) is a commercially valuable chemical with the potential to be a key building block for deriving many industrially important chemicals. However, its biological production has not been well documented. Our previous study demonstrated the feasibility of producing 3‐HP from glycerol using the recombinant Escherichia coli SH254 expressing glycerol dehydratase (DhaB) and aldehyde dehydrogenase (AldH), and reported that an “imbalance between the two enzymes” and the “instability of the first enzyme DhaB” were the major factors limiting 3‐HP production. In this study, the efficiency of the recombinant strain(s) was improved by expressing DhaB and AldH in two compatible isopropyl‐thio‐β‐galactoside (IPTG) inducible plasmids along with glycerol dehydratase reactivase (GDR). The expression levels of the two proteins were measured. It was found that the changes in protein expression were associated with their enzymatic activity and balance. While cloning an alternate aldehyde dehydrogenase (ALDH), α‐ketoglutaric semialdehyde dehydrogenase (KGSADH), instead of AldH, the recombinant E. coli SH‐BGK1 showed the highest level of 3‐HP production (2.8 g/L) under shake‐flask conditions. When an aerobic fed‐batch process was carried out under bioreactor conditions at pH 7.0, the recombinant SH‐BGK1 produced 38.7 g 3‐HP/L with an average yield of 35%. This article reports the highest level of 3‐HP production from glycerol thus far. Biotechnol. Bioeng. 2009; 104: 729–739 © 2009 Wiley Periodicals, Inc.
Safety of elastography applied to the placenta: Be careful with ultrasound radiation force

We read with interest the article entitled ‘Comparison of placental elasticity in normal and pre-eclamptic pregnant women by acoustic radiation force impulse elastosonography’, and we wish to thank the authors for this work. We share the authors’ view of the usefulness of elastography for placental exploration. However we would like to warn about the safety of ultrasound radiation force applied to pregnant women. Indeed, we do not know the exact values of the energy delivered by radiation force, whether it is thermal index (TI), mechanical index (MI), spatial peak-temporal average intensity (ISPTA) or spatial peak-pulse average intensity (ISPPA). Acceptable thresholds for these parameters are determined by several societies, such as the British Medical US Society (BMUS). There is a risk of tissue heating as soon as the TI is greater than 0.7. The duration of the examination must therefore be reduced. Beyond a TI of 3, the method should not be applied to pregnant women. The references cited by Karaman et al. do not allow the security of their system to be documented. The often-repeated assertion that the use of ultrasound radiation force is equivalent to that of Doppler ultrasonography is not supported by any specific data. Similarly, histopathological analyses of 115 placentas ex vivo by Sugitani et al. do not constitute a sufficient demonstration. This uncertainty of the safety of ultrasound radiation force has led some authors to prefer animal experimentation, which seems to be a measure of elementary prudence. Even in the absence of safety data, journals increasingly accept articles reporting the use of radiation force in pregnant women. However, we believe that such jurisprudence is not entirely acceptable. We know that calculation of the TI is difficult from a methodological point of view, and we would not want to block the use of these promising tools by an excess of precaution. While waiting for new data, we recall that some elastographic methods make it possible to avoid the use of radiation force, for example, strain elastography or transient elastography. Certainly, strain elastography gives only qualitative values about the relative elasticity of the tissues, which constitutes imperfect information. But transient elastography provides the same results as those of shear wave elastography or acoustic radiation force imaging, that is, Young’s Modulus and shear wave speed. This is the approach chosen by our team.
Electrophysiologically Interactive Computer Systems

Combining computing with physiological sensing technologies will transform human-machine interaction and usher in a wide range of new applications. electrophysiologically interactive computer systems (EpICS) combine physiological sensing technologies with interactive computer applications. These systems support a diverse range of monitoring and training disciplines. EpICS provide interesting usability metrics and form the backbone of brain-computer interfaces, prosthetics, and other hands-free control technologies. We have identified two basic EpIC systems. Monitoring EpICS quantify or measure an electrophysiological signal of interest against some scale. Training EpICS feed back physiological information to a subject in real time to enable operant conditioning or instrumental learning of control to occur - a process commonly known as biofeedback.
Difficult direct laryngoscopy in patients with cervical spine disease

Two hundred and fifty three patients were examined before surgery for cervical spine disease. The grade of glottic visibility was determined at direct laryngoscopy, using the classification proposed by Cormack and Lehane. The overall prevalence of difficulty (grades 3 and 4) was 20%. Patients with disease that includes the occipito‐atlanto‐axial complex have a higher prevalence of difficulty than those with disease below the axis vertebra. Occipito‐atlanto‐axial disease is associated with poor mandibular protrusion. The best single predictor of difficulty was reduced separation of the posterior elements of the first and second cervical vertebrae on lateral radiographs. The Mallampati examination was the best single predictor on physical examination. The Mallampati may be an indicator of poor cranio‐cervical extension. Difficulty was rare in patients with class A mandibular protrusion, and invariable in patients with class C protrusion.
Neurogenesis in Postnatal Mouse Dorsal Root Ganglia

Neurogenesis continues in various regions of the central nervous system (CNS) throughout life. As the mitogen basic fibroblast growth factor (bFGF) can proliferate neuronal precursors of CNS neurons in culture, and is also upregulated within adult dorsal root ganglia following axotomy, it is possible that the postnatal dorsal root ganglia contain bFGF-responsive neuronal precursors. We undertook cell culture of postnatal mouse dorsal root ganglia to demonstrate neurogenesis. Basic FGF induced a cellular proliferative response in dorsal root ganglia cell culture. After 2 weeks in serum-free medium containing bFGF, neurons were rarely observed. However, following removal of bFGF and addition of trophic factors, many cells were observed that morphologically resembled dorsal root ganglia neurons, stained for neuronal markers, and generated action potentials. Furthermore, bromodeoxyuridine, used as a marker of cytogenesis, was detected in neurofilament-160(+) and/or microtubule-associated protein-2(+) cells that morphologically resembled neurons. In addition to bFGF, epidermal growth factor, nerve growth factor, and sonic hedgehog were also capable of generating spherical cell clusters that contained cells that stained for neuronal markers following the addition of trophic factors. These results suggest that early postnatal dorsal root ganglia contain neural precursors that appear to proliferate in response to various factors and can then be induced to differentiate into neurons. In conclusion, the existence of neural precursors and the possibility of neurogenesis in postnatal dorsal root ganglia may provide a greater range of plasticity available to somatosensory systems during growth or following injury, perhaps to replace ineffectual or dying neurons.
Nuclear DNA sequence divergence between parapatric subspecies of the grasshopper Chorthippus parallelus

Sequence data from a non‐coding nuclear DNA segment (CpnI‐1) was used to investigate the divergence between Spanish and French subspecies of the grasshopper Chorthippuspara/us which form a hybrid zone in the Pyrenees. The spatial distribution of eighteen Cpnl‐1 sequence haplotypes from eighteen French and fifteen Spanish populations and phylogenetic analyses using both distance and parsimony procedures provide strong evidence that the Py renean hybrid zone was formed by postglacial secondary contact and that the French subspecies arose by range expansion from a Balkan or Italian refugium. In addition, the data provide evidence for subdivision between grasshoppers from Northern Spain and those from Central and Pyrenean Spanish populations.
Post-filter design for speech enhancement in various noisy environments

A microphone array post-filter design effective in various noise environments is proposed for implementation in a hands-free speech interface. Although various post-filter designs have been studied, few methods have been effective in practical use since different types of sound sources, such as spatially coherent target/interference sources and incoherent background noise, are included in the observation signals. This paper describes a post-filter that was designed after estimating the power spectral density (PSD) of each target/interference source and background noise to reduce the estimation error of the post-filter. This was achieved by assuming that the background noise was composed of stationary signals. Through experiments involving four microphones, we confirmed that our proposed method works well in certain noisy environments.
A high-fat diet suppresses de novo lipogenesis and desaturation but not elongation and triglyceride synthesis in mice[S]

Intracellular lipids and their synthesis contribute to the mechanisms and complications of obesity-associated diseases. We describe an NMR approach that provides an abbreviated lipidomic analysis with concurrent lipid biosynthetic fluxes. Following deuterated water administration, positional isotopomer analysis by deuterium NMR of specific lipid species was used to examine flux through de novo lipogenesis (DNL), FA elongation, desaturation, and TG-glycerol synthesis. The NMR method obviated certain assumptions regarding sites of enrichment and exchangeable hydrogens required by mass isotope methods. The approach was responsive to genetic and pharmacological gain or loss of function of DNL, elongation, desaturation, and glyceride synthesis. BDF1 mice consuming a high-fat diet (HFD) or matched low-fat diet for 35 weeks were examined across feeding periods to determine how flux through these pathways contributes to diet induced fatty liver and obesity. HFD mice had increased rates of FA elongation and glyceride synthesis. However DNL was markedly suppressed despite insulin resistance and obesity. We conclude that most hepatic TGs in the liver of HFD mice were formed from the reesterification of existing or ingested lipids, not DNL.
After the red passport: towards an anthropology of the everyday geopolitics of entrapment in the EU's ‘immediate outside’

Suggesting building bricks for an anthropology of everyday geopolitics, this text analyses affective engagements with regulation, here of cross-border mobility. Following the logic of the regulation that constitutes them, I conceptualize zones of humiliating entrapment through documentary requirements – experienced by citizens of Bosnia-Herzegovina and Serbia – as the EU's shrinking ‘immediate outside’. Using ethnography, I embed bodily experiences in visa queues in people's engagements with changing Eurocentric spatiotemporal rankings, refracting this entrapment against the privileges of certain foreigners (such as me) and against their own remembered mobility with the ‘red’ Yugoslav passport. I propose that complementing the dominant focus on the role of (national) identity politics in geopolitical affect with one on regulation and ranking is a central task for a critical anthropology of everyday geopolitics in peripheries. Resume L’auteur de cet article entend mettre en avant des elements pour constituer une anthropologie de la geopolitique quotidienne. Pour cela, il analyse l’abord affectif de la regulation, en l’occurrence celle des flux transfrontaliers. Suivant la logique de la reglementation qui les constitue, il conceptualise sous l’appellation « d’exterieur immediat » de l’Union europeenne des zones, de plus en plus exigues, ou les sujets (en l’occurrence des ressortissants de Bosnie-Herzegovine et de Serbie) sont pris dans le piege humiliant des exigences paperassieres. A l’aide de l’ethnographie, il incorpore le vecu physique des files d’attente de visas dans la confrontation des gens aux classements spatiotemporels eurocentriques mouvants, confrontant cette situation d’enlisement aux privileges de certains etrangers (comme lui-meme) et a leurs propres souvenirs de mobilite avec le passeport yougoslave « rouge ». L’auteur suggere qu’une anthropologie de la geopolitique quotidienne dans les zones peripheriques requiert de completer la focalisation sur le role de la politique identitaire (nationale) dans les affects geopolitiques par une attention soutenue aux regulations et aux classements.
Value of ultrasonography compared with physical examination for the detection of locoregional metastases in patients with cutaneous melanoma

&NA; In several studies the early detection of locoregional metastases in patients with cutaneous melanomas has been shown to be of prognostic value. Physical examination alone often fails to detect locoregional metastases or cannot unambiguously classify palpable lymph nodes. This study aimed to evaluate the usefulness of high resolution ultrasonography for the early detection of locoregional metastases and to compare the sensitivity and specificity of ultrasound and physical examination. A prospective study was performed between January 1997 and June 1999 in 1395 patients (721 men and 674 women) with invasive cutaneous melanoma, treated and followed up at the Department of Dermatology and Allergology, Ludwig‐Maximilian‐University, Munich, Germany. A total of 2650 physical and ultrasound examinations of lymphatic drainage areas were performed, and lesions suspicious for metastases were excised and diagnosed by histopathology. The results of physical and ultrasound examinations were compared. Of the 2650 ultrasound examinations, metastases were suspected in 153, whereas 290 of the 2650 physical examinations were suspicious for metastatic disease. A total of 168 patients with suspicious lesions underwent surgery; histopathological examination revealed 112 melanoma metastases and 56 other diagnoses, including one second malignancy, one neurinoma, one haemangioma and 54 reactive lymph nodes. Ultrasonographic diagnosis of melanoma metastases had a sensitivity of 92.2% and a specificity of 98.2%, whereas diagnosis by physical examination had a sensitivity of only 51.3% and a specificity of 90.9%. Thus ultrasound examination was found to be highly effective and superior to physical examination for the early detection of locoregional melanoma metastases.
Modelling the thermal conductivity of semiconductor NWs; a step forward to the increase of the thermoelectric figure of merit

Low dimensional semiconductor structures are very promising for thermoelectric conversion. In particular, the thermal conductivity of semiconductor nanowires (NWs) can be engineered in order to enhance the thermoelectric figure of merit. Modeling the thermal conductivity of NWs is a step forward to the design of advanced thermoelectric devices.
Theory of manual vehicular control.

The analytical basis of manual vehicular control theory is a combination of feedback systems analysis and mathematical models for human operators engaged in control tasks. Simplified representations for the operator-system combination are provided by the 'crossover model', which is described in detail. The system dynamics and average performance of the crossover model system are developed. With these as bases, case studies are presented to illustrate the types of result which can be obtained from application of the operator-vehicle control theory. Two aircraft control examples illustrate the use of the theory and its empirical correlates to estimate operator dynamic characteristics, system performance, pilot ratings, pilot commentary, design implications, and some experimental guidelines. A driver automobile example is presented to illustrate the use of the theory in structuring the key guidance and control features of the driver's visual field. A comprehensive bibliography of operator-vehicle system analysis applications is also provided.
Bacterial Two-component and Hetero-heptameric Pore-forming Cytolytic Toxins: Structures, Pore-forming Mechanism, and Organization of the Genes

Staphylococcal γ-hemolysin (Hlg), leukocidin (Luk), and Panton–Valentine leukocidin (PVL) are two-component and hetero-oligomeric pore-forming cytolytic toxins (or cytolysin), that were first identified in bacteria. No information on the existence of hetero-oligomeric pore-forming cytolytic toxins in bacteria except for staphylococcal strains is available so far. Hlg (Hlg1 of 34 kDa/Hlg2 of 32 kDa) effectively lyses erythrocytes from human and other mammalian species. Luk (LukF of 34 kDa/LukS of 33 kDa) is cytolytic toward human and rabbit polymorphonuclear leukocytes and rabbit erythrocytes, and PVL (LukF-PV of 34 kDa/LukS-PV of 33 kDa) reveals cytolytic activity with a high cell specificity to leukocytes. Hlg1 is identical to LukF and that the cell specificities of the cytolysins are determined by Hlg2 and LukS. Based on the primary and 3-dimensional structures of the toxin components, Hlg, Luk, and PVL are thought to form a family of proteins. In the first chapter of this article, we describe the molecular basis of the membrane pore-forming nature of Hlg, Luk, and PVL. We also describe a requirement of the phosphorylation of LukS and LukS-PV by protein kinase for their leukocytolytic activity besides their pore formation on human leukocytes. Recently, the assembly mechanism of the LukF and Hlg2 monomers into pore-forming hetero-oligomers of Hlg on human erythrocyte membranes has been clarified for the first time by our study using a single-molecular fluorescence imaging technique. We estimated 11 sequential equilibrium constants for the assembly pathway which includes the beginning with membrane binding of monomers, proceeds through single pore oligomerization, and culminates in the formation of clusters of the pores. In the second chapter of this article, we refer to an assembly mechanism of LukF and Hlg2 on human erythrocytes as well as the roles of the membranes of the target cells in pore formation by Hlg. The LukF, LukS, and Hlg2 proteins are derived from the Hlg locus (hlg), and have been found in 99% of clinical isolates of Staphylococcus aureus. In contrast, LukF-PV and LukS-PV are derived from the PVL locus (pvl) which is distinct from the hlg locus, and only a small percentage of clinically isolated S. aureus strains carries pvl. Recently, we discovered pvl on the genome of lysogenic bacteriophages, φPVL, and determined the entire gene of the phage. We also demonstrated the phage conversion of S. aureus leading to the production of PVL through the discovery of a PVL-carrying temperate phage, φSLT, from a clinical isolate of S. aureus. In the third chapter of this article, we discuss genetic analyses of the Hlg, Luk, and PVL genes. We also discuss the current status of knowledge of the genetic organization of PVL-converting phages in order to achieve an understanding of their molecular evolution.