Miracle-dz/UniFAR-FTUs huggingface dataset:
Visible and near infrared fluorescence spectral flow cytometry

There is a long standing interest in measuring complete emission spectra from individual cells in flow cytometry. We have developed flow cytometry instruments and analysis approaches to enable this to be done routinely and robustly. Our spectral flow cytometers use a holographic grating to disperse light from single cells onto a CCD for high speed, wavelength‐resolved detection. Customized software allows the single cell spectral data to be displayed and analyzed to produce new spectra‐derived parameters. We show that familiar reference and calibration beads can be employed to quantitatively assess instrument performance. We use microspheres stained with six different quantum dots to compare a virtual bandpass filter approach with classic least squares (CLS) spectral unmixing, and then use antibody capture beads and CLS unmixing to demonstrate immunophenotyping of peripheral blood mononuclear cells using spectral flow cytometry. Finally, we characterize and evaluate several near infrared (NIR) emitting fluorophores for use in spectral flow cytometry. Spectral flow cytometry offers a number of attractive features for single cell analysis, including a simplified optical path, high spectral resolution, and streamlined approaches to quantitative multiparameter measurements. The availability of robust instrumentation, software, and analysis approaches will facilitate the development of spectral flow cytometry applications. © 2012 International Society for Advancement of Cytometry
IS1630 of Mycoplasma fermentans, a Novel IS30-Type Insertion Element That Targets and Duplicates Inverted Repeats of Variable Length and Sequence during Insertion

ABSTRACT A new insertion sequence (IS) of Mycoplasma fermentansis described. This element, designated IS1630, is 1,377 bp long and has 27-bp inverted repeats at the termini. A single open reading frame (ORF), predicted to encode a basic protein of either 366 or 387 amino acids (depending on the start codon utilized), occupies most of this compact element. The predicted translation product of this ORF has homology to transposases of the IS30 family of IS elements and is most closely related (27% identical amino acid residues) to the product of the prototype of the group, IS30. Multiple copies of IS1630 are present in the genomes of at least two M. fermentans strains. Characterization and comparison of nine copies of the element revealed that IS1630 exhibits unusual target site specificity and, upon insertion, duplicates target sequences in a manner unlike that of any other IS element. IS1630 was shown to have the striking ability to target and duplicate inverted repeats of variable length and sequence during transposition. IS30-type elements typically generate 2- or 3-bp target site duplications, whereas those created by IS1630 vary between 19 and 26 bp. With the exception of two recently reported IS4-type elements which have the ability to generate variable large duplications (B. B. Plikaytis, J. T. Crawford, and T. M. Shinnick, J. Bacteriol. 180:1037–1043, 1998; E. M. Vilei, J. Nicolet, and J. Frey, J. Bacteriol. 181:1319–1323, 1999), such large direct repeats had not been observed for other IS elements. Interestingly, the IS1630-generated duplications are all symmetrical inverted repeat sequences that are apparently derived from rho-independent transcription terminators of neighboring genes. Although the consensus target site for IS30 is almost palindromic, individual target sites possess considerably less inverted symmetry. In contrast, IS1630appears to exhibit an increased stringency for inverted repeat recognition, since the majority of target sites had no mismatches in the inverted repeat sequences. In the course of this study, an additional copy of the previously identified insertion sequence ISMi1 was cloned. Analysis of the sequence of this element revealed that the transposase encoded by this element is more than 200 amino acid residues longer and is more closely related to the products of other IS3 family members than had previously been recognized. A potential site for programmed translational frameshifting in ISMi1 was also identified.
Monocyte chemoattractant protein-1 messenger RNA expression in rat ischemic cortex.

BACKGROUND AND PURPOSE Previously we demonstrated that focal cerebral ischemia results in an increased expression of several cytokines/chemokines that precede the infiltration of leukocytes into the ischemic cortex after focal stroke induced by occlusion of the middle cerebral artery (MCAO). Monocyte chemoattractant protein-1 (MCP-1) is a potent chemoattractant specific for monocytes. The aim of the present study was to examine whether MCP-1 messenger RNA (mRNA) is expressed in ischemic brain tissue after MCAO. METHODS The expression of MCP-1 mRNA in the ischemic cortex was first identified by means of a sensitive reverse transcription and polymerase chain reaction technique. The time course of expression of MCP-1 mRNA in the ischemic and nonischemic cerebral cortex after both permanent MCAO and temporary MCAO (160 minutes) with reperfusion was then examined by means of Northern blot analysis. RESULTS Almost no expression of MCP-1 mRNA was found in the sham-operated or nonischemic (contralateral) cortex. A significant increase in MCP-1 mRNA expression in the ischemic cortex was observed after either permanent or temporary MCAO. MCP-1 mRNA was elevated at 6 hours (4.4-fold increase over sham; n = 4), reached its highest expression from 12 hours to 2 days (22.7-fold at the peak level; P < .01), and remained elevated up to 5 days (5.6-fold; P < .01) after permanent MCAO. The profile of MCP-1 mRNA expression in the ischemic cortex after MCAO with reperfusion was similar to that of permanent MCAO except that MCP-1 mRNA was increased earlier (ie, 12.5-fold increase at 3 hours; n = 4; P < .01). Also, MCP-1 mRNA expression in the ischemic cortex after permanent MCAO was significantly greater in hypertensive rats than in two normotensive rats (n = 4; P < .05). CONCLUSIONS The demonstration of induced MCP-1 mRNA expression early after focal ischemia suggests that MCP-1 may represent a locally expressed monocyte chemoattractant that plays an important role in monocyte infiltration into ischemic tissue and therefore may contribute to the tissue injury in ischemic stroke. Further studies must concentrate on identifying the induced expression of MCP-1 and its cellular localization in the ischemic brain when the appropriate antibodies become available.
Near-infrared [Fe II] and H2 Line Mapping of the Supernova Remnant IC 443 with the IRSF/SIRIUS

We investigate properties of the interstellar medium (ISM) interacting with shocks around the Galactic supernova remnant IC 443, using the results of near-infrared [Fe ii] and H2 line mapping with the InfraRed Survey Facility/Simultaneous Infrared Imager for Unbiased Survey. In the present study, we newly performed H2 1–0 S(1) and 2–1 S(1) line mapping with the narrowband filters tuned for these lines, covering the entire remnant ( 30 ′ × 35 ′ ). Combined with an [Fe ii] line map, our result shows that the H2 line emission is significantly detected in the southern region, while the [Fe ii] line emission is detected all over the remnant, suggesting that slow and fast shocks propagate through the southern region and the entire remnant, respectively. In particular, the H2 line emission is relatively strong compared to the [Fe ii] line emission in the southwestern region, where TeV γ-ray emission is detected. As the strong H2 line emission indicates the dominance of the dense ISM, this result supports the scenario that the γ-ray emission is likely to be produced through a heavy interaction between cosmic-ray protons and the dense ISM in the southwestern shell. We also find that the H2 and [Fe ii] line emissions show an anti-correlated spatial distribution in the same region, suggesting the presence of the clumpy ISM. Such a clumpy morphology of the ISM around IC 443 may assist cosmic-ray protons to efficiently interact with large amounts of the ISM protons.
Clustering of C‐Type Lectin Natural Killer Receptor‐Like Loci in the Bony Fish Oreochromis niloticus

The genome of the cichlid (teleost) fish Oreochromis niloticus contains a set of genes which encode group V C‐type lectin proteins homologous to the mammalian NKG2/CD94 family of natural killer (NK) cell receptors. To determine the genomic organization of these killer cell‐like receptor (KLR) genes, an O. niloticus BAC library was screened with a cDNA probe derived previously from an expressed sequence tag of the related cichlid species Paralabidochromis chilotes. Four distinct KLR‐bearing BAC clones were analysed, three of which could be assembled into a contig. One of the clones was sequenced in its entirety, whereas the others were partially sequenced to identify the KLR loci borne by them. Altogether, 28 distinct KLR loci were identified, of which at least 26 occupy a single chromosomal region, the KLR complex. One half of the loci appear to be occupied by pseudogenes. Compared to the human NK cell receptor complex, the Oreochromis KLR complex is more compact and, apart from transposons, appears to contain only KLR loci. The gene density of the complex is one KLR locus per 18 kb of sequence. All the KLR loci constituting the complex are derived from a single most recent common ancestor, which is estimated to have existed 7.7 million years ago. The 180 kb of the determined sequence is a mosaic of blocks of similar segments reflecting a complex history of duplications, deletions and rearrangements. The transposons found in the sequenced part belong to the TC1, Xena, CR1 and TX1 families.
Evaluation of MR-Induced Hot Spots for Different Temporal SAR Modes Using a Time-Dependent Finite Difference Method With Explicit Temperature Gradient Treatment

An investigation of magnetic resonance (MR)-induced hot spots in a high-resolution human model is performed, motivated by safety aspects for the use of MR tomographs. The human model is placed in an MR whole body resonator that is driven in a quadrature excitation mode. The MR-induced hot spots are studied by varying the following: the temporal specific absorption rate (SAR) mode (ldquosteady imagingrdquo, ldquointermittent imagingrdquo), the simulation procedure (related to given power levels or to limiting temperatures), and different thermal tissue properties including temperature-independent and temperature-dependent perfusion models. Both electromagnetic and thermodynamic simulations have been performed. For the electromagnetic modeling, a commercial finite-integration theory (FIT) code is applied. For the thermodynamic modeling, a time-domain finite-difference (FD) scheme is formulated that uses an explicit treatment of temperature gradient components. This allows a flux-vector-based implementation of heat transfer boundary conditions on cubical faces. It is shown that this FD scheme significantly reduces the staircase errors at thermal boundaries that are locally sloped or curved with respect to the cubical grid elements.
Out with the old, in with the new? Comparing methods for measuring protein degradation

Protein degradation is a critical factor in controlling cellular protein abundance. Here, we compare classical methods for determining protein degradation rates to a novel GFP (green fluorescent protein) fusion protein based method that assesses the intrinsic stability of cloned cDNA library products by flow cytometry [ Yen et al. (2008) Science 322, 918]. While no method is perfect, we conclude that chimeric gene reporter approaches, though powerful, should be applied cautiously, due principally to GFP (or other reporter tag) interference with protein organelle targeting or incorporation into macromolecular assemblies, both of which cause spuriously high degradation rates.
Parity Striping of Disk Arrays: Low-Cost Reliable Storage with Acceptable Throughput

An analysis of mirrored discs and of RAID5 shows that mirrors have considerably better throughput, measured as requests/second on random requests of arbitrary size (up to 1MB). Mirrors have comparable or better response time for requests of reasonable size (less than 100KB). But mirrors have a 100% storage penalty: storing the data twice. Parity striping is a data layout that stripes the parity across the discs, but does not stripe the data. Parity striping has throughput almost as good as mirrors, and has cost/GB comparable to RAID5 designs -combing the advantages of both for high-traffic disc resident data. Parity striping has additional fault containment and software benefits as well. Parity striping sacrifices the high data transfer rates of RAID designs for high throughput. It is argued that response time and throughput are preferable performance metrics. Outline Introduction Why Striping and RAID Are Inappropriate for OLTP Systems Parity Striping: Cheap Reliable Storage Plus High Throughput An Analysis of Mirrors, RAID5, and Parity Stripe Performance Mirrored Discs Parity Stripe Discs RAID5 Discs Applying the Analysis to a 10+2 array The Read-Only Case The Write-Only Case Analyzing a High-Performance Disc Other Benefits of Parity Striping Summary Acknowledgments References Appendix: Spreadsheets Corresponding to the Graphs
Manipulating the mammalian genome by homologous recombination

Gene targeting in mammalian cells has proven invaluable in biotechnology, in studies of gene structure and function, and in understanding chromosome dynamics. It also offers a potential tool for gene-therapeutic applications. Two limitations constrain the current technology: the low rate of homologous recombination in mammalian cells and the high rate of random (nontargeted) integration of the vector DNA. Here we consider possible ways to overcome these limitations within the framework of our present understanding of recombination mechanisms and machinery. Several studies suggest that transient alteration of the levels of recombination proteins, by overexpression or interference with expression, may be able to increase homologous recombination or decrease random integration, and we present a list of candidate genes. We consider potentially beneficial modifications to the vector DNA and discuss the effects of methods of DNA delivery on targeting efficiency. Finally, we present work showing that gene-specific DNA damage can stimulate local homologous recombination, and we discuss recent results with two general methodologies—chimeric nucleases and triplex-forming oligonucleotides—for stimulating recombination in cells.
Harmonisation of food regulations and trade in the Single Market: evidence from disaggregated data

A structural gravity model is used to quantify the effect of harmonisation of EU food regulations on intra-EU trade during 1990-2001. We construct a database that identifies food products covered by harmonised regulations at a very detailed level. We find, at different levels of aggregation, that harmonisation of food regulations has led to more intra-EU trade, and that the tariff equivalents of the cost of not harmonising food regulations, subject to the sub-sector elasticity of substitution, vary significantly across some food sub-sectors.
MTMT in QALab-3: World History Essay Question Answering System that Utilizes Textbooks and Open Knowledge Bases

This paper introduces the system and its evaluation for answering world history essay questions by utilizing linked open data which assists machine translation. Since the target questions are the world history subject of the entrance examination of the University of Tokyo, most answers can be found in the Japanese world history textbooks. However, an equivalent content of high-quality English translation of the Japanese world history textbooks is not available. Therefore, we try to translate those textbooks utilizing linked open data, and using source language knowledge resource of which content is not equivalent with the target knowledge resource. The evaluation result indicates that the proposed system shows the best ROUGE-1 scores of all the end-to-end submissions [13]. The result of this paper concludes followings. 1) Simple neural translation of knowledge resource does not work for domain-specific cross-lingual question answering. 2) Linked open data is effective to find correct translation for difficult terms in machine translation process. 3) Adding source language open knowledge resource would help even if its content is not equivalent to the target knowledge resources.
Improved unsupervised NAP training dataset design for speaker recognition

The Nuisance Attribute Project (NAP) with labeled data provides an effective approach for improving the speaker recognition performance in the state-of-art speaker recognition system by removing unwanted channel and handset variation. However, the requirement for the labeled NAP training data may limit its practical application. In our previous study, a simple unsupervised clustering algorithm based on dot products between supervectors was introduced for designing NAP training dataset without a prior knowledge about channel and speaker information. Using such clustering results as the initial training dataset, in this paper, we make a further improvement of the training dataset by enhancing similarity measurement of supervectors via NAP projection and score normalization. The effectiveness of this unsupervised NAP training dataset design strategy has been verified in the experiments using the in-house development dataset of IIR submission for the 2012 NIST SRE.
Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset

Clinical coding is currently a labour-intensive, error-prone, but a critical administrative process whereby hospital patient episodes are manually assigned codes by qualified staff from large, standardised taxonomic hierarchies of codes. Automating clinical coding has a long history in NLP research and has recently seen novel developments setting new benchmark results. A popular dataset used in this task is MIMIC-III, a large database of clinical free text notes and their associated codes amongst other data. We argue for the reconsideration of the validity MIMIC-III’s assigned codes, as MIMIC-III has not undergone secondary validation. This work presents an open-source, reproducible experimental methodology for assessing the validity of EHR discharge summaries. We exemplify the methodology with MIMIC-III discharge summaries and show the most frequently assigned codes in MIMIC-III are undercoded up to 35%.
Extended safe havens and between-group dispersal of helpers in a cooperatively breeding cichlid

In cooperative breeders, between-group dispersal of helpers is expected to occur if it increases their fitness. Genetic data suggest that helpers in the cooperatively breeding Lake Tanganyika cichlid Neolamprologus pulcher occasionally migrate into nearby groups where they again become helpers. We studied in the field how and why helpers migrate between groups by recording their ranging and social behaviours. We found that helpers spent 5.3% of their time visiting other groups, where they received similar low levels of aggression as within their home group. Large helpers visited other groups more often than small helpers and helpers visited other groups more frequently when the queue in their home group was large, suggesting that helpers with low chances to inherit the territory search for alternatives. Our data show that helpers may use other groups' territories as a refuge, as helpers actively sought shelter within territories of neighbouring groups when we experimentally increased the perceived risk of staying in their home territory. We observed two attempted and one successful case of 'voluntary' (i.e., strategic) between-group dispersal, and experimentally induced three helpers to disperse into other groups. By regular visits, helpers appear to establish familiarity and social relationships with nearby groups, which serve as 'extended safe havens' to hide from predators. In the long run frequent visiting behaviour may facilitate between group dispersal.
KILLING OF SCHISTOSOMES BY ELASTASE AND HYDROGEN PEROXIDE: IMPLICATIONS FOR LEUKOCYTE-MEDIATED SCHISTOSOME KILLING

Activated leukocytes participate in immunity to infection by the parasitic blood fluke Schistosoma mansoni. They attach to the surface of schistosomes and secrete schistosomicidal substances. Cationic proteins, hydrolytic enzymes, and oxidants, produced by the leukocytes, have been implicated in the damage to the schistosomes. To examine the possible involvement of elastase in the killing of schistosomes by leukocytes, young and adult stages of S. mansoni were treated in vitro with pancreatic elastase (PE) and neutrophil elastase (NE). Schistosomula, lung-stage schistosomula (LSS), and adult worms (AW) have been found to be sensitive to both PE and NE. Male AW were more sensitive to PE than female AW. The enzymatic activity of elastase is essential for its toxic effect because heat-inactivation and specific elastase inhibitors prevented elastase-mediated schistosome killing. Thus, α1-antitrypsin and the chloromethyl ketone (CMK)–derived tetrapeptides Ala-Ala-Pro-Val-CMK and Ala-Ala-Pro-Ala-CMK but not Ala-Ala-Pro-Phe-CMK and Ala-Ala-Pro-Leu-CMK blocked PE caseinolytic and schistosomulicidal activities. As shown previously, schistosomes are also efficiently killed by hydrogen peroxide. LSS appear to be more resistant than AW and early-stage schistosomula to the lytic effects of hydrogen peroxide. Cotreatment experiments with both elastase and hydrogen peroxide indicated that they exert an additive toxic effect and that hydrogen peroxide sensitizes schistosomula to the toxic effect of elastase but not vice versa. These results demonstrate, for the first time, that elastases may be toxic molecules used by neutrophils, eosinophils, and macrophages to kill various developmental stages of S. mansoni.
Design, Synthesis and Anti-fibrosis Activity Study of N1-Substituted Phenylhydroquinolinone Derivatives

Pirfenidone (5-methyl-1-phenyl-2(1H)-pyridone, PFD) is a small-molecule compound acting on multiple targets involved in pathological fibrogenesis and is effective to increase the survival of patients with fibrosis, such as idiopathic pulmonary fibrosis. However, PFD is not active enough, requiring a high daily dose. In this study, to keep the multiple target profiles, N1-substituted phenylhydroquinolinone derivatives, which retain the 1-phenyl-2(1H)-pyridone scaffold were designed and synthesized. The preliminary anti-fibrosis activities for all target compounds were evaluated on a NIH3T3 fibroblast cell line using MTT assay methods. Most compounds showed significant inhibition on NIH3T3 cell proliferation with a IC50 range of 0.09–26 mM, among which 5-hydroxy-1-(4'-bromophenyl)-5,6,7,8-tetrahydroquinolin-2(1H)-one (6j) displayed 13 times higher potency (IC50 = 0.3 mM) than that of AKF-PD (IC50 = 4.2 mM). These results suggest that N1-substituted phenylhydroquinolinone is a promising scaffold which can be applied for further investigation and for developing novel anti-fibrosis agents.
Origins of Timing Errors in Human Sensorimotor Coordination

Abstract The authors analyzed fluctuations in timing errors when 8 human participants attempted to coordinate movement with external rhythmic signals. The temporal dynamics of the errors is usually described in terms of simple, self-correcting models. Here the authors demonstrate that timing errors are characterized by a 1/f α type of long memory process. The value of the exponent α differentiates different types of coordination states: synchronization and syncopation. More interesting, evidence was found that α can be changed when participants use different coordination strategies. Together with the authors' understanding of the generation mechanism for long memory processes, these results suggest that 1/fα type of long-range correlated timing errors are of higher cortical origin and are likely the outcome of distributed neural processes acting on multiple time scales.