Miracle-dz/UniFAR-FTUs huggingface dataset:
Five-parameter fluorescence imaging: wound healing of living Swiss 3T3 cells

Cellular functions involve the temporal and spatial interplay of ions, metabolites, macromolecules, and organelles. To define the mechanisms responsible for completing cellular functions, we used methods that can yield both temporal and spatial information on multiple physiological parameters and chemical components in the same cell. We demonstrated that the combined use of selected fluorescent probes, fluorescence microscopy, and imaging methods can yield information on at least five separate cellular parameters and components in the same living cell. Furthermore, the temporal and spatial dynamics of each of the parameters and/or components can be correlated with one or more of the others. Five parameters were investigated by spectrally isolating defined regions of the ultraviolet, visible, and near-infrared spectrum based on five distinct fluorescent probes. The parameters included nuclei (Hoechst 33342), mitochondria (diIC1-[5] ), endosomes (lissamine rhodamine B-dextran), actin (fluorescein), and the cell volume Cy7- dextran). Nonmotile, confluent Swiss 3T3 cells did not show any detectable polarity of cell shape, or distribution of nuclei, endosomes, or mitochondria. These cells also organized a large percentage of the actin into stress fibers. In contrast, cells migrating into an in vitro wound exhibited at least two stages of reorganization of organelles and cytoplasm. During the first 3 h after wounding, the cells along the edge of the wound assumed a polarized shape, carried the nuclei in the rear of the cells, excluded endosomes and mitochondria from the lamellipodia, and lost most of the highly organized stress fibers. The cell showed a dramatic change between 3 and 7 h after producing the wound. The cells became highly elongated and motile; both the endosomes and the mitochondria penetrated into the lamellipodia, while the nuclei remained in the rear and the actin remained in less organized structures. Defining the temporal and spatial dynamics and interplay of ions, contractile proteins, lipids, regulatory proteins, metabolites, and organelles should lead to an understanding of the molecular basis of cell migration, as well as other cellular functions.
Approach for physical design in sub-100 nm era

In sub-100 nm processes, various physical phenomena come up as critical red-brick in designing circuits and LSIs. We focus on design for variability (DFV) for LSI-chip design, taking within-die variations into consideration. The main approach for the purpose is a new test structure, TEG (test element group), to measure the within-die variation of elements (MOS, R, C) and ring-oscillators. The precise measurement has been achieved with careful TEG design, including on-chip circuit, such as CBCM, Kelvin pattern. Reliable measurement data were analyzed statistically. Variation-caused systematic and random physical sources have been successfully decomposed with a newly developed extraction strategy. The data exhibits an extremely large variation in N/PMOS drain current (I/sub ds/) and threshold voltage (V/sub th/). The main sources of the random variation are doping fluctuation and line edge roughness (LER) in small size MOS transistors. I/sub ds/ variation is affected by the doping fluctuation. On the other hand, V/sub th/ variation is sensitive to LER. Interconnect variation is essentially small compared with the I/sub ds//V/sub th/ variation of MOS transistors; however, its variation is systematic component dominant. Ring oscillator T/sub pd/ variation is found to be closely related to I/sub ds/ variation, showing a correlation coefficient of 0.9. Design for variability is one of the most difficult challenges in 65-90 nm processes. Statistical design in the early stages will be necessary.
The TRPM1 Channel Is Required for Development of the Rod ON Bipolar Cell-AII Amacrine Cell Pathway in the Retinal Circuit

Neurotransmission plays an essential role in neural circuit formation in the central nervous system (CNS). Although neurotransmission has been recently clarified as a key modulator of retinal circuit development, the roles of individual synaptic transmissions are not yet fully understood. In the current study, we investigated the role of neurotransmission from photoreceptor cells to ON bipolar cells in development using mutant mouse lines of both sexes in which this transmission is abrogated. We found that deletion of the ON bipolar cation channel TRPM1 results in the abnormal contraction of rod bipolar terminals and a decreased number of their synaptic connections with amacrine cells. In contrast, these histological alterations were not caused by a disruption of total glutamate transmission due to loss of the ON bipolar glutamate receptor mGluR6 or the photoreceptor glutamate transporter VGluT1. In addition, TRPM1 deficiency led to the reduction of total dendritic length, branch numbers, and cell body size in AII amacrine cells. Activated Goα, known to close the TRPM1 channel, interacted with TRPM1 and induced the contraction of rod bipolar terminals. Furthermore, overexpression of Channelrhodopsin-2 partially rescued rod bipolar cell development in the TRPM1−/− retina, whereas the rescue effect by a constitutively closed form of TRPM1 was lower than that by the native form. Our results suggest that TRPM1 channel opening is essential for rod bipolar pathway establishment in development. SIGNIFICANCE STATEMENT Neurotransmission has been recognized recently as a key modulator of retinal circuit development in the CNS. However, the roles of individual synaptic transmissions are not yet fully understood. In the current study, we focused on neurotransmission between rod photoreceptor cells and rod bipolar cells in the retina. We used genetically modified mouse models which abrogate each step of neurotransmission: presynaptic glutamate release, postsynaptic glutamate reception, or transduction channel function. We found that the TRPM1 transduction channel is required for the development of rod bipolar cells and their synaptic formation with subsequent neurons, independently of glutamate transmission. This study advances our understanding of neurotransmission-mediated retinal circuit refinement.
Motor–Language Coupling in Huntington’s Disease Families

Traditionally, Huntington’s disease (HD) has been known as a movement disorder, characterized by motor, psychiatric, and cognitive impairments. Recent studies have shown that motor and action–language processes are neurally associated. The cognitive mechanisms underlying this interaction have been investigated through the action compatibility effect (ACE) paradigm, which induces a contextual coupling of ongoing motor actions and verbal processing. The present study is the first to use the ACE paradigm to evaluate action–word processing in HD patients (HDP) and their families. Specifically, we tested three groups: HDP, healthy first-degree relatives (HDR), and non-relative healthy controls. The results showed that ACE was abolished in HDP as well as HDR, but not in controls. Furthermore, we found that the processing deficits were primarily linguistic, given that they did not correlate executive function measurements. Our overall results underscore the role of cortico-basal ganglia circuits in action–word processing and indicate that the ACE task is a sensitive and robust early biomarker of HD and familial vulnerability.
Effects of financial reform on productivity change

Purpose – The aim is to investigate the effects of the first financial restructuring (FFR) on productivity growth, technical progress and efficiency change, using data from 42 commercial banks in Taiwan from 2001 to 2004.Design/methodology/approach – Data envelopment analysis is applied to compute the Malmquist index of productivity change.Findings – It is found that Taiwan commercial banks on average experienced a 117.39 percent increase in productivity growth, of which is 2.11 percent is due to efficiency change and 115.28 percent to technical progress over the four year period. In addition, during the four year period, a 1 percent reduction in the nonperforming loan ratio resulted in 1.85 percent growth in productivity; a 1 percent increase in the capital adequacy ratio led to 2.15 percent growth in productivity.Practical implications – It can be concluded that after the FFR, the productivity growth, technical progress, and efficiency change all improve, with the lower nonperforming loan ratio contribu.
Nursing Activities Score and workload in the intensive care unit of a university hospital

Objective The nursing workload consists of the time spent by the nursing staff to perform the activities for which they are responsible, whether directly or indirectly related to patient care. The aim of this study was to evaluate the nursing workload in an adult intensive care unit at a university hospital using the Nursing Activities Score (NAS) instrument. Methods A longitudinal, prospective study that involved the patients admitted to the intensive care unit of a university hospital between March and December 2008. The data were collected daily to calculate the NAS, the Acute Physiology and Chronic Health Evaluation (APACHE II), the Sequential Organ Failure Assessment (SOFA) and the Therapeutic Intervention Scoring System (TISS-28) of patients until they left the adult intensive care unit or after 90 days of hospitalization. The level of significance was set at 5%. Results In total, 437 patients were evaluated, which resulted in an NAS of 74.4%. The type of admission, length of stay in the intensive care unit and the patients’ condition when leaving the intensive care unit and hospital were variables associated with differences in the nursing workload. There was a moderate correlation between the mean NAS and APACHE II severity score (r=0.329), the mean organic dysfunction SOFA score (r=0.506) and the mean TISS-28 score (r=0.600). Conclusion We observed a high nursing workload in this study. These results can assist in planning the size of the staff required. The workload was influenced by clinical characteristics, including an increased workload required for emergency surgical patients and patients who died.
Analysis of long-term acoustic datasets for baleen whales and beaked whales within the Mariana Islands Range Complex (MIRC) for 2010 to 2013

Cetacean distribution and abundance in the Mariana Archipelago was relatively unstudied until recently. Although there has been increasing effort to understand the occurrence of various cetacean species in both near shore and offshore waters, there is still relatively little known about their occurrence seasonally, or their prevalence relative to other regions. To better understand the seasonal distribution of cetaceans in the Marianas, the NOAA Pacific Islands Fisheries Science Center (PIFSC) deployed a longterm acoustic recorder in the region in 2010, expanded that effort to two sites in 2011, and has been monitoring both sites since that time.
Enrichment of Members of the Family Geobacteraceae Associated with Stimulation of Dissimilatory Metal Reduction in Uranium-Contaminated Aquifer Sediments

ABSTRACT Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.
NMR spectroscopy metabolomic profiling of exhaled breath condensate in patients with stable and unstable cystic fibrosis

Background Metabolomics could provide new insights into the pathophysiology of cystic fibrosis (CF) by identifying profiles of endogenous metabolites. Objectives To investigate whether metabolomics of exhaled breath condensate could discriminate between patients with unstable CF, stable CF and healthy subjects, and whether selected metabolites were responsible for between-group differences. Methods Twenty-nine patients with stable CF, 24 with unstable CF and 31 healthy subjects (age 9–24 years) participated in a cross-sectional study. Metabolomics was performed with high-resolution nuclear magnetic resonance spectroscopy. Partial least squares-discriminant analysis was used as classifier. The results were validated in a second independent study. Results Intraclass correlation coefficients for between-day and technical repeatability were 0.93 and 0.96, respectively. Bland–Altman analysis showed good within-day repeatability. Correct classification rate of CF (n=53) vs healthy subjects (n=31) was 96% (R2=0.84; Q2=0.79). Model validation with a testing sample set obtained from subjects not included in the primary analysis (23 CF and 25 healthy subjects) showed a sensitivity of 91% and a specificity of 96%. The classification rate of stable CF (n=29) vs unstable CF patients (n=24) was 95% (R2=0.82; Q2=0.78). Model external validation in 14 patients with stable CF and 16 with unstable CF showed a sensitivity of 86% and a specificity of 94%. Ethanol, acetate, 2-propanol and acetone were most discriminant between patients with CF and healthy subjects, whereas acetate, ethanol, 2-propanol and methanol were the most important metabolites for discriminating between patients with stable and unstable CF. Conclusions Nuclear magnetic resonance spectroscopy of exhaled breath condensate is reproducible, discriminates patients with CF from healthy subjects and patients with unstable CF from those with stable CF, and identifies the metabolites responsible for between-group differences.
A Hardware-Independent Colour Calibration Technique

Most colour‐normal human observers have no difficulty to adjust a coloured light such that it appears neither red nor green, or such that it appears neither yellow nor blue. Moreover, it has been shown that these hue judgements are not significantly influenced by language or age and individual differences in colour sensitivity are not reflected in the unique‐hue settings. Here we show how we can use the invariance of these unique‐hue judgements to develop a colour calibration technique for display devices, which eliminates the need for an external calibration standard or a measurement device.
Synergistic Effect of Nitric Oxide Synthase and Cyclooxygenase Inhibitors on Carrageenan-induced Paw Edema in Rats

Summary The present study examined the effects of L-nitroarginine methylester (L-NAME, CAS 50903–99–6), a non-selective nitric oxide synthase (NOS) inhibitor, indometa-cin (IND, CAS 3305–29–1), a non-selective cyclooxygenase (COX) inhibitor, and a combination of these agents (L-NAME + IND) on carrageenan-induced paw edema for 4 h after the injection of carrageenan in rats. L-NAME at 10 and 30 mg/kg but not 3 mg/kg (i.p.) decreased paw volume slightly but significantly only at 1 h after the carrageenan injection. IND reduced paw volume slightly at 1 and 3 mg/kg, and markedly at 10 mg/kg (p.o.). A combination of L-NAME and IND at a subthreshold dose (3 mg/kg, i.p. and 1 mg/kg, p.o., respectively) caused a marked reduction of paw edema, which was also confirmed by histopathological examinations. A combination of N-(3-(aminomethyl)benzyl)acetamidine (1400W, CAS 180001–34–7), a selective inhibitor of inducible NOS, and IND at 3 mg/kg, i.p., and 1 mg/kg, p.o. , respectively, did not show synergistic anti-inflammatory effects. In conclusion, the combination of non-selective NOS and COX inhibitors had synergistic anti-inflammatory effects on carrageenan-induced paw edema at an early stage, suggesting negative crosstalk between the endogenous NOS-NO and COX-PG pathways in the early stages of acute inflammation.
Stable tri-snRNP integration is accompanied by a major structural rearrangement of the spliceosome that is dependent on Prp8 interaction with the 5′ splice site

Exon definition is the predominant initial spliceosome assembly pathway in higher eukaryotes, but it remains much less well-characterized compared to the intron-defined assembly pathway. Addition in trans of an excess of 5′ss containing RNA to a splicing reaction converts a 37S exon-defined complex, formed on a single exon RNA substrate, into a 45S B-like spliceosomal complex with stably integrated U4/U6.U5 tri-snRNP. This 45S complex is compositonally and structurally highly similar to an intron-defined spliceosomal B complex. Stable tri-snRNP integration during B-like complex formation is accompanied by a major structural change as visualized by electron microscopy. The changes in structure and stability during transition from a 37S to 45S complex can be induced in affinity-purified cross-exon complexes by adding solely the 5′ss RNA oligonucleotide. This conformational change does not require the B-specific proteins, which are recruited during this stabilization process, or site-specific phosphorylation of hPrp31. Instead it is triggered by the interaction of U4/U6.U5 tri-snRNP components with the 5′ss sequence, most importantly between Prp8 and nucleotides at the exon–intron junction. These studies provide novel insights into the conversion of a cross-exon to cross-intron organized spliceosome and also shed light on the requirements for stable tri-snRNP integration during B complex formation.
An Algorithm of Receding Horizon Control for Two-Person Linear Quadratic Differential Games Using LMI Method

In this paper a linear quadratic differential gamesbased receding horizon control (RHC) algorithm is presented using linear matrix inequality (LMI) method, for which nominal closed-loop stability is guaranteed. The two-person control inputs are obtained by minimizing a quadratic performance index (cost function) over a finite horizon plus a time-varying terminal cost penalty, subject to input, state and output constraints. Under certain conditions, the weighting matrix in the terminal cost penalty enables one to specify an invariant ellipsoid in which the input, state and output constraints are satisfied. The main contribution of this paper is to apply LMI method to two-person differential games and to incorporate the calculation of that into the on-line optimization problem of the controller. The main advantage of this approach is that a natural and automatic trade-off between feasibility and optimality is obtained. The simulation results demonstrate that the approach can be useful for practical applications. Index Term-Differential Game, Receding Horizon Control, Linear Matrix Inequality, Algorithm, 4WS ;
A Case-Based Approach to Knowledge Acquisition for Domain-Specific Sentence Analysis

This paper describes a case-based approach to knowledge acquisition for natural language systems that simultaneously learns part of speech, word sense, and concept activation knowledge for all open class words in a corpus. The parser begins with a lexicon of function words and creates a case base of context-sensitive word definitions during a humansupervised training phase. Then, given an unknown word and the context in which it occurs, the parser retrieves definitions from the case base to infer the word's syntactic and semantic features. By encoding context as part of a definition, the meaning of a word can change dynamically in response to surrounding phrases without the need for explicit lexical disambiguation heuristics. Moreover, the approach acquires all three classes of knowledge using the same case representation and requires relatively little training and no hand-coded knowledge acquisition heuristics. We evaluate it in experiments that explore two of many practical applications of the technique and conclude that the case-based method provides a promising approach to automated dictionary construction and knowledge acquisition for sentence analysis in limited domains. In addition, we present a novel case retrieval algorithm that uses decision trees to improve the performance of a k-nearest neighbor similarity metric.
Use of an image-guided navigation system in dental implant surgery in anatomically complex operation sites.

INTRODUCTION Recent developments in computer assisted surgery have brought major improvements to maxillofacial surgery. Computer systems for intra-operative navigation have been introduced enabling the surgeon to locate the continually updated position of the instruments and the operation site on the patient's three-dimensional reconstructed image data set displayed on a monitor in the operating room. Complex surgical procedures can be performed according to the preoperative plan based on CT and/or MRI data minimizing surgical risks and optimizing clinical results. Nowadays computer-assisted-surgery has also proved effective in dental implantology. AIM The objective of this study was to compare the accuracy of conventional and computer-assisted dental implantation planning and surgery. Analyzing our early experiences, we aimed to evaluate the benefit from utilising computer assisted surgery (CAS). PATIENTS Five patients were treated with the aid of CAS, a total of 18 dental implants being placed. Only difficult operation sites, e.g. following bone augmentation or anatomically malformed jaws were included in this study. METHOD An infra-red light based navigation system (Vector Vision 2, BrainLAB, Munich, Germany) including a three-dimensional planning approach for maxillofacial surgery was used. Placement of dental implants in the maxilla included direct visualization when drilling the implant socket according to the axis previously planned on radiographs and CT scans. RESULTS In two cases the conventionally planned implant location had to be changed due to insufficient bone being available. With four implants, it proved possible to insert longer fixtures after the CAS system had evaluated all parameters of the surgical region. In one case a shorter implant was installed due to insufficient bone at the designated location. CONCLUSION The use of an image-guided navigation system provides a valuable tool in implant dentistry and proved superior to conventional implant surgery especially in difficult anatomical regions.