Miracle-dz/UniFAR-FTUs huggingface dataset:
Minimal Experience Required for Immediate-Early Gene Induction in Zebra Finch Neostriatum

We show that a single presentation of a zebra finch song, 2 s in duration, will induce an "immediate-early gene" response in the caudomedial neostriatum of zebra finches (Poephila guttata). Repetition of this stimulus 10 times is sufficient to induce a maximal increase in RNA and protein, detected 30 and 90 min later respectively. Thus very brief stimuli can set in motion a slow genomic process in the brain which takes hours to resolve. Immediate-early gene function is often considered in the context of a "feedback" model (i.e., to consolidate memories of the inducing event). However, based on the long lag observed here between initiation and full expression of the molecular response, we suggest an alternative, ethologically based, "feed-forward" model in which exposure to a novel or significant context triggers an increase in the efficiency of memory capture processes for subsequent experiences.
Hypochlorous acid regulates neutrophil extracellular trap release in humans

Neutrophil extracellular traps (NETs) comprise extracellular chromatin and granule protein complexes that immobilize and kill bacteria. NET release represents a recently discovered, novel anti‐microbial strategy regulated non‐exclusively by nicotinamide adenine dinucleotide phosphate (NADPH) oxidase generation of reactive oxygen intermediates (ROIs), particularly hydrogen peroxide. This study aimed to characterize the role of ROIs in the process of NET release and to identify the dominant ROI trigger. We employed various enzymes, inhibitors and ROIs to record their effect fluorometrically on in vitro NET release by human peripheral blood neutrophils. Treatment with exogenous superoxide dismutase (SOD) supported the established link between hydrogen peroxide and NET production. However, treatment with myeloperoxidase inhibitors and direct addition of hypochlorous acid (HOCl; generated in situ from sodium hypochlorite) established that HOCl was a necessary and sufficient ROI for NET release. This was confirmed by the ability of HOCl to stimulate NET release in chronic granulomatous disease (CGD) patient neutrophils which, due to the lack of a functional NADPH oxidase, also lack the capacity for NET release in response to classical stimuli. Moreover, the exogenous addition of taurine, abundantly present within the neutrophil cytosol, abrogated NET production stimulated by phorbol myristate acetate (PMA) and HOCl, providing a novel mode of cytoprotection by taurine against oxidative stress by taurine.
Modelling the Impact of Perceived Connectivity on the Intention to Use Social Media: Discovering Mediating Effects and Unobserved Heterogeneity

Early research examined the direct effect of perceived connectivity (PC) on intention to adopt information systems. In this study, we extend that research stream by examining the mediating effects of perceived enjoyment (PE) and perceived playfulness (PP) on the relationship between PC and the intention to use social media within the workplace. To test our proposed model, we collected data from 2,556 social media users from Australia, Canada, India, the UK, and the US. We applied the REBUS-PLS algorithm, a response-based method for detecting unit segments in PLS path modelling and assessing the unobserved heterogeneity in the data sample. Based on the strength of effects, the algorithm automatically detected two groups of users sharing the same intentions to use social media. A post hoc analysis of each group was done using contextual and demographic variables including geographic location, country, age, education and gender. Implications for practice and research are discussed.
[Differential diagnosis of axillary lymph nodes: Usefulness of gray-scale and color-power doppler sonography].

PURPOSE To evaluate and compare the usefulness of gray-scale and color-power Doppler sonography in differentiating benign from malignant axillary lymph nodes, and to find out whether the combined usage of both modalities increased the diagnostic accuracy. MATERIALS AND METHODS Sixty lymph nodes in 59 patients were evaluated by gray-scale and color-power Doppler sonography. Color-power Doppler evaluation was based on the morphological patterns of vascularity. Spectral wave form analysis was also performed. Sensitivity, specificity, positive and negative predictive values and overall accuracy were calculated for each modality and for the combined usage of both modalities. When two modalities were used in combination a lymph node was accepted to be 'malignant' if it was diagnosed as 'malignant' by either or both of the modalities. RESULTS Forty lymph nodes were confirmed to be malignant and 20 were benign by histopathologic or sytologic examination or by clinical and sonographic follow-up. Gray-scale and color-power sonography had sensitivities of 92%, 89%; specificities of 70%, 75%; positive predictive values of 86%, 87%; negative predictive values of 82%, 79%; and overall accuracies of 85%, 85% respectively. The combined usage of both modalities yielded a sensitivity of 98%, specificity of 70%, positive predictive value of 87%, negative predictive value of 88%, and an overall accuracy of 88%. CONCLUSION Gray-scale sonography and color-power Doppler examination have the same overall accuracy for the differentiation of benign from malignant axillary lymph nodes. Spectral wave form analysis was proved to be statistically insignificant. The combined usage of both modalities would decrease the number of false negative cases.
A Study of Ship Rotation Effects on SAR Image

Imaging distortions induced by each particular rotation of a moving ship are quantitatively investigated through numerical simulations. Two sets of dynamics are considered in the model, namely a ship with pitch, yaw, and roll rotations, and the time evolutions of its wake. To construct high-resolution synthetic aperture radar (SAR) images in spotlight mode, the time-varying scattering from the electrically very large scene is computed by a parallel quasi-stationary algorithm, in which the physical optics (PO) method is used to compute the scattering from the ship, and a PO phase correction of the two-scale model is used to take account of the Doppler effects caused by the wake. Reasonable agreement is obtained when comparisons are made between the simulated and real SAR images. A range of imaging distortions are observed and analyzed, such as the displacement, rotation, stretching/compressing, and broaden/narrow of the ship image. A systematic analysis shows that these distortions can be characterized by four main types of transformations, namely translation, rotation, scaling, and shearing. This paper presents quantitative insights into the data interpretation and signature classification of ship on SAR image.
Oxygen mapping: Probing a novel seeding strategy for bone tissue engineering

Bone tissue engineering (BTE) utilizing biomaterial scaffolds and human mesenchymal stem cells (hMSCs) is a promising approach for the treatment of bone defects. The quality of engineered tissue is crucially affected by numerous parameters including cell density and the oxygen supply. In this study, a novel oxygen‐imaging sensor was introduced to monitor the oxygen distribution in three dimensional (3D) scaffolds in order to analyze a new cell‐seeding strategy. Immortalized hMSCs, pre‐cultured in a monolayer for 30–40% or 70–80% confluence, were used to seed demineralized bone matrix (DBM) scaffolds. Real‐time measurements of oxygen consumption in vitro were simultaneously performed by the novel planar sensor and a conventional needle‐type sensor over 24 h. Recorded oxygen maps of the novel planar sensor revealed that scaffolds, seeded with hMSCs harvested at lower densities (30–40% confluence), exhibited rapid exponential oxygen consumption profile. In contrast, harvesting cells at higher densities (70–80% confluence) resulted in a very slow, almost linear, oxygen decrease due to gradual achieving the stationary growth phase. In conclusion, it could be shown that not only the seeding density on a scaffold, but also the cell density at the time point of harvest is of major importance for BTE. The new cell seeding strategy of harvested MSCs at low density during its log phase could be a useful strategy for an early in vivo implantation of cell‐seeded scaffolds after a shorter in vitro culture period. Furthermore, the novel oxygen imaging sensor enables a continuous, two‐dimensional, quick and convenient to handle oxygen mapping for the development and optimization of tissue engineered scaffolds. Biotechnol. Bioeng. 2017;114: 894–902. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
Nuclear disintegration as a leading step of glutamate excitotoxicity in brain neurons

Recent studies on ischemic brain disease in vivo and glutamate excitotoxicity in vitro suggest that apoptosis may play a role in excitotoxic neuronal death. To examine the possible involvement of apoptosis in glutamate excitotoxicity, we studied an early process of morphological changes in rat cortical neurons exposed to 1 mM glutamate. Observations under Nomarski optics combined with a digital image processor revealed a rapid change in the nucleus followed by a cellular swelling. The nucleus increased in granularity and swelled in 5 min, then became liquefied in 30 min. The cell body swelled slowly in 15–45 min. These changes could be prevented by treatment of the neuron with MK‐801 (dizocilpine maleate), a blocker of N‐methyl‐D‐aspartate (NMDA) receptor‐coupled ion channel. However, treatment of the neurons with NG‐nitro‐L‐arginine (N‐NORG), a nitric oxide synthase inhibitor, had no significant effect. Use of the in situ end‐labeling technique for the demonstration of free 3′‐hydroxyl ends revealed that DNA fragmentation took place within 1 hr after glutamate exposure. A change in intracellular Ca2+ concentration was examined with fluo‐3 under a confocal laser microscope. Application of 1 mM glutamate induced rapid Ca transients in the nucleus as well as in the cytoplasm. Both of these Ca responses were blocked by MK‐801. These results indicate that glutamate excitotoxicity in the brain neuron does not fulfill morphological criteria of apoptosis, but suggest that the nuclear disintegration associated with DNA fragmentation is involved as a leading step in glutamate excitotoxicity. © 1996 Wiley‐Liss, Inc.
The bacterial alarmone (p)ppGpp is required for virulence and controls cell size and survival of Pseudomonas syringae on plants.

The stringent response, mediated by second messenger (p)ppGpp, results in swift and massive transcriptional reprogramming under nutrient limited conditions. In this study, the role of (p)ppGpp on virulence of Pseudomonas syringae pv. syringae B728a (PssB728a) was investigated. The virulence of the relA/spoT (ppGpp(0) ) double mutant was completely impaired on bean, and bacterial growth was significantly reduced, suggesting that (p)ppGpp is required for full virulence of P. syringae. Expression of T3SS and other virulence genes was reduced in ppGpp(0) mutants. In addition, ppGpp deficiency resulted in loss of swarming motility, reduction of pyoverdine production, increased sensitivity to oxidative stress and antibiotic tolerance, as well as reduced ability to utilize γ-amino butyric acid. Increased levels of ppGpp resulted in reduced cell size of PssB728a when grown in a minimal medium and on plant surfaces, while most ppGpp(0) mutant cells were not viable on plant surfaces 24 h after spray inoculation, suggesting that ppGpp-mediated stringent response temporarily limits cell growth, and might control cell survival on plants by limiting their growth. These results demonstrated that ppGpp-mediated stringent response plays a central role in P. syringae virulence and survival and indicated that ppGpp serves as a global signal for regulating various virulence traits in PssB728a.
Implementing Basel II Loss Distribution Approach for Operational Risk

To quantify the operational risk capital charge under the current regulatory framework for banking supervision, referred to as Basel II, many banks adopt the Loss Distribution Approach. There are many modelling issues that should be resolved to use the approach in practice. In this paper we review the quantitative methods suggested in literature for implementation of the approach.
Benefits, Barriers, and Challenges to University-Level Food Waste Tracking

ABSTRACT The goal of this study was to assess the perceptions of dining services’ staff toward tracking food waste within a large university using focus group discussions and structured interviews. Participants reported that food waste tracking resulted in improved awareness of food waste, individually directed corrective action, lower food costs, increased accountability, and shifts in perspectives. Reported barriers included logistical concerns with weighing, such as time required, compliance, communication, and need for ongoing training. Recommendations ranged from establishing a university-wide policy instituting food waste tracking programs per facility to manipulating employee work schedules internally to accommodate tracking.
A Gait Generation Method for the Compass-type Biped Robot based on Discrete Mechanics

Abstract In this paper, we consider a new approach based on discrete mechanics to a gait generation problem for the compass-type biped robot. First, both continuous-time and discrete-time models of the compass-type biped robot are derived. We next formulate a discrete gait generation problem for the discrete compass-type biped robot as a finite dimensional nonlinear optimal control problem, and solve it by using the sequential quadratic programming. Then, we propose a transformation method of a discrete-time input into continuous one and apply it to gait generation for the continuous compass-type biped robot. Some simulations are also shown in order to verify the effectiveness of our approach.
Block principal component analysis with application to gene microarray data classification

We propose a block principal component analysis method for extracting information from a database with a large number of variables and a relatively small number of subjects, such as a microarray gene expression database. This new procedure has the advantage of computational simplicity, and theory and numerical results demonstrate it to be as efficient as the ordinary principal component analysis when used for dimension reduction, variable selection and data visualization and classification. The method is illustrated with the well‐known National Cancer Institute database of 60 human cancer cell lines data (NCI60) of gene microarray expressions, in the context of classification of cancer cell lines. Copyright © 2002 John Wiley & Sons, Ltd.
Expression and promoter activation of the Rpe65 gene in retinal pigment epithelium cell lines

Purpose. To examine the expression and promoter activation of the retinal pigment epithelium (RPE)-preferentially expressed Rpe65 gene in the commonly available RPE cell lines. Methods. Reverse transcription coupled to polymerase chain reaction (RT-PCR) was performed after total RNA extraction from different RPE (ARPE-19, monkey, hTERT-RP1 and D407) and non-RPE (COS-7, HeLa, HepG2 and HS27) cell lines. Promoter activity was assayed by transient transfection of luciferase reporter constructs containing nested deletions of the 5' flanking region of the mouse Rpe65 gene. The involvement of a putative TATA box in the basal promoter expression was studied by site-directed mutagenesis in D407 cells and binding of TATA box-related transcription factors to that region was demonstrated by Electrophoretic Mobility Shift Assays (EMSA). Results. Expression of the human RPE65 cDNA was observed in all the RPE cell lines tested, and in COS-7 cells (monkey RPE65 cDNA). Transient transfections of the mouse Rpe65 promoter/luciferase transgene containing nested deletions of the Rpe65 5' flanking region showed that fragments containing bases -655 to +48 and -1240 to +48 generated specific promoter activity only in the D407 cell line. A promoter fragment from -49 to +48 directed basal promoter activity in all the cell lines tested. Part of this basal activity was due to a putative TATA box that specifically binds transcription factors contained in a D407 nuclear extract. Conclusion. Although transcription of the Rpe65 gene occurs in all the tested cell lines, we find that the D407 cell line is the only one capable of directing specific mouse Rpe65 promoter activity. This limits the study of the transcriptional regulation of the mouse Rpe65 gene in vitro to this particular cell line.
Hypertrophic pachymeningitis as an initial and cardinal manifestation of microscopic polyangiitis

The authors describe a 68-year-old man who developed hypertrophic pachymeningitis as an initial and cardinal manifestation of microscopic polyangiitis. The patient had a high titer of antineutrophil cytoplasmic antibody for myeloperoxidase. Biopsies revealed necrotizing glomerulonephritis in the kidney, small vessel vasculitis in the sural nerve, and infiltration of plasma cells and eosinophils in the thickened dura mater.
Generation of Evc2/Limbin global and conditional KO mice and its roles during mineralized tissue formation

Ellis‐van Creveld (EvC) syndrome (OMIM 225500) is an autosomal recessive disease characterized with chondrodysplastic dwarfism in association with abnormalities in oral cavity. Ciliary proteins EVC and EVC2 have been identified as causative genes and they play an important role on Hedgehog signal transduction. We have also identified a causative gene LIMBIN for bovine chondrodysplastic dwarfism (bcd) that is later identified as the bovine ortholog of EVC2. Here, we report generation of conventional and conditional mutant Evc2/Limbin alleles that mimics mutations found in EvC patients and bcd cattle. Resulted homozygous mice showed no ciliary localization of EVC2 and EVC and displayed reduced Hedgehog signaling activity in association with skeletal and oral defects similar to the EvC patients. Cartilage‐specific disruption of Evc2/Limbin resulted in similar but milder skeletal defects, whereas osteoblast‐specific disruption did not cause overt changes in skeletal system. Neural crest‐specific disruption of Evc2/Limbin resulted in defective incisor growth similar to that seen in conventional knockouts; however, differentiation of amelobolasts was relatively normal in the conditional knockouts. These results showcased functions of EVC2/LIMBIN during formation of mineralized tissues. Availability of the conditional allele for this gene should facilitate further detailed analyses of the role of EVC2/LIMBIN in pathogenesis of EvC syndrome. genesis 53:612–626, 2015. © 2015 Wiley Periodicals, Inc.
Were genome‐wide linkage studies a waste of time? Exploiting candidate regions within genome‐wide association studies

A central issue in genome‐wide association (GWA) studies is assessing statistical significance while adjusting for multiple hypothesis testing. An equally important question is the statistical efficiency of the GWA design as compared to the traditional sequential approach in which genome‐wide linkage analysis is followed by region‐wise association mapping. Nevertheless, GWA is becoming more popular due in part to cost efficiency: commercially available 1M chips are nearly as inexpensive as a custom‐designed 10 K chip. It is becoming apparent, however, that most of the on‐going GWA studies with 2,000–5,000 samples are in fact underpowered. As a means to improve power, we emphasize the importance of utilizing prior information such as results of previous linkage studies via a stratified false discovery rate (FDR) control. The essence of the stratified FDR control is to prioritize the genome and maintain power to interrogate candidate regions within the GWA study. These candidate regions can be defined as, but are by no means limited to, linkage‐peak regions. Furthermore, we theoretically unify the stratified FDR approach and the weighted P‐value method, and we show that stratified FDR can be formulated as a robust version of weighted FDR. Finally, we demonstrate the utility of the methods in two GWA datasets: Type 2 diabetes (FUSION) and an on‐going study of long‐term diabetic complications (DCCT/EDIC). The methods are implemented as a user‐friendly software package, SFDR. The same stratification framework can be readily applied to other type of studies, for example, using GWA results to improve the power of sequencing data analyses. Genet. Epidemiol. 34: 107–118, 2010. © 2009 Wiley‐Liss, Inc.
Amplitude and time measurement ASIC with analog derandomization

We describe a new ASIC for accurate and efficient processing of high-rate pulse signals from highly segmented detectors. In contrast to conventional approaches, this circuit affords a dramatic reduction in data volume through the use of analog techniques (precision peak detectors and time-to-amplitude converters) together with fast arbitration and sequencing logic to concentrate the data before digitization. In operation the circuit functions like a data-driven analog first-in, first-out (FIFO) memory between the preamplifiers and the ADC. Peak amplitudes of pulses arriving at any one of the 32 inputs are sampled, stored, and queued for readout and digitization through a single output port. Hit timing, pulse risetime, and channel address are also available at the output. Prototype chips have been fabricated in 0.35 micron CMOS and tested. First results indicate proper functionality for pulses down to 30 ns peaking time and input rates up to 1.6 MHz/channel. Amplitude accuracy of the peak detect and hold circuit is 0.3% (absolute). TAC accuracy is within 0.3% of full scale. Power consumption is less than 2 mW/channel. Compared with conventional techniques such as track-and-hold and analog memory, this new ASIC will enable efficient pulse height measurement at 20 to 300 times higher rates.
Efficient frequency-domain realization of robust generalized, sidelobe cancellers

This paper deals with hands-free acoustical front-ends for human/machine interaction in competing talker situations using efficient frequency-domain implementations of a robust generalized sidelobe canceller (GSC). A new scheme is devised which leads to a factor of three of computational savings. The GSC tracking behavior is not impaired as the block lengths are kept sufficiently small.
Sleep Problems and Institutionalization of the Elderly

This study examined the role of sleep problems in the decisions of families to institutionalize elderly relatives. Previous work on institutionalization of the elderly has given little attention to the contribution of nocturnal, sleep-related problems. Seventy-three primary caregivers of elders recently admitted to a nursing home or psychiatric hospital were asked to identify the problems the elder was having during the night and day and rate the degree to which these influenced their decision to institutionalize the elder. Seventy percent of the caregivers in each sample cited nocturnal problems in their decision to institutionalize, often because their own sleep was disrupted. The most frequent disruptive nocturnal events were micturition, pain, and complaints of sleeplessness. Sleep problems of the elderly contribute heavily to the decision to institutionalize an elder and thus to the social and economic cost of institutional care. They appear to do this largely by interfering with the sleep of caregivers. The nature, prevalence, and treatability of the sleeping problems of both elders and their caregivers need further study. (J Geriatr Psychiatry Neurol 1991;4:204-210).