Miracle-dz/UniFAR-FTUs huggingface dataset:
A Rice Glutamyl-tRNA Synthetase Modulates Early Anther Cell Division and Patterning1[OPEN]

OsERS1, a glutamyl-tRNA synthetase, modulates early rice anther development through affecting metabolic homeostasis and redox status. Aminoacyl-tRNA synthetases (aaRSs) have housekeeping roles in protein synthesis, but little is known about how these aaRSs are involved in organ development. Here, we report that a rice (Oryza sativa) glutamyl-tRNA synthetase (OsERS1) maintains proper somatic cell organization and limits the overproliferation of male germ cells during early anther development. The expression of OsERS1 is specifically detectable in meristematic layer 2-derived cells of the early anther, and osers1 anthers exhibit overproliferation and disorganization of layer 2-derived cells, producing fused lobes and extra germ cells in early anthers. The conserved biochemical function of OsERS1 in ligating glutamate to tRNAGlu is enhanced by its cofactor aaRS OsARC. Furthermore, metabolomics profiling revealed that OsERS1 is an important node for multiple metabolic pathways, indicated by the accumulation of amino acids and tricarboxylic acid cycle components in osers1 anthers. Notably, the anther defects of the osers1 mutant are causally associated with the abnormal accumulation of hydrogen peroxide, which can reconstitute the osers1 phenotype when applied to wild-type anthers. Collectively, these findings demonstrate how aaRSs affect male organ development in plants, likely through protein synthesis, metabolic homeostasis, and redox status.
MRI progression of cerebral small vessel disease and cognitive decline in patients with hypertension

Objective: Hypertension is associated with cognitive deficits, probably because it is a major risk factor for the development of white matter hyperintensities (WMH), lacunes, and cerebral microbleeds, which are MRI markers of cerebral small vessel disease. Studies into associations between presence or progression of these MRI markers and cognitive decline in hypertensive patients are rare. We investigated the association of baseline presence and progression of MRI markers of cerebral small vessel disease with cognitive decline over 4 years in patients with hypertension. Methods: In this longitudinal study, hypertensive patients underwent neuropsychological assessments and brain MRI at baseline and after 4 years. Presence and progression of periventricular and subcortical WMH, lacunes, and cerebral microbleeds were visually rated. Results: In total, 128 hypertensive patients (90 patients with essential hypertension and 38 hypertensive lacunar stroke patients), mean age: 58.6 ± 12.2 years, were included. Progression of periventricular WMH was associated with cognitive decline in simple regression analysis (P = 0.001) and in multivariable analysis with correction for baseline WMH presence and potential confounders (P = 0.004). In this multivariable analysis, R2 of progression of periventricular WMH was 5.6%, whereas R2 of baseline presence of periventricular WMH was 0.6%. We did not find significant associations between baseline presence or progression of the other MRI markers and cognitive decline. Conclusion: In patients with hypertension, progression of periventricular WMH over 4 years is associated with cognitive decline, whereas we could not show an association between baseline periventricular WMH and cognitive decline. These results emphasize the importance of preventing progression of WMH in hypertensive patients.
Overnight Transcutaneous Carbon Dioxide Monitoring in Eucapnic Patients with Obstructive Sleep Apnea Syndrome.

OBJECTIVES We monitored increases in CO2 levels during sleep by measuring transcutaneous pCO2 (PtcCO2) to determine its relationship with polysomnographic data in normocapnic patients with obstructive sleep apnea syndrome (OSAS). MATERIAL AND METHODS Between October 2011 and December 2012, 139 patients underwent PtcCO2 monitoring with polysomnography. All patients were evaluated with arterial blood gas (ABG) measurements and pulmonary function tests (PFTs). We excluded 13 patients with COPD and/or daytime hypercapnia and 29 patients whose PtcCO2 records could not be evaluated. RESULTS The patients' mean age was 46.8±10.3 years. Fifty-nine patients (60.8%) were male, and 38 (39.2%) patients were female. The mean overnight PtcCO2 was ≤45 mm Hg in 84 (86.6%) patients and >45 mm Hg in 13 (13.4%) patients. In the group with PtcCO2>45 mm Hg, 10 patients had an apnea-hypopnea index (AHI) >15, and 3 patients had an AHI<15, without a statistically significant difference (p=0.078). The mean apnea and apnea/interapnea periods were similar. The mean PtcCO2 values correlated with time spent when the SpO2 was <90% (r=0.220, p<0.031). When we grouped the patients by AHI, 60 (61.8%) patients had an AHI>15 (moderate to severe OSAS), and 37 (37.2%) had an AHI<15 (mild OSAS). Of the former group, 16.7% had a mean PtcCO2 >45 mm Hg, whereas this ratio was 8.1% in the latter group. The difference was not statistically significant (p=0.359). In the group with an AHI>15, the highest PtcCO2 levels were significantly higher (p<0.05). CONCLUSION We conclude that seemingly eucapnic OSAS patients may experience hypercapnia when sleeping, and PtcCO2 monitoring may be useful in the early diagnosis of hypercapnia.
Power Budget Analysis for Waveguide-Enhanced Raman Spectroscopy

Waveguide-enhanced Raman spectroscopy (WERS) is emerging as an attractive alternative to plasmonic surface-enhanced Raman spectroscopy approaches as it can provide more reproducible quantitative spectra on a robust chip without the need for nanostructured plasmonic materials. Realizing portable WERS systems with high sensitivity using low-cost laser diodes and compact spectrometers requires a detailed analysis of the power budget from laser to spectrometer chip. In this paper, we describe theoretical optimization of planar waveguides for maximum Raman excitation efficiency, demonstrate WERS for toluene on a silicon process compatible high index contrast tantalum pentoxide waveguide, measure the absolute conversion efficiency from pump power to received power in an individual Raman line, and compare this with a power budget analysis of the complete system including collection with an optical fiber and interfacing to a compact spectrometer. Optimized 110 nm thick Ta2O5 waveguides on silica substrates excited at a wavelength of 637 nm are shown experimentally to yield overall system power conversion efficiency of ∼0.5 × 10−12 from the pump power in the waveguide to the collected Raman power in the 1002 cm−1 Raman line of toluene, in comparison with a calculated efficiency of 3.9 × 10−12. Collection efficiency is dictated by the numerical and physical apertures of the spectral detection system but may be improved by further engineering the spatial and angular Raman scattering distributions.
Study on Efficiency and Productivity of the Listed Commercial Banks in China——Based on Hicks-Moorsteen TFP Index

In this paper Hicks-Moorsteen TFP index is employed to investigate the productivity of the China's listed commercial banks during 2004—2011.It shows that the commercial banks with different property have distinct competitive advantages.Urban commercial banks have the advantages in technology and technical efficiency,and state-owned commercial banks have in scale efficiency,while joint-equity commercial banks have in scope efficiency.Secondly,the result shows that the total factor productivity of the listed commercial banks in China has declined 3.26 percent during this period.We also find that the slow technological progress is the main reason for the decline.Therefore,the increase of the efficiency in technology,scale economy and scope economy are key factors to improve the total factor productivity.Thirdly,based on efficiency-productivity comparative analysis,it shows that it is possible that the developments of bank industry may fall into the dilemma of "strong always strong,weak always weak". In sum,this paper investigates the effectiveness of China commercial bank reform,and provides some valuable insights into the new reform of commercial banks in China.
The fractional viscoelastic response of human breast tissue cells

The mechanical response of a living cell is notoriously complicated. The complex, heterogeneous characteristics of cellular structure introduce difficulties that simple linear models of viscoelasticity cannot overcome, particularly at deep indentation depths. Herein, a nano-scale stress-relaxation analysis performed with an atomic force microscope reveals that isolated human breast cells do not exhibit simple exponential relaxation capable of being modeled by the standard linear solid (SLS) model. Therefore, this work proposes the application of the fractional Zener (FZ) model of viscoelasticity to extract mechanical parameters from the entire relaxation response, improving upon existing physical techniques to probe isolated cells. The FZ model introduces a new parameter that describes the fractional time-derivative dependence of the response. The results show an exceptional increase in conformance to the experimental data compared to that predicted by the SLS model, and the order of the fractional derivative (α) is remarkably homogeneous across the populations, with a median value of 0.48 ± 0.06 for the malignant population and 0.51 ± 0.07 for the benign. The cells’ responses exhibit power-law behavior and complexity not associated with simple relaxation (SLS, α = 1) that supports the application of a fractional model. The distributions of some of the FZ parameters also preserve the distinction between the malignant and benign sample populations seen from the linear model and previous results while including the contribution of fast-relaxation behavior. The resulting viscosity, measured by a composite relaxation time, exhibits considerably less dispersion due to residual error than the distribution generated by the linear model and therefore serves as a more powerful marker for cell differentiation.
What Drives Emergency Department Patient Satisfaction? An Empirical Test using Structural Equation Modeling

Patient satisfaction determinants in emergency departments (EDs) have for decades been heavily investigated. Despite great focus, a lack of consensus about which parameters are deemed most important remains. This study proposes an integrated framework for ED patient satisfaction, testing four key hypotheses concerning effects between the latent constructs wait time, information delivery, safety, and infrastructure. The framework allow ED decision makers insight into the magnitude of the latent constructs’ importance with appertaining statistical significance based on an ample empirical sample. Such information is valuable to illuminate where to launch high impact initiatives to increase current ED patient satisfaction levels.
An approach to combining parallel and cross-over trials with and without run-in periods using individual patient data

Background In active run-in trials, where patients may be excluded after a run-in period based on their response to the treatment, it is implicitly assumed that patients have individual treatment effects. If individual patient data are available, active run-in trials can be modelled using patient-specific random effects. With more than one trial on the same medication available, one can obtain a more precise overall treatment effect estimate. Methods We present a model for joint analysis of a two-sequence, four-period cross-over trial (AABB/BBAA) and a three-sequence, two-period active run-in trial (AB/AA/A), where the aim is to investigate the effect of a new treatment for patients with pain due to osteoarthritis. Results Our approach enables us to separately estimate the direct treatment effect for all patients, for the patients excluded after the active run-in trial prior to randomisation, and for the patients who completed the active run-in trial. A similar model approach can be used to analyse other types of run-in trials, but this depends on the data and type of other trials available. Limitations We assume equality of the various carry-over effects over time. Conclusions The proposed approach is flexible and can be modified to handle other designs. Our results should be encouraging for those responsible for planning cost-efficient clinical development programmes.
Specific tyrosine phosphorylation sites on cortactin regulate Nck1-dependent actin polymerization in invadopodia

Invadopodia are matrix-degrading membrane protrusions in invasive carcinoma cells enriched in proteins that regulate actin polymerization. The on–off regulatory switch that initiates actin polymerization in invadopodia requires phosphorylation of tyrosine residues 421, 466, and 482 on cortactin. However, it is unknown which of these cortactin tyrosine phosphorylation sites control actin polymerization. We investigated the contribution of individual tyrosine phosphorylation sites (421, 466, and 482) on cortactin to the regulation of actin polymerization in invadopodia. We provide evidence that the phosphorylation of tyrosines 421 and 466, but not 482, is required for the generation of free actin barbed ends in invadopodia. In addition, these same phosphotyrosines are important for Nck1 recruitment to invadopodia via its SH2 domain, for the direct binding of Nck1 to cortactin in vitro, and for the FRET interaction between Nck1 and cortactin in invadopodia. Furthermore, matrix proteolysis-dependent tumor cell invasion is dramatically inhibited in cells expressing a mutation in phosphotyrosine 421 or 466. Together, these results identify phosphorylation of tyrosines 421 and 466 on cortactin as the crucial residues that regulate Nck1-dependent actin polymerization in invadopodia and tumor cell invasion, and suggest that specifically blocking either tyrosine 421 or 466 phosphorylation might be effective at inhibiting tumor cell invasion in vivo.
Role of Mitogen-Activated Protein Kinase Sty1 in Regulation of Eukaryotic Initiation Factor 2α Kinases in Response to Environmental Stress in Schizosaccharomyces pombe

ABSTRACT The mitogen-activated protein kinase (MAPK) Sty1 is essential for the regulation of transcriptional responses that promote cell survival in response to different types of environmental stimuli in Schizosaccharomyces pombe. In fission yeast, three distinct eukaryotic initiation factor 2α (eIF2α) kinases, two mammalian HRI-related protein kinases (Hri1 and Hri2) and the Gcn2 ortholog, regulate protein synthesis in response to cellular stress conditions. In this study, we demonstrate that both Hri1 and Hri2 exhibited an autokinase activity, specifically phosphorylated eIF2α, and functionally replaced the endogenous Saccharomyces cerevisiae Gcn2. We further show that Gcn2, but not Hri1 or Hri2, is activated early after exposure to hydrogen peroxide and methyl methanesulfonate (MMS). Cells lacking Gcn2 exhibit a later activation of Hri2. The activated MAPK Sty1 negatively regulates Gcn2 and Hri2 activities under oxidative stress but not in response to MMS. In contrast, Hri2 is the primary activated eIF2α kinase in response to heat shock. In this case, the activation of Sty1 appears to be transitory and does not contribute to the modulation of the eIF2α kinase stress pathway. In strains lacking Hri2, a type 2A protein phosphatase is activated soon after heat shock to reduce eIF2α phosphorylation. Finally, the MAPK Sty1, but not the eIF2α kinases, is essential for survival upon oxidative stress or heat shock, but not upon MMS treatment. These findings point to a regulatory coordination between the Sty1 MAPK and eIF2α kinase pathways for a particular range of stress responses.
Morphological Change of Inner Retinal Layer on Spectral-Domain Optical Coherence Tomography following Macular Hole Surgery

Background/Aims: To investigate the morphological changes of the inner retinal layer by spectral-domain optical coherence tomography (OCT) after idiopathic full-thickness macular hole (MH) surgery. Methods: In a retrospective study, the authors evaluated 52 eyes of 49 patients with MH closed following vitrectomy. All patients were followed postoperatively for more than 6 months. Cross-sectional and retinal surface images were obtained using Cirrus high-definition OCT before and after surgery. In 24 of the 52 eyes, fundus autofluorescence (FAF) was analyzed. Results: The incidence of dissociated optic nerve fiber layer (DONFL) increased gradually over time after surgery. 57.7% had defects of only the retinal nerve fiber layer (RNFL) and 30.8% had defects in the inner plexiform layer at 6 months after surgery. Postoperative best-corrected visual acuity did not differ significantly based on the depth of the DONFL (p = 0.299). There were no changes in FAF in the area with DONFL. Conclusions: DONFL is characterized by progressive defects that are not limited to RNFL thickness. The healing process after vitrectomy for MH is not limited in the RNFL affecting deeper structural changes. Further investigations are required to evaluate the pathophysiological mechanism of inner retinal change after MH surgery.
Flow‐cytometric analysis of rare antigen‐specific T cells

The cytometric enumeration and characterization of antigen‐specific lymphocytes, as introduced about 15 years ago, has contributed significantly to our understanding of adaptive immune responses in health and disease. Despite the development of several technologies, allowing to directly or indirectly analyze many aspects of lymphocyte specificity and function, several unresolved issues remain, due to the low frequency of certain antigen‐specific lymphocyte subsets and the complexity of T cell antigen recognition. This is especially true for CD4+ conventional as well as regulatory T cells, which bring major contributions to immune protection and pathology. Here we review the current technologies for the analysis of antigen specific T cells within the physiologic T cell repertoire and with a special focus on recent technologies addressing the analysis of rare antigen‐specific T cell populations including naive and regulatory T cells. © 2013 International Society for Advancement of Cytometry
Fusion Approach for Prognostics Framework of Heritage Structure

The Cutty Sark is undergoing major conservation to slow down the deterioration of the original Victorian fabric of the ship. While the conservation work being carried out is “state of the art,” there is no evidence at present of the effectiveness of the conservation work over the next fifty years. A prognostics framework is being developed to monitor the “health” of the ship's iron structures to help ensure a 50 year life once conservation is completed, with only minor deterioration taking place over time. This paper presents the prognostics framework being developed, which encompasses four approaches: 1-Canary and Parrot devices, 2-Physics-of-Failure (PoF) models, 3-Precursor Monitoring and Data Trend Analysis, and 4-Bayesian Networks. “Canary” and “Parrot” devices have been designed to mimic the actual mechanisms that would lead to failure of the iron structures, with canary devices failing faster to act as an indicator of forthcoming failures, while parrot devices fail at the same rate as the structure under consideration. A PoF model based on a decrease of the corrosion rate over time is used to predict the remaining life of an iron structure. Mahalanobis Distance (MD) is used as a precursor monitoring technique to obtain a single comparison metric from multiple sensor data to represent anomalies detected in the system. Bayesian Network models are then used as a fusion technique, integrating remaining life predictions from PoF models with information of possible anomalies from MD analysis to provide a new prediction of remaining life. This paper describes why, and how the four approaches are used for diagnostic and prognostics purposes, and how they are integrated into the prognostics framework.
An Energy-Efficient Digital ReRAM-Crossbar-Based CNN With Bitwise Parallelism

There is great attention to develop hardware accelerator with better energy efficiency, as well as throughput, than GPUs for convolutional neural network (CNN). The existing solutions have relatively limited parallelism as well as large power consumption (including leakage power). In this paper, we present a resistive random access memory (ReRAM)-accelerated CNN that can achieve significantly higher throughput and energy efficiency when the CNN is trained with binary constraints on both weights and activations, and is further mapped on a digital ReRAM-crossbar. We propose an optimized accelerator architecture tailored for bitwise convolution that features massive parallelism with high energy efficiency. Numerical experiment results show that the binary CNN accelerator on a digital ReRAM-crossbar achieves a peak throughput of 792 GOPS at the power consumption of 4.5 mW, which is 1.61 times faster and 296 times more energy-efficient than a high-end GPU.
Identification of a cytotoxic T-cell epitope on the recombinant nucleocapsid proteins of Rinderpest and Peste des petits ruminants viruses presented as assembled nucleocapsids.

The nucleocapsid protein (N) of morbilliviruses is not only a major structural protein but also the most abundant protein made in infected cells. We overexpressed the N proteins of Rinderpest virus and Peste des petits ruminants virus in E. coli, which assemble into nucleocapsids in the absence of viral RNA that resemble nucleocapsids made in the virus-infected cells. Employing these assembled structures resembling subviral particles, we studied the induction of both the antibody response and the cytotoxic T-lymphocyte (CTL) response in a murine model (BALB/c). A single dose of the purified recombinant nucleocapsids of both viruses in the absence of an adjuvant induces a strong CTL response. The CTLs generated are antigen specific and cross-reactive with respect to each virus and, furthermore, this CTL response is MHC class I restricted. Based on the prediction for H-2(d)-restricted T-cell motifs we tested the lysis of transfected P815 (H-2(d)) cells expressing a nine amino acid potential CTL epitope, by splenic T cells in vitro restimulated with bacterially expressed RPV or PPRV N proteins. We extended our study to the bovine system both to analyze the immunogenicity of these recombinant proteins in the natural hosts and to show that PBMC from cattle vaccinated with Rinderpest vaccine proliferate in vitro, in response to restimulation with soluble nucleocapsid proteins. Furthermore, the murine CTL epitope functions in the bovine system as a cytotoxic T-cell epitope. This sequence, which is conserved in the N proteins of morbilliviruses, conforms well to the predicted algorithm for some of the most common BoLA CTL antigenic peptides.
Supercontinuum Generation in Nonlinear Microstructured Fiber and Recent Advances

Supercontinuum (SC) is generated experimentally in nonlinear microstructured optical fibers (MOFs) which are designed and fabricated by stack and draw process. Effects of different drawing parameters on the MOF structures are studied and high air filling fraction is achieved by optimizing the drawing parameters. Different aspects of SC generation process is theoretically modeled and compared with the experimentally generated SC spectrum. Certain interesting physical processes that occur during SC generation are explained in detail.
Image segmentation and image models

This paper discusses image segmentation techniques from the standpoint of the assumptions that an image should satisfy in order for a particular technique to be applicable to it. These assumptions, which are often not stated explicitly, can be regarded as (perhaps informal) "models" for classes of images. The paper emphasizes two basic classes of models: statistical models that describe the pixel population in an image or region, and spatial models that describe the decomposition of an image into regions.