gebhart/patrepeval huggingface dataset:
Two Distinct EF-Tu Epitopes Induce Immune Responses in Rice and Arabidopsis (2013)

Plants sense potential pathogens by recognizing conserved pathogen-associated molecular patterns (PAMPs) that cause PAMP-triggered immunity (PTI). We previously reported that rice recognizes flagellin from the rice-incompatible N1141 strain of Acidovorax avenae and subsequently induces immune responses. Cell extracts isolated from flagellin-deficient N1141 (Δfla1141) still induced PTI responses, suggesting that Δfla1141 possesses an additional PAMP distinct from flagellin. Here, we show that elongation factor Tu (EF-Tu), one of the most abundant bacterial proteins, acts as a PAMP in rice and causes several PTI responses. In Brassicaceae species, EF-Tu and an N-acetylated peptide comprising the first 18 amino acids of the N-terminus, termed elf18, are fully active as inducers of PTI responses. By contrast, elf18 did not cause any immune responses in rice, whereas an EF-Tu middle region comprising Lys176 to Gly225, termed EFa50, is fully active as a PAMP in rice. In the leaves of rice plants, EF-Tu induced H2O2 generation and callose deposition, and also triggered resistance to coinfection with pathogenic bacteria. Taken together, these data demonstrate that rice recognizes EFa50, which is distinct from elf18, and that this epitope induces PTI responses.
Free-Living to Freewheeling: The Evolution of Vibrio cholerae from Innocence to Infamy (2004)

Toxigenic strains of the Gram-negative bacterium Vibrio cholerae cause the most severe form of dehydrating diarrhea known as cholera and have been responsible for at least seven distinct pandemics of cholera (Faruque et al., 1998a). Since the first recorded pandemic, which began in 1817, V. cholerae strains associated with different pandemics are assumed to have undergone phenotypic and genetic changes with time. For example, although the seventh pandemic was caused by the El Tor biotype of V. cholerae, the sixth and possibly earlier pandemics were caused by the classical biotype. The genetic changes in V. cholerae associated with epidemics and pandemics, however, were not fully appreciated until the development and application of molecular techniques to analyze strains.
Electrophysiological studies in spinocerebellar ataxia type 6 (2000)

In spinocerebellar ataxia type 6 (SCA6), the cerebellum is predominantly affected, but several electrophysiological studies have revealed subclinical disorders other than cerebellar lesions. We conducted statistical analyses by comparing SCA6 patients and age-matched normal controls to asses whether electrophysiological abnormalities are directly associated with SCA6 because late onset of SCA6 may involve senile changes. We performed brain stem auditory evoked potentials (BAEP), visual evoked potentials, somatosensory evoked potentials and nerve conduction studies in 10 SCA6 patients. The BAEP latencies of wave I was prolonged and compound muscle action potentials of peroneal nerve and sensory nerve action potentials of sural nerve reduced in SCA6 patients. Our results suggest an existence of peripheral impairment in the auditory pathway and axonal neuropathy in SCA6.
Scalable service gateway architecture for mobile SaaS platforms (2010)

New schemes such as SaaS and PaaS that let users access services over networks are widely used. Moreover, network operators must provide value-added services that enable service providers to create new services promptly and maintain performance as the number of service providers and users increases. To meet these requirements, we proposes a service gateway, which handles user messages (e.g., rewrites the message destination) on the basis of the user location, and a scalable control scheme for the SGW. And we implemented a prototype system to confirm scalability.
Dependence of the Fictive Temperature of Glass on Cooling Rate (1976)

An equation derived by Ritland relating the cooling rate and fictive temperature for glasses without memory is extended to those with memory, i.e. those which exhibit a spectrum of relaxation times. Provided that the spectrum of relaxation times is temperature‐independent, the limiting fictive temperature, T′ f , obtained when a glass is cooled through the transition region, is shown to be related to the cooling rate, q , by d In | q |/ d (1/ T'f )=‐Δ h ★/ R where R is the ideal gas constant and Δ h ★ the activation enthalpy for the relaxation times controlling the structural relaxation. Values of T′ f vs q obtained from enthalpy measurements by differential scanning calorimetry are presented for B 2 O 3 , 0.4Ca(NO 3 ) 2 —0.6KNO 3 , and borosilicate crown glasses; Δ h ★ is equal, within experimental error, to the activation enthalpy for shear viscosity. Values of T′ f from volume and enthalpy measurements obtained at the same cooling rate for the borosilicate crown glass are equal.
Exponential improvement in precision for Hamiltonian-evolution simulation (2013)

We provide a quantum method for simulating Hamiltonian evolution with complexity polynomial in the logarithm of the inverse error. This is an exponential improvement over existing methods for Hamiltonian simulation. In addition, its scaling with respect to time is close to linear, and its scaling with respect to the time derivative of the Hamiltonian is logarithmic. These scalings improve upon most existing methods. Our method is to use a compressed Lie-Trotter formula, based on recent ideas for efficient discrete-time simulations of continuous-time quantum query algorithms.
IFN-γ orchestrates tumor elimination, tumor dormancy, tumor escape, and progression (2018)

Tumor immunoediting consisting of three phases of elimination, equilibrium or dormancy, and escape has been supported by preclinical and clinical data. A comprehensive understanding of the molecular mechanisms by which antitumor immune responses regulate these three phases are important for developing highly tailored immunotherapeutics that can control cancer. To this end, IFN-γ produced by Th1 cells, cytotoxic T cells, NK cells, and NKT cells is a pleiotropic cytokine that is involved in all three phases of tumor immunoediting, as well as during inflammation-mediated tumorigenesis processes. This essay presents a review of literature and suggests that overcoming tumor escape is feasible by driving tumor cells into a state of quiescent but not indolent dormancy in order for IFN-γ-producing tumor-specific T cells to prevent tumor relapse.
An application ofin vivowhole body counting technique for studying strontium metabolism and internal dose reconstruction for the Techa River population (2006)

Nuclear techniques for direct assessment of internally deposited radionuclides are essential for monitoring and dosimetry of members of the public exposed due to radiation accidents. Selection of the methods for detection of internal contamination is determined by nuclear-physical characteristics of the deposits. For the population living in settlements located along the Techa River contaminated in 1950s by liquid radioactive wastes from the plutonium production complex Mayak (Southern Urals, Russia) the main dose-forming radionuclide was 90Sr. It is a bone-seeking radionuclide that incorporates in the skeleton and remains there for many years so it can be detected for long periods after the intake occurred. Measurements of pure beta-emitting 90Sr are possible through detection of bremsstrahlung from the 90Sr/90Y beta rays in the low energy range (30-160 keV) using phoswich detectors. This suggested the development of a unique whole body counter in 1974 for monitoring of the 90Sr- and 137Cs-body burden in the Techa River population with the use of phoswich detectors. Long-term observations with the WBC covering more than 38,000 measurements on over 20,000 people have been made. This has created a unique database for studying strontium and calcium metabolism and for assessment of the internal dose for residents of the Techa River settlements due to ingestion of 90Sr. This paper describes the main results obtained for the Techa River population essential for bone metabolism and dosimetry, epidemiological studies, and radiation protection.
Regionalization of Critical Care Medicine (1995)

Thompson, Dan R. MD FCCM; Clemmer, Terry P. MD FCCMS; Applefeld, Jack J. MD FCCM; Crippen, David W. MD FCCM; Wedel, Suzanne K. MD FCCM Author Information
Coordinate regulation of the human TAP1 and LMP2 genes from a shared bidirectional promoter. (1995)

Recently, four genes (TAP1, TAP2, LMP2, LMP7) involved or potentially involved in the processing and transport of major histocompatibility complex class I-associated antigen to the endoplasmic reticulum have been identified. We now report the initial characterization of the bidirectional promoter for the human transporter associated with antigen processing 1 (TAP1) and low molecular mass polypeptide 2 (LMP2) genes. These genes are divergently transcribed from a central promoter region of only 593 bp. Functional analysis using a bidirectional reporter system demonstrates the minimal 593-bp promoter is sufficient for concurrent expression in both directions. There is no TATA box homology at either end but there is a prevalence of GC boxes. Transcription is initiated at multiple sites for each gene without any of the TAP1 transcripts overlapping with the LMP2 transcripts. The region proximal to the TAP1 gene is required for maximal basal level expression of not only TAP1 but also LMP2. Furthermore, this region is necessary for tumor necrosis factor alpha (TNF-alpha) induction of both genes. Site-specific mutations of an NF-kappa B element in the TAP1 proximal region blocked induction by TNF-alpha in both the TAP1 and LMP2 directions. An adjacent GC box was required for basal expression of both genes as well as augmenting the TNF-alpha induction of the distal LMP2 gene. In vivo genomic foot-printing of this region revealed strong protein/DNA interactions at the NF-kappa B and GC box consensus sequences. In vitro binding studies confirmed the capacity of the NF-kappa B site to bind p50/p65 and p52/p65 heterodimers and of the GC box to bind Sp1. Thus, the promoter elements proximal to the TAP1 gene play a significant role in regulating basal and induced expression of both TAP1 and LMP2. The findings presented in this report clearly link LMP2 expression with TAP1 expression and provide additional suggestive evidence linking LMP2 to class I antigen presentation.
High infection rates ofTriatoma dimidiataare associated with low levels ofTrypanosoma cruziseroprevalence in Pedro Carbo, Ecuador. Use of atc24 gene-based PCR approach (2005)

In control programs for vectorial transmission of Chagas' disease, conventional microscopic procedures are generally performed to determine baseline levels of infectivity of vectors. Reported here are data using Polymerase Chain Reaction in the detection of Trypanosoma cruzi in Triatoma dimidiata, one of the principal vectors of Chagas' disease in Ecuador. The microscopy and PCR techniques showed a high percentage of vector infection in Pedro Carbo, province of Guayas (Ecuador), with 44.16% and 46.13% positive insects, respectively. This contrasted with the very low Chagas seropositivity recorded (0.5%). Since T. dimidiata was the only vector of the Chagas' disease found in Pedro Carbo and looking at the vector behavior, our data suggest that despite the high T. dimidiata infection, the low Chagas seropositivity detected is closely associated with the epidemiological and ecological context of T. dimidiata in Pedro Carbo.
Synthesis and Crystal Structure Determination of Ag9FeS4.1Te1.9, the First Example of an Iron Containing Argyrodite (2013)

Ag9FeS4.1Te1.9 was prepared by solid state synthesis from stoichiometric amounts of the elements at 873 K. The compound forms gray crystals which are stable against air and moisture. The crystal structure was determined by X-ray diffraction from selected single crystals. Ag9FeS4.1Te1.9 crystallizes in the space group F4̅3m, a = 11.0415(7) Å, V = 1346.1(1) Å3, and Z = 4 (powder data at 293 K). The compound shows a reversible phase transition upon cooling to the space group P213, a = 11.0213(1) Å, V = 1338.75(2) Å3, and Z = 4 (single crystal data at 200 K). The title compound is the first example of an iron containing argyrodite-type material with Fe3+ located in tetrahedral sites. Silver atoms are disordered at room temperature which was taken into account by nonharmonic refinement of the silver positions. The refinement converged to R1 = 3.51% and wR2 = 10.66% for the room temperature measurement and to R1 = 1.55% and wR2= 5.23% for the 200 K data set (all data). Impedance measurements were performed in the temperature range from 323 to 473 K. Ionic conductivity values are 1.81 × 10–2 S cm–1 at 323 K and 1.41 × 10–1 S cm–1 at 468 K. The activation energy is 0.19 eV from 323 to 423 K and 0.06 eV from 393 to 473 K. DTA measurements reveal congruent melting at 907 K. A phase transition temperature of 232 K with an enthalpy of 7.9 kJ/mol was determined by DSC measurements. 57Fe Mössbauer spectra show one signal at 298 K and a doublet at 78 K, indicating Fe3+ and structural distortions upon cooling the samples. Hyperfine field splitting of iron is observed at 5 K. Measurements of the molar susceptibility revealed that the compound is paramagnetic down to a Néel temperature of TN = 22.1(5) K. Antiferromagnetic ordering is observed at lower temperatures.
Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids (2016)

Global mechanization, urbanization, and various natural processes have led to the increased release of toxic compounds into the biosphere. These hazardous toxic pollutants include a variety of organic and inorganic compounds, which pose a serious threat to the ecosystem. The contamination of soil and water are the major environmental concerns in the present scenario. This leads to a greater need for remediation of contaminated soils and water with suitable approaches and mechanisms. The conventional remediation of contaminated sites commonly involves the physical removal of contaminants, and their disposition. Physical remediation strategies are expensive, non-specific and often make the soil unsuitable for agriculture and other uses by disturbing the microenvironment. Owing to these concerns, there has been increased interest in eco-friendly and sustainable approaches such as bioremediation, phytoremediation and rhizoremediation for the cleanup of contaminated sites. This review lays particular emphasis on biotechnological approaches and strategies for heavy metal and metalloid containment removal from the environment, highlighting the advances and implications of bioremediation and phytoremediation as well as their utilization in cleaning-up toxic pollutants from contaminated environments.
Reduction of Recurrence Risk of Pancreatitis in Cystic Fibrosis With Ivacaftor (2017)

The effect of ivacaftor in patients with cystic fibrosis (CF) with recurrent pancreatitis is unknown. We conducted a multicenter retrospective study of patients with CF taking ivacaftor who had a history of recurrent pancreatitis. During the first 3 months of therapy, only 1 of the 6 patients had an episode of pancreatitis, which was managed on an outpatient basis. Between 3 and 12 months on ivacaftor therapy, none of the patients had recurrence of pancreatitis or required hospitalization. The use of ivacaftor was associated with a reduced frequency and recurrence rate of pancreatitis in patients with CF.
A vision based relative navigation framework for formation flight (2014)

Unmanned aerial vehicle (UAV) formation flight can vastly increase operational range and persistence through autonomous aerial refuelling or efficient flight on a wingman's wake vortices. Differencing individual UAV state estimates is not sufficiently accurate for close formation operations and must be augmented with vehicle-to-vehicle observations. To this end, we propose a quaternion based unscented Kalman filter to fuse information from each UAV sensor suite with relative vision observations. The result is a vastly improved relative state estimate that is resilient to brief vision dropouts and degrades gracefully during extended dropouts. Simulated formation flight results validate the approach and provide a numerical analysis of the algorithm performance. Ground based experiments demonstrate the algorithm running in real-time on a dual-UAV system. This represents a significant step towards an airborne implementation.
Embedding tree metrics into low dimensional Euclidean spaces (1999)

We consider embedding metrics induced by trees into Euclidean spaces with a restricted number of dimensions. We show that any weighted tree T with n vertices and L leaves can be embedded into d -dimensional Euclidean space with O (L1/(d-1)) distortion. Furthermore, we exhibit an embedding with almost the same distortion which can be computed efficiently. This distortion substantially improves the previous best upper bound of \tilde O (n2/d) and almost matches the best known lower bound of Ω(L1/d) .
Delving into High-Quality Synthetic Face Occlusion Segmentation Datasets (2022)

This paper performs comprehensive analysis on datasets for occlusion-aware face segmentation, a task that is crucial for many downstream applications. The collection and annotation of such datasets are time-consuming and labor-intensive. Although some efforts have been made in synthetic data generation, the naturalistic aspect of data remains less explored. In our study, we propose two occlusion generation techniques, Naturalistic Occlusion Generation (NatOcc), for producing high-quality naturalistic synthetic occluded faces; and Random Occlusion Generation (RandOcc), a more general synthetic occluded data generation method. We empirically show the effectiveness and robustness of both methods, even for unseen occlusions. To facilitate model evaluation, we present two high-resolution real-world occluded face datasets with fine-grained annotations, RealOcc and RealOcc-Wild, featuring both careful alignment preprocessing and an in-the-wild setting for robustness test. We further conduct a comprehensive analysis on a newly introduced segmentation benchmark, offering insights for future exploration.
Evaluation of the sodium-glutamate blocker riluzole in a preclinical model of cervical spinal cord injury (2010)

A total of 92.3% of injured rats that received repeated dose of 6 mg/kg riluzole survived during the term of 6 weeks, showing tolerance to this dosage. In contrast, higher doses of riluzole (8mg/kg IP q12h post-injury) were associated with significant respiratory depression and high mortality (7/10 rats). Riluzole treatment (P1 group) decreased the functional deficit significantly (P < 0.05) at 6 weeks after injury by showing 11.4 in BBB, 3.8 in BBB subscore and 2.8 in grid walk test, compared with 10.25 in BBB, 1.1 in BBB subscore, and 8.0 in grid walk test of control group (Figure 1). Quantitative analysis of SSEPs confirmed the neuroprotective effects of riluzole (P1 group) by showing significantly larger amplitude (control = 20.67 µV, P1 = 42.67 µV and P3 = 37.00 µV, Figure 2) and reduced response latency (control = 4.05 ms and P1 = 3.9 ms). Western blotting of NF200 indicated greater axonal preservation with riluzole treatment (P1 group) at 1 week after injury. The P3 group showed trends to improved neurobehavioral recovery and axonal preservation that did not attain significance. HPLC showed riluzole penetrated into the spinal cord as fast as 15 minutes, accumulated in the spinal cord at a concentration six times higher than in plasma, and two times higher than in brain. The drug stayed in spinal cord with a high concentration before the next injection. Figure 1 Riluzole treatment improved functional recovery. The most robust effects were seen when the drug was injected at one hour after SCIFigure 2 Riluzole treatment increased amplitude of somatosensory evoked potentials Conclusions: The sodium-glutamate blocker riluzole confers neurobehavioral and anatomical neuroprotection when administered one hour after moderately severe cervical contusive/compressive injury.
Continuum approximation techniques for the design of integrated package distribution systems (2007)

Abstract Complex package distribution systems are designed using idealizations of network geometries, operating costs, demand and customer distributions, and routing patterns. The goal is to find simple, yet realistic, guidelines to design and operate a network integrated both by transportation mode and service level; i.e., overnight (express) and longer (deferred) deadlines. The decision variables and parameters that define the problem are presented along with the models to approximate total operating cost. The design problem is then reduced to a series of optimization subproblems that can be solved easily. The proposed approach provides valuable insight for the design and operation of integrated package distribution systems. Qualitative conclusions suggest that benefits of integration are greater when deferred demand exceeds express demand. This insight helps to explain the different business strategies of package delivery firms today. © 2007 Wiley Periodicals, Inc. NETWORKS, Vol. 50(3), 183–196 2007
Experimental demonstration of ultra-compact directional couplers based on silicon hybrid plasmonic waveguides (2012)

Hybrid plasmonic waveguides and directional couplers have been experimentally demonstrated. Using a direct measurement method, the propagation loss of a 170 nm wide waveguide is measured to be 0.08 dB/μm at 1550 nm when the thickness of low-index region is 56 nm. Ultra-compact directional couplers based on such hybrid plasmonic waveguides are demonstrated with gaps of 140 nm, 185 nm, 235 nm, and 290 nm. The corresponding coupling lengths measured are 1.55 μm, 2.2 μm, 3.2 μm, and 4.8 μm, respectively, which are in very good agreement with the simulations. These ultra-compact devices can be potentially used in future ultra-dense photonic integrated circuits.
Human Adipose Tissue Extract Induces Angiogenesis and Adipogenesis In Vitro (2011)

The induction of adequate vascularization, a major challenge in tissue engineering, has been tried with numerous methods but with unsatisfactory results. Adipose tissue, an active endocrine organ with dense vasculature, secretes a wide number of angiogenic and adipogenic factors and seems an attractive source for these bioactive factors. We produced a novel cell-free extract from mature human adipose tissue (adipose tissue extract [ATE]) and analyzed the ability of this extract to induce angiogenesis and adipogenesis in vitro and studied the cytokine and growth factor composition of ATE with ELISA and cytokine array. We demonstrate that ATE, when added as cell culture supplement, effectively induced triglyceride accumulation in human adipose stem cells at concentrations from 200 μg/mL upward in less than a week and caused elevated levels of adipocyte differentiation markers (proliferator-activated receptor gamma and acyl-CoA-binding protein) when treated with at least 350 μg/mL of ATE. ATE induced angiogenesis from 450 μg/mL upward after a week in vitro. ATE contained numerous angiogenic and adipogenic factors, for example, vascular endothelial growth factor, basic fibroblast growth factor, interleukin-6, adiponectin, angiogenin, leptin, and insulin-like growth factor-I, as well as lower levels of a wide variety of other cytokines. We here present a novel cell-free angiogenesis- and adipogenesis-inducing agent that is cell-free and easy to produce, and its effect is dose dependent and its composition can be easily modified. Therefore, ATE is a promising novel agent to be used for angiogenesis induction to overcome the challenge of vascularization and for adipogenesis induction in a wide variety of tissue engineering applications in vitro and in vivo. ATE is also efficient for reproduction and modeling of natural adipogenesis in vitro for, for example, obesity and diabetes studies.