gebhart/patrepeval huggingface dataset:
The role of TOR in autophagy regulation from yeast to plants and mammals (2008)

The target of rapamycin (TOR) is a conserved Ser/Thr kinase that controls cell growth by activating an array of anabolic processes including protein synthesis, transcription and ribosome biogenesis, and by inhibiting catabolic processes such as mRNA degradation and autophagy. Control of autophagy by TOR occurs primarily at the induction step, and involves activation of the ATG1 kinase, a conserved component of the autophagic machinery. A substantial number of genes participating in autophagy have been originally identified in yeast. Most of these genes have mammalian homologues and many have apparent homologues in plants, indicating that autophagy is conserved among eukaryotes. The recent identification of TOR as a key element in cell growth control in plants and algae opens the way for future studies to investigate whether this signaling pathway may also control autophagy in photosynthetic organisms.
Free-standing and binder-free lithium-ion electrodes based on robust layered assembly of graphene and Co3O4 nanosheets (2013)

Free-standing and binder-free Co3O4/graphene films were fabricated through vacuum filtration and thermal treatment processes, in which sheet-like Co3O4 and graphene were assembled into a robust lamellar hierarchical structure via electrostatic interactions. The morphological compatibility coupled with strong interfacial interactions between Co3O4 and graphene significantly promoted the interfacial electron and lithium ion transport. When used as a binder-less and free-standing electrode for lithium-ion batteries, the hybrid film delivered a high specific capacity (~1400 mA h g(-1) at 100 mA g(-1) based on the total electrode weight), enhanced rate capability and excellent cyclic stability (~1200 mA h g(-1) at 200 mA g(-1) after 100 cycles). This effective strategy will provide new insight into the design and synthesis of many other composite electrodes for high-performance lithium-ion batteries.
SecLaaS: Secure Logging-as-a-Service for Cloud Forensics (2013)

Cloud computing has emerged as a popular computing paradigm in recent years. However, today's cloud computing architectures often lack support for computer forensic investigations. Analyzing various logs (e.g., process logs, network logs) plays a vital role in computer forensics. Unfortunately, collecting logs from a cloud is very hard given the black-box nature of clouds and the multi-tenant cloud models, where many users share the same processing and network resources. Researchers have proposed using log API or cloud management console to mitigate the challenges of collecting logs from cloud infrastructure. However, there has been no concrete work, which shows how to provide cloud logs to investigator while preserving users' privacy and integrity of the logs. In this paper, we introduce Secure-Logging-as-a-Service (SecLaaS), which stores virtual machines' logs and provides access to forensic investigators ensuring the confidentiality of the cloud users. Additionally, SeclaaS preserves proofs of past log and thus protects the integrity of the logs from dishonest investigators or cloud providers. Finally, we evaluate the feasibility of the scheme by implementing SecLaaS for network access logs in OpenStack - a popular open source cloud platform.
Silencing of Six Hydrophobins in <i>Cladosporium fulvum</i> : Complexities of Simultaneously Targeting Multiple Genes (2008)

In this study, we have constructed and expressed inverted repeat chimeras from the first exons of the six known hydrophobins of the fungus Cladosporium fulvum, the causal agent of tomato leaf mold. We used quantitative PCR to measure specifically the expression levels of the hydrophobins. The targeted genes are silenced to different degrees, but we also detected clear changes in the expression levels of nontargeted genes. This work highlights the difficulties that are likely to be encountered when attempting to silence more than one gene in a multigene family.
Practical Implementation of a Multiplex PCR for Acute Respiratory Tract Infections in Children (2004)

Molecular testing for acute respiratory infections (ARIs) has documented value but limited implementation due to questions that typically slow the acceptance of new tests. This study sought to address these questions and achieve implementation. Rhinovirus was added to a nested multiplex PCR (M-PCR), increasing its diagnostic yield. Over one winter, three hospital pediatric departments used the M-PCR to complement their direct fluorescent-antibody assay (DFA) for respiratory syncytial virus (RSV). Clinicians recorded "pretest probability estimates" (using continuous scales for various pathogen groups) for comparison with test results; treatments and test turnaround times were also recorded. Transnasal and throat swabs, with or without nasopharyngeal aspirate (NPA), were M-PCR tested. NPA-containing sample sets found to be RSV positive by DFA were not further tested. Single PCR for human metapneumovirus (hMPV) was performed retrospectively. Of 178 ARI episodes representing 172 patients, NPA was included in 97 sample sets; 54 (56%) were determined to be RSV positive. The other NPA-containing sample sets (n = 43) yielded 27 findings (63%), and the swab-only sets (n = 81) yielded 47 findings (58%); rhinovirus was found most often. Testing for hMPV yielded seven positive results. M-PCR median turnaround times were 4 days in swab-only samples and 5 days with NPA. Antibiotics were prescribed in 50 episodes, at rates similar for RSV and rhinovirus. Pretest probability estimates of a viral cause were lower in episodes caused by rhinovirus than in episodes caused by RSV. The hospitals continued to use M-PCR for NPA-containing samples found to be RSV negative by DFA. Test implementation is more likely with higher diagnostic yield and a protocol that reflects day-to-day clinical and laboratory operations.
Energy harvesting from underwater base excitation of a piezoelectric composite beam (2013)

In this paper, we investigate energy harvesting from underwater base excitation of a piezoelectric composite beam. Four different geometric configurations are experimentally studied in which the beam is either fully submerged or is partially immersed, with an eighth, a quarter, or a half of its length vibrating underwater. The frequency and the amplitude of base excitation are systematically varied along with the shunting resistance to investigate the principles of piezoelectric energy harvesting from underwater vibrations. Results demonstrate that increasing the wet length produces a consistent reduction of the resonance frequency and the quality factor of underwater vibrations. On the other hand, the harvested power is found to generally decrease as the submersion length is increased. Experimental results are interpreted through a distributed piezohydroelastic model that accounts for added mass and nonlinear hydrodynamic damping effects. A reduced order modal model is further established to parametrically explore the system response across a variety of geometrical and physical parameters.
Faster defect localization in nanometer technology based on defective cell diagnosis (2007)

In this paper we present practical techniques that enable diagnosis of defective library cells in a failing die. Our technique can handle large industrial designs and practical situations like compressed test patterns with multiple exercising conditions per pattern and sequence dependent defects. Being able to accurately differentiate between cell-internal and interconnect defects leads to a faster root cause failure analysis at a reduced cost. This capability was applied on an AMD graphics chip using 90nm at TSMC. In all of the failing dies that underwent physical failure analysis, the defective library cell identified by diagnosis was verified to be correct by failure analysis. Currently this capability is successfully used to diagnose another design using TSMC’s 65nm technology.
Identification and characterization of amylase-binding protein C from<i>Streptococcus mitis</i>NS51 (2010)

A substantial proportion of the streptococcal species found in dental plaque biofilms are able to interact with the abundant salivary enzyme alpha-amylase. These streptococci produce proteins that specifically bind amylase. An important plaque species, Streptococcus mitis, secretes a 36-kDa amylase-binding protein into the extracellular milieu. Proteins precipitated from S. mitis NS51 cell culture supernatant by the addition of purified salivary amylase were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to a membrane, and a prominent 36-kDa band was cut from the membrane and sequenced to yield the N-terminal amino acid sequence DSQAQYSNGV. Searching the S. mitis genome sequence database revealed a single open reading frame containing this sequence, and the gene was amplified by the S. mitis genomic DNA polymerase chain reaction. The coding region of this open reading frame, designated amylase-binding protein C (AbpC), was cloned into an Escherichia coli expression vector and the recombinant AbpC (rAbpC) was purified from the soluble fraction of the E. coli cell lysate. Purified AbpC was found to interact with immobilized amylase, confirming AbpC as a new streptococcal amylase-binding protein.
Three‐dimensional structure of (1–71)bacterioopsin solubilized in methanol/chloroform and SDS micelles determined by <sup>15</sup>N‐<sup>1</sup>H heteronuclear NMR spectroscopy (1994)

Spatial structures of a chymotryptic fragment C2 (residues 1-71) of bacterioopsin from Halobacterium halobium, solubilized in a mixture of methanol/chloroform (1:1, by vol.) and 0.1 M 2HCO2NH4, or in perdeuterated sodium (2H)dodecyl sulfate (SDS) micelles in the presence of perdeuterated (2,2,2-2H)trifluoroethanol, were determined by two-dimensional and three-dimensional heteronuclear 15N-1H NMR techniques. The influence of (2,2,2-2H)trifluoroethanol on the conformational dynamics of C2 in micelles and the effect of the salt (organic mixture) were studied. Under the best conditions, 1H and 15N resonances of 15N-uniformly enriched protein were assigned in both milieus by homonuclear two-dimensional NOE (NOESY) and two-dimensional total-correlated (TOCSY) spectra and heteronuclear three-dimensional NOESY-multiple-quantum-correlation (HMQC) and TOCSY-HMQC spectra. 651 (organic mixture) and 520 (micelles) interproton-distance constraints, derived from volumes of cross-peaks in two-dimensional NOESY and three-dimensional NOESY-HMQC spectra, along with deuterium exchange rates of amide groups measured in both milieus and 51 HN-C alpha H coupling constants obtained in the case of the organic mixture, were used in the construction of C2 spatial structures. Obtained structures are similar in both milieus and have two right-handed alpha-helical regions stretching from Pro8 to Met32 and Phe42 to Tyr64 (organic mixture), and from Pro8 to Met32 and Ala39 to Leu62 (micelles). In micelles, the second alpha helix is terminated by C-cap Gly63, adopting a conformation characteristic of a left-handed helix. Residues Gly65 to Thr67 from the turn of a right-handed helix. In the isotropic medium of the organic mixture, the C-terminal region of residues 65-71 lacks an ordered structure. Torsion angles chi 1 were unequivocally determined for 18 alpha-helical residues in both milieus. In the isotropic organic mixture and anisotropic micellar system, C2 remains a compact structure with a characteristic size of 3.0-3.5 nm. C2 seems to be present in at least two conformational states, packed and unpacked. Using NMR data, along with the electron cryomicroscopy model of bacteriorhodopsin [Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckman, E. & Downing, K. H. (1990) J. Mol. Biol. 213, 899-929], we suggested a model for the conformation of C2 in this putative close-packed state. However, no NOE contact between alpha helices was found in either milieu.
CHAOTIC SIGNAL SYNTHESIS WITH REAL-TIME CONTROL: SOLVING DIFFERENTIAL EQUATIONS IN PD, MAX/MSP, AND JMAX (2003)

Chaotic signals are useful in two different levels in audio synthesis: as sound material or control structure. Patching languages such as Pd, Max/MSP, and jMAX provide easier mechanisms for generating chaotic structures at control level. We can generate deterministic chaotic signals either by finding numerical solutions to differential equations or by using first return maps. While generating the next sample, both of these methods require calculations with the knowledge of the previous sample. Most signal processing environments for computer music, such as Pd, Max/MSP, and jMAX, transfer audio data among their objects by vectors (blocks). In such environments, finding numerical solutions to differential equations or generating signals based on first return maps, will require writing external objects or setting the block-size to 1. Writing external objects can be time consuming and the real-time control of the calculations have to be embedded in the external object, which will require a recompilation for every change to the mechanism. Setting the block-size to 1 can make writing the patch cumbersome and sometimes very confusing. In this paper we shall present the fexpr# object, implemented for Pd, Max/MSP, and jMAX, which can be used for finding numerical solutions to differential equations by simply entering the difference equations as part of the object arguments. The object parameters can then be controlled in real-time using the host patching language. As examples, solutions to Lorenz Equations, Chua&apos;s Oscillators, Duffing&apos;s equation, and the use of first return maps will be presented using the fexpr# object.
Safety and Immunogenicity of Vaccination With MART-1 (26–35, 27L), gp100 (209–217, 210M), and Tyrosinase (368–376, 370D) In Adjuvant With PF-3512676 and GM-CSF In Metastatic Melanoma (2012)

The effectivenes of cancer vaccines in inducing CD8(+) T-cell responses remains a challenge, resulting in a need for testing more potent adjuvants. Our objective was to determine the safety and immunogenicity of vaccination against melanoma-related antigens employing MART-1, gp100, and tysosinase paptides combined with the TLR9 agonist PF-3512676 and local granulocyte macrophage-colony stimulating factor in oil emulsion. Using continuous monitoring of safety and a 2-stage design for immunologic efficacy, 20 immune response evaluable patients were targetted. Vaccinations were given subcutaneously on days 1 and 15 per cycle (1cycle=28 d) for up to 13 cycles. Interferon-γ enzyme-linked immunosorbent spot was used as the primary assay measuring the frequency of peripheral antigen-specific CD8(+) T cells at days 50 and 90 compared with baseline (target ≥ 9/20 immunologic responses). Clinical responses were measured by Response Evaluation Criteria In Solid Tumors every 8 weeks. Twenty-two (including 20 immune response evaluable) melanoma patients were enrolled. All had American Joint Committe on Cancer stage IV (5M1a, 6M1b, 11M1c) and most had previously received therapy. Eight had previously treated brain metastases. An average of 3.5 cycles of vaccination per patient was administered. Clinical response data were available for 21 patients. There were 2 partial response and 8 stable disease lasting 2-7 months. One patient with ongoing partial response continued on treatment. At a median follow-up of 7.39 months (range, 3.22-20.47 mo), median progression-free survival was 1.9 months (90% confidence interval, 1.84-3.68) and median overall survival was 13.4 months (90% confidence interval,11.3-∞). No regimen-related grade 3/4/5 toxicities were observed. There were 9/20 patients with positive enzyme-linked immunosorbent spot at day 50 and/or day 90. Our adjuvant regimen combining PF-3512676 and granulocyte macrophage-colony stimulating factor was safe and is worthy of further testing with these or alternative peptides, potentially in combination with antibodies that target immunoregulatory checkpoints.
Fusion of time delayed measurements with uncertain time delays (2005)

In this paper we consider the problem of estimating the state of a dynamic system from a sequence of observations that are imprecisely timestamped. We argue that this problem can be addressed using the covariance union (CU) technique, and we demonstrate its application in a particular example.
Syntheses and reactions of the bis-boryloxide O(Bpin)2(pin = O2C2Me4) (2005)

The reaction of the phosphine oxides, OPEt31 and OPn-Bu32 with pinacolborane (HBpin) results in phosphine oxide reduction and the formation of O(Bpin)23. In contrast, the phosphine oxide OPn-Bu3 reacts with HB(C6F5)2 or B(C6F5)3 to give only the donor-acceptor adducts. Compound 3 reacts with HNPt-Bu3 to give the phosphinimonium borate salt, [t-Bu3PNH2][(Bpin(OBpin)2]6, while reaction with Cp2ZrMe2 affords the species Cp2Zr(OBpin)27.
Design and Experimental Validation of a Cooperative Driving System in the Grand Cooperative Driving Challenge (2012)

In this paper, we present the Cooperative Adaptive Cruise Control (CACC) architecture, which was proposed and implemented by the team from Chalmers University of Technology, Göteborg, Sweden, that joined the Grand Cooperative Driving Challenge (GCDC) in 2011. The proposed CACC architecture consists of the following three main components, which are described in detail: 1) communication; 2) sensor fusion; and 3) control. Both simulation and experimental results are provided, demonstrating that the proposed CACC system can drive within a vehicle platoon while minimizing the inter-vehicle spacing within the allowed range of safety distances, tracking a desired speed profile, and attenuating acceleration shockwaves.
<title>Multispectral tissue classification of MR images using sensor fusion approaches</title> (1990)

Multi-spectral image data fusion techniques for tissue classification of magnetic resonance (MR) images are presented. Using MR it is possible to obtain imagesof proton density the spin-lattice relaxation time constant ( T1) and the spin-spin relaxation time constant (T2) of the same anatomical section of the human body. In this paper we adopt a sensor fusion approach to tissue classification and segmentation in which each of the three images are treated as the output of different sensors. Regions of the images are modeled as noncausal Gaussian Markov random fields (GMRFs) and the underlying tissue label image is also assumed to follow a Gibbs distribution. Two different multi-spectral tissue labeling algorithms maximum a posteriori (MAP) estimation and the Dempster-Shafer evidential reasoning technique are presented. In the Bayesian MAP approach we use an independent opinion pool for data fusion and a deterministic relaxation to obtain the MAP solution. In practice the Bayesian approach may be too restrictive and a likelihood represented by a point probability value is usually an overstatement of what is actually known. In the Dempster-Shafer approach we adopt Dempster''s rule of combination for data fusion using belief intervals and ignorance to represent our confidence in a particular labeling and we present a new deterministic relaxation scheme that updates the belief intervals. Results obtained from real MR images are presented. 1.
Retinoic acid promotes transcription of the platelet-derived growth factor alpha-receptor gene. (1990)

Retinoic acid together with dibutyryl cyclic AMP stimulated transcription of the platelet-derived growth factor alpha-receptor gene in embryonal carcinoma cells (line F9). Processed mRNA transcripts appeared within 4 h after exposure to these agents, and functional alpha:alpha homodimers appeared within 24 h.
Fluorocarbon‐Based in vivo Oxygen Transport and Delivery Systems (1991)

The approval of Fluosol, a fluorocarbon emulsion for oxygenating the myocardium during the transluminal coronary angioplasty procedure, is a landmark in the field of injectable oxygen carriers, the so-called blood substitutes. This review discusses the advances made since this first emulsion was initially developed about 12 years ago. Attention is focused on the progress achieved in the preparation and selection of new, better-defined and faster-excreted fluorocarbons, and better surfactants, improved emulsions, knowledge of structure/property relationships along with an improved understanding of the physiologic response to their administration. These advances have led to the development of a second generation of highly concentrated, fluid and stable injectable oxygen carriers suitable for a broad range of clinical applications. Prospects for further progress and future generations of emulsions are also outlined.
Generalized Displacement Structure for Block-Toeplitz, Toeplitz-Block, and Toeplitz-Derived Matrices (1994)

The concept of displacement structure has been used to solve several problems connected with Toeplitz matrices and with matrices obtained in some way from Toeplitz matrices (e.g., by combinations of multiplication, inversion, and factorization). Matrices of the latter type will be called Toeplitz-derived (or Toeplitz-like, close-to-Toeplitz). This paper introduces a generalized definition of displacement for block-Toeplitz and Toeplitz-block arrays. It will turn out that Toeplitz-derived matrices are perhaps best regarded as particular Schur complements obtained from suitably defined block matrices. The new displacement structure is used to obtain a generalized Schur algorithm for fast triangular and orthogonal factorizations of all such matrices and well-structured fast solutions of the corresponding exact and overdetermined systems of linear equations. Furthermore, this approach gives a natural generalization of the so-called Gohberg–Semencul formulas for Toeplitz-derived matrices.
BIER — Boosting Independent Embeddings Robustly (2017)

Learning similarity functions between image pairs with deep neural networks yields highly correlated activations of large embeddings. In this work, we show how to improve the robustness of embeddings by exploiting independence in ensembles. We divide the last embedding layer of a deep network into an embedding ensemble and formulate training this ensemble as an online gradient boosting problem. Each learner receives a reweighted training sample from the previous learners. This leverages large embedding sizes more effectively by significantly reducing correlation of the embedding and consequently increases retrieval accuracy of the embedding. Our method does not introduce any additional parameters and works with any differentiable loss function. We evaluate our metric learning method on image retrieval tasks and show that it improves over state-ofthe- art methods on the CUB-200-2011, Cars-196, Stanford Online Products, In-Shop Clothes Retrieval and VehicleID datasets by a significant margin.
Facile optical resolution of DL-1,4,5,6-tetra-O-benzyl-myo-inositol: Key synthons for the phosphoinositides (1994)

The facile preparation of 1D-1,4,5,6,-tetra-O-benzyl-myo-inositol and its enantiomer 1L-1,4,5,6-tetra-O-benzyl-myo-inositol from the corresponding racemate via the 1-(1′S)-(−)-camphanic acid esters is described.
Synthesis and Application of a Water-Soluble Near-Infrared Dye for Cancer Detection Using Optical Imaging (2005)

A novel water-soluble 2-[2-(2-chloro-3-{2-[3,3-dimethyl-5-sulfo-1-(4-sulfo-butyl)-3H-indol-2-yl]-vinyl}-cyclohex-2-enylidene)-ethylidene]-3,3-dimethyl-1-(4-sulfo-butyl)-2,3-dihydro-1H-indole-5-carboxylic acid (dye 2) was developed via an asymmetric approach. With an additional sulfonate group, the near-infrared feature of this dye exhibited a 2-fold increase in quantum yield compared to the previous generation. The current synthetic strategy provided a single carboxylic group as a handle for conjugation, thus allowing selectivity for bioconjugation. The stability of this dye was demonstrated by labeling peptides via solid-phase peptide chemistry. The in vivo optical imaging showed potential and broad applications of this dye in developing molecular-based beacons for cancer detection.