gebhart/patrepeval huggingface dataset:
Rice-induced secondary metabolite gene expression inAspergillus nidulans (2020)

Activation of silent biosynthetic gene clusters in fungi remains a challenge for discovery of new useful natural products. In this work, we identify a group of silent secondary metabolite gene clusters in Aspergillus nidulans that are induced by rice (Oryza sativa). Using reverse phase HPLC purification on extracts of rice, we identified the plant hormone gibberellic acid as one compound present in rice extracts that induced these silent genes. Additionally, select secondary metabolite (SM) genes activated by rice were tested for responses to several plant hormones which produced distinctly different transcriptomic profiles in A. nidulans. These observations support the idea that phytohormones play an important role in regulating fungal SM biosynthesis while additionally serving as a source of natural product chemical libraries to screen for useful compounds.
SIGMOD Digital Symposium Collection (DiSC) Editor's Message. (2000)

There were some practical problems in using the SF-36 in an acutely unwell stroke population. However, analysis of psychometric properties suggested that most of the subscales were adequately reliable and valid. Sensitivity to change was poorer in the later stages of the study.
Short-range ordered photonic structures of lamellae-forming diblock copolymers for excitation-regulated fluorescence enhancement (2016)

Photonic crystals can be represented by periodic nanostructures with alternating refractive indices, which create artificial stop bands with the appearance of colors. In this regard, nanodomains of block copolymers and the corresponding structural colors have been intensively studied in the past. However, the practical application of photonic crystals of block copolymers has been limited to a large degree because of the presence of large defects and grain boundaries in the nanodomains of block copolymers. The present study focuses on the alternative opportunity of short-range ordered nanodomains of block copolymers for fluorescence enhancement, which also has a direct relevance to the development of fluorescence sensors or detectors. The enhancement mechanism was found to be interconnected with the excitation process rather than the alternation of the decay kinetics. In particular, we demonstrate that randomly oriented, but regular grains of lamellae of polystyrene-block-polyisoprene, PS-b-PI, diblock copolymers and their blend with PS homopolymers can behave as Bragg mirrors to induce multiple reflections of the excitation source inside the photonic structures. This process in turn significantly increases the effective absorption of the given fluorophores inside the polymeric photonic structures to amplify the fluorescence signal.
In Vivo Optical Molecular Imaging:Principles and Signal Processing Issues (2006)

In vivo optical molecular imaging involves the use of light emitting tracers combined with sophisticated sensing modalities to perform in vivo imaging of genetic and molecular information. In contrast to the classical diagnostic imaging tools which image the end effects of the diseases, optical molecular imaging could enhance our knowledge of biological phenomena, monitor genetic expression and the alteration of cells, and lead to earlier detection of diseases. With the development of exotic molecular probes with easily detectable bioluminescence and fluorescence labels, optical molecular imaging has emerged as an important new field within biomedical imaging. This paper reviews this state-of-the-art imaging technology and signal processing issues to monitor molecular and cellular events in living organisms.
Self-homodyne coherent system based on polarization-multiplexed pilot-carrier (2015)

This paper proposes an original self-homodyne coherent system based on the copropagating pilot carrier, which does not require the SOP tracking at the receiver. The system allows to double the whole transported capacity with respect to the standard on-off keying (OOK) modulation thanks to a tailored modulation scheme combined with a specific transmitter (TX) based on the direct modulation of a single laser to achieve both the carrier and the signal, and a RX architecture based on direct detection. By means of suitable simulations, the performance of the proposed system is compared with respect to the employment of 4-level pulse-amplitude modulation (4PAM), which is a very effective modulation format able to double the capacity exploiting direct detection suitable for short-reach applications. Moreover, also polarization shift keying (POLSK) modulation is taken into account in the comparison. Finally, experimental measures confirm the feasibility of the proposed system.
Microbial laboratory evolution in the era of genome‐scale science (2011)

Laboratory evolution studies provide fundamental biological insight through direct observation of the evolution process. They not only enable testing of evolutionary theory and principles, but also have applications to metabolic engineering and human health. Genome-scale tools are revolutionizing studies of laboratory evolution by providing complete determination of the genetic basis of adaptation and the changes in the organism's gene expression state. Here, we review studies centered on four central themes of laboratory evolution studies: (1) the genetic basis of adaptation; (2) the importance of mutations to genes that encode regulatory hubs; (3) the view of adaptive evolution as an optimization process; and (4) the dynamics with which laboratory populations evolve.
AudioChalk: Idiosyncratic Software For Sketching Spectral Music (2015)

This Thesis describes the design of the proof-of-concept software application, AudioChalk. AudioChalk, which combines a vector graphics editor with a oscillator bank synthesizer, lets users algorithmically generate, manipulate, or sketch partials by hand in the time frequency domain via intuitive graphical elements. The purpose of developing AudioChalk was to study, from a software developerâs perspective, how content creation software for experimental musicians can be designed to offer both a flexible and efficient workflow. Simultaneously precise and efficient control are gained by sacrificing some of the softwareâs flexibility. However, if losses of flexibility are carefully considered to not significantly interfere with intended use cases, users often do not perceive a loss of possible functionality. The design choices regarding tradeoffs between efficiency and flexibility that were considered while developing AudioChalk are distilled into a rubric, called idiosyncrasy. Idiosyncrasy as a rubric attempts to generalize the consequences of software design choices from the intended usersâ perspective. The intended users in the case of AudioChalk are composers of experimental electronic music.
State of the art for treatment of bony defects around anterior shoulder instability—the American perspective (2021)

Abstract While arthroscopic Bankart repair yields high success rates, bone loss on the glenoid or humeral head can portend a poor outcome. The authors recommend a thorough evaluation including computed tomography (CT) scanning to best evaluate the amount of bone loss. Multiple studies have shown that the outcomes of revision stabilization procedures are inferior to the respective primary procedure; thus, it is of paramount importance to select the correct index procedure to optimize patient outcome. The authors present the American perspective on treating shoulder instability. For patients with a small on-track Hill Sachs lesion and less than 10 % glenoid bone loss, an isolated arthroscopic Bankart repair is appropriate. This procedure is also recommended for bony Bankart lesions, as well as in overhead throwing athletes. With an engaging Hill Sachs lesion and less than 15 % glenoid bone loss, the authors recommend the addition of a remplissage to the arthroscopic Bankart repair. For patients with up to 15 % bone loss or following a failed previous arthroscopic repair, the authors advocate for open Bankart repair. They recommend Latarjet in patients with a non-engaging Hill Sachs lesion greater than 15 % bone loss. Patients with bone loss over 30 % would benefit from bone grafting with iliac crest autograft or distal tibia allograft for stabilization. In summary, the authors believe that the index procedure provides an opportunity to optimize patient outcome and careful consideration of the treatment options is warranted.
Nonlinear stochastic resonance: The saga of anomalous output-input gain (2000)

We reconsider stochastic resonance (SR) for an overdamped bistable dynamics driven by a harmonic force and Gaussian noise from the viewpoint of the gain behavior, i.e., the signal-to-noise ratio (SNR) at the output divided by that at the input. The primary issue addressed in this work is whether a gain exceeding unity can occur for this archetypal SR model, for subthreshold signals that are beyond the regime of validity of linear response theory: in contrast to nondynamical threshold systems, we find that the nonlinear gain in this conventional SR system exceeds unity only for suprathreshold signals, where SR for the spectral amplification and/or the SNR no longer occurs. Moreover, the gain assumes, at weak to moderate noise strengths, rather small (minimal) values for near-threshold signal amplitudes. The SNR gain generically exhibits a distinctive nonmonotonic behavior versus both the signal amplitude at fixed noise intensity and the noise intensity at fixed signal amplitude. We also test the validity of linear response theory; this approximation is strongly violated for weak noise. At strong noise, however, its validity regime extends well into the large driving regime above threshold. The prominent role of physically realistic noise color is studied for exponentially correlated Gaussian noise of constant intensity scaling and also for constant variance scaling; the latter produces a characteristic, resonancelike gain behavior. The gain for this typical SR setup is further contrasted with the gain behavior for a "soft" potential model.
Frontispiz: polyMOFs: A Class of Interconvertible Polymer‐Metal‐Organic‐Framework Hybrid Materials (2015)

Hybridmaterialien In der Zuschrift auf S. 6250 ff. beschreiben S. M. Cohen et al. die Umwandlung von nichtporösen, eindimensionalen, amorphen Polymeren in kristalline polymerbasierte Metall-organische Gerüstmaterialien.
Structures of two hydrated cage diketones (1990)

Le 2,3,5,6-tetrachloro-8,11-dihydroxy-4,4-dimethoxy-8,11-epoxy pentacyclo [5.4.0.0 2,6 •O 3,10 •O 5,9 ] undecane, C 13 H 12 Cl 4 O 5 , cristallise dans P2 1 /n avec a=7,392, b=12,726, c=16,107 A, β=95,64 o Z=4; affinement jusqu'a R=0,0395. Le 1,9-dibromo-11,11-dihydroxy-5-methylpentacyclo [5.4.0.0 2,6 •O 3,10 •O 5,9 ] undecane-8-one, C 12 H 12 Br 2 O 3 , cristallise dans P1 avec a=6,713, b=14,013, c=14,579 A, α=113,29, β=99,58, μ=99,31 o , Z=4; affinement jusqu'a R=0,0640. Les groupes dicetone dans les deux composes initiaux sont additionnes a de l'eau et forment un dihydrate et un monohydrate
Development and Feasibility of a Real-Time Clinical Decision Support System for Traumatic Brain Injury Anesthesia Care (2017)

CDS implementation is feasible and acceptable with a high rate of case capture and appropriate generation of alert and guidance messages for TBI anesthesia care.
A Voltage-Based Leakage Current Calculation Scheme and its Application to Nanoscale MOSFET and FinFET Standard-Cell Designs (2014)

Logic-level estimators of leakage currents, in nanoscale standard-cell-based designs, are relevant for the dramatic speed advantage with respect to analog SPICE-level simulation. We propose a novel logic-level leakage estimation model based on the characterization of voltages at the internal nodes of digital cells, in conjunction with the characterization of leakage currents in a single field-effect transistor (FET) device and with the input-dependent Kirchhoff current law expression of the total current in the cell topology. The voltage-based nature of the approach simplifies the inclusion of supply voltage variation/scaling impact, as well as of output voltage drop (loading effect), on leakage currents. The method has been implemented in hardware description language models of a complete cell library. Exhaustive tests report average accuracy below 1% error in 22-nm CMOS and 20-nm FinFET technologies, when compared with SPICE BSIM simulation results.
5,5-Fused thiophene γ-lactams as templates for serine protease inhibition (2002)

Novel 5,5-fused thiophene lactams are potent inhibitors and acylating agents of HNE and PPE.
Redesigning active and passive microring resonators (2013)

Even after decades of investigation, microring resonator devices remain mostly in the realm of research. Reconsiderations of microring designs lead to improved fabrication tolerance, modulation performance, and functionality, paving the path toward practical implementations.
62.1: High‐Performance Solution‐Processed OLED Enhanced by Evaporated Common Layer (2011)

Abstract In order to improve the performances of the solution processed full‐color Organic Light Emitting Diodes (OLEDs), we develop “the advanced hybrid device structure”. This new hybrid device has the hybrid connecting layer (HCL) which is fabricated as a common layer on the solution processed red‐green layers, and under the evaporated blue common layer. This HCL has two different roles depending on each color, the first is improvement of hole injection to the blue emissive layer, and the second is confinement of triplet excitons for red and green emissive layer. We found that HCL can operate as an efficiency enhancement layer for all emissive layers.
Non-Paraxial Accelerating Beams (2012)

We present the spatially accelerating solutions of the Maxwell equations. Such beams accelerate along a circular trajectory extending beyond the paraxial regime, thus generalizing the concept of accelerating Airy beams.
Lymphoid origin of intrinsically activated plasmacytoid dendritic cells in mice (2018)

Abstract We identified a novel mouse plasmacytoid dendritic cell (pDC) lineage derived from the common lymphoid progenitors (CLPs) that is dependent on expression of Bcl11a . These CLP-derived pDCs, which we refer to as “B-pDCs”, have a unique gene expression profile that includes hallmark B cell genes, normally not expressed in conventional pDCs. Despite expressing most classical pDC markers such as SIGLEC-H and PDCA1, B-pDCs lack IFN-α secretion, exhibiting a distinct inflammatory profile. Functionally, B-pDCs induce T cell proliferation more robustly than canonical pDCs following Toll-like receptor 9 (TLR9) engagement. B-pDCs, along with another homogeneous subpopulation of myeloid derived pDCs, display elevated levels of the cell-surface receptor tyrosine kinase AXL, mirroring human AXL + transitional DCs in function and transcriptional profile. Murine B-pDCs therefore represent a phenotypically and functionally distinct CLP-derived DC lineage specialized in T cell activation and previously not described in mice.
Programmable high frequency RC oscillator (2005)

Conventional RC oscillators, though offer inexpensive components as resistors and capacitors, are not suitable for frequencies beyond few MHz. Here, a VCO based RC oscillator is proposed, where the output frequency can be programmed finely with digital codes over range of higher frequencies on the fly. In this architecture, divided output frequency of a VCO is compared precisely against an external RC time-constant at regular calibration interval and the VCO frequency is adjusted. The calibration rate can be adjusted by programmable choice of capacitor, to avoid any beat frequency with any system requirement. The circuit is designed and fabricated in a 0.18/spl mu/m technology for low voltage operation.
A Review of Data Mining Techniques for Health Care Analytics (2018)

We now live in an era of complex data explosion with unprecedented flow. Drowning with data and Starving for Knowledge,has become the scenario. Especially in health care sector, the data is rich and massively flooded. With the application of Data Mining techniques, novel, useful and actionable insights can be uncovered to bring win-win strategy for both doctors as well as patients. Medical Diagnosis is an intricate task that needs to be carried out precisely and efficiently. This paper throws light into the Data Mining techniques used for medical prognosis and diagnosis.
In situ low temperature As-doping of Ge films using As(SiH3)3 and As(GeH3)3: fundamental properties and device prototypes (2015)

We report the development of a new method to systematically and controllably achieve very high carrier concentrations in As-doped germanium using ultra-low temperature, high efficiency routes based on the structurally and chemically compatible inorganic hydrides As(SiH3)3 and As(GeH3)3. The Ge n-layers are grown on Ge-buffered Si(100) using in situ depositions of the compounds with Ge3H8 at 330 °C. The as-grown films are found to exhibit excellent crystallinity, defect-free interfaces, atomically smooth surfaces and flat doping profiles with abrupt edges. The active carrier densities are measured to be in the range of 1 × 1019–8.4 × 1019 cm−3 irrespective of the precursor type. These carrier densities are in close agreement with atomic As concentrations measured by secondary ion mass spectrometry, indicating that the growth mechanism promotes the nearly complete substitutional incorporation of dopant atoms while suppressing the formation of non-active clusters and defects. In spite of the lower solubility of As in Ge relative to that of P, the maximum carrier concentrations obtained with As(SiH3)3 and As(GeH3)3 are roughly 30% higher than those found with the analogous P(SiH3)3 and P(GeH3)3. This result, along with the close similarity in band gap narrowing observed for the two methods, suggests that the As-doping route may be advantageous for optical devices that require the highest possible carrier concentrations to populate the conduction band valley associated with direct gap emission. On the other hand—due to the inherently shorter carrier relaxation times in As-doped Ge—the lowest observed resistivity of 5 × 10−4 Ω cm is slightly higher than the lowest resistivity from P-doped analogs. Finally, optical responsivity, electroluminescence and I–V properties of photodiodes fabricated using As(SiH3)3 and As(GeH3)3 are found to be on par with those observed from Ge-on-Si reference analogs, indicating that the chemistry approach described here represents a viable and straightforward route to doping and activation of device-quality materials.
Non-coding regions are the main source of targetable tumor-specific antigens – DATASETS (k=33) (2018)

Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but few have been identified thus far. We therefore developed a proteogenomic approach to enable the high-throughput discovery of TSAs coded by potentially all genomic regions. In two murine cancer cell lines and seven human primary tumors, we identified a total of 40 TSAs, about 90% of which derived from allegedly non-coding regions and would have been missed by standard exome-based approaches. Moreover, the majority of these TSAs derived from non-mutated yet aberrantly expressed transcripts (such as endogenous retroelements) that could be shared by multiple tumor types. In mice, the efficacy of TSA vaccination was influenced by two parameters that can be estimated in humans and could serve for TSA prioritization in clinical studies: TSA expression and the frequency of TSA-responsive T cells in the pre-immune repertoire. In conclusion, the strategy reported herein could considerably facilitate the identification and prioritization of actionable human TSAs.
The cost of QoS support in edge devices an experimental study (1999)

This paper investigates the problem of making QoS guarantees available in access devices such as edge routers, that are commonly deployed in today's IP networks. We propose a specific design which we evaluate by carrying out a complete implementation, whose performance we then measure in the context of an experimental testbed. The results indicate that a reasonable level of service differentiation, i.e., rate and delay guarantees, can be provided with a minimal impact on the raw packet forwarding performance of edge devices.
Phase II Study of the Mitogen-Activated Protein Kinase 1/2 Inhibitor Selumetinib in Patients With Advanced Hepatocellular Carcinoma (2011)

PURPOSE Hepatocellular carcinoma (HCC) is a common and deadly malignancy with few systemic therapy options. The RAF/mitogen-activated protein kinase kinase (MEK)/extracellular signal-related kinase (ERK) pathway is activated in approximately 50% to 60% of HCCs and represents a potential target for therapy. Selumetinib is an orally available inhibitor of MEK tyrosine kinase activity. PATIENTS AND METHODS Patients with locally advanced or metastatic HCC who had not been treated with prior systemic therapy were enrolled on to the study. Patients were treated with selumetinib at its recommended phase II dose of 100 mg twice per day continuously. Cycle length was 21 days. Imaging was performed every two cycles. Biopsies were obtained at baseline and at steady-state in a subset of patients, and pharmacokinetic (PK) analysis was performed on all patients. Results Nineteen patients were enrolled, 17 of whom were evaluable for response. Most (82%) had Child-Pugh A cirrhosis. Toxicity was in line with other studies of selumetinib in noncirrhotic patients. PK parameters were also comparable to those in noncirrhotic patients. No radiographic response was observed in this group, and the study was stopped at the interim analysis. Of 11 patients with elevated α-fetoprotein, three (27%) had decreases of 50% or more. Median time to progression was 8 weeks. Inhibition of ERK phosphorylation was demonstrated by Western blotting. CONCLUSION In this study of selumetinib for patients with HCC, no radiographic responses were seen and time to progression was short, which suggests minimal single-agent activity despite evidence of suppression of target activation.
Functional characterization of the L-type pyruvate kinase gene glucose response complex. (1993)

L-type pyruvate kinase (L-PK) gene expression is modulated by hormonal and nutritional conditions. We have previously shown that the glucose/insulin response element (GlRE) of the L-PK gene is built around two noncanonical E boxes (element L4) that cooperate closely with a contiguous binding site (element L3). We present in this report the identification of proteins that interact with both elements. The L3 site binds hepatocyte nuclear factor 4 (HNF4)- and COUP/TF-related proteins. In fibroblasts, the overexpression of HNF4 transactivates the L-PK promoter. On the contrary, COUP/TF strongly inhibits the active promoter in hepatocytes. The L4 site binds the major late transcription factor (MLTF) in vitro and ex vivo; mutations that suppress this binding activity also inactivated the GlRE function. Mutations transforming one or two noncanonical E boxes of element L4 into consensus MLTF/USF binding sites strongly increase the affinity for MLTF/USF and do not impair the glucose responsiveness. However, merely the ability to bind MLTF/USF does not seem to be sufficient to confer a GlRE activity: those elements in which one E box has been destroyed and the other has been transformed into a consensus MLTF/USF sequence bind MLTF/USF efficiently but do not confer a high glucose responsiveness on the L-PK gene promoter. Consequently, the full activity of the L-PK GlRE seems to require the cooperation between two putative MLTF/USF binding sites located in the vicinity of an HNF4 binding site.