gebhart/patrepeval huggingface dataset:
Helical Oligopeptides of a Quaternized Amino Acid with Tunable Chiral‐Induction Ability and an Anomalous pH Response (2017)

A series of octamer (8-mer) and hexadecamer (16-mer) oligopeptides of 4-aminopiperidine-4-carboxylic acid (Api) with l-leucine as a chiral auxiliary at their N or C termini were synthesized. By using circular dichroism spectroscopy, the conformational profiles of the peptides were systematically studied, which revealed that the α-helix-formation ability of the peptides is determined by the combination of parameters, which includes peptide length, state of the piperidine groups in the Api units, and position of the chiral auxiliary. When the piperidines were in the free-base state, the peptides showed a low propensity to form helical structures. However, the protonation and acylation of the piperidines enhanced the formation of helical structures, such that the order for helix-formation ability was protonated>acylated>free base. In terms of peptide length, the 16-mers generally showed higher helix-formation ability than the corresponding 8-mers, and one of the 16-mers showed helicity at the highest level reported thus far for oligopeptides of a similar length. It was also found that the sensitivity of the helical structure towards the state of the piperidine groups changed drastically depending on the chiral auxiliary position; the N-terminal chiral peptides were more sensitive than the C-terminal chiral analogues.
Approaching Theoretical Performances of Electrocatalytic Hydrogen Peroxide Generation by Cobalt‐Nitrogen Moieties (2023)

Electrocatalytic oxygen reduction reaction (ORR) has been intensively studied for environmentally benign applications. However, insufficient understanding of ORR 2 e<sup>-</sup> -pathway mechanism at the atomic level inhibits rational design of catalysts with both high activity and selectivity, causing concerns including catalyst degradation due to Fenton reaction or poor efficiency of H<sub>2</sub> O<sub>2</sub> electrosynthesis. Herein we show that the generally accepted ORR electrocatalyst design based on a Sabatier volcano plot argument optimises activity but is unable to account for the 2 e<sup>-</sup> -pathway selectivity. Through electrochemical and operando spectroscopic studies on a series of CoN<sub>x</sub> /carbon nanotube hybrids, a construction-driven approach based on an extended "dynamic active site saturation" model that aims to create the maximum number of 2 e<sup>-</sup> ORR sites by directing the secondary ORR electron transfer towards the 2 e<sup>-</sup> intermediate is proven to be attainable by manipulating O<sub>2</sub> hydrogenation kinetics.
Novel Synthesis of HEX-2-Enopyranosides (1987)

Abstract The usefulness of thioglycosides, particularly 2-thiopyridyl glycosides2 having a suitable activating group at the anomeric center for glycosylation, has been well documented. Glycosylations of 2-thiopyridyl 4,6-di–acetyl-2,3-dideoxy-α-D-erythro-hex-2-enopyranoside (1) with aglycones to furnish the corresponding 2,3-unsaturated-∼-glycosides have been studied. The latter compounds are suitable for the preparation of 2,3-dideoxy-sugar glycosides.
Combined Guided Tracking and Matching with Adaptive Track Initialization (2005)

Point feature tracking is the key step in solving such problems as camera calibration and 3d reconstruction. In this paper, we propose a new feature-tracking framework that is based on combination of guided tracking and matching approaches. The proposed framework raises the quality of tracking in terms of mean track lengths and fraction of successfully tracked features. We also propose an adaptive track initialization scheme based on spatial partitioning of detected features into bins that reduces the influence of dominant planes on outlier segmentation. Results are given for a number of real image sequences. The algorithm is demonstrated to outperform previous approaches.
Data from Somatic Tissue Engineering in Mouse Models Reveals an Actionable Role for WNT Pathway Alterations in Prostate Cancer Metastasis (2023)

&lt;div&gt;Abstract&lt;p&gt;To study genetic factors influencing the progression and therapeutic responses of advanced prostate cancer, we developed a fast and flexible system that introduces genetic alterations relevant to human disease directly into the prostate glands of mice using tissue electroporation. These electroporation-based genetically engineered mouse models (EPO-GEMM) recapitulate features of traditional germline models and, by modeling genetic factors linked to late-stage human disease, can produce tumors that are metastatic and castration-resistant. A subset of tumors with &lt;i&gt;Trp53&lt;/i&gt; alterations acquired spontaneous WNT pathway alterations, which are also associated with metastatic prostate cancer in humans. Using the EPO-GEMM approach and an orthogonal organoid-based model, we show that WNT pathway activation drives metastatic disease that is sensitive to pharmacologic WNT pathway inhibition. Thus, by leveraging EPO-GEMMs, we reveal a functional role for WNT signaling in driving prostate cancer metastasis and validate the WNT pathway as therapeutic target in metastatic prostate cancer.&lt;/p&gt;Significance:&lt;p&gt;Our understanding of the factors driving metastatic prostate cancer is limited by the paucity of models of late-stage disease. Here, we develop EPO-GEMMs of prostate cancer and use them to identify and validate the WNT pathway as an actionable driver of aggressive metastatic disease.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 890&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Knowledge encapsulation for focused search from pervasive devices (2002)

Mobile knowledge seekers often need access to information on the Web during a meeting or on the road, while away from their desktop. A common practice today is to use pervasive devices such as Personal Digital Assistants or mobile phones. However, these devices have inherent constraints (e.g., slow communication, form factor) which often make information discovery tasks impractical.In this paper, we present a new focused-search approach specifically oriented for the mode of work and the constraints dictated by pervasive devices. It combines focused search within specific topics with encapsulation of topic-specific information in a persistent repository. One key characteristic of these persistent repositories is that their footprint is small enough to fit on local devices, and yet they are rich enough to support many information discovery tasks in disconnected mode. More specifically, we suggest a representation for topic-specific information based on "knowledge-agent bases" that comprise all the information necessary to access information about a topic (under the form of key concepts and key Web pages) and assist in the full search process from query formulation assistance to result scanning on the device itself. The key contribution of our work is the coupling of focused search with encapsulated knowledge representation making information discovery from pervasive devices practical as well as efficient. We describe our model in detail and demonstrate its aspects through sample scenarios.
Accelerating Progress Towards Practical Quantum Advantage: The Quantum Technology Demonstration Project Roadmap (2022)

Quantum information science and technology (QIST) is a critical and emerging technology with the potential for enormous world impact and is currently invested in by over 40 nations. To bring these large-scale investments to fruition and bridge the lower technology readiness levels (TRLs) of fundamental research at universities to the high TRLs necessary to realize the promise of practical quantum advantage accessible to industry and the public, we present a roadmap for Quantum Technology Demonstration Projects (QTDPs). Such QTDPs, focused on intermediate TRLs, are large-scale public-private partnerships with a high probability of translation from laboratory to practice. They create technology demonstrating a clear 'quantum advantage' for science breakthroughs that are user-motivated and will provide access to a broad and diverse community of scientific users. Successful implementation of a program of QTDPs will have large positive economic impacts.
Advanced chemical deposition techniques - from research to production (2001)

Abstract Chemical deposition techniques show distinct advantages for research tasks as well as for microelectronic production lines. This review will summarize the state of the art of the Chemical Solution Deposition (CSD) and of the Metal-Organic Chemical Vapor Deposition (MOCVD) processes for high-permittivity, ferroelectric, and other complex electronic oxide thin films as well as their applications in integrated capacitors, FeRAMs, etc Emphasis will be laid on the selection and the properties of the precursors, the microscopic mechanisms of film deposition, and the tailoring of the microstructure by the deposition parameters. In the main part of the review, topics of current interest will be specifically discussed: (1) the deposition of ultrathin films, (2) device integration issues, and (3) lateral nanostructuring and the formation of single grains. The techniques will be evaluated for their potential use in a future nanotechnology environment. Besides these research-oriented topics, both CSD and MOCVD show features which render the techniques highly suitable for large-wafer, high through-put production. The migration path from R&D systems to production tools will be outlined. Key Words: Chemical Solution DepositionMOCVDultrathin filmsnanotechnologysingle grainsferroelectricsdielectricsmicrostructureintegrated devices
Angiosarcoma of bone marrow with unusual expression of chymase: diagnosis in a trephine biopsy specimen (2007)

Angiosarcoma is a very rare vascular neoplasm, comprising less than 1% of all sarcomas. Involvement of the bone marrow is distinctly uncommon and almost invariably seen in patients with disseminated disease. Primary angiosarcoma of the bone/bone marrow, however, is extremely rare and, to the best of the authors knowledge, has not been reported to be diagnosed in a trephine biopsy.1

A 77-year-old woman presented with acute back pain. A mastectomy had been performed for carcinoma of the left breast 16 years previously. Her past medical history was otherwise unremarkable. On physical examination, the patient showed hemisensory loss of the left leg. MRI and radionuclide bone scan revealed a large tumour mass …
Control of cyclin‐dependent kinase 5 (Cdk5) activity by glutamatergic regulation of p35 stability (2005)

Although the roles of cyclin-dependent kinase 5 (Cdk5) in neurodevelopment and neurodegeneration have been studied extensively, regulation of Cdk5 activity has remained largely unexplored. We report here that glutamate, acting via NMDA or kainate receptors, can induce a transient Ca(2+)/calmodulin-dependent activation of Cdk5 that results in enhanced autophosphorylation and proteasome-dependent degradation of a Cdk5 activator p35, and thus ultimately down-regulation of Cdk5 activity. The relevance of this regulation to synaptic plasticity was examined in hippocampal slices using theta burst stimulation. p35(-/-) mice exhibited a lower threshold for induction of long-term potentiation. Thus excitatory glutamatergic neurotransmission regulates Cdk5 activity through p35 degradation, and this pathway may contribute to plasticity.
Efficient distributed control of light-emitting diode array lighting systems (2012)

We consider illumination rendering with distributed control of a lighting system with an array of light-emitting diodes (LEDs). As low-cost microprocessors become standard components in LED drivers, distributing the computation of the control signals to individual LED drivers becomes attractive. Common distributed control algorithms require each individual controller to exchange information with all the others and process it. This incurs too large a communication and processing overhead for a low-cost local controller. In this Letter, we propose a distributed control algorithm for achieving global illumination rendering, wherein a controller only needs to communicate within a selected neighborhood. We present design criteria for defining the communication neighborhood and study its impact on rendering performance.
Improved murine glioma detection following modified diet and photobleaching of skin PpIX fluorescence (2007)

The Aminolevulinic Acid (ALA) - Protoporphyrin IX (PpIX) system is unique in the world of photosensitizers in that the prodrug ALA is enzymatically transformed via the tissue of interest into fluorescently detectable levels of PpIX. This system can be used to monitor cellular metabolism of tumor tissue for applications such as therapy monitoring. Detecting PpIX fluorescence noninvasively has proven difficult due to the high levels of PpIX produced in the skin compared to other tissue both with and without ALA administration. In the current study, methods to decrease skin PpIX autofluorescence and skin PpIX fluorescence following ALA administration have been examined. Use of a purified diet is found to decrease both skin PpIX autofluorescence and skin PpIX fluorescence following ALA administration, while addition of a broad spectrum antibiotic to the water shows little effect. Following ALA administration, improved brain tumor detection is seen when skin PpIX fluorescence is photobleached via blue light prior to transmission spectroscopic measurements of tumor bearing and control animals. Both of these methods to decrease skin PpIX autofluorescence and skin PpIX fluorescence following ALA administration are shown to have a large effect on the ability to detect tumor tissue PpIX fluorescence noninvasively <i>in vivo</i>.
Building HMM-TTS Voices on Diverse Data (2014)

The statistical models of hidden Markov model based text-to-speech (HMM-TTS) systems are typically built using homogeneous data. It is possible to acquire data from many different sources but combining them leads to a non-homogeneous or diverse dataset. This paper describes the application of average voice models (AVMs) and a novel application of cluster adaptive training (CAT) with multiple context dependent decision trees to create HMM-TTS voices using diverse data: speech data recorded in studios mixed with speech data obtained from the internet. Training AVM and CAT models on diverse data yields better quality speech than training on high quality studio data alone. Tests show that CAT is able to create a voice for a target speaker with as little as 7 seconds; an AVM would need more data to reach the same level of similarity to target speaker. Tests also show that CAT produces higher quality voices than AVMs irrespective of the amount of adaptation data. Lastly, it is shown that it is beneficial to model the data using multiple context clustering decision trees.
TiB2 Formation Using Thermite Ignition (2008)

Determination of particle size and packing density effects on thermite ignition temperatures of three stoichiometric mixtures was made. The three mixtures were 3TiO2 + 4Al; B2O3 + 2Al and 3TiO2 + 3B3O3 +10AI. Comparisons were made of products formed by igniting loose powder and pressed pellets at room temperature and in a furnace pre-heated to 1260°C.
Linear dependence of spin exchange coupling constant on bridge angle in phenoxy-bridged dinickel(II) complexes (1994)

A magneto-structural relationship showing linear dependence of antiferromagnetic exchange coupling constant (–J) on Ni–O–Ni bridge angle as well as the intramolecular Ni ⋯ Ni distance has been obtained with a series of phenoxy-bridged macrocyclic dinickel(II) complexes with centrosymmetric structures.
Chemical deglycosylation on a micro‐scale of membrane glycoproteins with retention of phosphoryl‐protein linkages (1989)

We provide here an easy and convenient procedure for the chemical deglycosylation of membrane glycoproteins that can be done rapidly and inexpensively on large numbers of membrane samples on a microscale without prior isolation of the glycoprotein in question. We have used the procedure successfully on three different glycoproteins and additionally have shown that covalent linkages of the polypeptide to phosphoryl residues are preserved.
Nanotube Network Transistors from Peptide‐Wrapped Single‐Walled Carbon Nanotubes (2005)

Nanotube network transistors have been prepared by pin-point microfluidic deposition of peptide-wrapped unbundled single-walled carbon nanotubes (see picture). Functioning devices exhibited n-type behavior with on/off ratios up to 4×103 in vacuum. Networks of different composition (nanotubes and dispersants) can be deposited in a controlled manner at specific positions on substrates, thus offering great flexibility.
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology (2021)

In polypharmacology drugs are required to bind to multiple specific targets, for example to enhance efficacy or to reduce resistance formation. Although deep learning has achieved a breakthrough in de novo design in drug discovery, most of its applications only focus on a single drug target to generate drug-like active molecules. However, in reality drug molecules often interact with more than one target which can have desired (polypharmacology) or undesired (toxicity) effects. In a previous study we proposed a new method named DrugEx that integrates an exploration strategy into RNN-based reinforcement learning to improve the diversity of the generated molecules. Here, we extended our DrugEx algorithm with multi-objective optimization to generate drug-like molecules towards multiple targets or one specific target while avoiding off-targets (the two adenosine receptors, A<sub>1</sub>AR and A<sub>2A</sub>AR, and the potassium ion channel hERG in this study). In our model, we applied an RNN as the agent and machine learning predictors as the environment. Both the agent and the environment were pre-trained in advance and then interplayed under a reinforcement learning framework. The concept of evolutionary algorithms was merged into our method such that crossover and mutation operations were implemented by the same deep learning model as the agent. During the training loop, the agent generates a batch of SMILES-based molecules. Subsequently scores for all objectives provided by the environment are used to construct Pareto ranks of the generated molecules. For this ranking a non-dominated sorting algorithm and a Tanimoto-based crowding distance algorithm using chemical fingerprints are applied. Here, we adopted GPU acceleration to speed up the process of Pareto optimization. The final reward of each molecule is calculated based on the Pareto ranking with the ranking selection algorithm. The agent is trained under the guidance of the reward to make sure it can generate desired molecules after convergence of the training process. All in all we demonstrate generation of compounds with a diverse predicted selectivity profile towards multiple targets, offering the potential of high efficacy and low toxicity.
High-Level Design and Validation of the BlueSPARC Multithreaded Processor (2010)

This paper presents our experiences in using high-level methods to design and validate a 16-way multithreaded microprocessor called BlueSPARC. BlueSPARC is an in-order, high-throughput processor supporting complex features such as privileged-mode operations, memory management, and a nonblocking cache subsystem. Using a high-level design language called Bluespec System Verilog (BSV), our final implementation achieves comparable synthesis quality to a similar commercial microprocessor developed using conventional register transfer level flows, and is capable of running unmodified commercial applications while hosted on a Xilinx XCV2P70 field-programmable gate array (FPGA) at 90 MHz. To validate our implementation, an FPGA-accelerated approach was developed to efficiently check the correct execution of real, nondeterministic multithreaded programs running on the BlueSPARC processor. Together, the high-level language features of BSV along with our validation approach enabled us to achieve a working FPGA-based implementation in less than one man-year.
Effect of Plane of Arm Elevation on Glenohumeral Kinematics (2013)

Scapulohumeral rhythm significantly decreased as the plane of arm elevation moved in an anterior arc from abduction to forward flexion. The amount of physiologic glenohumeral excursion varied significantly with the plane of elevation, was smallest for scaption, and showed inconsistent patterns across subjects with the exception of consistent inferior translation during abduction.
The granulin-epithelin precursor/PC-cell-derived growth factor is a growth factor for epithelial ovarian cancer. (2003)

cDNA library preparation from microdissected tumor epithelium provided a selective advantage for the identification of growth factors for epithelial ovarian cancer. Differential granulin expression in tumor samples and the antiproliferative effects of its antisense down-regulation suggest that GEP may be a new autocrine growth factor and molecular target for epithelial ovarian cancer.
The effects of irradiation on the expression of a tumour rejection antigen (heat shock protein gp96) in human cervical cancer (1998)

Recently, gp96 molecules have been implicated in the presentation of endogenous and viral antigens. A number of key elements in this pathway, including major histocompatibility complex (MHC) class I molecules as well as adhesion/co-stimulation molecules such as ICAM-1, are known to be sensitive to irradiation effects. The results show that radiation can also increase the expression of other immunologically important cell molecules such as a tumour rejection antigen (heat shock protein gp96) in human cervical cancer. Such findings may partially explain the increased immunogenicity of tumour cells following irradiation and further support a role for local radiation therapy as a powerful biologic response modifier.
Terahertz transmission properties of an individual slit in a thin metallic plate (2009)

We report on the terahertz transmission properties through a single slit in a thin metallic film. The properties are studied by comparing the transmissions of TE- and TM-polarized electromagnetic waves over a broad spectral range from the geometrical regime to the subwavelength limit. In the geometrical regime, the remarkable terahertz transmission due to guided modes is observed even without the contribution of surface waves. Whereas in the subwavelength limit, the surface charge oscillations associated with the TM-polarized guided mode give rise to strong transmission enhancement. The nature of the mechanisms for the terahertz transmission is elucidated using theoretical simulations of the near-field distributions and electromagnetic energy flow.
Circulating Tissue Kallikrein Levels Correlate With Severity of Carotid Atherosclerosis (2004)

Angiogenic factors are heterogeneously expressed in patients with carotid atherosclerosis. The tK measurement may be useful for the diagnosis and monitoring of atherosclerotic disease.
Session Initiation Protocol (SIP) Session Mobility (2009)

Session mobility is the transfer of media of an ongoing communication session from one device to another.This document describes the basic approaches and shows the signaling and media flow examples for providing this service using the Session Initiation Protocol (SIP).Service discovery is essential to locate targets for session transfer and is discussed using the Service Location Protocol (SLP) as an example.This document is an informational document.