gebhart/patrepeval huggingface dataset:
Chemical development of the vasopressin receptor 2 antagonist SR-121463 (2001)

Abstract A facile convergent total synthesis of the selective, potent, and orally active V2 non-peptide antagonist, SR-121463, was developed by modification of the discovery route. One of the late intermediates, the sulfonyl chloride 1, was synthesized from 3-hydroxybenzoic acid (19) by regioselective sulfonation, O-methylation and amidation in four steps. Another late intermediate, indolin-2-one 2, was prepared from p-phenetidine (8) through the indolin-2-one 16, where the cyclohexanone moiety of 27 was introduced into the active 3-methylene group of 16 by sequential transformation using methyl acrylate and KOtBu. After formation of the cyclic ketal moiety of 13, its ring-opening was achieved by using NaBH4 in the presence of CCl3COOH. The morpholino group in 2 was introduced in accordance with the discovery approach, starting from the 2-hydroxyethoxy derivative 14 through the tosyloxy derivative 15 with morpholine in a one-pot reaction. In this way, the indolin-2-one 2 was synthesized from 8 in six steps. Finally, acylation of the indolin-2-one 2 was achieved with the sulfonyl chloride 1 in the presence of KOtBu in dimethyl sulfoxide (DMSO) at room temperature. This synthetic route proved to be applicable for the large-scale synthesis of SR-121463.
Cooperative driving according to Scoop (2011)

KTH Royal Institute of Technology and Scania are entering the GCDC 2011 under the name Scoop –Stockholm Cooperative Driving. This paper is an introduction to their team and to the technical approac ...
Surface Changes in Mild Steel Coupons from the Action of Corrosion-Causing Bacteria (1981)

Changes which occur on the surface of mild steel coupons submerged in cultures of an Fe(III)-reducing bacterium, isolated from corroded pipe systems carrying crude oil, were studied microscopically to investigate the interaction between the corrosion-causing bacterium and the corroding mild steel coupon. Under micro-aerobic conditions and in the absence of the bacteria, a dense, crystalline, amorphous coat formed on the surface of the steel coupons. In the presence of bacteria the surface coat was extensively removed, exposing the bare metal to the environment. After about 2 weeks of exposure, the removal of the surface coating was followed by colonization of the metal surface by the bacteria. Colonization was mediated by fibrous, exopolysaccharidic material formed by the bacteria. Extension of studies to other bacteria isolated from crude oil and corroded pipes reveals that the formation of exopolysaccharide fibers and possession of adherent properties are common characteristics of bacteria from crude oil systems.
Direct Template Approach for the Formation of (Anisotropic shape) Hollow Silicate Microparticles (2011)

Non-uniform bulk or surface morphology of hollow particles has been an emerging interest because of the potential applications involving chemical storage, delivery and self-assembly for novel functional materials. There had been reports that experimental anisotropic (non-uniform) particles are much more difficult than synthesizing particles with uniform bulk and surface. Hence, this study reported a simple direct approach for the formation of unique hollow anisotropic amorphous silicate microparticles (10 to 20 μm). This was successfully prepared at room temperature via hydrolysis and condensation of tetraethylorthosilicate (TEOS), with ammonia water (NH4OH) as catalyst, ethanol (EtOH) and inorganic micro-size calcium carbonate (CaCO3) as template. The molar ratio used was 1.88:28.85:1:2.85 (CaCO3: EtOH: TEOS: NH4OH), mixed/stirred (at room temperature for 2 h), then filtered/washed by ethanol/water, after then dried and acid treated (3.0 mole/L) to obtained a micro-sized hollow SiO2 particles. This simple approach for the formation of unique anisotropic shape hollow silicate micro-sized particles can be a good alternative for a possible application as large porous carrier for nanoparticles (large drug delivery (LPP's)).
Hard and Wear Resistant Surfaces for Load Bearing Metal Implants (2011)

This chapter contains sections titled: Introduction Laser Engineered Net Shaping (Lens™) Compostionally and Structurally Graded Implants Summary
The FrankenPipe (2007)

The FrankenPipe project is an attempt to convert a traditional Highland Bagpipe into a controller capable of driving both real-time synthesis on a laptop as well as a radio-controlled (RC) car. Doing so engages musical creativity while enabling novel, often humorous, performance art. The chanter is outfitted with photoresistors (CdS photoconductive cells) underneath each hole, allowing a full range of MIDI values to be produced with each finger and giving the player a natural feel. An air-pressure sensor is also deployed in the bag to provide another element of control while capturing a fundamental element of bagpipe performance. The final product navigates the realm of both musical instrument and toy, allowing the performer to create a novel yet rich performance experience for the audience.
SEM for the 21st Century—Scanning Ion Microscopy (2012)

Abstract This article provides an introduction to scanning ion microscopy, explaining how it overcomes one of the biggest limitations of SEMs, namely the tradeoff between spatial resolution and depth of field, while also providing significantly more surface detail, a wide range of novel and familiar contrast mechanisms, and the potential for new microanalytical techniques that combine nanometer spatial resolution and single monolayer sensitivity. In addition to describing the capabilities of scanning ion microscopes, the article also addresses the issue of sample charging and the potential for physical damage that can result from ion beam irradiation.
Computational Investigation of the Ordered Water System Around Microtubules: Implications for Protein Interactions (2022)

The existence of an exclusion zone in which particles of a colloidal suspension in water are repelled from hydrophilic surfaces has been experimentally demonstrated in numerous studies, especially in the case of Nafion surfaces. Various explanations have been proposed for the origin of this phenomenon, which is not completely understood yet. In particular, the existence of a fourth phase of water has been proposed by G. Pollack and if this theory is proven correct, its implications on our understanding of the properties of water, especially in biological systems, would be profound and could give rise to new medical therapies. Here, a simple approach based on the linearized Poisson-Boltzmann equation is developed in order to study the repulsive forces mediated by ordered water and involving the following interacting biomolecules: 1) microtubule and a tubulin dimer, 2) two tubulin dimers and 3) a tubulin sheet and a tubulin dimer. The choice of microtubules in this study is motivated because they could be a good candidate for the generation of an exclusion zone in the cell and these models could be a starting point for detailed experimental investigations of this phenomenon.
Figure S2 from HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figure S2. PT2385 does not affect HIF-1 complexes.&lt;/p&gt;
Converged Wireless Network Architecture for Homeland Security (2006)

We propose a converged wireless network architecture that allows both emerging IP-based multimedia services and mission-critical services to be supported for public safety end users. The proposed network architecture allows the technology and cost advantages of commercial wireless technologies (3G cellular, IEEE 802.x) to be leveraged while preserving existing investments in land mobile radio networks. The proposed converged network architecture also fulfils the key requirement of enabling interoperable mission-critical communications between public safety end users during times of need - a current limitation of public safety networks.
Reverse β-oxidation pathways for efficient chemical production (2022)

Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.
CORRELATION OF THE ASYMMETRIC AND SYMMETRIC POO<sup>-</sup>FREQUENCIES WITH THE IONIC POTENTIAL OF THE METAL ION IN COMPOUNDS OF ORGANOPHOSPHORUS ACID EXTRACTANTS : A SHORT REVIEW* (1998)

ABSTRACT The correlation between [(VASYM(POO-) - VASYM (POO-)], Av, and the ionic potential of the metal ion in metal compounds of alkylsubstituted diphosphonic acid extractants is reviewed. Similar correlations of the ionic potential of the metal ion with Δv in organosubstituted monophosphate, organosubstituted monophosphonate, carbonate and nitrate compounds have been previously demonstrated. In this paper, we discuss the origin, general validity, and utility of the correlation for organophosphorus compounds. Far-infrared and 54Fe -labeled data were used to identify metal-oxygen stretching vibrations and establish that for some metal ions, e.g., Fe(III) and possibly Th(IV), the metal-oxygen interaction has substantial covalent character. The correlation appears to be valid not only for materials in which the metal-oxygen interaction is predominantly ionic, but also for compounds characterized by a covalent metal-oxygen bonding as well as for polymeric materials, providing the POO- stretching vibrations are assignable. The
An NAK-based hierarchical ARQ scheme for reliable data multicast in integrated communication and broadcast networks (2008)

In this paper we propose a hierarchical architecture of the return channel in ICBN and an NAK-based hierarchical ARQ scheme (H-ARQ). The H-ARQ scheme can alleviate the NAK implosion and balance the retransmission traffic between broadcast and communication networks. The users are divided into regions in the communication network, and each region has a Local Recovery Router (LRR), which cooperates with the Data Broadcast Server (DBS) to decide the retransmission method. The impact of the ARQ scheme on the data broadcast performance is analyzed, and the NAK arrivals in ICBN are modeled and simulated.We also propose an algorithm to optimize the parameters and cost functions in the H-ARQ scheme. At last we give some simulation results to validate the improvement of the H-ARQ scheme running on the hierarchical system architecture.
VISUAL AND QUANTITATIVE MRI EVALUATION OF HIPPOCAMPUS AND FORNIX IN INTRACTABLE COMPLEX PARTIAL EPILEPSY (1996)

Browd, Samuel R.; Gilmore, Robin; Quisling, Ronald; Leonard, Christina M.; Roper, Steven N.; Lucas, Timothy H. Author Information
Neuronal avalanches change from wakefulness to deep sleep - a study of intracranial depth recordings in humans (2013)

Poster presentation: Twenty Second Annual Computational Neuroscience Meeting: CNS*2013. Paris, France. 13-18 July 2013.
Neuronal dynamics differs between wakefulness and sleep stages, so does the cognitive state [1]. In contrast, a single attractor state, called self-organized critical (SOC), has been proposed to govern human brain dynamics for its optimal information coding and processing capabilities [2]. Here we address two open questions: First, does the human brain always operate in this computationally optimal state, even during deep sleep? Second, previous evidence for SOC was based on activity within single brain areas [3-5], however, the interaction between brain areas may be organized differently. Here we asked whether the interaction between brain areas is SOC.
We addressed these questions by characterizing neuronal avalanches [3] - spatiotemporal waves of enhanced activity - from up to 61 local field potential (LFP) channels of intracranial depth recordings (5 human patients, two recording nights each, summing up to ~100h of recordings). The recording contacts were distributed inside the entire brain. Note that ~60 contacts are sufficient to avoid major subsampling effects: Subsampling may heavily distort results in SOC systems due to an insufficient number of sampling sites [5]. In addition, we compared the experimental results to results from a subsampled SOC model of integrate- and fire neurons, which can be tuned to the sub- and supercritical regime.
We show that avalanche distributions closely follow a power law - the hall mark feature of SOC systems. This result held for each vigilance state, and independent of the threshold and the temporal scale. This indicates first that the interaction between brain areas are close to SOC, and second that the dynamics of all cognitive states, from wakefulness to deep sleep are close to SOC. Minor differences between cognitive states are, however, reflected in the avalanche distributions: Slow wave sleep (s3/s4) showed larger and longer neuronal avalanches than REM sleep, while wakefulness showed intermediate ones (p < 0.05). The SOC neuronal model, together with the data, suggested first that these differences are mediated by global but tiny changes in synaptic strength, and second, that the changes with vigilance states reflect small deviations from criticality to the subcritical regime, implying that the human brain does not operate in the SOC state proper - contrary to previous believes. Independent of criticality, the analysis confirmed that slow wave sleep shows increased correlations between cortical areas, and revealed that REM sleep shows more fragmented cortical dynamics.
Role of fingerprint-inspired relief structures in elastomeric slabs for detecting frictional differences arising from surface monolayers (2018)

The perception of fine texture of an object is influenced by its microscopic topography and surface chemistry-i.e., the topmost layer of atoms and molecules responsible for its surface energy, adhesion, and friction generated when probed by a fingertip. Recently, it has been shown that human subjects can discriminate high-energy (i.e., hydrophilic), oxidized silicon from low-energy (i.e., hydrophobic), fluorinated alkylsilane-coated silicon. The basis of discrimination was consistent with differences between stick-slip friction frequencies generated when sliding the fingertip across the two surfaces. One aspect that was not examined was the presence of surface relief structures on the fingertip. Indeed, papillary ridges-fingerprints-may be involved in enhanced discrimination of fine textures arising from surface roughness, but how (or whether) fingerprints may also be involved in the discrimination of surface chemistry-through its effect on friction-is unknown. Here, using a mock finger made from a slab of silicone rubber shows that relief structures amplify differences in stick-slip friction when slid across either a hydrophilic oxide or a hydrophobic monolayer on silicon. We quantify the similarity between the friction traces of the mock fingers sliding across hydrophilic and hydrophobic surfaces under varying velocities and applied masses using a cross-correlation analysis. We then convert the cross-correlational data into convenient "discriminability matrices." These matrices identify combinations of downward forces and sliding velocities that enhance differences in friction between hydrophilic and hydrophobic monolayers. In addition, a computational model of macroscopic, "rate-and-state" friction confirms that frictional differences in chemistry are amplified when elastic slabs bear a patterned interface. This biomimetic approach to engineering sliding interfaces may inform the development of improved electronic skin and haptic devices and may contribute to understanding the role of relief structure in tactile perception.
Method for continuous control of composition and doping of pulsed laser deposited films (2023)

A method for growing a deposit upon a substrate of semiconductor material involves the utilization of pulsed laser deposition techniques within a low-pressure gas environment. The substrate and a target of a first material are positioned within a deposition chamber and a low-pressure gas atmosphere is developed within the chamber. The substrate is then heated, and the target is irradiated, so that atoms of the target material are ablated from the remainder of the target, while atoms of the gas simultaneously are adsorbed on the substrate/film surface. The ablated atoms build up upon the substrate, together with the adsorbed gas atoms to form the thin-film deposit on the substrate. By controlling the pressure of the gas of the chamber atmosphere, the composition of the formed deposit can be controlled, and films of continuously variable composition or doping can be grown from a single target of fixed composition.
MiR-31 promotes mammary stem cell expansion and breast tumorigenesis by suppressing Wnt signaling antagonists (2017)

MicroRNA-mediated post-transcriptional regulation plays key roles in stem cell self-renewal and tumorigenesis. However, the in vivo functions of specific microRNAs in controlling mammary stem cell (MaSC) activity and breast cancer formation remain poorly understood. Here we show that miR-31 is highly expressed in MaSC-enriched mammary basal cell population and in mammary tumors, and is regulated by NF-κB signaling. We demonstrate that miR-31 promotes mammary epithelial proliferation and MaSC expansion at the expense of differentiation in vivo. Loss of miR-31 compromises mammary tumor growth, reduces the number of cancer stem cells, as well as decreases tumor-initiating ability and metastasis to the lung, supporting its pro-oncogenic function. MiR-31 modulates multiple signaling pathways, including Prlr/Stat5, TGFβ and Wnt/β-catenin. Particularly, it activates Wnt/β-catenin signaling by directly targeting Wnt antagonists, including Dkk1. Importantly, Dkk1 overexpression partially rescues miR31-induced mammary defects. Together, these findings identify miR-31 as the key regulator of MaSC activity and breast tumorigenesis.
Nanoanalytical Electron Microscopy Reveals a Sequential Mineralization Process Involving Carbonate-Containing Amorphous Precursors (2016)

A direct observation and an in-depth characterization of the steps by which bone mineral nucleates and grows in the extracellular matrix during the earliest stages of maturation, using relevant biomineralization models as they grow into mature bone mineral, is an important research goal. To better understand the process of bone mineralization in the extracellular matrix, we used nanoanalytical electron microscopy techniques to examine an in vitro model of bone formation. This study demonstrates the presence of three dominant CaP structures in the mineralizing osteoblast cultures: <80 nm dense granules with a low calcium to phosphate ratio (Ca/P) and crystalline domains; calcium phosphate needles emanating from a focus: "needle-like globules" (100-300 nm in diameter) and mature mineral, both with statistically higher Ca/P compared to that of the dense granules. Many of the submicron granules and globules were interspersed around fibrillar structures containing nitrogen, which are most likely the signature of the organic phase. With high spatial resolution electron energy loss spectroscopy (EELS) mapping, spatially resolved maps were acquired showing the distribution of carbonate within each mineral structure. The carbonate was located in the middle of the granules, which suggested the nucleation of the younger mineral starts with a carbonate-containing precursor and that this precursor may act as seed for growth into larger, submicron-sized, needle-like globules of hydroxyapatite with a different stoichiometry. Application of analytical electron microscopy has important implications in deciphering both how normal bone forms and in understanding pathological mineralization.
Activation of Acute Phase Response Factor (APRF)/Stat3 Transcription Factor by Growth Hormone (1995)

The mechanism by which the binding of growth hormone (GH) to its cell surface receptor elicits changes in gene transcription are largely unknown. The transcription factor Stat1/p91 has been shown to be activated by GH. Here we show that acute phase response factor or Stat3 f1p4an antigenically related protein), is also activated by GH. Stat3 has been implicated in the interleukin-6-dependent induction of acute phase response genes. GH promotes in 3T3-F442A fibroblasts the tyrosyl phosphorylation of a protein immunoprecipitated by antibodies to Stat3. This protein co-migrates with a tyrosyl phosphorylated protein from cells treated with leukemia inhibitory factor, a cytokine known to activate Stat3. Tyrosyl phosphorylated Stat3 is also observed in response to interferon-gamma. Stat3 is present in GH-inducible DNA-binding complexes that bind the sis-inducible element in the c-fos promoter and the acute phase response element in the alpha 2-macroglobulin promoter. The ability of GH to activate both Stat1 and Stat3 (i.e. increase their tyrosyl phosphorylation and ability to bind to DNA) suggests that gene regulation by GH involves multiple Stat proteins. Shared transcription factors among hormones and cytokines that activate JAK kinases provide an explanation for shared responses, while the ability of the different ligands to differentially recruit various Stat family members suggests mechanisms by which specificity in gene regulation could be achieved.
Sampling variability between two mid-turbinate swabs of the same patient has implications for influenza viral load monitoring (2014)

Influenza viral load monitoring in nasal swabs could be very valuable as virological endpoints in clinical trials to monitor treatment efficacy, in analogy to HIV, HBV & HCV viral load monitoring. However, the differences between left and right nostrils, as observed in this study, highlight the importance of proper sampling and the need for standardized sampling procedures.
A Hybrid Approach for Multi-User Massive MIMO Sparse Channel Estimation Based on Bayesian Recovery and Hard Thresholding (2015)

We propose an efficient sparse channel estimation algorithm based on the compressed sensing (CS) approach for large scale multi-user (MU) MIMO systems. The proposed scheme is a hybrid one comprising Bayesian and greedy methods. It can improve the estimation performance by incorporating the spatial channel knowledge that the neighboring antennas in an array share the same support. The pilot overhead can be reduced by utilizing the data symbols using a reliability measure for channel estimation. Moreover, the effect of interfering and non-interfering pilots on the estimation performance will be investigated. It will be shown that the proposed hybrid technique performs similar or better than the Bayesian method with substantially reduced complexity.