gebhart/patrepeval huggingface dataset:
Physical studies of DNA premelting equilibria in duplexes with and without homo dA.cntdot.dT tracts: correlations with DNA bending (1990)

We have employed a variety of physical methods to study the equilibrium melting and temperature-dependent conformational dynamics of dA.dT tracts in fractionated synthetic DNA polymers and in well-defined fragments of kinetoplast DNA (kDNA). Using circular dichroism (CD), we have detected a temperature-dependent, "premelting" event in poly(dA).poly(dT) which exhibits a midpoint near 37 degrees C. Significantly, we also detect this CD "premelting" behavior in a fragment of kDNA. By contrast, we do not observe this "premelting" behavior in the temperature-dependent CD spectra of poly[d(AT)].poly[d(AT)], poly(dG).poly(dC), poly[d(GC)].poly[d(GC)], or calf thymus DNA. Thus, poly(dA).poly(dT) and kDNA exhibit a common CD-detected "premelting" event which is absent in the other duplex systems studied in this work. Furthermore, we find that the anomalous electrophoretic retardation of the kDNA fragments we have investigated disappears at temperatures above approximately 37 degrees C. We also observe that the rotational dynamics of poly(dA).poly(dT) and kDNA as assessed by singlet depletion anisotropy decay (SDAD) and electric birefringence decay (EBD) also display a discontinuity near 37 degrees C, which is not observed for the other duplex systems studied. Thus, in the aggregate, our static and dynamic measurements suggest that the homo dA.dT sequence element [common to both poly(dA).poly(dT) and kDNA] is capable of a temperature-dependent equilibrium between at least two helical states in a temperature range well below that required to induce global melting of the host duplex. We suggest that this "preglobal" melting event may correspond to the thermally induced "disruption" of "bent" DNA.
Resource Management in Wireless Networks via Multi-Agent Deep Reinforcement Learning (2021)

We propose a mechanism for distributed resource management and interference mitigation in wireless networks using multi-agent deep reinforcement learning (RL). We equip each transmitter in the network with a deep RL agent that receives delayed observations from its associated users, while also exchanging observations with its neighboring agents, and decides on which user to serve and what transmit power to use at each scheduling interval. Our proposed framework enables agents to make decisions simultaneously and in a distributed manner, unaware of the concurrent decisions of other agents. Moreover, our design of the agents' observation and action spaces is scalable, in the sense that an agent trained on a scenario with a specific number of transmitters and users can be applied to scenarios with different numbers of transmitters and/or users. Simulation results demonstrate the superiority of our proposed approach compared to decentralized baselines in terms of the tradeoff between average and 5 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> percentile user rates, while achieving performance close to, and even in certain cases outperforming, that of a centralized information-theoretic baseline. We also show that our trained agents are robust and maintain their performance gains when experiencing mismatches between train and test deployments.
Archaeal viruses from Yellowstone’s high temperature environments (2005)

In general, our understanding of Archaea lags far behind our knowledge of the other two domains of life—Bacteria and Eukarya. Unlike the other domains of life, very few viruses of Archaea have been characterized. Of the approximately 4000 viruses described to date, only 36 are associated with archaeal hosts--many of these from thermophilic Crenarchaeota. In this work we describe the discovery, isolation and preliminary characterization of viruses and novel virus-like particles isolated directly from diverse thermal environments in Yellowstone National Park.
Spacecraft Thermal Control Management Using Electrochromics (2000)

Abstract : Thin-film multilayer electrochromic coatings for thermal control of spacecraft were designed, built and tested. Design was for a 300 degrees K spacecraft. but coatings would also work well for warmer surface emittance control. Changes in emissivity of dE=0.2, and ratios of on to off emissivity were as high as 3.5. Further work is needed to improve reproducibility of results and long-term stability.
Accumulation of urokinase plasminogen activator (uPA) in the synovial fluid of patients with rheumatoid arthritis (RA) (2011)

<b>Copyright information:</b>Taken from "Urokinase, a constitutive component of the inflamed synovial fluid, induces arthritis"Arthritis Research &amp; Therapy 2002;5(1):R9-R17.Published online 17 Oct 2002PMCID:PMC154426.Copyright © 2003 Jin et al., licensee BioMed Central Ltd. This is an Open Access article: Media for any non-commercial purpose, provided this notice is presented along with the articles original URL. The level of uPA is presented as the mean ± SEM (ng/ml). Significance regarding differences between the groups is indicated.
ChemInform Abstract: Palladium(II) and Platinum(II) Complexes with Chelating Sulfinyl Functions. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Color-Doppler guided high intensity focused ultrasound for hemorrhage control (2005)

To determine efficacy of high intensity focused ultrasound (HIFU) in occlusion of pelvic vessels a 3.2 MHz HIFU transducer was synchronized with color-Doppler ultrasound imaging for real-time visualization of flow within blood vessels during HIFU therapy. HIFU was applied to pig and rabbit pelvic vessels in vivo, both transcutaneously and with skin removed. The in situ focal intensity was 4000 W/cm2 on average. Vessel occlusion was confirmed by color or audio Doppler, and gross and histological observations. In rabbits, five out of 10 femoral arteries (diameter of 2 mm) were occluded after 30–60 s of HIFU application. The average blood flow reduction of 40% was observed in the remaining arteries. In pigs, out of 7 treated superficial femoral arteries (2 mm in diameter), 4 were occluded, one had 80% blood flow reduction, and 2 were patent. In addition, 3 out of 4 superficial femoral arteries, punctured with 18 gauge needle, were occluded after 60–90 s of HIFU application. Larger vessels (diameter of 4 mm) were patent after HIFU treatment. Doppler-guided HIFU has potential application in occlusion of injured pelvic vessels similar to angiographic embolization.
SILICA-CAST REPLICAS FOR MORPHOLOGY STUDIES ON SPRUCE AND BIRCH XYLEM (2004)

Sol-gel mineralization has been used and evaluated as a tool for morphological studies on Picea abies and Betula verrucosa . Wood specimens and a pulped spruce sample were impregnated with a silica sol-gel and subsequently heated (calcined) to condense the surfactant-templated polysilicic acid into structured mesoporous silica. During this calcination process, the wood substance and the surfactant were removed and a silica-cast replica of the sample was obtained. The sol-gel mineralization method produced replicas that were studied by environmental scanning and transmission electron microscopy (ESEM, TEM) without additional sample preparation. The calcination induced some shrinkage above the fiber level, but the ultrastructural dimensions were not discernibly affected. The silica-cast replica method may therefore be a useful tool for studies of the wood ultrastructure, including the cell-wall pore structure (microcavities), down to the nanometer level.
Narrow-Band Channel-Dropping Filter Based on Side-Polished Fiber with Long Interaction Length (2004)

We demonstrate an all-fiber channel-dropping filter comprising a 2 ×2 side-polished fiber coupler with long coupling length and a narrow-band fiber Bragg grating. The side-polished fibers are fabricated on a silicon wafer acting as a polishing substrate while the alignment V-grooves are simultaneously prepared. Two polished fibers with an intracore Bragg grating between them are combined as a grating-frustrated coupler, and a low-loss channel-dropping filter was achieved with the spectral bandwidth less than 2 nm (25 dB), dropping efficiency greater than 98% and channel isolation greater than 25 dB. The filter can be manufactured through a fast and reliable fabrication process.
Synthesis and Biological Evaluation of Some Acyclic Pyridine C-Nucleosides. Part One (1994)

Abstract The reaction between 3-bromo-5-chloromethylpyridine hydrochloride (4) with the mono sodium salt of ethylene glycol was investigated. 3-Bromo-5-(2-hydroxyethoxymethyl)-pyridine (5) was synthesized and converted to the 3-carboxy analogue using butyllithium and CO2. Subsequent treatment with diazomethane and ammonolysis gave the corresponding acyclic nicotinamide C-nucleosides. The latter compounds were converted into the thioamide analogues by reaction with Lawesson's reagent. The pyridine N-oxide derivatives were obtained by treatment with peracetic acid or hydrogen peroxide. All compounds were identified with the aid of 1H- and 13C-NMR and mass spectrometry. The acyclic pyridine C-nucleosides were evaluated against a number of viral strains and cancer cell lines but no significant biological activity was found.
Lubricant replacement in rolling element bearings for weapon surety devices (1996)

Stronglink switches are a weapon surety device that is critical to the nuclear safety theme in modem nuclear weapons. These stronglink switches use rolling element bearings which contain a lubricant consisting of low molecular weight polytetrafluoroethylene (PTFE) fragments. Ozone-depleting solvents are used in both the manufacture and application of this lubricant. An alternate bearing lubrication for stronglink switches is needed that will provide long-term chemical stability, low migration and consistent performance. Candidates that were evaluated include bearings with sputtered MoS{sub 2} on the races and retainers, bearings with TiC-coated balls, and bearings with Si{sub 3}N{sub 4} balls and steel races. These candidates were compared to the lubricants currently used which are bearings lubricated with PTFE fragments of low molecular weight in a fluorocarbon solvent. The candidates were also compared to bearings lubricated with a diester oil which is representative of bearing lubricants used in industrial applications. Evaluation consisted of cycling preloaded bearings and subjecting them to 23 gRMS random vibration. All of the candidates are viable substitutes for low load application where bearing preload is approximately 1 pound. For high load applications where the bearing preload is approximately 10 pounds, bearings with sputtered MoS{sub 2} on the races and retainers appear to be the best substitutes. Bearings with TiC-coated balls also appear to be a viable candidate but these bearings did not perform as well as the sputtered MoS{sub 2}.
Aortic Aneurysm, Thoracoabdominal Aneurysm, Juxtarenal Aneurysm, Fenestrated Endografts, Branched Endografts, and Endovascular Aneurysm Repair (2006)

The development of endovascular devices to treat aneurysms that abut or involve the visceral vessels has occurred in an effort to reduce the significant procedural morbidity and mortality associated with conventional repair. To accomplish this, three systems have been trialed. The first technique was developed to treat juxtarenal aneurysms and involves the placement of customized fenestrations strategically placed within the fabric of the graft. These are aligned with the ostia of the visceral vessels incorporated by the repair and supplemented by the placement of a balloon expandable stent. In a similar fashion, aneurysms that involve the visceral vessels can be treated with a fenestrated graft where the fenestration is reinforced with a nitinol ring. This is then mated with a balloon-expandable stentgraft, allowing the devices to seal at the level of the nitinol ring. An alternative means of incorporating the visceral vessels is to use directional branches where one or more additional limbs (typically 8 mm) are anastomosed to the aortic graft, through which access into the visceral vessel is attained. Mating stentgrafts for the later design can be of a self-expanding or balloon expandable nature. The experience with fenestrated devices is mature and associated with a low perioperative mortality (<2%) without many long-term complications. The treatment of thoracoabdominal aneurysms with branches has provided us with optimism regarding the technique, but results are only short term in nature. Further device development is ongoing and dissemination of this technology is now occurring in Europe, Australia and Canada.
Optimization of a Degradable Polymer–Lipid Nanoparticle for Potent Systemic Delivery of mRNA to the Lung Endothelium and Immune Cells (2018)

mRNA therapeutics hold great potential for treating a variety of diseases through protein-replacement, immunomodulation, and gene editing. However, much like siRNA therapy the majority of progress in mRNA delivery has been confined to the liver. Previously, we demonstrated that poly(β-amino esters), a class of degradable polymers, are capable of systemic mRNA delivery to the lungs in mice when formulated into nanoparticles with poly(ethylene glycol)-lipid conjugates. Using experimental design, a statistical approach to optimization that reduces experimental burden, we demonstrate herein that these degradable polymer-lipid nanoparticles can be optimized in terms of polymer synthesis and nanoparticle formulation to achieve a multiple order-of-magnitude increase in potency. Furthermore, using genetically engineered Cre reporter mice, we demonstrate that mRNA is functionally delivered to both the lung endothelium and pulmonary immune cells, expanding the potential utility of these nanoparticles.
Protein Folding and the IBM BlueGene Supercomputer (2002)

Understanding how proteins fold is an important step in uncovering the mysteries of protein function. To date, the computational resources needed to simulate even the shortest and simplest protein folds have been astronomical. Simulation of larger and more complex folds has been prohibitively expensive. In 1999, IBM announced the start of an effort to build a supercomputer, the BlueGene, to be applied to biomolecular problems such as protein folding. This paper provides an overview of the problem of protein folding, a description of IBM’s BlueGene project, and what we may hope to gain once the machine is fully operational. 1
[Endothelin receptor antagonist]. (2008)

Pulmonary arterial hypertension(PAH) is an uncommon disease characterised by a progressive increase in pulmonary vascular resistance. An imbalance between vasoconstrictor/vasodilator activities could be responsible for altered pulmonary vascular tone and structure. In PAH patients, endothelin are increased. Restoration of this imbalance by targeted therapies such as endothelin receptor antagonists should further improve treatment options for the management of PAH. Current treatment algorithms for PAH recommend bosentan as first-line treatment for PAH in functional class III. Recent many trials suggested that endothelin receptor antagonist, bosentan, caused good results in idiopathic PAH and PAH associated with chronic thromboembolism, collagen diseases, and congenital heart diseases.
High-Speed Optical Vector Modulation for Coherent Transmission Systems (2009)

We reviewed recent results in high-speed optical vector modulation, where inphase and quadrature
A catalytic enantioselective stereodivergent aldol reaction (2023)

The aldol reaction is among the most powerful and strategically important carbon-carbon bond-forming transformations in organic chemistry. The importance of the aldol reaction in constructing chiral building blocks for complex small-molecule synthesis has spurred continuous efforts toward the development of direct catalytic variants. The realization of a general catalytic aldol reaction with control over both the relative and absolute configurations of the newly formed stereogenic centers has been a longstanding goal in the field. Here, we report a decarboxylative aldol reaction that provides access to all four possible stereoisomers of the aldol product in one step from identical reactants. The mild reaction can be carried out on a large scale in an open flask, and generates CO<sub>2</sub> as the only by-product. The method tolerates a broad substrate scope and generates chiral β-hydroxy thioester products with substantial downstream utility.
Streaked laser absorption measurements of density and temperature profiles in a high density Z pinch (1995)

A nonresonant laser absorption technique is described for studying the density and temperature profiles in a high density z-pinch discharge. A long pulse (700-ns) dye laser backlights the pinch and a streak camera records the transmitted laser intensity. Spatially and temporally resolved absorption coefficients are inferred from the fractional transmission through the plasma. The measured values are related to plasma density and temperature profiles using theoretical calculated absorption coefficients and equations of state. The results demonstrate the fine spatial resolution that can be obtained with this technique, reveal a complex radial structure in z-pinch discharges not observable in emission light streak photographs, and establish the practicality of using the technique to evaluate and benchmark theoretical model predictions.
A de novo redesign of the WW domain (2003)

We have used a sequence prediction algorithm and a novel sampling method to design protein sequences for the WW domain, a small beta-sheet motif. The procedure, referred to as SPANS, designs sequences to be compatible with an ensemble of closely related polypeptide backbones, mimicking the inherent flexibility of proteins. Two designed sequences (termed SPANS-WW1 and SPANS-WW2), using only naturally occurring L-amino acids, were selected for study and the corresponding polypeptides were prepared in Escherichia coli. Circular dichroism data suggested that both purified polypeptides adopted secondary structure features related to those of the target without the aid of disulfide bridges or bound cofactors. The structure exhibited by SPANS-WW2 melted cooperatively by raising the temperature of the solution. Further analysis of this polypeptide by proton nuclear magnetic resonance spectroscopy demonstrated that at 5 degrees C, it folds into a structure closely resembling a natural WW domain. This achievement constitutes one of a small number of successful de novo protein designs through fully automated computational methods and highlights the feasibility of including backbone flexibility in the design strategy.
Analytical Validation of a Proliferation-Based Molecular Signature Used as a Prognostic Marker in Early Stage Lung Adenocarcinoma (2015)

These studies demonstrate that the gene signature is robust and reproducible, making it suitable for use in a clinical setting.
Nano Recording and Readout on Optical Disk (2006)

Nano recording and readout on optical disk are investigated by a novel characterization method with ultrahigh resolution. Optical and thermal mechanisms of nano recording and readout on phase-change disk are discussed and proposed
Effects of nicotinamide mononucleotide on older patients with diabetes and impaired physical performance: A prospective, placebo‐controlled, double‐blind study (2022)

In older male patients with diabetes and impaired physical performance, NMN supplementation for 24 weeks was safe, but did not improve grip strength and walking speed. Geriatr Gerontol Int 2023; 23: 38-43.
Throughput increase by adjustment of the BARC drying time with coat track process (2005)

Throughput of a coater module within the coater track is related to the solvent evaporation rate from the material that is being coated. Evaporation rate is controlled by the spin dynamics of the wafer and airflow dynamics over the wafer. Balancing these effects is the key to achieving very uniform coatings across a flat unpatterned wafer. As today’s coat tracks are being pushed to higher throughputs to match the scanner, the coat module throughput must be increased as well. For chemical manufacturers the evaporation rate of the material depends on the solvent used. One measure of relative evaporation rates is to compare flash points of a solvent. The lower the flash point, the quicker the solvent will evaporate. It is possible to formulate products with these volatile solvents although at a price. Shipping and manufacturing a more flammable product increase chances of fire, thereby increasing insurance premiums. Also, the end user of these chemicals will have to take extra precautions in the fab and in storage of these more flammable chemicals. An alternative coat process is possible which would allow higher throughput in a distinct coat module without sacrificing safety. A tradeoff is required for this process, that being a more complicated coat process and a higher viscosity chemical. The coat process uses the fact that evaporation rate depends on the spin dynamics of the wafer by utilizing a series of spin speeds that first would set the thickness of the material followed by a high spin speed to remove the residual solvent. This new process can yield a throughput of over 150 wafers per hour (wph) given two coat modules. The thickness uniformity of less than 2 nm (3 sigma) is still excellent, while drying times are shorter than 10 seconds to achieve the 150 wph throughput targets.
Toward Real-World Voice Disorder Classification (2021)

Objective: Voice disorders significantly compromise individuals' ability to speak in their daily lives. Without early diagnosis and treatment, these disorders may deteriorate drastically. Thus, automatic classification systems at home are desirable for people who are inaccessible to clinical disease assessments. However, the performance of such systems may be weakened due to the constrained resources and domain mismatch between the clinical data and noisy real-world data. Methods: This study develops a compact and domain-robust voice disorder classification system to identify the utterances of health, neoplasm, and benign structural diseases. Our proposed system utilizes a feature extractor model composed of factorized convolutional neural networks and subsequently deploys domain adversarial training to reconcile the domain mismatch by extracting domain invariant features. Results: The results show that the unweighted average recall in the noisy real-world domain improved by 13% and remained at 80% in the clinic domain with only slight degradation. The domain mismatch was effectively eliminated. Moreover, the proposed system reduced the usage of both memory and computation by over 73.9%. Conclusion: By deploying factorized convolutional neural networks and domain adversarial training, domain-invariant features can be derived for voice disorder classification with limited resources. The promising results confirm that the proposed system can significantly reduce resource consumption and improve classification accuracy by considering the domain mismatch. Significance: To the best of our knowledge, this is the first study that jointly considers real-world model compression and noise-robustness issues in voice disorder classification. The proposed system is intended for application to embedded systems with limited resources.
Supplementary Methods from Small-Molecule Inhibitors of USP1 Target ID1 Degradation in Leukemic Cells (2023)

&lt;p&gt;PDF - 86KB, Additional supplementary methods.&lt;/p&gt;