gebhart/patrepeval huggingface dataset:
A high performance catalyst of shape-specific ruthenium nanoparticles for production of primary amines by reductive amination of carbonyl compounds (2018)

The creation of metal catalysts with highly active surfaces is pivotal to meeting the strong economic demand of the chemical industry. Specific flat-shaped pristine fcc ruthenium nanoparticles having a large fraction of atomically active {111} facets exposed on their flat surfaces have been developed that act as a highly selective and reusable heterogeneous catalyst for the production of various primary amines at exceedingly high reaction rates by the low temperature reductive amination of carbonyl compounds. The high performance of the catalyst is attributed to the large fraction of metallic Ru serving as active sites with weak electron donating ability that prevail on the surface exposed {111} facets of flat-shaped fcc Ru nanoparticles. This catalyst exhibits a highest turnover frequency (TOF) of <i>ca.</i> 1850 h<sup>-1</sup> for a model reductive amination of biomass derived furfural to furfurylamine and provides a reaction rate approximately six times higher than that of an efficient and selective support catalyst of Ru-deposited Nb<sub>2</sub>O<sub>5</sub> (TOF: <i>ca.</i> 310 h<sup>-1</sup>).
Decreased Pulmonary Radiation Resistance of Manganese Superoxide Dismutase (MnSOD)-Deficient Mice is Corrected by Human Manganese Superoxide Dismutase-Plasmid/Liposome (SOD2-PL) Intratracheal Gene Therapy (2000)

The pulmonary ionizing radiation sensitivity of C57BL/6 Sod2(+/-) mice heterozygous for MnSOD deficiency was compared to that Sod2(+/+) control littermates. Embryo fibroblast cell lines from Sod2(-/-) (neonatal lethal) or Sod2(+/-) mice produced less biochemically active MnSOD and demonstrated a significantly greater in vitro radiosensitivity. No G(2)/M-phase cell cycle arrest after 5 Gy was observed in Sod2(-/-) cells compared to the Sod2(+/-) or Sod2(+/+) lines. Subclonal Sod2(-/-) or Sod2(+/-) embryo fibroblast lines expressing the human SOD2 transgene showed increased biochemical activity of MnSOD and radioresistance. Sod2(+/-) mice receiving 18 Gy whole-lung irradiation died sooner and had an increased percentage of lung with organizing alveolitis between 100 and 160 days compared to Sod2(+/+) wild-type littermates. Both Sod2(+/-) and Sod2(+/+) littermates injected intratracheally with human manganese superoxide dismutase-plasmid/liposome (SOD2-PL) complex 24 h prior to whole-lung irradiation showed decreased DNA strand breaks and improved survival with decreased organizing alveolitis. Thus underexpression of MnSOD in the lungs of heterozygous Sod2(+/-) knockout mice is associated with increased pulmonary radiation sensitivity and parallels increased radiation sensitivity of embryo fibroblast cell lines in vitro. The restoration of cellular radioresistance in vitro and in lungs in vivo by SOD2-PL transgene expression supports a potential role for SOD2-PL gene therapy in organ-specific radioprotection.
Genetic approaches to disease and regeneration (2004)

Cardiovascular disease is largely a consequence of coronary artery blockage through excessive proliferation of smooth muscle cells. It in turn leads to myocardial infarction and permanent and functionally devastating tissue damage to the heart wall. Our studies have revealed that elastin is a primary player in maintaining vascular smooth muscle cells in their dormant state and thus may be a useful therapeutic in vascular disease. By studying zebrafish, which unlike humans, can repair damage to heart muscle, we have begun to uncover some of the genes that seem necessary to undertake the de-differentiation steps that currently fail and prevent the formation of new proliferating cardiomyocytes at the site of damage in a mammalian heart.
Reduced Exercise Capacity, Chronotropic Incompetence, and Early Systemic Inflammation in Cardiopulmonary Phenotype Long Coronavirus Disease 2019 (2023)

Cardiopulmonary symptoms >1 year after COVID-19 were associated with reduced exercise capacity, which was associated with earlier inflammatory markers. Chronotropic incompetence may explain exercise intolerance among some with "long COVID."
Emergence of IFN-alpha TRAIL-expressing killer pDCs (IKpDCs) as a consequence of a crosstalk with NK cells. Influence of HIV-1 infection and implication of HMGB1 (2012)

Background Plasmacytoid dendritic cells (pDCs) mainly contribute to antiviral immunity through recognition of viral components resulting in the production of type-I interferon (IFN), a powerful innate antiviral cytokine. IFN-alpha production by pDCs is promoted by a cross-talk with NK cells, that triggers in return the cytotoxicity of NK cells. Given the essential role of pDCs and NK cells in viral control, we addressed the question of the impact of HIV on NK-pDC cross-talk, and the consequences on viral innate immunity.
Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector (2019)

Borrelia burgdorferi, the causative agent of Lyme disease in humans, is maintained in a complex biphasic life cycle, which alternates between tick and vertebrate hosts. To successfully survive and complete its enzootic cycle, B. burgdorferi adapts to diverse hosts by regulating genes required for survival in specific environments. Here we describe the first ever use of transposon insertion sequencing (Tn-seq) to identify genes required for B. burgdorferi survival in its tick host. We found that insertions into 46 genes resulted in a complete loss of recovery of mutants from larval Ixodes ticks. Insertions in an additional 56 genes resulted in a >90% decrease in fitness. The screen identified both previously known and new genes important for larval tick survival. Almost half of the genes required for survival in the tick encode proteins of unknown function, while a significant portion (over 20%) encode membrane-associated proteins or lipoproteins. We validated the results of the screen for five Tn mutants by performing individual competition assays using mutant and complemented strains. To better understand the role of one of these genes in tick survival, we conducted mechanistic studies of bb0017, a gene previously shown to be required for resistance against oxidative stress. In this study we show that BB0017 affects the regulation of key borrelial virulence determinants. The application of Tn-seq to in vivo screening of B. burgdorferi in its natural vector is a powerful tool that can be used to address many different aspects of the host pathogen interaction.
Synthesis, characterization, and oxygenation of bis-fenced porphyrinato iron(II) and cobalt(II) complexes (1990)

The both-faces-hindered and highly symmetric complexes 5,10,15,20-tetra(2′,6′-dipivaloyl-oxyphenyl)porphyrinato-iron(II) and -cobalt(II), which have no amide residues but ester ones in the fence groups, have been synthesized. The iron(II) complex formed stable and reversible dioxygen adducts in toluene at 25 °C. The half-life for irreversible oxidation is longer than 1 d. The ligation properties for this complex with imidazole derivatives or dioxygen have been determined and compared to those of one-face-hindered porphyrinatoiron complexes. The bulky groups on both sides of the macrocycle decrease the binding constants for imidazole and for dioxygen. The binding characteristics of an imidazole derivative, which is sterically restrained by the bulky groups, have been clarified by Mössbauer and i.r. spectroscopic measurements. A kinetic study of dioxygen association and dissociation suggests that the low oxygen affinity is brought about primarily by the high rate of ligand dissociation.
Restoring the function of the glutamate-nitric oxide –cGMP pathway by treatments acting on different brain targets restores cognitive function in rats with minimal hepatic encephalopathy (2015)

Chronic liver disease (e.g. cirrhosis) affects brain function. There is a high incidence of mild cognitive impairment and psychomotor slowing in patients with cirrhosis. This condition, known as minimal hepatic encephalopathy (MHE) affects more than 2 million people in the European Union and has serious health, social and economic consequences. There are no effective treatments for MHE. Rat models of MHE reproduce cognitive and motor alterations seen in patients, showing reduced performance in different types of cognitive tests, including learning a conditional discrimination task in a Y maze. We have shown that reduced ability to learn the Y maze task is due to reduced function of the glutamate-nitric oxide (NO)-cGMP pathway in cerebellum, assessed in vivo by microdialysis. This results in reduced formation of cGMP in response to activation of NMDA receptors and impairment of learning ability. We have found that both hyperammonemia and neuroinflammation contribute to impair this pathway. The effect is mediated by enhanced tonic activation of NMDA and GABAA receptors and of MAP-kinase p38. Based on this mechanistic studies, we have designed and tested new therapeutic strategies acting on specific targets in the brain, which have successfully restored the function of the glutamate-NO-cGMP pathway in vivo and learning ability in rats with MHE. This can be achieved by therapeutic treatments using: a) phosphodiesterase 5 inhibitors (sildenafil, zaprinast), that increase cGMP levels by reducing its degradation b) extracellular cGMP c) antagonists of type A GABA receptors (bicuculline) d) neurosteroids that modulate GABAergic tone (pregnenolone sulfate) e) inhibitors of cyclooxygenase (ibuprofen) which reduce neuroinflammation f) inhibitors of MAP- kinase p38 (SB239063), that reduce microglial activation and neuroinflammation g) Translation of some of these treatments to clinical practice would improve cognitive function, quality of life and life span of patients with cirrhosis and MHE and reduce health systems costs.
Phenylalanine Effects on Brain Function in Adult Phenylketonuria (2020)

Our study provides strong evidence for a correlation between phenylalanine levels and clinical, neuropsychological, neurophysiologic, biochemical, and imaging alterations in adult patients with phenylketonuria.
Improved Face Model Fitting on Video Sequences (2007)

Active Appearance Models (AAMs) represent the shape and appearance of an object via two low-dimensional subspaces, one for shape and one for appearance.AAMs for facial images are currently receiving considerable attention from the computer vision community.However, most existing work focuses on fitting AAMs to a single image.For many applications, effectively fitting an AAM to video sequences is of critical importance and challenging, especially considering the varying quality of real-world video content.This paper proposes a hybrid model to address this problem.Both a generic AAM and a subject-specific model are employed simultaneously in the proposed fitting scheme.Experimental results from outdoor surveillance video sequences demonstrate the improved image registration across video frames and faster fitting convergence.
SuFEx Activation with Ca(NTf2)2: A Unified Strategy to Access Sulfamides, Sulfamates and Sulfonamides from S(VI) Fluorides (2020)

&lt;p&gt;&lt;br&gt;&lt;/p&gt; &lt;p&gt;A method to activate sulfamoyl fluorides, fluorosulfates, and sulfonyl fluorides with calcium triflimide, and DABCO for SuFEx with amines is described. The reaction was applied to a diverse set of sulfamides, sulfamates, and sulfonamides at room temperature under mild conditions. Additionally, we highlight the application of this transformation to parallel medicinal chemistry to generate a broad array of nitrogen-based S(VI) compounds. &lt;/p&gt;
Perspectives on influenza evolution and the role of research (2010)

Influenza is a highly contagious respiratory pathogen that continues to evolve and threaten both veterinary and human public health. Influenza A viruses are continually undergoing molecular changes through mutations, reassortment, and, in rare instances, recombination. While they generally cause benign enteric infection in their natural reservoir of wild aquatic birds, they can cause catastrophic and potentially lethal disease outbreaks in humans, domestic poultry, and pigs when they cross the host species barrier. The continuing circulation of highly pathogenic (HP) H5N1 influenza viruses in domestic poultry in parts of Eurasia and the emergence and global spread of pandemic H1N1 2009 are current examples of influenza evolution. The spread of both HP H5N1 and pandemic H1N1 to multiple hosts emphasizes the potential for continued evolution. In this review, we discuss the current understanding of influenza A virus structure and strategies of variation, with a specific focus on the HP H5N1 and pandemic H1N1 influenza viruses. Additionally, we attempt to identify the gaps in our knowledge of H5N1 and pandemic H1N1 influenza viruses. These gaps include (i) an understanding of the molecular determinants of influenza virus and the host that permit efficient transmissibility and pandemic potential, (ii) the urgent need for prospective surveillance in apparently healthy swine, (iii) the molecular determinants of high pathogenicity in poultry, pigs, and people, (iv) the genetic basis of host susceptibility, (v) antigenic variability, (vi) the use of vaccine to control influenza, (vii) the role of wild birds as the reservoir of highly pathogenic avian influenza, (viii) the problems with vaccines, (ix) seasonality, (x) co-infections, and (xi) anti-influenza drug resistance. Our failure to eradicate HP H5N1 globally and to explain why H5N1 does not transmit efficiently in humans while an H1N1 pandemic virus of swine origin spread globally in months are key examples that emphasize the critical need to bridge these knowledge gaps. Future directions in influenza research that will help us resolve each of the above-mentioned knowledge gaps include complete genomic and proteomic analysis of both the virus and the host with the prospect of designing new control strategies and the development of genetically resistant hosts.
Catecholamine‐associated changes in the state of leukocyte adhesiveness/aggregation in the peripheral blood (1993)

Abstract This article further explores the effects of stress on leukocyte adhesiveness. The concentration of plasma catecholamines as well as the LAA values were examined in 16 volunteers during a cold pressor test and in 15 volunteers following physical activity. A significant correlation between LAA values and plasma norepinephrine, dopamine and epinephrine was noted. In addition, experimental studies of anaesthetized dogs infused with dopamine and norepinephrine showed increased LAA values, and an insulin‐induced hypoglycaemic animal model for adrenergic stress indicated an inverse correlation between serum glucose concentrations and LAA values. Finally, in the presence of an MAO inhibitor, norepinephrine significantly increased the state of LAA in vitro. Thus, there exists an association between adrenergic stress and the appearance of sticky leukocytes in the circulating pool. We assume that, at least in part, this stickiness results from a direct effect of the catecholamines on the adhesive properties of the cells. Other factors might be related to the decreased endothelial adhesiveness towards the white blood cells as well as the concomitant effect of other mediators released during stress. This study also supports our notion that the state of LAA in the peripheral blood can serve as a useful stress marker.
Signal-to-Noise Ratio Enhancement in Cardiac Pulse Measurements Using Multitap CMOS Image Sensors With In-Pixel Temporal Redundant Samplings (2021)

Insufficient signal-to-noise ratio (SNR) limits the quality of cardiac pulses measured by multitap CMOS image sensors (CISs). We present an in-pixel temporal redundant samplings (TRS) method for enhancing the SNR through sampling the charges originated by one individual optical scene into the multiple storage taps in turn with the identical time window, enabling magnification of the image signal in shot noise domain. Modeling indicates that the linear SNR increases with a factor square root of TRS sampling number, which is also verified by characterization results utilizing a four-tap CIS. Application results show that the high-frequency (HF) noise components observed in the measured cardiac pulses can be attenuated by 67.9%, 48%, and 53.6% with heart rate detection accuracies up to 99.7%, 99.3%, and 98.7% by applying TRS modes under given conditions of stable ambient, background light (BGL) variation, and motion disturbance, respectively. Moreover, the proposed method is as well foreseeable to be extended to other multitap-involved imaging applications.
Issues in handling impression materials. (2002)

Implant restorations require extreme accuracy since the implants are rigidly fixed. Although impression materials can be highly accurate, small inaccuracies are acceptable because the periodontal ligament allows for tooth movement. This luxury is not available with implants. A problem is the rotation of direct impression copings and distortion of interabutment positions in the master cast. Wee investigated the amount of torque required to displace a coping in eight impression material groups and the positional accuracy of the materials. The initial examination of torque narrowed the acceptable materials to a medium viscosity polyether, a high viscosity addition silicone, and a medium viscosity polysulfide-condensation silicones were eliminated. The results showed that the polyether and addition silicone produced casts with minimal distortion. Finally, it always is prudent to read the manufacturer's recommendations for use of impression materials. Catalyst-to-base ratios vary, as do working and setting times, depending on exact compositions. Impression materials also have various degrees of compatibility with stone, particularly the hydrocolloids, and it is advisable to use the recommended stone. Adhesives should be applied at least 15 minutes prior to loading the impression material. If at all possible, use of a rigid tray is recommended and impressions should be poured in the dental office; this minimizes the error produced at the beginning of the fabrication process. Elimination of errors early in fabrication of a prosthesis help prevent their magnification and result in a better-fitting restoration, requiring minimal adjustment in the end.
TensorFlow Eager: A Multi-Stage, Python-Embedded DSL for Machine Learning (2019)

TensorFlow Eager is a multi-stage, Python-embedded domain-specific language for hardware-accelerated machine learning, suitable for both interactive research and production. TensorFlow, which TensorFlow Eager extends, requires users to represent computations as dataflow graphs; this permits compiler optimizations and simplifies deployment but hinders rapid prototyping and run-time dynamism. TensorFlow Eager eliminates these usability costs without sacrificing the benefits furnished by graphs: It provides an imperative front-end to TensorFlow that executes operations immediately and a JIT tracer that translates Python functions composed of TensorFlow operations into executable dataflow graphs. TensorFlow Eager thus offers a multi-stage programming model that makes it easy to interpolate between imperative and staged execution in a single package.
Multi-block ADMM Heuristics for Mixed-Binary Optimization on Classical and Quantum Computers (2020)

Solving combinatorial optimization problems on current noisy quantum devices is currently being advocated for (and restricted to) binary polynomial optimization with equality constraints via quantum heuristic approaches. This is achieved using, e.g., the variational quantum eigensolver (VQE) and the quantum approximate optimization algorithm (QAOA). We present a decomposition-based approach to extend the applicability of current approaches to "quadratic plus convex" mixed binary optimization (MBO) problems, so as to solve a broad class of real-world optimization problems. In the MBO framework, we show that the alternating direction method of multipliers (ADMM) can split the MBO into a binary unconstrained problem (that can be solved with quantum algorithms), and continuous constrained convex subproblems (that can be solved cheaply with classical optimization solvers). The validity of the approach is then showcased by numerical results obtained on several optimization problems via simulations with VQE and QAOA on the quantum circuits implemented in Qiskit, an open-source quantum computing software development framework.
Distinguishability and identifiability testing of contact state models (2005)

An important component of compliant motion control is the estimation of contact states during task execution. This paper addresses two fundamental questions that must be answered when formulating mathematical descriptions of contact states: are the contact states distinguishable from each other? and can the unknown or imprecisely known parameters in these descriptions be identified? An analytical method is presented for evaluating the distinguishability and identifiability questions of a set of contact state models described by non-linear algebraic equations. In contrast to existing, on-line numerical techniques, this approach can be used during the design phase of a contact state estimator to select contact models and robot sensors to ensure feasibility of the estimator. The approach is illustrated using contacts between polygonal and polyhedral objects.
Characterization of the DNA repair spore photoproduct lyase enzyme from Clostridium acetobutylicum: A radical-SAM enzyme (2007)

Spore photoproduct lyase (SPL) is a “Radical-SAM” repair enzyme which catalyzes the cleavage of spore photoproduct (SP, 5-thyminyl-5,6-dihydrothymine), a specific lesion found in bacterial spore DNA, to thymine monomers by a free-radical mechanism. The enzyme requires S -adenosyl- l -methionine (SAM) and a [4Fe–4S] cluster for activity. SPL from Bacillus subtilis has been difficult to isolate and characterize due to problems with the solubility and stability of the overexpressed protein in Escherichia coli and the lability of the [Fe–S] cluster, even if the protein was purified under strictly anaerobic conditions. In order to overcome these problems we searched for another SPL enzyme and we found that the recombinant SPL enzyme from Clostridium acetobutylicum , isolated either aerobically or anaerobically from overexpressing E. coli , behaves more stably than the B. subtilis one. We report here a complete spectroscopic and biochemical characterization of this enzyme. In particular we show for the first time that, using HYSCORE spectroscopy, SAM binds to the cluster as observed in the case of other members of the “Radical-SAM” enzyme family such as the activases of pyruvate formate lyase and ribonucleotide reductase.
Nanoscale thin single-crystal silicon and its application to electronics (2004)

We demonstrate a method for achieving thin (tens of nanometers) single-crystal silicon films with electronic-quality bulk and surface properties, atomic-scale surface roughness, and suitable for use in complex multilayered structures. The thin silicon film is achieved by defining thickness through the use of oxidation depth as a reference, transfer of film structure by exfoliation, and chemical-mechanical polishing for selective thin film definition. Such structures are useful in a variety of directions: in electronic devices such as field-effect transistors, in characterization studies such as those utilizing vertical transport using thicknesses of the order of mean free path length, etc. We demonstrate its use in a silicon metal-oxide-semiconductor transistor with two gates, one on each side of the thin silicon film on a planar substrate.