gebhart/patrepeval huggingface dataset:
Biosynthesis of synthons in two-liquid-phase media (2000)

The Pseudomonas oleovorans alkane hydroxylase and xylene oxygenase from Pseudomonas putida are versatile mono-oxygenases for stereo- and regioselective oxidation of aliphatic and aromatic hydrocarbons. Pseudomonas oleovorans and alkanol dehydrogenase deficient mutants of Pseudomonas have previously been used to produce alkanols from various alkanes and optically active epoxides from alkenes. Similarly, P. putida strains have been used to produce aromatic alcohols, aromatic acids, and optically active styrene oxides. A limitation in the use of Pseudomonas strains for bioconversions is that these strains can degrade some of the products formed. To counter this problem, we have constructed Escherichia coli recombinants, which contain the alk genes from the OCT plasmid of P. oleovorans [E. coli HB101 (pGEc47)] and the xylMA genes from the TOL plasmid of P. putida mt-2 [E. coli HB101 (pGB63)], encoding alkane hydroxylase and xylene oxygenase, respectively. Escherichia coli HB101 (pGEc47) was used to produce octanoic acid from n-octane and E. coli HB101 (pBG63) was put to use for the oxidation of styrene to styrene oxide in two-liquid phase biocatalysis at high cell densities. The alk(+) recombinant strain E. coli HB101 (pGEc47) was grown to 40 g/L cell dry mass in the presence of n-octane, which was converted to octanoic acid by the alkane oxidation system, the product accumulating in the aqueous phase. The xyl(+) recombinant E. coli HB101 (pBG63) was grown to a cell density of 26 g/L cell dry mass in the presence of around 7% (v/v) n-dodecane, which contained 2% (v/v) styrene. The recombinant E. coli (xyl(+)) converted styrene to (S)-(+)-styrene oxide at high enantiomeric excess (94% ee) and this compound partitioned almost exclusively into the organic phase. Using these high-cell-density two-liquid-phase cultures, the products accumulated rapidly, yielding high concentrations of products (50 mM octanoic acid and 90 mM styrene oxide) in the respective phases.
Mutated Toll-like receptor 9 increases Alzheimer’s disease risk by compromising innate immunity protection (2023)

The development of Alzheimer's disease (AD) involves central and peripheral immune deregulation. Gene identification and studies of AD genetic variants of peripheral immune components may aid understanding of peripheral-central immune crosstalk and facilitate new opportunities for therapeutic intervention. In this study, we have identified in a Flanders-Belgian family a novel variant p.E317D in the Toll-like receptor 9 gene (TLR9), co-segregating with EOAD in an autosomal dominant manner. In human, TLR9 is an essential innate and adaptive immune component predominantly expressed in peripheral immune cells. The p.E317D variant caused 50% reduction in TLR9 activation in the NF-κB luciferase assay suggesting that p.E317D is a loss-of-function mutation. Cytokine profiling of human PBMCs upon TLR9 activation revealed a predominantly anti-inflammatory response in contrast to the inflammatory responses from TLR7/8 activation. The cytokines released upon TLR9 activation suppressed inflammation and promoted phagocytosis of Aβ<sub>42</sub> oligomers in human iPSC-derived microglia. Transcriptome analysis identified upregulation of AXL, RUBICON and associated signaling pathways, which may underline the effects of TLR9 signaling-induced cytokines in regulating the inflammatory status and phagocytic property of microglia. Our data suggest a protective role of TLR9 signaling in AD pathogenesis, and we propose that TLR9 loss-of-function may disrupt a peripheral-central immune crosstalk that promotes dampening of inflammation and clearance of toxic protein species, leading to the build-up of neuroinflammation and pathogenic protein aggregates in AD development.
The structure of hidamicin, a polyether antibiotic. (1989)

Hidamicin, a member of polyether antibiotic,1} was found in the fermentation broth of an actinomycetes, MI429-38F1, which had been isolated from a soil sample collected at Takayama-city, Gifu Prefecture, Japan. The strain MI429-38F1 was shown to be closely related to Actinomadura verrucososporcP by taxonomic studies.
Design, Synthesis, and Pharmacological Evaluation ofN-Acylhydrazones and Novel Conformationally Constrained Compounds as Selective and Potent Orally Active Phosphodiesterase-4 Inhibitors (2012)

Among a small series of tested N-acylhydrazones (NAHs), the compound 8a was selected as a selective submicromolar phosphodiesterase-4 (PDE4) inhibitor associated with anti-TNF-α properties measured both in vitro and in vivo. The recognition pattern of compound 8a was elucidated through molecular modeling studies based on the knowledge of the 3D-structure of zardaverine, a PDE4 inhibitor resembling the structure of 8a, cocrystallized with the PDE4. Based on further conformational analysis dealing with N-methyl-NAHs, a quinazoline derivative (19) was designed as a conformationally constrained NAH analogue and showed similar in vitro pharmacological profile, compared with 8a. In addition 19 was found active when tested orally in LPS-evoked airway hyperreactivity and fully confirmed the working hypothesis supporting this work.
Physically-based simulation of twilight phenomena (2005)

We present a physically-based approach to compute the colors of the sky during the twilight period before sunrise and after sunset. The simulation is based on the theory of light scattering by small particles. A realistic atmosphere model is assumed, consisting of air molecules, aerosols, and water. Air density, aerosols, and relative humidity vary with altitude. In addition, the aerosol component varies in composition and particle-size distribution. This allows us to realistically simulate twilight phenomena for a wide range of different climate conditions. Besides considering multiple Rayleigh and Mie scattering, we take into account wavelength-dependent refraction of direct sunlight as well as the shadow of the Earth. Incorporating several optimizations into the radiative transfer simulation, a photo-realistic hemispherical twilight sky is computed in less than two hours on a conventional PC. The resulting radiometric data is useful, for instance, for high-dynamic range environment mapping, outdoor global illumination calculations, mesopic vision research and optical aerosol load probing.
Control of Pollution in Singapore (1993)

Intensive industrialization efforts since the 1960s and rapid urbanisation have transformed Singapore into a highly urbanised and compact society. Not surprisingly, pollution control in Singapore is capable of centralised control and stringent enforcement in a way which may not perhaps be possible in other societies with much larger lands and with a much more dispersed population.
Deep Multiview Collaborative Clustering (2021)

The clustering methods have absorbed even-increasing attention in machine learning and computer vision communities in recent years. In this article, we focus on the real-world applications where a sample can be represented by multiple views. Traditional methods learn a common latent space for multiview samples without considering the diversity of multiview representations and use K -means to obtain the final results, which are time and space consuming. On the contrary, we propose a novel end-to-end deep multiview clustering model with collaborative learning to predict the clustering results directly. Specifically, multiple autoencoder networks are utilized to embed multi-view data into various latent spaces and a heterogeneous graph learning module is employed to fuse the latent representations adaptively, which can learn specific weights for different views of each sample. In addition, intraview collaborative learning is framed to optimize each single-view clustering task and provide more discriminative latent representations. Simultaneously, interview collaborative learning is employed to obtain complementary information and promote consistent cluster structure for a better clustering solution. Experimental results on several datasets show that our method significantly outperforms several state-of-the-art clustering approaches.
Diabetes induces stable intrinsic changes to myeloid cells that contribute to chronic inflammation during wound healing in mice (2013)

Acute inflammation in response to injury is a tightly regulated process by which subsets of leukocytes are recruited to the injured tissue and undergo behavioural changes that are essential for effective tissue repair and regeneration. The diabetic wound environment is characterised by excessive and prolonged inflammation that is linked to poor progression of healing and, in humans, the development of diabetic foot ulcers. However, the underlying mechanisms contributing to excessive inflammation remain poorly understood. Here we show in a murine model that the diabetic environment induces stable intrinsic changes in haematopoietic cells. These changes lead to a hyper-responsive phenotype to both pro-inflammatory and anti-inflammatory stimuli, producing extreme M1 and M2 polarised cells. During early wound healing, myeloid cells in diabetic mice show hyperpolarisation towards both M1 and M2 phenotypes, whereas, at late stages of healing, when non-diabetic macrophages have transitioned to an M2 phenotype, diabetic wound macrophages continue to display an M1 phenotype. Intriguingly, we show that this population predominantly consists of Gr-1(+) CD11b(+) CD14(+) cells that have been previously reported as 'inflammatory macrophages' recruited to injured tissue in the early stages of wound healing. Finally, we show that this phenomenon is directly relevant to human diabetic ulcers, for which M2 polarisation predicts healing outcome. Thus, treatments focused at targeting this inflammatory cell subset could prove beneficial for pathological tissue repair.
The convex hull of the AC power flow equations in rectangular coordinates (2016)

Obtaining the convex hull of the alternating current (AC) power flow equations is largely beneficial in the convexification of the optimization problems in power systems where the AC power flow constraints are taken into account. In this paper, the AC power flow formulation in rectangular coordinates which is a non-convex quadratic equality is equivalently decomposed into four quadratic inequalities whose coefficient matrices are positive semidefinite. Two of the quadratic inequalities are convex while the other two are not. The proposed decomposition facilitates the convexification of the power flow equations much. A convex hull formulation is proposed for the resulting non-convex quadratic inequalities. This formulation is applied to study the convex hull of the AC power flow.
CNPUF: A Carbon Nanotube-based Physically Unclonable Function for secure low-energy hardware design (2014)

Physically Unclonable Functions (PUFs) are used to provide identification, authentication and secret key generation based on unique and unpredictable physical characteristics. Carbon Nanotube Field Effect Transistors (CNFETs) were shown to have excellent electrical and unique physical characteristics and are promising candidates to replace silicon transistors in future Very Large Scale Integration (VLSI) designs. We present Carbon Nanotube PUF (CNPUF), the first PUF design that takes advantage of unique CNFET characteristics. CNPUF achieves higher reliability against environmental variations and increased resistance against modeling attacks. Furthermore, CNPUF has a considerable power and energy reduction in comparison to previous ultra-low power PUF designs of 89.6% and 98%, respectively. Additionally, CNPUF allows power-security tradeoff.
An Assessment of Blood Vessel Remodeling of Nanofibrous Poly(ε-Caprolactone) Vascular Grafts in a Rat Animal Model (2023)

The development of an ideal vascular prosthesis represents an important challenge in terms of the treatment of cardiovascular diseases with respect to which new materials are being considered that have produced promising results following testing in animal models. This study focuses on nanofibrous polycaprolactone-based grafts assessed by means of histological techniques 10 days and 6 months following suturing as a replacement for the rat aorta. A novel stereological approach for the assessment of cellular distribution within the graft thickness was developed. The cellularization of the thickness of the graft was found to be homogeneous after 10 days and to have changed after 6 months, at which time the majority of cells was discovered in the inner layer where the regeneration of the vessel wall was found to have occurred. Six months following implantation, the endothelialization of the graft lumen was complete, and no <i>vasa vasorum</i> were found to be present. Newly formed tissue resembling native elastic arteries with concentric layers composed of smooth muscle cells, collagen, and elastin was found in the implanted polycaprolactone-based grafts. Moreover, the inner layer of the graft was seen to have developed structural similarities to the regular aortic wall. The grafts appeared to be well tolerated, and no severe adverse reaction was recorded with the exception of one case of cartilaginous metaplasia close to the junctional suture.
Finding Frequent Patterns in a Large Sparse Graph (2004)

This paper presents two algorithms based on the horizontal and vertical pattern discovery paradigms that find the connected subgraphs that have a sufficient number of edge-disjoint embeddings in a single large undirected labeled sparse graph. These algorithms use three different methods to determine the number of the edge-disjoint embeddings of a subgraph that are based on approximate and exact maximum independent set computations and use it to prune infrequent subgraphs. Experimental evaluation on real datasets from various domains show that both algorithms achieve good performance, scale well to sparse input graphs with more than 100,000 vertices, and significantly outperform a previously developed algorithm.
Development of a large-area, low-cost solar water-heating system for South Africa with a high thermal energy collection capacity (2019)

A low-cost heat-exchanger system that can be used in high-pressure/low-pressure isolated solar water-heating systems in South Africa was developed for household applications. The combination of a copper coil and electrical heater allowed for isolation of the high-pressure and low-pressure sections of the system and enabled the utilisation of large low-cost solar heat-absorber platforms that operated at low pressure with a low risk of fouling and leaking. The design comprised a copper coil heat exchanger to be installed inside a conventional geyser, to replace the normal heating element and thermostat system in a conventional commercially available household geyser. The electric heating element still supplements the system in low solar energy conditions. The circulation in the system is created by a small separate photovoltaic panel and a circulation pump. An integrated switch allows the system to alternate between conventional electrical heating and solar water-heating according to prevailing weather conditions. Current tests show that the system of 15 m2 area can be installed at a cost of approximately ZAR 10 000–12 000. The system can provide hot water at approximately 12 cents per kWh, with a total heat storage capacity of up to 10 kWh per day. This implies a saving to the customer of up to ZAR 600 per month. The accumulated saving to a household over the ten-year lifetime of the product is estimated at ZAR 200 000. As the thermal energy storage capacity of current systems as available on the local market is approximately 1 kWhr per day for a 2 m2 collector. A typical increase in thermal energy collection capacity of tenfold more than the capability of conventional systems on the market is hence achieved. The system offers implementation possibilities for South Africa’s low-cost housing schemes and can provide for creating numerous new business and job opportunities on the African continent with its abundant solar irradiation resources.
Synthesis and microstructure of manganese ferrite colloidal nanocrystals (2010)

The atomic level structure of a series of monodisperse single crystalline nanoparticles with a magnetic core of manganese ferrite was studied using X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) techniques at both the Fe and Mn K-edges, and conventional and high resolution transmission electron microscopy (TEM and HRTEM). In particular, insights on the non-stoichiometry and on the inversion degree of manganese ferrite nanocrystals of different size were obtained by the use of complementary structural and spectroscopic characterization techniques. The inversion degree of the ferrite nanocrystals, i.e. the cation distribution between the octahedral and tetrahedral sites in the spinel structure, was found to be much higher (around 0.6) than the literature values reported for bulk stoichiometric manganese ferrite (around 0.2). The high inversion degree of the nanoparticles is ascribed to the partial oxidation of Mn(2+) to Mn(3+) which was evidenced by XANES, leading to non-stoichiometric manganese ferrite.
Dynamic Material Properties Experiments Using Pulsed Magnetic Compression. (2010)

Abstract not provided.
Features and outcome of neonatal leukemia in Japan: Experience of the Japan Infant Leukemia Study Group (2005)

These results suggest an improvement attributable to treatment of neonatal leukemia. International-based collaborative studies are necessary to investigate the biology of this condition and to establish appropriate therapeutic strategies.
Partition of Graphs and Hypergraphs into Monochromatic Connected Parts (2012)

We show that two results on covering of edge colored graphs by monochromatic connected parts can be extended to partitioning. We prove that for any $2$-edge-colored non-trivial $r$-uniform hypergraph $H$, the vertex set can be partitioned into at most $\alpha (H)-r+2$ monochromatic connected parts, where $\alpha (H)$ is the maximum number of vertices that does not contain any edge. In particular, any $2$-edge-colored graph $G$ can be partitioned into $\alpha(G)$ monochromatic connected parts, where $\alpha (G)$ denotes the independence number of $G$. This extends König's theorem, a special case of Ryser's conjecture. Our second result is about Gallai-colorings, i.e. edge-colorings of graphs without $3$-edge-colored triangles. We show that for any Gallai-coloring of a graph $G$, the vertex set of $G$ can be partitioned into monochromatic connected parts, where the number of parts depends only on $\alpha(G)$. This extends its cover-version proved earlier by Simonyi and two of the authors.
A BENCHMARK DATA SET FOR VALIDITY EVALUATION OF ROAD NETWORK SIMULATION MODELS (1998)

We have been developing and validating a traffic simulator AVENUE which deals with urban road networks. Through the experience of the model validation, we have spent substantial effort to collect precise data set including time-varying O-D demand and individual vehicle trajectories. In this paper, the outline of the survey in Kichijoji-Mitaka area is described at first. In order to collect precise data, the survey was made with recording number plates for &amp;apos;every &amp;apos; vehicles traveling the area. Then, the extraction of individual vehicle trajectories from the survey data is briefly explained. The extraction process interpolates misreading data by observers with heuristics rules. The extracted vehicle trajectories are subsequently aggregated to time-varying O-D demand. Finally, the validation of AVENUE is presented as an example of the usage of this benchmark data set. The recommended model validation process and the future
Primary versus Secondary Ovarian Malignancy: Imaging Findings of Adnexal Masses in the Radiology Diagnostic Oncology Group Study (2001)

For malignant ovarian masses, multilocularity at MR imaging or US favors the diagnosis of primary ovarian malignancy rather than secondary neoplasm, but it is difficult to accurately distinguish between primary and secondary ovarian malignancies.
Operative Treatment of Fifth Metatarsal Jones Fractures (Zones II and III) in the NBA (2016)

Category: Sports. Introduction/Purpose: Proximal fractures (Zones II and III) of the fifth metatarsal are common in the elite athlete population with basketball players being especially prone to developing these injuries. Fractures in Zones II and III of the fifth metatarsal can be difficult to treat due to tendency toward delayed union, nonunion, or refracture. The purpose of this case series is to report our experience in treating 10 professional basketball players from the National Basketball Association (NBA) for proximal fifth metatarsal fractures and determine the healing rate, return to play, refracture rate and role of foot type in these athletes. Methods: The records of 10 professional basketball players who were treated for fifth metatarsal fractures between September 2008 and October 2014 were retrospectively reviewed. Seven athletes underwent standard percutaneous internal fixation with bone marrow aspirate concentrate (BMAC) while the other 3 had open bone grafting primarily in addition to fixation and BMAC. Radiographic features associated with recurrent fifth metatarsal fractures were reported including fourth-fifth intermetatarsal (IMA4-5), fifth metatarsal lateral deviation (MT5-LD), calcaneal pitch (CP), and metatarsus adductus (MAA) angles. Differences in clinical and radiographic features were assessed between athletes who refractured (n=3) and those who did not (n=7). Results: Radiographic healing was observed at an overall average of 7.5 weeks and return to play was 9.8 weeks. Three athletes experienced refractures. When comparing the refracture group (n=3) with the control group (n=7), there were no significant differences in clinical features or radiographic measurements except that the refracture group had the highest measured MAA. Four of 10 fit the criteria for having metatarsus adductus as measured by the Sgarlato method (MAA greater than 14 degrees) while 5 of 10 had metatarsus adductus using the Engel method (greater than 24 degrees). All refractures had an abnormal angle using the Engel method. Seven of the 10 athletes were classified as pes planus and 9/10 had a bony prominence under the proximal base of their fifth metatarsals styloid. Conclusion: This is the largest series of operatively treated professional basketball players that possess a unique foot type that seems to be associated with increased risk of fifth metatarsal fracture and refracture. This foot type is one which has forefoot metatarsus adductus and a fifth metatarsal that is curved with a prominent base. We continue to use standard internal fixation with bone marrow aspirate but advocate additional prophylactic open bone grafting in patients with high IMA4-5, MT5-LD and MAA angles as well as prominent fifth metatarsal styloids in order to improve fracture healing and potentially decrease the risk of refracture.
Planar-constructed spatial micro-stage (2023)

A multiple degree of freedom platform assembly formed from a plurality of thin films on a substrate can, when activated, move out of the plane of the substrate without additional manufacturing steps. The platform is connected to the substrate by at least three linkages, each linkage being pivotally connected to the platform and the base. At least two of the base connections are to powered traveling devices that are manufactured at one end of a path and which may be moved to locations along the path to cause the platform to move to predetermined positions. The entire assembly, including hinges, is manufactured as planar structures; preferably by a thin film technology such as MEMS.
A viologen phosphorus dendritic molecule as a carrier of ATP and Mant-ATP: spectrofluorimetric and NMR studies (2014)

A viologen phosphorus dendritic molecule is able to create non-covalent interactions with model molecules of drugs belonging to the group of nucleoside analogues.