gebhart/patrepeval huggingface dataset:
Computational analysis of binding between benzamide-based derivatives and Abl wt and T315I mutant kinases (2016)

An integrated computational study was performed to identify the binding mechanisms of benzamide-based derivatives with Abl_wt/Abl_T315I kinases for designing Abl inhibitors.
Ectopic Gene Expression and Organogenesis inArabidopsisMutants Missing BRU1 Required for Genome Maintenance (2011)

Chromatin reconstitution after DNA replication and repair is essential for the inheritance of epigenetic information, but mechanisms underlying such a process are still poorly understood. Previously, we proposed that Arabidopsis BRU1 functions to ensure the chromatin reconstitution. Loss-of-function mutants of BRU1 are hypersensitive to genotoxic stresses and cause release of transcriptional gene silencing of heterochromatic genes. In this study, we show that BRU1 also plays roles in gene regulation in euchromatic regions. bru1 mutations caused sporadic ectopic expression of genes, including those that encode master regulators of developmental programs such as stem cell maintenance and embryogenesis. bru1 mutants exhibited adventitious organogenesis, probably due to the misexpression of such developmental regulators. The key regulatory genes misregulated in bru1 alleles were often targets of PcG SET-domain proteins, although the overlap between the bru1-misregulated and PcG SET-domain-regulated genes was limited at a genome-wide level. Surprisingly, a considerable fraction of the genes activated in bru1 were located in several subchromosomal regions ranging from 174 to 944 kb in size. Our results suggest that BRU1 has a function related to the stability of subchromosomal gene regulation in the euchromatic regions, in addition to the maintenance of chromatin states coupled with heritable epigenetic marks.
A portable artificial robotic hand controlled by EMG signal using ANN classifier (2015)

This paper aims at building a portable robotic hand for physically disabled people to perform basic hand movements. Surface Electromyography(EMG) signal is collected from muscles of human forearm to extract the subject's intentions of action, where six kinds of gestures are selected for discussion. An Artificial Neural Network(ANN) is trained and utilized to distinguish the desired movement according to the features picked up from the myoelectric signal. A simple robotic hand with seven degrees of freedom has been built and hardware circuits including signal acquisition, power management, and microprocessor are designed with no wire connecting to computer, making it compact and convenient to use. At last, experiments have been conducted to verify the validity of the whole system. The results show an efficient and relatively accurate recognition performance of this work.
NUTRITIONAL CHARACTERISTICS OF GREENHOUSE CHERRY TOMATOES (2003)

Cherry tomatoes are characterized by relatively high levels of antioxidants, particularly lycopene, and high antioxidant ability; in Sicily they are produced in cold greenhouses within production cycles that cover all the year. Considering this we have investigated the changes of some compositional parameters (sugars, ascorbic acid, α-tocopherol, carotenoids, phenolic compounds, antioxidant activity) associated to the nutritional value and to the health-related properties of fruits harvested in Sicily at different times of the year. Sampled fruits had particularly high levels of sugars, ascorbic acid and carotenoids, which, on the other hand, had a considerable variability; in spite of this variability of ascorbic acid and carotenoid content, one serving of raw tomatoes (100 g) can provide a relevant amount of vitamin C and A (respectively, 50÷120% and 12÷25% of the recommended daily intake) and lycopene (7060÷11970 μg/100g) throughout the year. The content of main phenolic compounds (particularly the flavonoids rutin and naringenin) evidenced the highest variability among tomato antioxidants. None of the parameters had a significant relationship with mean solar radiation measured during the ripening period of the fruits.
Manifold learning using Euclidean k-nearest neighbor graphs [image processing examples] (2004)

In the manifold learning problem one seeks to discover a smooth low dimensional surface, i.e., a manifold embedded in a higher dimensional linear vector space, based on a set of n measured sample points on the surface. In this paper, we consider the closely related problem of estimating the manifold's intrinsic dimension and the intrinsic entropy of the sample points. Specifically, we view the sample points as realizations of an unknown multivariate density supported on an unknown smooth manifold. In previous work, we introduced a geometric probability method called the geodesic minimal spanning tree (GMST) to obtain asymptotically consistent estimates of manifold dimension and entropy. In this paper, we present a simpler method, based on the k-nearest neighbor (k-NN) graph that does not require estimation of geodesic distances on the manifold. The algorithm is applied to standard synthetic manifolds as well as real data sets consisting of images of faces.
Epidural Anesthesia for Cesarean Section in Diabetic Parturients (1981)

Acid-base status and blood levels of bupivacaine were determined in 16 diabetic parturients and their infants after epidural anesthesia for cesarean section. The newborn infants were divided into two groups based on umbilical artery pH at birth. Group A consisted of 10 infants who had a pH of >7.2 and group B consisted of six infants with a pH of <7.2. Neonatal acidosis was related to both the severity of maternal diabetes and the presence of maternal hypotension after epidural anesthesia. In addition, the half-life of bupivacaine was prolonged in acidotic infants. The placental transfer of bupivacaine, as judged by umbilical vein/maternal vein ratios, was significantly greater in acidotic infants.
Mutagenesis and homology modeling reveal a predicted pocket of lysophosphatidylcholine acyltransferase 2 to catch Acyl‐CoA (2021)

Platelet-activating factor (PAF) is a potent proinflammatory phospholipid mediator that elicits various cellular functions and promotes several pathological events, including anaphylaxis and neuropathic pain. PAF is biosynthesized by two types of lyso-PAF acetyltransferases: lysophosphatidylcholine acyltransferase 1 (LPCAT1) and LPCAT2, which are constitutive and inducible forms of lyso-PAF acetyltransferase, respectively. Because LPCAT2 mainly produces PAF under inflammatory stimuli, understanding the structure of LPCAT2 is important for developing specific drugs against PAF-related inflammatory diseases. Although the structure of LPCAT2 has not been determined, the crystal structure was reported for Thermotoga maritima PlsC, an enzyme in the same gene family as LPCAT2. Here, we identified residues in mouse LPCAT2 essential for its enzymatic activity and a potential acyl-coenzyme A (CoA)-binding pocket, based on homology modeling of mouse LPCAT2 with PlsC. We also found that Ala115 of mouse LPCAT2 was important for acyl-CoA selectivity. In conclusion, these results predict the three-dimensional (3D) structure of mouse LPCAT2. Our findings have implications for the future development of new drugs against PAF-related diseases.
Molecular epidemiology of noroviruses and sapoviruses and their role in Australian outbreaks of acute gastroenteritis (2012)

Every winter since 2004, (except 2005) there have been outbreaks of acute gastroenteritis across Australia, caused by norovirus (NoV). These outbreaks are frequently seen in aged-care facilities, hospitals and cruise ships. Why has this become the norm and what has happened in virological terms to cause this? A single genetic lineage of NoV has emerged as the major cause of pandemic and epidemic viral gastroenteritis. The first reported pandemic of acute gastroenteritis occurred in 1996, discovered through the advent of molecular detection assays. Following a second pandemic in 2002, NoV-associated pandemics of gastroenteritis have occurred with increasing frequency. Here we describe the current molecular epidemiological trends of human NoV, and its milder cousin, sapovirus (SaV), and explain why, in particular, NoV has become the biggest player in the field of viral gastroenteritis. With encouraging results from the first vaccine trial recently reported and continuing research towards the development of vaccines and antiviral agents, we ask whether better weapons to fight and deter gastroenteritis viruses will be available in the future?
The Multiplicity of Human Pancreatic Secretory Trypsin Inhibitor (1985)

Four forms of pancreatic secretory trypsin inhibitor (PSTI; A1, A2, B, and C) were purified from human pancreatic juice. According to sequence results, the primary structure of B was different from that reported earlier (Greene, L.J., et al. (1976) Method Enzymol. 45, 813-825) at two positions, i.e. Asn21----Asp21, Asp29----Asn29. A1 and A2 were deamidated forms of B judging from peptide mappings with Staphylococcus aureus V8 protease. Gln45 in B was replaced by Glu in A1 and Gln51 in B was replaced by Glu in A2. C was an inhibitor lacking five amino acid residues from the amino terminal of B. B and C inhibited human cationic trypsin activity stoichiometrically with similar dissociation constants, but A1 and A2 showed poorer trypsin inhibitory activity than B and C.
Linearity and temperature dependence of large-area processed high-q barium strontium titanate thin-film varactors [Correspondence] (2010)

Ba(0.6)Sr(0.4)TiO(3) (BST) thin-films with large dielectric tunability as high as 4:1 were obtained using a large-area pulsed laser deposition process, with low loss-tangents below 0.01 at zero-bias and 10 GHz. This paper summarizes experimental results obtained on large-area processed BST thin films on 100-mm-diameter sapphire substrates characterized using a varactor shunt switch test structure. Varactors with 0.25-mumthick BST films exhibited large dielectric tunability, the relative dielectric permittivity at zero bias of 990 tuned to 250 at an electric field of 320 kV/cm. The leakage current through the BST film was below 2 nA up to 6 V dc bias. The quality factor (Q) exceeded 300 at relatively low 6 V dc bias for the BST varactors at 1 GHz. These results confirm that large-area processed BST thin films are ready to compete with semiconductor varactors for commercial applications at RF, microwave, and millimeterwave frequencies.
2098-P: The Accuracy of Meal Test to Diagnose Hypoglycemia after Gastric Bypass (2019)

Gastric bypass (GB) alters postprandial glucose pattern with a higher peak of glucose and lower glucose nadir. Glycemic effects of GB is exaggerated in patients suffering from postprandial hyperinsulinemic hypoglycemia. Diagnosis is complex and requires documentation of concurrent symptoms with low glucose that are relieved by carbohydrate (CHO) intake (Whipple’s triad). Mixed meal tolerance test (MTT) is often used to provoke hypoglycemia but glucose threshold to fulfill Whipple’s triad remains unknown. Here we measured accuracy of 350-kcal MTT (Ensure Plus®, 51 g CHO) to diagnose hypoglycemia in 95 GB subject (43 with prior documented hypoglycemia [H] and 52 asymptomatic [A]). In addition, measured outcomes were compared with those during isovolemic 250-kcal liquid MTT (Ensure®, 40 g CHO) in a separate cohort of 49 GB subjects (31 H vs. 18 A). Time and weight loss since surgery, BMI, and A1c were similar between H and A. The H subjects had lower fasting glucose (80±1 vs. 84±1 mg/dL, P&amp;lt;0.05) and nadir glucose levels (51±2 vs. 67±2 mg/dL, P&amp;lt;0.001). Nadir glucose values were associated with fasting glucose (r=0.6, P&amp;lt;0.001). Plotting true positive rate (sensitivity) against false positive rates (1-specificity) for nadir glucose during MTT yielded an area under the Receiver Operating Characteristics (ROC) curve of 0.80±0.05. A nadir blood glucose cut-off of 53 mg/dL produced the highest sum of sensitivity (65%) and specificity (88%) for detecting hypoglycemia. Lower CHO ingestion (40 g) did not significantly affect the accuracy of MTT to diagnose hypoglycemia (AUC ROC: 0.69±0.08). Our findings indicates that mixed meals containing 40-50 g of CHO have good discriminatory value to diagnose hypoglycemia after GB using blood glucose threshold of &amp;lt;54mg/dL. Disclosure H. Honka: None. R.A. DeFronzo: Advisory Panel; Self; AstraZeneca, Boehringer Ingelheim Pharmaceuticals, Inc., Elcelyx Therapeutics, Inc., Intarcia Therapeutics, Inc., Janssen Pharmaceuticals, Inc., Novo Nordisk Inc. Research Support; Self; AstraZeneca, Boehringer Ingelheim Pharmaceuticals, Inc., Janssen Pharmaceuticals, Inc., Merck &amp; Co., Inc. Speaker's Bureau; Self; AstraZeneca, Novo Nordisk Inc. M.E. Patti: Consultant; Self; Eiger BioPharmaceuticals. Research Support; Self; Dexcom, Inc., Janssen Pharmaceuticals, Inc., MedImmune, Xeris Pharmaceuticals, Inc. M. Salehi: None. Funding National Institutes of Health (DK105379, DK083554 to M.S.); National Center for Advancing Translational Sciences (8UL1TR000077); Finnish Cultural Foundation (00180071)
Beyond the simple models (1991)

Models of the mechanical behaviour of soils have served two purposes in this book: they have been used primarily to illustrate facets of the observed behaviour of soils which might at first sight be considered extraordinary but which, with even a simple model of soil behaviour, can in fact be anticipated; however, Section 11.3 has shown how such models can be used in finite element analyses of geotechnical problems of practical importance. There are different requirements for models used for purely illustrative purposes and for models used for predicting the response of geotechnical structures. The illustrative model is expected to give a simplified but overall picture of soil behaviour, but the predictive model must be able to match rather closely the behaviour of the elements of real soil which are being deformed in a particular prototype. Some of the simplifying assumptions of the illustrative model are inappropriate for the predictive model if the predictions are to be useful. Many implicit or explicit assumptions have been made in this book in presenting the simple models; the effects of relaxing some of these assumptions are discussed briefly in this chapter.
Rhodium-Catalyzed Hydroformylation Promoted by Modified Cyclodextrins:Current Scope and Future Developments (2008)

The contribution of modified cyclodextrins in aqueous biphasic rhodium-catalyzed hydroformylation of higher olefins is tackled, taking into account previous results and new experimental data. The role of the cyclodextrins is emphasized and discussed through the analysis of numerous parameters. Development outlooks are also presented. Keywords: Hydroformylation, cyclodextrin, rhodium, aqueous catalysis, interface
Palmar and dorsal fixed-angle plates in AO C-type fractures of the distal radius: is there an advantage of palmar plates in the long term? (2012)

Functional advantage of palmar plates gained within the first 6 weeks prevails over the course of a year. Both groups demonstrate further gradual increase of function after 6 months, although dorsal plates did not catch up completely. Improved early postoperative function seems to be the cornerstone for the best possible results. Patients with dorsal plates benefit from hardware removal more than palmar plates in terms of reduction of pain levels. The advantage of palmar plates is a faster functional recovery with lower complication rates. This is especially important in the elderly population. Radiological results did not show a superiority of palmar plates over dorsal plates.
The Ability to Promote Efflux Via ABCA1 Determines the Capacity of Serum Specimens With Similar High-Density Lipoprotein Cholesterol to Remove Cholesterol From Macrophages (2010)

Sera with similar HDL-C or apoA-I differ in their ability to promote macrophage efflux because of differences in the concentration of pre beta-1 HDL.
Steroidal Lactones from Withania somnifera, an Ancient Plant for Novel Medicine (2009)

Withania somnifera, commonly known as Ashwagandha, is an important medicinal plant that has been used in Ayurvedic and indigenous medicine for over 3,000 years. In view of its varied therapeutic potential, it has also been the subject of considerable modern scientific attention. The major chemical constituents of the Withania genus, the withanolides, are a group of naturally occurring C28-steroidal lactone triterpenoids built on an intact or rearranged ergostane framework, in which C-22 and C-26 are appropriately oxidized to form a six-membered lactone ring. In recent years, numerous pharmacological investigations have been carried out into the components of W. somnifera extracts. We present here an overview of the chemical structures of triterpenoid components and their biological activity, focusing on two novel activities, tumor inhibition and antiangiogenic properties of withaferin A and the effects of withanolide A on Alzheimer's disease. The most recent attempts in biotechnological production of withanolides are also discussed.
Femtosecond Broadband Frequency Switch of Terahertz Three-Dimensional Meta-Atoms (2021)

We present the experimental demonstration of a subpicosecond all-optical THz switch based on three-dimensional (3D) terahertz meta-atoms. Combining a special design of 3D meta-devices and the ultrafast dynamics of low temperature grown gallium arsenide, we can modulate the reflectance of the THz microcavities within 2.2 ps. The device enables a 280 GHz switch in resonance frequency within less than 200 fs. The switch back to the original resonance takes 800 fs. Experimental results show that the speed values are strongly convoluted by the THz probing field and, thus, the real switching times are even shorter, in the few 100 fs range.
ChemInform Abstract: Synthesis of Fused 1λ4,2‐Thiazines (2‐Azathiabenzenes). (1986)

Abstract The azidothiophene CELTb ‐ aldehyde (I) reacts with methylene compounds (II) to give the azides (III), whic:h on heating in toluene yield the cyclic sulphimides (IV).
Control of posture with FES systems (2002)

One of the major obstacles in restoration of functional FES supported standing in paraplegia is the lack of knowledge of a suitable control strategy. The main issue is how to integrate the purposeful actions of the non-paralysed upper body when interacting with the environment while standing, and the actions of the artificial FES control system supporting the paralyzed lower extremities. In this paper we provide a review of our approach to solving this question, which focuses on three inter-related areas: investigations of the basic mechanisms of functional postural responses in neurologically intact subjects; re-training of the residual sensory-motor activities of the upper body in paralyzed individuals; and development of closed-loop FES control systems for support of the paralyzed joints.
Interpretation and Application of Borehole Image Logs in a New Generation of Reservoir Models for a Cluster of Fields in Southern Oman (2010)

Borehole imaging is among the fastest and most accurate methods for collecting high resolution subsurface data. Recent breakthroughs in acquisition, tool design, and modeling software provide real-time subsurface images of incredible detail, from the drill bit straight to a workstation. Associated interpretation workflows offer the high level of detail that is needed to make operational decision and to increase the predictability of subsurface models. Many exploration and production companies have acquired a wealth of dipmeter and image log data. The data are readily available and provide, for example the orientation of fractures and fluvial channels in space. Further applications of borehole imaging technology include matrix and fracture characterization, pore-type partitioning, geosteering, and in-situ stress determination. Exciting new applications are found in enhanced oil recovery, carbon dioxide sequestration, and geothermal projects. In addition, borehole image data are paramount to unlocking unconventional plays such as shale gas and coal-bed methane. AAPG Memoir 92 portrays key applications of dipmeter and image log data across the exploration and production life cycle. (Continued)
Giant coercivity and spin clusters in high pressure polymorphs of Mn2LiReO6. (2022)

New high-pressure ordered-ilmenite and double-perovskite polymorphs of Mn 2 LiReO 6 are unprecedented A-site manganites with B/B′ +/7+ oxidation states. They show cluster spin-cluster-glass behaviour and giant coercivity without spin–orbit-coupling.
Processing of twin-roll cast thin AlFeSi strips for the manufacture of aluminium finstock (2017)

The thin strips produced with the new generation twin roll casters experience profoundly different temperature and strain gradients in the caster roll gap and thus require different down stream processing cycles. An attempt was made in the present work to identify processing cycles for the manufacture of finstock from thin AlFeSi strips. The grain structure in strips homogenized directly at the cast gauge is reorganized through growth processes while the grain structure in strips homogenized after cold rolling is reorganized via recrystallization. Finstock samples cold rolled without a homogenization treatment start to recrystallize at 300 °C in a very sluggish fashion whereas finstock samples submitted to a homogenization treatment undergo a faster recrystallization starting at 225 °C. Finstock with intermediate temper mechanical properties can be more easily achieved with a back-annealing process cycle without a homogenization treatment owing to a sluggish recrystallization. Soft temper finstock, on the other hand, requires a process cycle with a homogenization treatment.
A Systematic and Functional Classification of Streptococcus pyogenes That Serves as a New Tool for Molecular Typing and Vaccine Development (2014)

Streptococcus pyogenes ranks among the main causes of mortality from bacterial infections worldwide. Currently there is no vaccine to prevent diseases such as rheumatic heart disease and invasive streptococcal infection. The streptococcal M protein that is used as the substrate for epidemiological typing is both a virulence factor and a vaccine antigen. Over 220 variants of this protein have been described, making comparisons between proteins difficult, and hindering M protein-based vaccine development. A functional classification based on 48 emm-clusters containing closely related M proteins that share binding and structural properties is proposed. The need for a paradigm shift from type-specific immunity against S. pyogenes to emm-cluster based immunity for this bacterium should be further investigated. Implementation of this emm-cluster-based system as a standard typing scheme for S. pyogenes will facilitate the design of future studies of M protein function, streptococcal virulence, epidemiological surveillance, and vaccine development.
Polarization-Based Radar Detection in Sea Clutter (2015)

Abstract : The goal of the proposed research is to characterize and model polarization-related behaviors of sea clutter and to use these models to develop and evaluate methods for radar detection/characterization of a target on the surface of the sea. The specific propagation phenomenology that is to be exploited in this new form of detection is termed polarization mode dispersion (PMD), which is characterized by a spread in the received signal polarization state versus the signal frequency components in the radar returns. PMD is traditionally not analyzed in radar returns, but the hypothesis is that knowledge of the PMD in the returns (which is embedded via distributed clutter and target reflections) contains new forms of information.