gebhart/patrepeval huggingface dataset:
FlexSADRA: Flexible Structural Alignment using aDimensionality Reduction Approach (2005)

A topic of research that is frequently studied in Structural Biology is the problem of determining the degree of similarity between two protein structures. The most common solution is to perform a three dimensional structural alignment on the two structures. Rigid structural alignment algorithms have been developed in the past to accomplish this but treat the protein molecules as immutable structures. Since protein structures can bend and flex, rigid algorithms do not yield accurate results and as a result, flexible structural alignment algorithms have been developed. The problem with these algorithms is that the protein structures are represented using thousands of atomic coordinate variables. This results in a great computational burden due to the large number of degrees of freedom required to account for the flexibility. Past research in dimensionality reduction techniques has shown that a linear dimensionality reduction technique called Principal Component Analysis (PCA) is well suited for high dimensionality reduction. This thesis introduces a new flexible structural alignment algorithm called FlexSADRA, which uses PCA to perform flexible structural alignments. Test results show that FlexSADRA determines better alignments than rigid structural alignment algorithms. Unlike existing rigid and flexible algorithms, FlexSADRA addresses the problem in a significantly lower dimensionality problem space and assesses not only the structural fit but the structural feasibility of the final alignment.
BRAF Mutation Analysis in Fine Needle Aspiration (FNA) Cytology of the Thyroid (2006)

BRAF mutations have been detected in 30% to 80% of papillary thyroid carcinomas (PTC). Several detection methods for BRAF mutation have been reported, but a direct comparison between different assay methods has not been previously reported. In this study, we examined the diagnostic utility of BRAF (T1799A) mutation in 71 cases of thyroid fine needle aspiration specimens using 4 different methods, including direct sequencing, Colorimetric Mutector Assay, real-time LightCycler polymerase chain reaction (LC PCR) with fluorescence resonance energy transfer probes, and an allele-specific LC PCR with CYBR green 1. BRAF mutation was detected in 31 of 58 cases of PTC, but not in 13 cases of non-PTC lesions. The 4 assay methods used in this study were sensitive, reliable, and comparable with each other (100% of specificity and 53.5% of sensitivity). PTC harboring BRAF mutation had higher extrathyroidal invasion and/or lymph node metastasis than PTC with wild-type BRAF. BRAF mutation analysis should be useful for the clinical diagnosis of PTC in cases of indeterminate fine needle aspiration specimen, because of the high degree of specificity. Our results indicate that there is similar sensitivity for the four detection methods. However, the allele-specific LC PCR with CYBR green 1 method is most rapid, easier to perform, and least expensive technique, and it can be readily performed in most molecular diagnostic laboratories.
Simultaneous interpenetrating networks consisting of polyurethane and graft vinyl ester resin: Effect of different radical initiators (2002)

Abstract A series of well‐defined graft vinyl ester resins (graft VER), composed of butanol side chain (BO) or poly(oxypropylene) side chains with different molecular weights (200 or 390), were synthesized and characterized. The simultaneous interpenetrating networks (SINs) of graft VER and polyurethane (PU) were prepared. The effect of initiators for graft VER on the morphologies and mechanical properties of PU/graft VER SINs was studied through DSC, SEM, and FTIR observations. For PU/graft VER SIN formed with AIBN as initiator, the morphology and structure of these SINs are mainly controlled by the PU network formed first, and the structure of graft VER has almost no influence on the long‐range order structure of hard segments in SIN. For PU/graft VER SIN prepared with BPO/DMA as initiator (redox system), the side‐chain structure of graft VER greatly affects the morphologies of these SINs, although the PU network and graft VER network formed almost simultaneously. The reinforcement effect of the graft VER network on the PU network is significantly different by using these two different initiators for graft VER, which could be related with the morphologies of SINs and the formation rate of the two networks. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 1629–1636, 2002; DOI 10.1002/app.10502
INHIBITION BY COCAINE OF NORADRENALINE RELEASE FROM SYMPATHETIC NERVES IN THE RABBIT EAR ARTERY (1988)

1. Effects of cocaine on release of noradrenaline (NA) from sympathetic nerves were studied in the isolated perfused central artery of the rabbit ear. Indices of release were the vasoconstrictor response to nerve stimulation and stimulation-induced overflow of radioactivity after the nerves had been loaded with [3H]-NA. The overflow studies were carried out on phenoxybenzamine-treated arteries to eliminate the effect of cocaine on neuronal uptake. 2. Cocaine enhanced the constrictor responses of the artery to stimulation in concentrations of 3 and 30 mumols/l, but in higher concentrations (tested up to 300 mumols/l) the enhancement declined and was replaced by inhibition. Responses to extraluminal NA remained enhanced throughout the concentration range (tested up to 150 mumols/l). 3. In contrast, cocaine depressed the overflow of radioactivity, the effect being detectable in a concentration of 3 mumols/l (a decrease of 15%); the decrease was 40% at the highest concentration tested (90 mumols/l). 4. It is suggested that when assessed in terms of the vasoconstrictor response, inhibition of transmitter release by cocaine is masked by inhibition of neuronal uptake except in high concentrations of cocaine.
Stable Neo-Hookean Flesh Simulation (2018)

Nonlinear hyperelastic energies play a key role in capturing the fleshy appearance of virtual characters. Real-world, volume-preserving biological tissues have Poisson’s ratios near 1/2, but numerical simulation within this regime is notoriously challenging. In order to robustly capture these visual characteristics, we present a novel version of Neo-Hookean elasticity. Our model maintains the fleshy appearance of the Neo-Hookean model, exhibits superior volume preservation, and is robust to extreme kinematic rotations and inversions. We obtain closed-form expressions for the eigenvalues and eigenvectors of all of the system’s components, which allows us to directly project the Hessian to semipositive definiteness, and also leads to insights into the numerical behavior of the material. These findings also inform the design of more sophisticated hyperelastic models, which we explore by applying our analysis to Fung and Arruda-Boyce elasticity. We provide extensive comparisons against existing material models.
Intramolecular Hydroboration of Unsaturated Phosphine Boranes (2004)

Homoallylic phosphine boranes undergo intramolecular hydroboration upon activation by triflic acid. The reaction occurs via an intermediate B-trifluorosulfonyloxyborane complex such as 15, followed by S(N)1-like or S(N)2-like displacement of the triflate leaving group, apparently leading to the formation of a four-center transition state. In the case of trisubstituted double bonds, as in the substrates 29 and 32, ionic hydrogenation of the alkene competes with internal hydroboration.
DARBE GENİŞLİK MODÜLASYONU İLE SÜRÜLEN SİSTEMLERE GİRDİ ŞEKİLLENDİRME TEKNİĞİNİN UYGULANABİLİRLİĞİ (2019)

Bu çalışmada, darbe genişlik modülasyonu ile sürülen esnek sistemlerde oluşan artık titreşimin azaltılması amacıyla, alternatif bir girdi şekillendirme metodu sunulmuştur. Sistem doğal frekansı ve sönüm oranı gibi parametrelerinin tam olarak bilinmemesi ya da hatalı tahmin edilmesi durumunda dahi gürbüz bir girdi şekillendirme metodu oluşturulmaya çalışılmıştır. Birim genlik kullanılarak elde edilen girdi şekillendirme metoduyla çok sayıda darbeye sahip girdi şekillendirici üretilebilir ve bu girdi şekillendirici sistemdeki artık titreşimi yok edebilmektedir ya da azaltabilmektedir. Girdi şekillendirme tekniklerinde, darbe zamanları tekniğin performansını belirlemektedir. Önerilen metotta darbe zamanları referans hareket profilinin, değişken frekanslı üçgen dalgalarla kesiştirilmesiyle bulunur. Önerilen metot, çok bilinen sıfır titreşim metodu ile karşılaştırılıp, sunulan girdi şekillendirme metodunun performans karakteristiği ve sistemin cevabıyla ilgili grafikler sunulmuştur. Ayrıca girdi şekillendirme tekniğinin, seyahat süresinin daha kısa olması istenilen durumlarda da gürbüz olarak çalıştığı görülmektedir.
New Light on NO Bonding in Fe(III) Heme Proteins from Resonance Raman Spectroscopy and DFT Modeling (2010)

Visible and ultraviolet resonance Raman (RR) spectra are reported for Fe(III)(NO) adducts of myoglobin variants with altered polarity in the distal heme pockets. The stretching frequencies of the Fe(III)-NO and N-O bonds, nu(FeN) and nu(NO), are negatively correlated, consistent with backbonding. However, the correlation shifts to lower nu(NO) for variants lacking a distal histidine. DFT modeling reproduces the shifted correlations and shows the shift to be associated with the loss of a lone-pair donor interaction from the distal histidine that selectively strengthens the N-O bond. However, when the model contains strongly electron-withdrawing substituents at the heme beta-positions, nu(FeN) and nu(NO) become positively correlated. This effect results from Fe(III)-N-O bending, which is induced by lone-pair donation to the N(NO) atom. Other mechanisms for bending are discussed, which likewise lead to a positive nu(FeN)/nu(NO) correlation, including thiolate ligation in heme proteins and electron-donating meso-substituents in heme models. The nu(FeN)/nu(NO) data for the Fe(III) complexes are reporters of heme pocket polarity and the accessibility of lone pair, Lewis base donors. Implications for biologically important processes, including NO binding, reductive nitrosylation, and NO reduction, are discussed.
ChemInform Abstract: LONG‐RANGE STERIC EFFECTS IN RHODIUM(I) CLEAVAGES OF SECOPENTAPRISMANES. A REVERSIBLE RHODIUM(I)‐MEDIATED CYCLOBUTANE‐DIOLEFIN CONVERSION (1978)

Abstract Umsetzung der Secopentaprismane (Ia)‐(Ic) mit dem Rh‐Komplex (V) liefert die Komplexe (II) und freies Norbornadien (III).
Diamond for Biosensing: Electrochemical Detection of NOx Species with Thiol-Amine Functionalized Diamond (2015)

Diamond has long been of interest as a biomaterial due to its expected biocompatibility and chemical stability. Progress in surface functionalization of diamond and diamond electrochemistry has extended this interest to use as a biosensor platform. The sensitivity and selectivity of the diamond surface can be enhanced by covalently attaching carbon-based biochemicals. In this communication, an amine-thiol molecule was attached to a boron-doped diamond (BDD) surface to produce an enhanced ability to detect NO species. In the case of hydrogen terminated BDD, it was found that NO (aqueous) oxidation was insufficiently distinct to electrochemically detect NO. However, the amine-thiol functionalized BDD surface provided a distinct oxidation peak from 65 nanomolar to 236 nanomolar concentrations. Multiple cyclic voltammagrams with amine-thiol functionalized BDD electrode in (HPLC-quality) purified water indicated that the covalently attached surface molecules resisted decomposition during both anodic and cathodic polarization.
Reducing the carbon footprint from water distribution systems by using a lower discount rate (2010)

Climate change, especially global warming caused by human activities, presents serious global risks. Mitigating global warming by reducing greenhouse gas (GHG) emissions is a unique challenge facing our generation. For all industries, actions must be taken to reduce emissions and the water industry must play its part. Previous research on water distribution system (WDS) optimisation has found that the discount rate used in the conceptual design process of a WDS involving pumping has a significant impact on the final design of the network, which in turn has an impact on the greenhouse gas (GHG) emissions generated from the system. In this paper, the impact of the discount rate used in project planning on the final decision making of WDS design is investigated via a one-pipe water transmission system. Two different pumping systems with pipe lengths of 15 km and 150 km are used as case studies. The total cost of the WDS with different pipe diameters has been evaluated using a high and a low discount rate in the literature. The total GHG emissions from these systems are also calculated in this paper. The computation shows that different discount rates lead to different least-cost WDS networks. A lower discount rate than the cost of capital can lead to a final WDS design with significant GHG reductions.
Antioxidant Activity of Jojoba (Simmondsia chinensis) Seed Residue Extract (2020)

Jojoba ( Simmondsia chinensis (Link)) is a shrub plant that widely used as cosmetic ingredients especially jojoba oil. When making jojoba oil, the residue still reminds and become waste. This study aimed to determine the antioxidant activity of jojoba seed residue (JSR). Jojoba seed residue was collected from Sudan. The JSR extracted by maceration with n -hexane, ethyl acetate, and 70% ethanol solvent. The antioxidant activity was determined using DPPH (2,2-diphenyl-1-picrylhydrazyl) assay. The result showed that 70% ethanol extract of JSR had the highest antioxidant activity with 50% Inhibition Concentration (IC 50 ) value of 219.42 mg/L. The 70% ethanol extract was fractionated by using silica gel column chromatography with gradient elution produced 10 fractions. All fractions showed antioxidant activity (IC 50 106-447 mg/L). Fraction 3 had the highest antioxidant activity with IC 50 value of 106.26 mg/L. Therefore, JSR has a great potential for use as a raw material in cosmetic and pharmaceutical products industry, or as a source of bioactive compounds.
Relation between functional magnetic resonance imaging (fMRI) and single neuron, local field potential (LFP) and electrocorticography (ECoG) activity in human cortex (2013)

The relation between changes in the blood oxygen dependent metabolic changes imaged by functional magnetic resonance imaging (fMRI) and neural events directly recorded from human cortex from single neurons, local field potentials (LFPs) and electrocorticogram (ECoG) is critically reviewed, based on the published literature including findings from the authors' laboratories. All these data are from special populations, usually patients with medically refractory epilepsy, as this provides the major opportunity for direct cortical neuronal recording in humans. For LFP and ECoG changes are often sought in different frequency bands, for single neurons in frequency of action potentials. Most fMRI studies address issues of functional localization. The relation of those findings to localized changes in neuronal recordings in humans has been established in several ways. Only a few studies have directly compared changes in activity from the same sites in the same individual, using the same behavioral measure. More often the comparison has been between fMRI and electrophysiologic changes in populations recorded from the same functional anatomic system as defined by lesion effects; in a few studies those systems have been defined by fMRI changes such as the "default" network. The fMRI-electrophysiologic relationships have been evaluated empirically by colocalization of significant changes, and by quantitative analyses, often multiple linear regression. There is some evidence that the fMRI-electrophysiology relationships differ in different cortical areas, particularly primary motor and sensory cortices compared to association cortex, but also within areas of association cortex. Although crucial for interpretation of fMRI changes as reflecting neural activity in human cortex, controversy remains as to these relationships. Supported by: Dutch Technology Foundation and University of Utrecht Grant UGT7685, ERC-Advanced grant 320708 (NR) and NIH grant NS065186 (JO).
IRL‐1620, a tumor selective vasodilator, augments the uptake and efficacy of chemotherapeutic agents in prostate tumor rats (2007)

IRL-1620 significantly enhanced the uptake and efficacy of anticancer agents in prostate cancer.
An efficient reduction technique for degree-constrained subgraph and bidirected network flow problems (1983)

Efficient algorithms are given for the bidirected network flow problem and the degree-constrained subgraph problem. Four versions of each are solved, depending on whether edge capacities/multiplicities are one or arbitrary, and whether maximum value/maximum cardinality or minimum cost/maximum weight is the objective. A version of the shortest path problem is also efficiently solved. The algorithms use a reduction technique that solves one problem instance by reducing to a number of problems.
Evaluation of Single Pixel Step Sizes in Visual Acuity Assessment (2010)

Letter sizes that do not conform to a multiple of 5 pixel letter height yield valid acuity scores. This facilitates adaptive psychometric procedures for acuity testing, such as ZEST and QUEST, in which letter sizes are selected to be as close to the current estimate of threshold size as possible.
Survival of Cats with Naturally Occurring Chronic Renal Failure Is Related to Severity of Proteinuria (2006)

Abstract Background: Tubulointerstitial kidney disease is a common cause of illness and death in pet cats and is typically not associated with overt proteinuria. Hypothesis: Proteinuria would be independently related to survival in cats with renal failure, with or without hypertension. Animals: The study included 136 client-owned cats; 28 apparently normal, 14 hypertensive but not azotemic, 66 azotemic but not hypertensive, and 28 both hypertensive and azotemic. Methods: Cox's proportional hazards model was used to determine the influence of initial plasma creatinine concentration, proteinuria (urine protein-to-creatinine ratio or albumin-to-creatinine ratio), age, and systemic hypertension on the risk of death or euthanasia during the follow-up period. Multivariable linear regression was used to determine the relation between severity of proteinuria and predictive variables, including age, plasma creatinine concentration, systolic blood pressure, sex, and urine specific gravity. Results: Plasma creatinine concentration and proteinuria were very highly related to survival. The hazard ratio (95% confidence intervals) for death or euthanasia was 2.9 (1.4–6.3) and 4.0 (2.0–8.0) for urine protein-to-creatinine ratio 0.2-0.4 and &amp;gt;0.4, respectively, compared with the baseline group with a urine protein-to-creatinine ratio of &amp;lt;0.2 and were 2.4 (1.2–4.8) and 4.9 (2.3–10.2) for an albumin-to-creatinine ratio of 30–82 mg/g and &amp;lt;82 mg/g, respectively, compared with a baseline group with albumin-to-creatinine ratio of &amp;lt;30 mg/g. Treated hypertensive cats did not have reduced survival, although systolic blood pressure, together with plasma creatinine concentration was positively related to the magnitude of proteinuria. Conclusions and Clinical Importance: Despite the relatively low concentrations of proteinuria typical of chronic renal disease in cats, this measurement is of prognostic significance.
Echtzeit-Optimierung von Kontaktkräften in mehrfingrigen Manipulationssystemen (Realtime Optimization of Robot Hand Grasping Forces) (2002)

In diesem Beitrag wird ein für den Einsatz im geschlossenen Regelkreis geeignetes Echtzeitoptimierungsverfahren zur Berechnung von optimalen Greifkräften bei mehrfingrigen Handmanipulationsvorgängen vorgestellt. Das Verfahren basiert auf einer Problemformulierung der unilateralen mechanischen Bindungen zwischen Finger und Objekt als semidefinite Programmierungsaufgabe, die durch ein zeitdiskretisiertes Gradientenfluss-basiertes numerisches Iterationsverfahren in wenigen Millisekunden gelöst werden kann. Experimentelle Resultate mit der Tokyo Institute of Technology Hand zeigen die überlegenen Eigenschaften des Optimierungsansatzes bei mehrfingrigen Manipulationsaufgaben. In einem Multimedia-Anhang zu diesem Artikel werden eine prototypische Implementierung des Ansatzes, einige experimentelle Daten und Kurzfilme der Experimente zur Verfügung gestellt. Den Multimedia-Download zu diesem Beitrag finden Sie unter www.rs.tu-berlin.de/~roha
The justification for application and development trendsof non-conventional rodenticides in protection of alfalfa from rodents (2012)

This paper presents the harmful rodents in alfalfa in Serbia in the first decade of this century. We also review the products registered and assessed the efficiency of conventional (acute) rodenticides, anticoagulant and rodenticides based on environmentally friendly active ingredients. In addition to anticoagulants of second generation, whose mechanism of action is based on a synthesis of the factors preventing blood coagulation, in the latest of the eighties, and in early of nineties introduced products based on vitamin D3-cholecalciferol. Their mechanism of action is based on the mobilization of calcium from bone and tissue and calcification of blood vessels, kidney, liver, heart muscle leading to delays in the work of these bodies. The last decade of the last century have been recorded and products based on trace element selenium (Se), the mechanism of action is based on the replacement of thiol functional enzymes SS groups. Also presents the possibility of application of ecological cellulose product in the field. In the world, so far, cellulose based rodenticides are only registered in municipal buildings. Its mechanism of action is based on interference with the absorption of water leading to dehydration in rodents. Rodents do not develop resistance to products based on vitamin D3 and selenium, a cellulose product is favourable toxicological and eco-toxicological point.
Role of Additives in Composite PEI/Oxide CO2 Adsorbents: Enhancement in the Amine Efficiency of Supported PEI by PEG in CO2 Capture from Simulated Ambient Air (2015)

Supported amines are promising candidate adsorbents for the removal of CO2 from flue gases and directly from ambient air. The incorporation of additives into polymeric amines such as poly(ethylenimine) (PEI) supported on mesoporous oxides is an effective strategy to improve the performance of the materials. Here, several practical aspects of this strategy are addressed with regards to direct air capture. The influence of three additives (CTAB, PEG200, PEG1000) was systematically explored under dry simulated air capture conditions (400 ppm of CO2, 30 °C). With SBA-15 as a model support for poly(ethylenimine) (PEI), the nature of the additive induced heterogeneities in the deposition of organic on the interior and exterior of the particles, an important consideration for future scale up to practical systems. The PEG200 additive increased the observed thermodynamic performance (∼60% increase in amine efficiency) of the adsorbents regardless of the PEI content, while the other molecules had less positive effects. A threshold PEG200/PEI value was identified at which the diffusional limitations of CO2 within the materials were nearly eliminated. The threshold PEG/PEI ratio may have physical origin in the interactions between PEI and PEG, as the optimal ratio corresponded to nearly equimolar OH/reactive (1°, 2°) amine ratios. The strategy is shown to be robust to the characteristics of the host support, as PEG200 improved the amine efficiency of PEI when supported on two varieties of mesoporous γ-alumina with PEI.