gebhart/patrepeval huggingface dataset:
Saliency Tree: A Novel Saliency Detection Framework (2014)

This paper proposes a novel saliency detection framework termed as saliency tree. For effective saliency measurement, the original image is first simplified using adaptive color quantization and region segmentation to partition the image into a set of primitive regions. Then, three measures, i.e., global contrast, spatial sparsity, and object prior are integrated with regional similarities to generate the initial regional saliency for each primitive region. Next, a saliency-directed region merging approach with dynamic scale control scheme is proposed to generate the saliency tree, in which each leaf node represents a primitive region and each non-leaf node represents a non-primitive region generated during the region merging process. Finally, by exploiting a regional center-surround scheme based node selection criterion, a systematic saliency tree analysis including salient node selection, regional saliency adjustment and selection is performed to obtain final regional saliency measures and to derive the high-quality pixel-wise saliency map. Extensive experimental results on five datasets with pixel-wise ground truths demonstrate that the proposed saliency tree model consistently outperforms the state-of-the-art saliency models.
Bio-functionalisation of polyether ether ketone using plasma immersion ion implantation (2015)

Plasma immersion ion implantation (PIII) is used here to improve the surface bioactivity of polyether ether ketone (PEEK) by modifying the chemical and mechanical properties and by introducing radicals. Modifications to the chemical and mechanical properties are characterised as a function of ion fluence (proportional to treatment time) to determine the suitability of the treated surfaces for biological applications. Radical generation increases with treatment time, where treatments greater than 400 seconds result in a high concentration of long-lived radicals. Radical reactions are responsible for oxidation of the surface, resulting in a permanent increase in the polar surface energy. The nano-scale reduced modulus was found to increase with treatment time at the surface from 4.4 to 5.2 GPa. The macromolecular Young’s modulus was also found to increase, but by an amount corresponding to the volume fraction of the ion implanted region. The treated surface layer exhibited cracking under cyclical loads, associated with an increased modulus due to dehydrogenation and crosslinking, however it did not show any sign of delamination, indicating that the modified layer is well integrated with the substrate – a critical factor for bioactive surface coatings to be used in-vivo. Protein immobilisation on the PIII treated surfaces was found to saturate after 240 seconds of treatment, indicating that there is room to tune surface mechanical properties for specific applications without affecting the protein coverage. Our findings indicate that the modification of the chemical and mechanical properties by PIII treatments as well as the introduction of radicals render PEEK well suited for use in orthopaedic implantable devices.
Isolation of Human Myoblasts with the Fluorescence-Activated (1988)

We have established procedures for the rapid and efficient purification of human myoblasts using the fluorescence-activated cell sorter. Our approach capitalizes on the specific reaction of monoclonal antibody 5.1H 11 with a human muscle cell surface antigen. For each of the five samples analyzed, an enrichment of myoblasts to greater than 99% of the cell population was immediately achieved. Following 3 to 4 weeks of additional growth in vitro, sorted myoblast cultures remained 97% pure. Differentiation of the sorted myoblast cultures, assessed by creatine kinase activity and isozyme content, was comparable to that of pure myoblast cultures obtained by cloning, and was significantly greater than that of mixed tibroblast and myoblast cultures. An average of lo4 viable myoblasts can be obtained per 0.1 g tissue, each with the potential to undergo approximately 40 cell divisions. Accordingly, if only two-thirds of this proliferative capacity is utilized, the potential yield approximates 10” myoblasts, equivalent to 1 kg of cells. Human myogenesis in vitro is no longer limited by cell number and is now amenable to molecular and biochemical analysis on a large SCak. @ 1988 Academic Press, Inc.
ChemInform Abstract: Synthesis of New Donor—Acceptor—Donor Materials via Au‐Catalyzed Double Cascade Cyclization. (2012)

Abstract Double cascade cyclization of arenyl tetraynes gives benzothiadiazole derivatives and related compounds.
Mechanism of the efflux transport of demethoxycurcumin-O-glucuronides in HeLa cells stably transfected with UDP-glucuronosyltransferase 1A1 (2019)

Demethoxycurcumin (DMC) is a safe and natural food-coloring additive, as well as an agent with several therapeutic properties. However, extensive glucuronidation in vivo has resulted in its poor bioavailability. In this study, we aimed to investigate the formation of DMC-O-glucuronides by uridine 5'-diphospho-glucuronosyltransferase 1A1 (UGT1A1) and its transport by breast cancer resistance protein (BCRP) and multidrug resistance-associated proteins (MRPs) in HeLa cells stably transfected with UGT1A1 (named HeLa1A1 cells). The chemical inhibitors Ko143 (a selective BCRP inhibitor) and MK571 (a pan-MRP inhibitor) both induced an obvious decrease in the excretion rate of DMC-O-glucuronides and a significant increase in intracellular DMC-O-glucuronide concentrations. Furthermore, BCRP knock-down resulted in a marked reduction in the level of excreted DMC-O-glucuronides (maximal 55.6%), whereas MRP1 and MRP4 silencing significantly decreased the levels of excreted DMC-O-glucuronides (a maximum of 42.9% for MRP1 and a maximum of 29.9% for MRP3), respectively. In contrast, neither the levels of excreted DMC-O-glucuronides nor the accumulation of DMC-O-glucuronides were significantly altered in the MRP4 knock-down HeLa cells. The BCRP, MRP1 and MRP3 transporters were identified as the most important contributors to the excretion of DMC-O-glucuronides. These results may significantly contribute to improving our understanding of mechanisms underlying the cellular disposition of DMC via UGT-mediated metabolism.
On recognizing and positioning curved 3-D objects from image contours (1990)

An approach for explicitly relating the shape of image contours to models of curved three-dimensional objects is presented. This relationship is used for object recognition and positioning. Object models consist of collections of parametric surface patches and their intersection curves; this includes nearly all representations used in computer-aided geometric design and computer vision. The image contours considered are the projections of surface discontinuities and occluding contours. Elimination theory provides a method for constructing the implicit equation of these contours for an object observed under orthographic or perspective projection. This equation is parameterized by the object's position and orientation with respect to the observer. Determining these parameters is reduced to a fitting problem between the theoretical contour and the observed data points. The proposed approach readily extends to parameterized models. It has been implemented for a simple world composed of various surfaces of revolution and tested on several real images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sensing of minute airflow motions near walls using pappus-type nature-inspired sensors (2017)

This work describes the development and use of pappus-like structures as sensitive sensors to detect minute air-flow motions. We made such sensors from pappi taken from nature-grown seed, whose filiform hairs' length-scale is suitable for the study of large-scale turbulent convection flows. The stem with the pappus on top is fixated on an elastic membrane on the wall and tilts under wind-load proportional to the velocity magnitude in direction of the wind, similar as the biological sensory hairs found in spiders, however herein the sensory hair has multiple filiform protrusions at the tip. As the sensor response is proportional to the drag on the tip and a low mass ensures a larger bandwidth, lightweight pappus structures similar as those found in nature with documented large drag are useful to improve the response of artificial sensors. The pappus of a Dandelion represents such a structure which has evolved to maximize wind-driven dispersion, therefore it is used herein as the head of our sensor. Because of its multiple hairs arranged radially around the stem it generates uniform drag for all wind directions. While still being permeable to the flow, the hundreds of individual hairs on the tip of the sensor head maximize the drag and minimize influence of pressure gradients or shear-induced lift forces on the sensor response as they occur in non-permeable protrusions. In addition, the flow disturbance by the sensor itself is limited. The optical recording of the head-motion allows continuously remote-distance monitoring of the flow fluctuations in direction and magnitude. Application is shown for the measurement of a reference flow under isothermal conditions to detect the early occurrence of instabilities.
Integral and impossible‐differential attacks on the reduced‐round Lesamnta‐LW‐BC (2021)

Abstract Lesamnta‐LW‐BC is the internal block cipher of the Lesamnta‐LW lightweight hash function, specified in ISO/IEC 29192‐5:2016. It is based on the unbalanced Feistel network and Advanced Encryption Standard round function. In this study, the security of Lesamnta‐LW‐BC against integral and impossible‐differential attacks is evaluated. Specifically, the authors searched for the integral distinguishers and impossible differentials with Mixed‐Integer Linear Programming‐based methods. As a result, the discovered impossible differential can reach up to 21 rounds, while three integral distinguishers reaching 18, 19 and 25 rounds are obtained, respectively. Moreover, it is also feasible to construct a 47‐round integral distinguisher in the known‐key setting. Finally, a 20‐round key‐recovery attack is proposed based on the discovered 18‐round integral distinguisher and a 19‐round key‐recovery attack using a 17‐round impossible differential. To the best of the authors' knowledge, this is the first third‐party cryptanalysis of Lesamnta‐LW‐BC.
Image deblurring, spectrum interpolation and application to satellite imaging (2000)

This paper deals with two complementary methods in noisy image deblurring: a nonlinear shrinkage of wavelet-packets coefficients called FCNR and Rudin-Osher-Fatemi's variational method. The FCNR has for objective to obtain a restored image with a white noise. It will prove to be very efficient to restore an image after an invertible blur but limited in the opposite situation. Whereas the Total Variation based method, with its ability to reconstruct the lost frequencies by interpolation, is very well adapted to non-invertible blur, but that it tends to erase low contrast textures. This complementarity is highlighted when the methods are applied to the restoration of satellite SPOT images.
Antibodies to S. aureus LukS-PV Attenuated Subunit Vaccine Neutralize a Broad Spectrum of Canonical and Non-Canonical Bicomponent Leukotoxin Pairs (2015)

S. aureus vaccine development has proven particularly difficult. The conventional approach to achieve sterile immunity through opsonophagocytic killing has been largely unsuccessful. S. aureus is highly toxigenic and a great body of evidence suggests that a successful future vaccine for this organism should target extracellular toxins which are responsible for host tissue destruction and immunosuppression. Major staphylococcal toxins are alpha toxin (a single subunit hemolysin) along with a group of bicomponent pore-forming toxins (BCPFT), namely Panton-Valentine leukocidin (PVL), gamma hemolysins (HlgCB and AB), LukAB and LukED. In our previous report, an attenuated mutant of LukS-PV (PVL- S subunit) named as "LukS-mut9" elicited high immunogenic response as well as provided a significant protection in a mouse sepsis model. Recent discovery of PVL receptors shows that mice lack receptors for this toxin, thus the reported protection of mice with the PVL vaccine may relate to cross protective responses against other homologous toxins. This manuscript addresses this issue by demonstrating that polyclonal antibody generated by LukS-mut9 can neutralize other canonical and non-canonical leukotoxin pairs. In this report, we also demonstrated that several potent toxins can be created by non-canonical pairing of subunits. Out of 5 pairs of canonical and 8 pairs of non-canonical toxins tested, anti-LukS-mut9 polyclonal antibodies neutralized all except for LukAB. We also studied the potential hemolytic activities of canonical and noncanonical pairs among biocomponent toxins and discovered that a novel non-canonical pair consisting of HlgA and LukD is a highly toxic combination. This pair can lyse RBC from different species including human blood far better than alpha hemolysin. Moreover, to follow-up our last report, we explored the correlation between the levels of pre-existing antibodies to new sets of leukotoxins subunits and clinical outcomes in adult patients with S. aureus bacteremia. We found that there is an inversed correlation between the antibody titer to sepsis for leukotoxins LukS-mut9, LukF-PV, HlgC, LukE and LukAB, suggesting the risk of sepsis was significantly lower in the patients with higher antibody titer against those toxins.
Crystal structure of PI3Kgamma with a dihydropurinone inhibitor (compound 4) (2019)

DNA-PK is a key component within the DNA damage response, as it is responsible for recognizing and repairing double-strand DNA breaks (DSBs) via non-homologous end joining. Historically it has been challenging to identify inhibitors of the DNA-PK catalytic subunit (DNA-PKcs) with good selectivity versus the structurally related PI3 (lipid) and PI3K-related protein kinases. We screened our corporate collection for DNA-PKcs inhibitors with good PI3 kinase selectivity, identifying compound <b>1</b>. Optimization focused on further improving selectivity while improving physical and pharmacokinetic properties, notably co-optimization of permeability and metabolic stability, to identify compound <b>16</b> (AZD7648). Compound <b>16</b> had no significant off-target activity in the protein kinome and only weak activity versus PI3Kα/γ lipid kinases. Monotherapy activity in murine xenograft models was observed, and regressions were observed when combined with inducers of DSBs (doxorubicin or irradiation) or PARP inhibition (olaparib). These data support progression into clinical studies (NCT03907969).
Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells (2017)

Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division consistent with substrate replete conditions. Planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. This study demonstrates that microbial attachment to cellulose substrate produces widespread gene expression changes for critical functions of this organism and provides physiological insights for two cells populations relevant for engineering of industrially-ready phenotypes.
ChemInform Abstract: THE PREPARATION OF SOME CYCLIC PHOSPHONATES AND THEIR USE IN OLEFIN SYNTHESIS (1978)

Abstract Die Arbusov‐Reaktion der cyclischen Phosphite (I) mit den Chlor‐ bzw. Bromessigestern oder Chloracetonitril (II) liefert die sechsgliedrigen cyclischen Phosphonate (IIIa‐c) und die fünfgliedrigen cyclischen Phosphonate (IIIa) und (IIIb), letztere als Gemisch der racemischen und meso‐Isomeren, die auch von (IIIa) einzeln bei Einsatz reiner racemischer oder meso‐Ausgangsverbindung (Ia) erhältlich sind.
A Sinusoidal Encoder-to-Digital Converter Based on an Improved Tangent Method (2017)

Sinusoidal encoders are used for the measurement of angular position and linear displacement. These provide electrical signals dependent on the sine and cosine of the position θ of their moving part relative to the stationary one. Conventional tangent/cotangent converters for determining θ from the encoder signals produce alternating highly non-linear segments of tangent and cotangent. Lookup tables are used for determining θ. This paper presents a novel converter for estimating θ without the lookup table. The method is based on dividing the circle angular interval into N sections. A crude or coarse measure θ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</sub> of the unknown angle θ is first determined by identifying the section in which θ is located. This is followed by the determination of a fine measure θ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> . These measures are combined to yield a precise measure of θ; the maximum error of the method depends on N. The converter has been implemented on a dSPACE set and has been successfully tested both with a sensor emulator and a real Hall-Effect sinusoidal encoder. This paper describes full details of the theory, simulation, and experimental results. The experimental results demonstrate excellent agreement with theory and simulation.
Neuronal activity regulates expression of tyrosine hydroxylase in adult mouse substantia nigra pars compacta neurons (2010)

Striatal delivery of dopamine (DA) by midbrain substantia nigra pars compacta (SNc) neurons is vital for motor control and its depletion causes the motor symptoms of Parkinson's disease. While membrane potential changes or neuronal activity regulates tyrosine hydroxylase (TH, the rate limiting enzyme in catecholamine synthesis) expression in other catecholaminergic cells, it is not known whether the same occurs in adult SNc neurons. We administered drugs known to alter neuronal activity to mouse SNc DAergic neurons in various experimental preparations and measured changes in their TH expression. In cultured midbrain neurons, blockade of action potentials with 1 μM tetrodotoxin decreased TH expression beginning around 20 h later (as measured in real time by green fluorescent protein (GFP) expression driven off TH promoter activity). By contrast, partial blockade of small-conductance, Ca(2+) -activated potassium channels with 300 nM apamin increased TH mRNA and protein between 12 and 24 h later in slices of adult midbrain. Two-week infusions of 300 nM apamin directly to the adult mouse midbrain in vivo also increased TH expression in SNc neurons, measured immunohistochemically. Paradoxically, the number of TH immunoreactive (TH+) SNc neurons decreased in these animals. Similar in vivo infusions of drugs affecting other ion-channels and receptors (L-type voltage-activated Ca(2+) channels, GABA(A) receptors, high K(+) , DA receptors) also increased or decreased cellular TH immunoreactivity but decreased or increased, respectively, the number of TH+ cells in SNc. We conclude that in adult SNc neurons: (i) TH expression is activity-dependent and begins to change ∼20 h following sustained changes in neuronal activity; (ii) ion-channels and receptors mediating cell-autonomous activity or synaptic input are equally potent in altering TH expression; and (iii) activity-dependent changes in TH expression are balanced by opposing changes in the number of TH+ SNc cells.
Subcellular distribution of glycogen and decreased tetanic Ca<sup>2+</sup> in fatigued single intact mouse muscle fibres (2014)

In skeletal muscle fibres, glycogen has been shown to be stored at different subcellular locations: (i) between the myofibrils (intermyofibrillar); (ii) within the myofibrils (intramyofibrillar); and (iii) subsarcolemmal. Of these, intramyofibrillar glycogen has been implied as a critical regulator of sarcoplasmic reticulum Ca(2+) release. The aim of the present study was to test directly how the decrease in cytoplasmic free Ca(2+) ([Ca(2+)]i) during repeated tetanic contractions relates to the subcellular glycogen distribution. Single fibres of mouse flexor digitorum brevis muscles were fatigued with 70 Hz, 350 ms tetani given at 2 s (high-intensity fatigue, HIF) or 10 s (low-intensity fatigue, LIF) intervals, while force and [Ca(2+)]i were measured. Stimulation continued until force decreased to 30% of its initial value. Fibres were then prepared for analyses of subcellular glycogen distribution by transmission electron microscopy. At fatigue, tetanic [Ca(2+)]i was reduced to 70 ± 4% and 54 ± 4% of the initial in HIF (P < 0.01, n = 9) and LIF (P < 0.01, n = 5) fibres, respectively. At fatigue, the mean inter- and intramyofibrillar glycogen content was 60-75% lower than in rested control fibres (P < 0.05), whereas subsarcolemmal glycogen was similar to control. Individual fibres showed a good correlation between the fatigue-induced decrease in tetanic [Ca(2+)]i and the reduction in intermyofibrillar (P = 0.051) and intramyofibrillar (P = 0.0008) glycogen. In conclusion, the fatigue-induced decrease in tetanic [Ca(2+)]i, and hence force, is accompanied by major reductions in inter- and intramyofibrillar glycogen. The stronger correlation between decreased tetanic [Ca(2+)]i and reduced intramyofibrillar glycogen implies that sarcoplasmic reticulum Ca(2+) release critically depends on energy supply from the intramyofibrillar glycogen pool.
Pilot report: non-operative treatment of Mayo Type II olecranon fractures in any-age adult patient (2017)

In this pilot report, Mayo Type II olecranon fractures were treated non-operatively to discharge. Good to excellent results were obtained in all patients according to the MEPI. Supportive care of these fractures should be comparatively studied. A downside risk to providing supportive care for these fractures was not identified.