gebhart/patrepeval huggingface dataset:
Preferential and Comprehensive Reconstitution of Severely Damaged Sciatic Nerve Using Murine Skeletal Muscle-Derived Multipotent Stem Cells (2014)

Loss of vital functions in the somatic motor and sensory nervous systems can be induced by severe peripheral nerve transection with a long gap following trauma. In such cases, autologous nerve grafts have been used as the gold standard, with the expectation of activation and proliferation of graft-concomitant Schwann cells associated with their paracrine effects. However, there are a limited number of suitable sites available for harvesting of nerve autografts due to the unavoidable sacrifice of other healthy functions. To overcome this problem, the potential of skeletal muscle-derived multipotent stem cells (Sk-MSCs) was examined as a novel alternative cell source for peripheral nerve regeneration. Cultured/expanded Sk-MSCs were injected into severely crushed sciatic nerve corresponding to serious neurotmesis. After 4 weeks, engrafted Sk-MSCs preferentially differentiated into not only Schwann cells, but also perineurial/endoneurial cells, and formed myelin sheath and perineurium/endoneurium, encircling the regenerated axons. Increased vascular formation was also observed, leading to a favorable blood supply and waste product excretion. In addition, engrafted cells expressed key neurotrophic and nerve/vascular growth factor mRNAs; thus, endocrine/paracrine effects for the donor/recipient cells were also expected. Interestingly, skeletal myogenic capacity of expanded Sk-MSCs was clearly diminished in peripheral nerve niche. The same differentiation and tissue reconstitution capacity of Sk-MSCs was sufficiently exerted in the long nerve gap bridging the acellular conduit, which facilitated nerve regeneration/reconnection. These effects represent favorable functional recovery in Sk-MSC-treated mice, as demonstrated by good corduroy walking. We also demonstrated that these differentiation characteristics of the Sk-MSCs were comparable to native peripheral nerve-derived cells, whereas the therapeutic capacities were largely superior in Sk-MSCs. Therefore, Sk-MSCs can be a novel/suitable alternative cell source for healthy nerve autografts.
3-Phenyl-4-acyl-5-isoxazolonate complex of Tb3+ doped into poly-β-hydroxybutyrate matrix as a promising light-conversion molecular device (2009)

A novel class of efficient antenna complexes of Tb3+ based on the use of 3-phenyl-4-acyl-5-isoxazolone ligands has been designed, synthesized, characterized and their photophysical properties evaluated . The new heterocyclic β-diketonate complexes of Tb3+ exhibit high green luminescence efficiency in the solid state with quantum yields between 59–72%. Furthermore in this work, the synthesis, characterization and luminescent properties of poly-β-hydroxybutyrate (PHB) polymer films doped with Tb3+-3-phenyl-4-acyl-5-isoxazolonate complexes at 5, 10, 15 and 20% (mass) are reported. The fact that the luminescent efficiency of doped films is enhanced (quantum yields between 74–86%) compared with precursor samples revealed that the polymer matrix acts as a co-sensitizer for Tb3+centers. The luminescence intensity decreases, however, with increasing precursor concentration in the doped PHB to greater than 15% where a saturation effect is observed, indicating that changes in the polymer matrix improve the absorption properties of the film, consequently quenching the luminescent effect. Synthesized luminescent polymers containing Tb3+-hetrocyclic β-diketonate complexes showed promising photoluminescence efficiency for applications to polymer light-emitting diodes and active polymer optical fibers.
Nemacol is a small molecule inhibitor of C. elegans vesicular acetylcholine transporter with anthelmintic potential (2023)

Nematode parasites of humans and livestock pose a significant burden to human health, economic development, and food security. Anthelmintic drug resistance is widespread among parasites of livestock and many nematode parasites of humans lack effective treatments. Here, we present a nitrophenyl-piperazine scaffold that induces motor defects rapidly in the model nematode Caenorhabditis elegans. We call this scaffold Nemacol and show that it inhibits the vesicular acetylcholine transporter (VAChT), a target recognized by commercial animal and crop health groups as a viable anthelmintic target. We demonstrate that it is possible to create Nemacol analogs that maintain potent in vivo activity whilst lowering their affinity to the mammalian VAChT 10-fold. We also show that Nemacol enhances the ability of the anthelmintic Ivermectin to paralyze C. elegans and the ruminant nematode parasite Haemonchus contortus. Hence, Nemacol represents a promising new anthelmintic scaffold that acts through a validated anthelmintic target.
Local stability of Belief Propagation algorithm with multiple fixed points (2012)

A number of problems in statistical physics and computer science can be expressed as the computation of marginal probabilities over a Markov random field. Belief propagation, an iterative message-passing algorithm, computes exactly such marginals when the underlying graph is a tree. But it has gained its popularity as an efficient way to approximate them in the more general case, even if it can exhibits multiple fixed points and is not guaranteed to converge. In this paper, we express a new sufficient condition for local stability of a belief propagation fixed point in terms of the graph structure and the beliefs values at the fixed point. This gives credence to the usual understanding that Belief Propagation performs better on sparse graphs.
Formation of Double-Strand Dimetallic Helicates with a Terpyridine-Based Macrocycle (2014)

The macrocyclic ligand (L), containing two terpyridine (terpy) and two ethylenediamine (en) groups arranged in a cyclic terpy-en-terpy-en sequence, forms a double-strand helicate Cu2L(4+) complex made especially stable by the formation of interstrand π-π stacking interactions involving opposite pyridine rings. The crystal structure of this complex shows the Cu(2+) cations in square pyramidal coordination environments defined by the donor atoms of half ligand chain composed, in sequence, by one pyridine ring, the connected ethylenediamine moiety and the two adjacent pyridine rings of the successive terpyridine. In aqueous solution, L forms both mono- and binuclear complexes with Cu(2+). The stability constants determined for these complexes evidence the combined action of the two metal ions in the assembly of the very stable helicate species, the binding of the first metal ion favoring the entrance of the second one. UV adsorption and emission spectra corroborate these equilibrium results. Furthermore, the Cu2L(4+) complex shows a significant inertness toward dissociation in acidic solutions. Also Zn(2+) forms mono- and binuclear complexes with L, although the Zn2L(4+) complex is much weaker than the Cu2L(4+) helicate and gives rise to fast dissociation reactions in acidic media. Experimental evidence allows neither to say that also the Zn(2+) complex has a helicate structure nor to exclude it.
Marked enhancement of the photoresponsivity and minority-carrier lifetime of BaSi2 passivated with atomic hydrogen (2019)

Passivation of barium disilicide ($\mathrm{BaS}{\mathrm{i}}_{2}$) films is very important for their use in solar cell applications. In this paper, we demonstrated the effect of hydrogen (H) passivation on both the photoresponsivity and minority-carrier lifetime of $\mathrm{BaS}{\mathrm{i}}_{2}$ epitaxial films grown by molecular beam epitaxy. First, we examined the growth conditions of a 3-nm-thick hydrogenated amorphous silicon (a-Si) capping layer formed on a 500-nm-thick $\mathrm{BaS}{\mathrm{i}}_{2}$ film and found that an H supply duration (${t}_{\mathrm{a}\text{\ensuremath{-}}\mathrm{Si}:\mathrm{H}}$) of 15 min at a substrate temperature of 180 \ifmmode^\circ\else\textdegree\fi{}C sizably enhanced the photoresponsivity of the $\mathrm{BaS}{\mathrm{i}}_{2}$ film. We next supplied atomic H to $\mathrm{BaS}{\mathrm{i}}_{2}$ epitaxial films at 580 \ifmmode^\circ\else\textdegree\fi{}C and changed supply duration (${t}_{\mathrm{BaSi};\mathrm{H}}$) in the range of 1--30 min, followed by capping with an a-Si layer. The photoresponsivity of the films changed considerably depending on ${t}_{\mathrm{BaSi};\mathrm{H}}$ and reached a maximum of 2.5 A/W at a wavelength of 800 nm for the sample passivated for ${t}_{\mathrm{BaSi};\mathrm{H}}=15$ min under a bias voltage of 0.3 V applied to the front-surface indium-tin-oxide electrode with respect to the back-surface aluminum electrode. This photoresponsivity is approximately one order of magnitude higher than the highest value previously reported for $\mathrm{BaS}{\mathrm{i}}_{2}$. Microwave photoconductivity decay measurements revealed that the minority-carrier lifetime of the $\mathrm{BaS}{\mathrm{i}}_{2}$ film with the highest photoresponsivity was 14 \ensuremath{\mu}s, equivalent to its bulk carrier lifetime ever reported. We performed theoretical analyses based on a rate equation including several recombination mechanisms and reproduced the experimentally obtained decay curves. We also calculated the total density of states of $\mathrm{BaS}{\mathrm{i}}_{2}$ by ab initio studies when one Si vacancy existed in a unit cell and one, two, and three H atoms occupied Si vacancy or interstitial sites. A Si vacancy caused a localized state with two energy bands to appear close to the middle of the band gap. In certain cases, H passivation of the Si dangling bonds can markedly decrease trap concentration. From both experimental and theoretical viewpoints, we conclude that an atomic H supply is beneficial for $\mathrm{BaS}{\mathrm{i}}_{2}$ solar cells.
Ribonuclease activity associated with human eosinophil-derived neurotoxin and eosinophil cationic protein. (1986)

The eosinophil granule contains a series of basic proteins, including major basic protein, eosinophil peroxidase, eosinophil-derived neurotoxin (EDN), and eosinophil cationic protein (ECP). Both EDN and ECP are neurotoxins and helminthotoxins. Comparison of the partial N-terminal amino acid sequences of EDN and ECP showed 67% identity; surprisingly, they also showed structural homology to pancreatic ribonuclease (RNase). Therefore, we determined whether EDN and ECP possess RNase enzymatic activity. By spectrophotometric assay of acid soluble nucleotides formed from yeast RNA, purified EDN showed RNase activity similar to bovine pancreatic RNase, whereas ECP was 50 to 100 times less active. The RNase activity associated with ECP was not significantly inhibited after exposure of ECP to polyclonal or monoclonal antibody to EDN. These results indicate that EDN and ECP both possess RNase activity, the RNase activity of EDN and ECP is specific, and EDN and ECP have maintained not only structural but also functional homology to pancreatic RNase.
Robust contextual models for in-session personalization (2019)

Most online activity happens in the context of a session; to enable better user experience many online platforms aim to dynamically refine their recommendations as sessions progress. A popular approach is to continuously re-rank recommendations based on current session activity and past session logs. This motivates the 2019 ACM RecSys Challenge organised by Trivago. Using the session log dataset released by Trivago, the challenge aims to benchmark models for in-session re-ranking of hotel recommendations. In this paper we present our approach to this challenge where we first contextualize sessions in a global and local manner, and then train gradient boosting and deep learning models for re-ranking. Our team achieved 2nd place out of over 570 teams, with less than 0.3% relative difference in Mean Reciprocal Rank from the 1st place team. Code for our approach can be found here: https://github.com/layer6ai-labs/RecSys2019
Design and Realization of a Non-Circular Cable Spool to Synthesize a Nonlinear Rotational Spring (2012)

Abstract In this paper we present a cable mechanism that realizes a nonlinear rotational spring from a linear translational spring. The spring is pulled by a cable wound around a non-circular spool, which is rigidly attached to the joint. The non-circular shape of the spool induces a nonlinear relationship between its angular position and the torque created by the tension of the cable. Depending on the shape of the spool, various torque–angle relationships can be realized. We show that for a given nonlinear torque–angle relationship, there is an explicit expression (closed-form solution) of the shape of the spool that synthesizes this function. First, we present the geometry of the problem. Then, we derive the methodology to calculate the shape of the spool to synthesize a prescribed torque–angle relationship. Finally, we verify the design methodology by experiments with three different spools realizing a constant force spring, an exponential softening spring and a cubic polynomial spring. We discuss the possible sources of errors between the theoretical and experimental results. Keywords: NONLINEAR SPRINGNONLINEAR STIFFNESSTENDON-DRIVEN MECHANISMMECHANICAL SYNTHESIS
Advection-Based Adjustment of Radar Measurements (2011)

When making radar-based precipitation products, a radar measurement is commonly taken to represent the geographical location vertically below the contributing volume of the measurement sample. However, when wind is present during the fall of the hydrometeors, precipitation will be displaced horizontally from the geographical location of the radar measurement. Horizontal advection will introduce discrepancies between the radar-measured and ground level precipitation fields. The significance of the adjustment depends on a variety of factors related to the characteristics of the observed precipitation as well as those of the desired end product. In this paper the authors present an advection adjustment scheme for radar precipitation observations using estimated hydrometeor trajectories obtained from the High-Resolution Limited-Area Model (HIRLAM) MB71 NWP model data. They use the method to correct the operational Finnish radar composite and evaluate the significance of precipitation advection in typical Finnish conditions. The results show that advection distances on the order of tens of kilometers are consistently observed near the edge of the composite at ranges of 100–250 km from the nearest radar, even when using a low elevation angle of 0.3°. The Finnish wind climatology suggests that approximately 15% of single radar measurement areas are lost on average when estimating ground level rainfall if no advection adjustment is applied. For the Finnish composite, area reductions of approximately 10% have been observed, while the measuring area is extended downstream by a similar amount. Advection becomes increasingly important at all ranges in snowfall with maximum distances exceeding 100 km.
Adaptive control of a class of multivariable nonaffine systems (2007)

A neural synthesis method is considered for a class of multivariable nonaffine uncertain systems. The method extends the previous approach developed in a single-input single-output system to a mufti-input multi-output system without resorting to a fixed-point assumption or boundedness assumption on the time derivative of a control effectiveness term. By assuming that the uncertain input matrix term is dominated by the known part of the input matrix, we show that a new inverting method can be developed taking nonaffineness into account for its synthesis procedure. Using Lyapunov’s direct method, it is shown that all the signals of the closed-loop system are uniformly ultimately bounded, and that the tracking error converges to an adjustable neighborhood of the origin. Simulation with a double Van Der Pol system having nonaffine control terms illustrates the approach.
ChemInform Abstract: Reactions of Substituted 2,3‐Dihydro‐1H‐indol‐3‐ones and Pyrrolo[2,3‐b]pyridin‐3‐ones with Wittig and Horner—Emmons Reagents: Synthesis of 7‐Azatryptamine. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Electron microscopy reveals that archaeal box C/D sRNPs are di‐sRNPs (2009)

Methylation of ribosomal RNA (rRNA) is required for optimal protein synthesis. Multiple 2′‐O‐ribose methylations are carried out by small (nucleolar) box C/D guide ribonucleoproteins (s(no)RNPs), which are ubiquitous in nature from archaea to eukaryotes. Each site of methylation is dictated by base pairing between the specific guide s(no)RNA component of the s(no)RNP and the target rRNA. We have determined the first structure of a reconstituted and catalytically active box C/D sRNP by electron microscopy and single particle analysis. Our results reveal that archaeal box C/D sRNPs form an unexpected di‐sRNP structure which is required for efficient methylation activity, challenging the conventional paradigm of box C/D s(no)RNP architecture. This work was supported by the NIH and the Boehringer Ingelheim Fonds.
Computer‐aided diagnosis of pulmonary nodules on CT scans: Segmentation and classification using 3D active contours (2006)

We are developing a computer-aided diagnosis (CAD) system to classify malignant and benign lung nodules found on CT scans. A fully automated system was designed to segment the nodule from its surrounding structured background in a local volume of interest (VOI) and to extract image features for classification. Image segmentation was performed with a three-dimensional (3D) active contour (AC) method. A data set of 96 lung nodules (44 malignant, 52 benign) from 58 patients was used in this study. The 3D AC model is based on two-dimensional AC with the addition of three new energy components to take advantage of 3D information: (1) 3D gradient, which guides the active contour to seek the object surface, (2) 3D curvature, which imposes a smoothness constraint in the z direction, and (3) mask energy, which penalizes contours that grow beyond the pleura or thoracic wall. The search for the best energy weights in the 3D AC model was guided by a simplex optimization method. Morphological and gray-level features were extracted from the segmented nodule. The rubber band straightening transform (RBST) was applied to the shell of voxels surrounding the nodule. Texture features based on run-length statistics were extracted from the RBST image. A linear discriminant analysis classifier with stepwise feature selection was designed using a second simplex optimization to select the most effective features. Leave-one-case-out resampling was used to train and test the CAD system. The system achieved a test area under the receiver operating characteristic curve (A(z)) of 0.83 +/- 0.04. Our preliminary results indicate that use of the 3D AC model and the 3D texture features surrounding the nodule is a promising approach to the segmentation and classification of lung nodules with CAD. The segmentation performance of the 3D AC model trained with our data set was evaluated with 23 nodules available in the Lung Image Database Consortium (LIDC). The lung nodule volumes segmented by the 3D AC model for best classification were generally larger than those outlined by the LIDC radiologists using visual judgment of nodule boundaries.
Heat Inactivation of Milk-Clotting Enzymes at Different pH (1979)

Thermal-death-time characteristics were determined for three milk-clotting enzymes and one mixture of enzymes for pH from 4.5 to 6.5 in Jenness-Koops buffer. Means for temperature dependence coefficients (z) in this pH range were 4.22 C for Mucor michel protease, 4.62 C for Mucor pusillus protease, 5.40 C for rennet, and 5.23 C for a 50:50 blend of rennet and pepsin. Activation energies were calculated for each enzyme or the mixture of rennet and pepsin and means were 131.5 kcal/mole for Mucor miebei protease, 116.8 kcal/mole for Mucor pusillus protease, 97.0 kcal/mole for rennet, and 99.6 kcal/mole for 50:50 rennet-pepsin mixture. For each enzyme, heat resistance increased as pH decreased. To accomplish 90% inactivation of each enzyme and the mixture in 15 s at pH 6.0, these temperature treatments were required: Mucor miebei, 77 C; Mucor pusillus protease, 71 C; and rennet and rennet-pepsin, 67 C.
Central depressant effect of l-tetrahydroberberine-d-camphor sulfonate (THB-CS) Electroencephalographic study. (1986)

Effects of l-tetrahydroberberine-d-camphor sulfonate (THB-CS) on spontaneous EEG, arousal response and recruiting response were investigated in rabbits and rats in comparison with those of chlorpromazine. The spontaneous EEG recorded from the motor cortex and hippocampus showed a prominent resting pattern 3-5 min after intravenous administration of THB-CS in doses more than 0.01 mg/kg in rabbits and 30 min after oral administration of the drug in doses more than 1 mg/kg in rats. These effects lasted for 30-60 min after i.v. administration and 60-90 min after oral administration; however, the effects were not proportional to the doses up to 8 mg/kg (i.v.) and 12.5 mg/kg (p.o.). The abnormal characteristics of the EEG pattern such as seizure pattern and flattening were not observed. Chlorpromazine also produced the resting pattern in doses of 2 mg/kg (i.v.) in rabbits and 1 mg/kg (p.o.) in rats. THB-CS and chlorpromazine produced a slight elevation of threshold for the EEG arousal response elicited by high frequency stimulation of the midbrain reticular formation, but did not alter the recruiting response elicited by low frequency stimulation of the centromedian nucleus of the thalamus. These results suggest that the effects of THB-CS resemble those of chlorpromazine, but are different from those of barbiturates.
Isolation of Circulating Tumor Cells by Size Exclusion using Lithography Fabricated Precision Microfilters (2011)

rapid and highly efficient isolation of circulating tumor cells (CTCs) from peripheral blood. Isolation of CTCs by size exclusion is a widely researched technique with the advantage of capturing tumor cells without reliance on cell surface expression markers. For many years CTC filtration has relied on track-etch filters with randomly distributed pores and lowporosity. Our lithography based fabrication method makes precise, high porosity microfilters suitable for microfiltration applications. These microfilters are strong, transparent, and have high CTC capture efficiency. Isolation of Circulating Tumor Cells by Size Exclusion using Lithography Fabricated Precision Microfilters