gebhart/patrepeval huggingface dataset:
Discovery of a Frank-Kasper σ Phase in Sphere-Forming Block Copolymer Melts (2010)

Sphere-forming block copolymers are known to self-assemble into body-centered cubic crystals near the order-disorder transition temperature. Small-angle x-ray scattering and transmission electron microscopy experiments on diblock and tetrablock copolymer melts have revealed an equilibrium phase characterized by a large tetragonal unit cell containing 30 microphase-separated spheres. This structure, referred to as the sigma (σ) phase by Frank and Kasper more than 50 years ago, nucleates and grows from the body-centered cubic phase similar to its occurrence in metal alloys and is a crystal approximant to dodecagonal quasicrystals. Formation of the σ phase in undiluted linear block copolymers (and certain branched dendrimers) appears to be mediated by macromolecular packing frustration, an entropic contribution to the interparticle interactions that control the sphere-packing geometry.
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis (2014)

To discover potential false positive functional pathway candidates and to support the results from standard statistical tests such as the Hypergeometric test, permutation tests of case control data should be carried out. The most reasonable alternative was case-control permutation, if this is not possible, SNP permutations may be carried out. Our study also demonstrates that significance values converge rapidly with an increasing number of permutations. By applying the described statistical framework we were able to discover axon guidance, focal adhesion and calcium signaling as important DCM-related pathways and Intestinal immune network for IgA production as most significant UC pathway.
Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes (2014)

Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean habitats. Strain R1(T) was isolated from a hot spring (Kunashir Island, Russia) and strain SBP2(T) was isolated from a deep gold mine (South Africa). Both isolates grew in the temperature range 30-60 °C and pH range 5.0-8.0. Strain R1(T) grew optimally at 60 °C and pH 6.0-6.5; for SBP2(T) optimal conditions were at 52 °C and pH 7.5-8.0. Both strains were capable of anaerobic respiration with nitrate and nitrite as electron acceptors as well as of microaerobic growth. They also could grow by fermentation of mono-, di- and polysaccharides. Based on their phylogenetic position and phenotypic features we suggest that the new isolates represent two novel species belonging to a new genus in the order Planctomycetales, for which the names Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov. are proposed. The type strain of Thermogutta terrifontis, the type species of the genus, is R1(T) ( = DSM 26237(T) = VKM B-2805(T)), and the type strain of Thermogutta hypogea is SBP2(T) ( = JCM 19991(T) = VKM B-2782(T)).
Supplementary Figure 1 from DLL4-Notch Signaling Mediates Tumor Resistance to Anti-VEGF Therapy <i>In Vivo</i> (2023)

&lt;p&gt;PDF file - 473K, Blockade of Notch signaling in endothelial cells by DBZ in vitro. Western blotting showed that the protein levels of activated Notch intracellular domain (NICD) and Hes-1 were significantly reduced by DBZ in human umbilical vein endothelial cells (HUVEC). HUVEC were grown to confluence and treated with increasing concentrations of DBZ for 8 hours.&lt;/p&gt;
Analysis of static versus fully-dynamic routing in IP/GMPLS over WDM optical networks with physical-layer impairment constraints (2009)

We investigate static and dynamic routing approaches in overlay IP/GMPLS over optical networks. Dynamic operation for full-wavelength services benefits from physical-layer impairment aware routing whereas static routing with sub-wavelength granularity demands relaxes transparent reach requirements.
Development of a MASH TL-3 median barrier gate. (2011)

Report regarding a median barrier gate designed to both offer protection to motorists and easier cross-median access for emergency and maintenance vehicles.
Octa: Omissions and Conflicts in Target-Aspect Sentiment Analysis (2020)

Sentiments in opinionated text are often determined by both aspects and target words (or targets). We observe that targets and aspects interrelate in subtle ways, often yielding conflicting sentiments. Thus, a naive aggregation of sentiments from aspects and targets treated separately, as in existing sentiment analysis models, impairs performance.
STRUCTURAL VIOLENCE AND WORK INJURY: THE EXPERIENCE OF UNDOCUMENTED DAY LABORERS IN SAN FRANCISCO (2000)

STRUCTURAL VIOLENCE AND WORK INJURY: THE EXPERIENCE OF UNDOCUMENTED DAY LABORERS IN SAN FRANCSICO by Nicholas David Walter B.A. (Middlebury College) 1994 A thesis submitted in partial satisfaction of the requirements for the degree of Masters of Science in Health and Medical Sciences in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, BERKELEY Committee in charge: Professor Nancy Scheper-Hughes, Chair Professor Philippe Bourgois Professor Tomas Boyce Assistant Professor Margarita Loinaz Spring 2000
BodyPart Detection in X-Ray Images (2008)

Medical Image Classification&amp; Retrieval is nowadays a hot topic. Many projects already exist in this field, like the IRMA project, but the obtained results are not yet good enough for real implementation. The goal of this report is to investigate in features that could enable a good performance for a multiclass classification task. First the database used for this student project is presented. Then, several features are described and evaluated on a benchmarked dataset. Finally, after conclusion, some indications of future work to improve the performance of such system are given.
Lysosome-associated membrane protein 3 misexpression in salivary glands induces a Sjögren's syndrome-like phenotype in mice (2021)

These results show a critical role for lysosomal trafficking in the development of SS and establish a causal relationship between LAMP3 misexpression and the development of SS.
Spatially resolved combustion measurements using crossed-beam saturated absorption spectroscopy (1982)

A technique has been developed for spatially resolved measurements of unstable radical species (such as OH, NH, CH, and CN) in combustion gases. White these species typically occur in concentrations of 0.1 % or less, they are important reaction intermediates. The development of techniques for measuring the concentration of these species is therefore of interest in combustion research.
Solvent Dependency in Stereoselective δ‐Lactam Formation of Chiral α‐Fluoromalonate Derivatives: Stereodivergent Synthesis of Heterocycles with Fluorine Containing Stereocenters Adjacent to Tertiary Stereocenters (2022)

Abstract The discovery and investigation of solvent dependency in stereoselective intramolecular amidation of chiral 5‐aminofunctionalized‐2‐fluoromalonate ester derivatives, which gives access to highly functionalized δ‐lactams with a quaternary fluorine‐containing stereocenter, is disclosed. Experimental work together with density functional theory calculations led to understanding of how to direct and switch the stereochemical outcome of the stereoselective δ‐lactam formation. The merging of this solvent‐dependent stereoselective switch with asymmetric catalysis and cascade reactions gives access to an unprecedented strategy for stereodivergent synthesis of all possible stereoisomers of fluorine‐containing stereocenters adjacent to tertiary stereocenters of a wide range of heterocyclic compounds with 95‐&gt;99% ee in one‐pot. It is also useful for application in total synthesis of fluorine‐containing pharmaceuticals. magnified image
ChemInform Abstract: REACTIONS OF DICARBONYL COMPOUNDS WITH β‐OXOGLUTARIC ACID‐ SYNTHESIS OF 4‐HYDROXY‐3,4‐DIPHENYLCYCLOPENT‐2‐ENONE‐2‐CARBOXYLIC ACID (1977)

Abstract Die Wiederaufnahme der Reaktion von Benzil (I) mit der Ketoglutarsäure (II) ergibt die erwartete Hydroxycyclopentencarbonsäure (III).
Effects of Glutamine‐Enriched Parenteral Nutrition on the Exocrine Pancreas (1990)

Total parenteral nutrition (TPN) is associated with intestinal and pancreatic atrophy and pancreatic exocrine insufficiency. Recent investigations have demonstrated that the addition of glutamine to intravenous feedings attenuates TPN-associated intestinal atrophy. However, the effect of glutamine-supplemented intravenous feedings on the pancreas of intact animals is unknown. This study compared the effects of an intravenous infusion of a 2% glutamine-enriched diet (GLN) with an isonitrogenous, isocaloric diet without glutamine (CONT) on the composition and structure of the exocrine pancreas in laboratory rats with and without a 60% small bowel resection. In nonresected, TPN-fed animals, pancreatic weight was significantly increased in the GLN group when compared to CONT (645 +/- 33 g vs 554 +/- 20 g, p less than 0.05). Nonresected GLN animals also had increased pancreatic DNA (3.82 +/- 0.19 mg vs 2.91 +/- 0.49 mg, p less than 0.005) and protein contents (93.0 +/- 5.9 mg vs 76.6 +/- 7.0 mg, p = 0.08) compared to control. Similar significant increases in pancreatic weight, DNA, and protein were observed in intestinally resected animals fed the glutamine diet. When data from CONT and GLN animals were pooled and analyzed together, glutamine significantly increased total pancreatic trypsinogen and lipase contents (p less than 0.05). The increase in trypsinogen in resected GLN animals was significantly greater than in CONT animals (283 +/- 22 vs 139 +/- 23, p less than 0.005). Biochemical and morphometric observations demonstrated that the trophic effects of glutamine on the exocrine pancreas were manifest by acinar hyperplasia and not hypertrophy. Glutamine appears to be an important nutrient for pancreatic exocrine tissue during TPN.(ABSTRACT TRUNCATED AT 250 WORDS)
Jam Sessions: Analysis and Experimental Evaluation of Advanced Jamming Attacks in MIMO Networks (2019)

In advanced jamming, the adversary intentionally concentrates the available energy budget on specific critical components (e.g., pilot symbols, acknowledgement packets, etc.) to (i) increase the jamming effectiveness, as more targets can be jammed with the same energy budget; and (ii) decrease the likelihood of being detected, as the channel is jammed for a shorter period of time. One of the fundamental challenges in designing defense mechanisms against an advanced jammer is understanding which jamming strategies yields the lowest throughput, for a given channel condition and a given amount of energy. To the best of our knowledge, this problem still remains unsolved. To fill this gap, in this paper we conduct a comparative analysis of several most viable advanced jamming schemes in the widely-used MIMO networks. We first mathematically model a number of advanced jamming schemes at the signal processing level, so that a quantitative relationship between the jamming energy and the jamming effect is established. Based on the model, theorems are derived on the optimal advanced jamming scheme for an arbitrary channel condition. The theoretical findings are validated through extensive simulations and experiments on a 5-radio 2x2 MIMO testbed. Our results show that the theorems are able to predict jamming efficiency with high accuracy. Moreover, we show that the theorems can be incorporated to state-of-art reinforcement learning based jamming algorithms and boost the action exploration phase so that a faster convergence is achieved.
Quantifying the Effect of Multivalent Ions in Polyelectrolyte Solutions (2021)

We implemented a scaling approach, based on the relationship between the solution correlation length ξ = lgν/B and the number of repeat units per correlation blob g for polymers with repeat unit projection length l, to quantify properties of solutions of carboxymethylcellulose and polystyrene sulfonate with monovalent and divalent counterions. The parameter B is equal to Bpe, Bg, Bth, and 1, and the exponent v = 1, 0.588, 0.5, and 1 in semidilute polyelectrolyte solutions, solutions of overlapping electrostatic and thermal blobs, and concentrated polymer solutions, which are separated by crossover concentrations cD, cth, and c**, respectively. The values of the B-parameters are obtained using the linear relationship between the specific viscosity ηsp(c) in the unentangled solution regime and the number of correlation blobs Nw/g per chain, with the weight-average degree of polymerization, Nw, and g = B3/(3ν–1)(cl3)1/(1–3ν) as a function of the repeat unit concentration, c, and the B-parameters in different solution regimes. This analysis shows that (i) there is only a small fraction of free counterions, f* < 12%; (ii) divalent ions have a strong effect on the renormalization of the excluded volume, reducing it by a factor of 2; and (iii) the effect of divalent counterions is much weaker on the renormalization of the Kuhn length, accounting for an increase of up to 10%. In combination, these effects significantly reduce chain stretching, increase the number of repeat units per solution correlation length, and promote chain disentanglement in polyelectrolyte solutions with divalent ions in comparison with that in solutions with monovalent counterions. There is an indication of chain bridging by Ca2+ ions in concentrated solutions of carboxymethylcellulose, manifested as an increase in solution viscosity. The concentration dependence of the solution correlation length ξ calculated using the set of B-parameters is in good agreement with that obtained from the peak position of the scattering function for concentrations c < cD.
VO2 electro-optic memory and oscillator for neuromorphic computing (2020)

We demonstrate optical memory and light-triggered electrical oscillations in a VO2 electro optic micro-wire device for potential applications in neuromorphic computing architectures.
Effect of ibrutinib treatment on hemolytic anemia and acrocyanosis in cold agglutinin disease/cold agglutinin syndrome (2021)

Cold antibody-mediated autoimmune hemolytic anemia (cAIHA) is a rare disease, usually related to an underlying indolent clonal B-cell lymphoproliferative disorder. Jalink and colleagues describe an international retrospective analysis of Bruton tyrosine kinase (BTK) inhibition in patients with cAIHA. The data indicate a rapid and notable improvement in both the hemolytic anemia as well as acrocyanosis, suggesting that this may be an effective approach, regardless of underlying pathology or MYD88 mutational status.
Fluidic self-assembly of micromirrors onto microactuators using capillary forces (2002)

The authors discuss the application of self-assembly techniques for positioning microscopic components onto a substrate in a desired configuration. The basis is a fluidic self-assembly technique in which capillary forces assemble microparts with submicrometer alignment precision. A heat-curable acrylate-based adhesive is used to provide the capillary forces for assembly and is then polymerized in a bath of water at 80/spl deg/C for 16 h with continuous nitrogen bubbling. The application we describe is self-assembly of flat silicon micromirrors; onto surface-micromachined actuators for use in an adaptive-optics mirror array. Photolithography defines shapes of hydrophobic self-assembled monolayers for self-assembly. Mirrors with fill factors up to 95% were assembled. Mirrors 464 /spl mu/m in diameter and assembled onto actuators remain flat to within 6 nm rms. This mirror quality would be difficult to attain without the process decoupling afforded by microassembly. The general self-assembly approach described here can be applied to parts ranging in size from the nanometer to the millimeter scale and to a variety of part and substrate materials.
Parameter Selection for Wyner–Ziv Coding of Laplacian Sources with Additive Laplacian or Gaussian Innovation (2009)

A large number of practical coding scenarios deal with sources such as transform coefficients that can be well modeled as Laplacians. For regular coding of such sources, samples are often quantized by a family of uniform quantizers possibly with a deadzone, and then entropy coded. For the Wyner-Ziv coding problem when correlated side-information is available at the decoder, the side-information can be modeled as obtained by independent additive Laplacian or Gaussian innovation on the source. This paper deals with optimal choice of parameters for practical Wyner-Ziv coding in such scenarios, using the same quantizer family as in the regular codec to cover a range of rate-distortion tradeoffs, given the variances of the source and additive noise. We propose and analyze a general encoding model based on multilevel coset codes that combines source coding and channel coding and show that at practical block lengths and code complexities, not pure channel coding but a hybrid combination of source coding and channel coding with right parameters provide optimal rate-distortion performance. We also provide a framework for on-the-fly parameter choice based on nonparametric representation of a set of seed functions, for use in scenarios where variances are estimated during encoding. A good insight in the optimal parameter selection mechanism is essential for building practical distributed codecs.
Supplementary Figure 3 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition (2023)

Supplementary Figure 3 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition
A novel similarity-invariant line descriptor for geometric map registration (2013)

In this paper we present a new line descriptor that can be used in the process of tracking 2D navigation maps that are low in texture details. The problem of tracking this kind of maps is very important in the development and testing phases of a navigation system. In order to track the motion of the map, which could be a translation, rotation, or scale (also known as similarity transform), line segments are used as features and are matched between two consecutive frames using the proposed descriptor in order to determine the motion between the frames. The descriptor is shown to be very robust against typical translation, rotation, and scale transformations, while requiring an acceptable processing time.
60. USEFULNESS OF KINEMATIC ANALYSIS AND EMG FOR THERAPEUTIC DECISION MAKING FOR UPPER LIMB DISORDERS IN CEREBRAL PALSY CHILDREN (2011)

Purpose of the study: Clinical assessment of the upper limb in the cerebral palsy child remains difficult, and minimally reproducible. Thus many authors use for the upper limb, as for the lower limb, movement analysis to aid in decision making and obtain an objective measurement of postoperative results. Material and method: Kinematic analysis and EMG were performed with the Vicon system in 27 cerebral palsy children with a spastic upper limb. The patients were compared with data obtained in a control population of 12 children. Eight patients had a second assessment after treatment. The experimental protocol followed the recommendations of the International Society of Biomechanics. The muscles targeted by the treatment were the pronator teres, the flexor carpi ulnaris, and the adductor pollicis (lengthening, transfer, toxin injection). Results: Significant kinematic anomalies (p Discussion: Kinematic and EMG anomalies involving the trunk, shoulder and elbow represent motor strategies compensating for distal anomalies: – recruitment of the biceps allows improved supination, pulls the elbow in flexion. Since the patient cannot extend the elbow to achieve a task, compensation with the trunk increases the amplitude of the flexion-extension movement; – ‘extrinsic’ supination is achieved via an increase in external rotation of the arm in relation to the trunk and homolateral inclination of the trunk. Conclusion: These observations have therapeutic implications: clinical, kinematic or EMG anomalies involving the trunk, shoulder, and elbow should not be treated per se but reevaluated after treatment of more distal anomalies.
Autoinhibitory regulation of S100A8/S100A9 alarmin activity locally restricts sterile inflammation (2018)

Autoimmune diseases, such as psoriasis and arthritis, show a patchy distribution of inflammation despite systemic dysregulation of adaptive immunity. Thus, additional tissue-derived signals, such as danger-associated molecular patterns (DAMPs), are indispensable for manifestation of local inflammation. S100A8/S100A9 complexes are the most abundant DAMPs in many autoimmune diseases. However, regulatory mechanisms locally restricting DAMP activities are barely understood. We now unravel for the first time, to our knowledge, a mechanism of autoinhibition in mice and humans restricting S100-DAMP activity to local sites of inflammation. Combining protease degradation, pull-down assays, mass spectrometry, and targeted mutations, we identified specific peptide sequences within the second calcium-binding EF-hands triggering TLR4/MD2-dependent inflammation. These binding sites are free when S100A8/S100A9 heterodimers are released at sites of inflammation. Subsequently, S100A8/S100A9 activities are locally restricted by calcium-induced (S100A8/S100A9)2 tetramer formation hiding the TLR4/MD2-binding site within the tetramer interphase, thus preventing undesirable systemic effects. Loss of this autoinhibitory mechanism in vivo results in TNF-α-driven fatal inflammation, as shown by lack of tetramer formation in crossing S100A9-/- mice with 2 independent TNF-α-transgene mouse strains. Since S100A8/S100A9 is the most abundant DAMP in many inflammatory diseases, specifically blocking the TLR4-binding site of active S100 dimers may represent a promising approach for local suppression of inflammatory diseases, avoiding systemic side effects.
Inhibition of breast cancer metastasis to the lungs with UBS109 (2018)

Synthetic monocarbonyl analogs of curcumin (MACs) are cytotoxic against several cancers including head and neck cancer, pancreatic cancer, colon cancer, and breast cancer. Mechanisms of action include depolarization of the mitochondrial membrane potential and inhibition of NF-κB, leading to apoptosis. We previously demonstrated that UBS109 (MAC), has preventive effects on bone loss induced by breast cancer cell lines. We determined whether UBS109 could inhibit and prevent lung metastasis, since lung metastasis of breast cancer is a major problem in addition to bone metastasis. A breast cancer lung metastasis (colonization) model was created by injection of breast cancer cells MDA-MB-231 into the tail vein of athymic nude mice, nu/nu. Animals were treated with vehicle or UBS109 at 5 or 15 mg/kg body weight by intraperitoneal injection once daily 5 days a week for 5 weeks. UBS109 at 15 mg/kg significantly inhibited lung metastasis/colonization as demonstrated by reduced lung weight consisting of tumor nodules. The body weight of animals treated with UBS109 15 mg/kg remained the same as in the other groups. UBS109 killed completely (100%) MDA-MB-231 breast cancer cells at 1.25 μM in a cytotoxicity assay <i>in vitro</i>. UBS109 15 mg/kg i.p. showed a maximal blood concentration (C<sub>max</sub>) of 432 ± 387 ng/mL at 15 min post injection. This is approximately 1.5 ng/ml in the blood of mice and equals 1.5 μM of UBS109. These <i>in vitro</i> and <i>in vivo</i> results are consistent with each other.