gebhart/patrepeval huggingface dataset:
Attention Models with Random Features for Multi-layered Graph Embeddings. (2018)

Modern data analysis pipelines are becoming increasingly complex due to the presence of multi-view information sources. While graphs are effective in modeling complex relationships, in many scenarios a single graph is rarely sufficient to succinctly represent all interactions, and hence multi-layered graphs have become popular. Though this leads to richer representations, extending solutions from the single-graph case is not straightforward. Consequently, there is a strong need for novel solutions to solve classical problems, such as node classification, in the multi-layered case. In this paper, we consider the problem of semi-supervised learning with multi-layered graphs. Though deep network embeddings, e.g. DeepWalk, are widely adopted for community discovery, we argue that feature learning with random node attributes, using graph neural networks, can be more effective. To this end, we propose to use attention models for effective feature learning, and develop two novel architectures, GrAMME-SG and GrAMME-Fusion, that exploit the inter-layer dependencies for building multi-layered graph embeddings. Using empirical studies on several benchmark datasets, we evaluate the proposed approaches and demonstrate significant performance improvements in comparison to state-of-the-art network embedding strategies. The results also show that using simple random features is an effective choice, even in cases where explicit node attributes are not available.
Microbiology of Borrelia burgdorferi (1997)

This article reviews the natural history, taxonomy, physical structure, growth requirements, and molecular structure of Borrelia burgdorferi sensu lato, the causative agent of Lyme disease. These spirochetal bacteria are maintained in nature through an infectious cycle between wild mammals and ticks. Borreliae are fastidious, slow-growing bacteria, found only in association with their arthropod or mammalian hosts in nature, and propagatable in the laboratory in a rich growth medium. The characteristic shape of borreliae is imposed by periplasmic flagella, located beneath the outer membrane and attached to the protoplasmic cylinder. The outer membrane of borreliae contains a number of abundant lipoproteins that are of serodiagnostic utility and currently under consideration as vaccine targets. The borrelial genome is unique in structure, organization, and copy number. Recent experiments demonstrate the feasibility of specific gene inactivation as a means with which to study the biology of borreliae and the pathogenesis of Lyme disease.
Low work function electron emitter hexaborides (1978)

Desirable properties of potential electron emitter materials include a high melting point, low vapor pressure and compound stability at elevated temperatures, in addition to a favorable work function φ and Richardson number. The rare-earth hexaborides combine many of these properties. We have evaluated and intercompared these properties in an attempt to establish groups of materials desirable for useful thermionic electron emitters. We find that La, Pr, and Nd hexaborides exhibit the most desirable combination of the above properties. Compounds of Pr or NdB6 with 10%–30% additions of LaB6 appear most promising as future emitter materials.
Improving Limited Labeled Dialogue State Tracking with Self-Supervision (2020)

Existing dialogue state tracking (DST) models require plenty of labeled data. However, collecting high-quality labels is costly, especially when the number of domains increases. In this paper, we address a practical DST problem that is rarely discussed, i.e., learning efficiently with limited labeled data. We present and investigate two self-supervised objectives: preserving latent consistency and modeling conversational behavior. We encourage a DST model to have consistent latent distributions given a perturbed input, making it more robust to an unseen scenario. We also add an auxiliary utterance generation task, modeling a potential correlation between conversational behavior and dialogue states. The experimental results show that our proposed self-supervised signals can improve joint goal accuracy by 8.95% when only 1% labeled data is used on the MultiWOZ dataset. We can achieve an additional 1.76% improvement if some unlabeled data is jointly trained as semi-supervised learning. We analyze and visualize how our proposed self-supervised signals help the DST task and hope to stimulate future data-efficient DST research.
Synthetic Biology Approaches to Produce C3-C6 Alcohols from Microorganisms (2012)

Biofuels synthesized from renewable resources are of increasing interest because of global energy and environmental problems. Compared to the traditional biofuel, ethanol, higher alcohols such as isobutanol and 1-butanol offer advantages such as higher energy density, lower hygroscopicity, lower vapor pressure, and compatibility with existing transportation infrastructure. Some Clostridia species are known to naturally produce isopropanol and 1-butanol. However, these fuels are not synthesized economically using native organisms. Additionally, other C3-C6 alcohols are not produced in large quantities by natural microorganisms. Synthetic biology offers an alternative approach in which synthetic pathways are engineered into user-friendly hosts for the production of these fuel molecules. These hosts could be readily manipulated to improve the production efficiency. This review summarizes recent progress in the engineering of microorganisms to produce C3-C6 alcohols.
Making single crystal colloids for photonic bandgaps in the optical domain. (1998)

We describe novel methods for making good quality colloidal crystals. We use polymethylmethacrylate (PMMA) spheres of diameter 0.8microns suspended in organic solvents between glass plates separated by about 10 microns. We have characterised the phase diagram in this confined system as a function of volume fraction and find that at volume concentrations beyond 49% a significant fraction of the suspended PMMA spheres are forced to crystallise into random close packed structures. The crystallite size is typically small (100microns) and the predominant structure is random close packed. This we confirm by single crystal light scattering measurements. We do find small areas of face centred cubic structure in these samples which we assume arises simply by chance stacking as the crystallites are typically only 10-15 layers thick. However the crystallite size can be increased simply by shearing the suspension during preparation. We also find conditions under which the formation of face centred cubic crystals can be preferential. We would present video footage of diffraction patterns formed during the shearing process where we can see clear evidence of the transition from random packing to FCC ordering.
Endocannabinoids and Peripheral Pain (2000)

For centuries cannabis has been used for the management of pain, however, clinical studies have not led to a uniform idea regarding the analgesic effectiveness of cannabis and its constituent Δ9-tetrahydrocannabinol (Δ9-THC). The discovery of anandamide and 2-arachidonylglycerol, two endogenous ligands for cannabinoid receptors, has aroused interest about the possible role for these molecules in modulation of pain perception.



The analgesic effects observed are mediated through cannabinoid receptors, localized in the brain, that interact with the noradrenergic and κ-opioid system; in the spinal cord, modulating the nociceptive perception, and on peripheral sensory neurons regulating the afferent stimulations. Anandamide is an effective antinociceptive agent, acting centrally as well as on peripheral neurons, modulating pain perception and initiation.
Discovery and Potency Optimization of 2‐Amino‐5‐arylmethyl‐1,3‐thiazole Derivatives as Potential Therapeutic Agents for Prostate Cancer (2009)

A new chemical series was identified via high-throughput screening as having antiproliferative activity on DU-145 human prostate carcinoma cell line (hit compound potency - 2.9 microM). Medicinal chemistry optimization of two peripheral diversity vectors of the hit molecule, independently, led to SAR generalizations and identification of the 'best' moieties. The latter were merged in a single compound that exhibited an over 100-fold better potency than the hit compound. For the most potent compounds it was confirmed that the observed antiproliferative potency was not associated with the compounds' non-specific cytotoxicity.
Measurement of electron emission due to energetic ion bombardment in plasma source ion implantation (1991)

An experimental procedure has been developed to measure electron emission due to energetic ion bombardment during plasma source ion implantation. Spherical targets (radius=2 cm) of copper, stainless steel, graphite, titanium alloy (Ti-6Al-4V) and aluminum alloy (6061) were biased negatively to 20, 30, and 40 kV in argon and nitrogen plasmas. A Langmuir probe was used to detect the propagating sheath edge and a Rogowski transformer was used to measure the current to the target. The measurements of electron emission coefficients compare well with those measured under similar conditions [B. Szapiro and J. J. Rocca, J. Appl. Phys. 65, 3713 (1989)].
Mechanics of the occlusive arm cuff and its application as a volume sensor (1993)

Although a common medical instrument, the mechanical function of an occlusive arm cuff has not been fully described in an engineering sense. The occlusive arm cuff is examined here using a mathematical mechanics model and experimental measurements. Cuff stretch was modeled by a nonlinear pressure-volume function. Air compression was represented by Boyle's law. An apparatus was developed to measure pressure due to the air volume pumped into the cuff for fixed arm volume. Data were obtained for two different cuff designs, and reveal a nonlinear cuff pressure-volume relationship that could be represented accurately by the mathematical model. Calibration constants are provided for the two types of occlusive cuff. Thus, the cuff pressure was found to consist of a balance between that produced by stretch of the elastic cuff bladder and that of the compression of the air contained within the bladder. The use of the gas law alone was found to be inadequate to represent the cuff mechanics. When applying the cuff to measure change in arm volume, such as during plethysmography or oscillometry, it cannot be assumed that the cuff sensitivity is constant. More precisely, it was found that the occlusive cuff is a transducer with a volume sensitivity that increases with cuff pressure and volume until it becomes nearly constant at high levels of cuff pressure (150 mmHg). A hypothetical case of a linear elastic artery with constant pulse pressure was used as input to the cuff model to illustrate the change in cuff pressure oscillations that occurs while cuff pressure is released.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis of Heparin Oligosaccharides (2003)

An efficient preparation of rare 2-O-benzoyl-3-O-benzyl-1,6-anhydro-β-l-idopyranose from commercially available diacetone α-d-glucose in five straightforward steps is described here. With this key building block in hand, the total syntheses of heparin oligosaccharides with three, five, seven, and nine sugar units are successfully carried out.
Polymer–Protein Core–Shell Nanoparticles for Enhanced Antigen Immunogenicity (2017)

Nanoengineered vaccine platforms can be modeled after viruses and other pathogens with highly organized and repetitive structures that trigger the host immune system. Here we demonstrated a pyridine-grafted poly(ε-caprolactone)-based polymer-protein core-shell nanoparticles (PPCS-NPs) platform can effectively trigger the host immune system and lead to significantly higher antibody titers.
1106 Vortical Flow Fields Around Splitter Blades in a Transonic Centrifugal Compressor Impeller (2009)

The interaction between the tip leakage vortex of the full blade and the splitter blade has been investigated on a transonic centrifugal compressor impeller with a vaneless diffuser, using large-scale numerical simulations and a vortex identification method. The interaction causes the formation of a horseshoe vortex around the leading edge of the splitter blade. The horseshoe vortex dominates the compressor performance at low flow rate. It is found that the formation process of the horseshoe vortex from its inception to its growth is greatly influenced by the circumferential position of the splitter blade.
Optical design of a variable view imaging system with the combination of a telecentric scanner and double wedge prisms (2010)

Recent developments in micro-electro-mechanical systems and biotechnology have presented an emerging need for observation of dynamic targets in three-dimensional space. Unfortunately, conventional microscopes with fixed optical parameters have difficulty supplying sufficient vision information because of occlusion, small field of view, and low depth resolution. This paper introduces the design of a variable view imaging system that can supply a flexible view with a relatively large zenith angle and simple kinematics. Because of several performance factors, a multiobjective optimization process is applied to achieve an appropriate design. A prototype system is developed and used to verify the proposed design.
Folate gene prediction of treatment response to 5-FU and leucovorin in advanced colorectal cancer. (2018)

3550 Background: 5-fluorouracil (5-FU) with the folate pro-drug leucovorin (LV) has long been backbone of chemotherapy for colorectal cancer (CRC). Low expression of folate-related genes may lead to poor response to 5-FU + LV (FLV) since poor transport and metabolization of LV yield insufficient co-factor ([6R]-5,10-methylenetetrahydrofolate) and weak inhibition of the target gene thymidylate synthase (TYMS). We have previously found a positive correlation between survival and expression of folate pathway genes in stage III CRC treated with adjuvant FLV. The aim of the present study was to relate progression-free survival (PFS) with gene expression in tumors from patients with metastasizing CRC (mCRC). Methods: Tissue samples of primary tumors were obtained at surgery from patients with mCRC (n = 143) prior to FLV-based chemotherapy. Outcome data were extracted from the Sahlgrenska University Hospital data base. Gene expression was determined with qPCR. Results: Significant positive correlations between PFS and expression of several folate relevant genes were found. After adjustment in a multiple Cox analysis of all analyzed genes, only ABCC3 remained significant (p < 0.0002). The ABCC3 protein is involved in outward transport of folates, and has preference for 10-formyltetrahydrofolate. This folate inhibits the first conversion step of LV to active co-factor. High expression of ABCC3 may therefore cause a high conversion rate of LV to co-factor, and enhanced inhibition of TYMS. After Cox analysis, ABCC3 expression levels were divided into tertiles; the low, intermediate and high levels. The intermediate and low tertiles had near identical outcomes and were combined. The high expression group had a median PFS of 10.1 months compared to 6.5 months among patients in the low expression group. Conclusions: Folate-related genes predict response to treatment with FLV in stage III and IV CRC. Outcome study after direct treatment with the direct co-factor diastereoisomer is warranted.
Blocking antibody to the β-subunit of FSH prevents bone loss by inhibiting bone resorption and stimulating bone synthesis (2012)

Low estrogen levels undoubtedly underlie menopausal bone thinning. However, rapid and profuse bone loss begins 3 y before the last menstrual period, when serum estrogen is relatively normal. We have shown that the pituitary hormone FSH, the levels of which are high during late perimenopause, directly stimulates bone resorption by osteoclasts. Here, we generated and characterized a polyclonal antibody to a 13-amino-acid-long peptide sequence within the receptor-binding domain of the FSH β-subunit. We show that the FSH antibody binds FSH specifically and blocks its action on osteoclast formation in vitro. When injected into ovariectomized mice, the FSH antibody attenuates bone loss significantly not only by inhibiting bone resorption, but also by stimulating bone formation, a yet uncharacterized action of FSH that we report herein. Mesenchymal cells isolated from mice treated with the FSH antibody show greater osteoblast precursor colony counts, similarly to mesenchymal cells isolated from FSH receptor (FSHR)(-/-) mice. This suggests that FSH negatively regulates osteoblast number. We confirm that this action is mediated by signaling-efficient FSHRs present on mesenchymal stem cells. Overall, the data prompt the future development of an FSH-blocking agent as a means of uncoupling bone formation and bone resorption to a therapeutic advantage in humans.
Sustainable drug release from polycaprolactone coated chitin-lignin gel fibrous scaffolds (2020)

Non-healing wounds have placed an enormous stress on both patients and healthcare systems worldwide. Severe complications induced by these wounds can lead to limb amputation or even death and urgently require more effective treatments. Electrospun scaffolds have great potential for improving wound healing treatments by providing controlled drug delivery. Previously, we developed fibrous scaffolds from complex carbohydrate polymers [i.e. chitin-lignin (CL) gels]. However, their application was limited by solubility and undesirable burst drug release. Here, a coaxial electrospinning is applied to encapsulate the CL gels with polycaprolactone (PCL). Presence of a PCL shell layer thus provides longer shelf-life for the CL gels in a wet environment and sustainable drug release. Antibiotics loaded into core-shell fibrous platform effectively inhibit both gram-positive and -negative bacteria without inducting observable cytotoxicity. Therefore, PCL coated CL fibrous gel platforms appear to be good candidates for controlled drug release based wound dressing applications.
Phase Dependent Voltage Contrast - An Inexpensive SEM Addition for LSI Failure Analysis (1981)

A simple and inexpensive SEM voltage contrast technique has been developed which displays die-level logic-state information by distinguishing between in- and out-of-phase signals with respect to a reference signal. The technique as currently implemented also permits on-chip delay measurements down to 75 ns with ±10% resolution. Electron beam blanking is not required.
P2‐372: Development of oligomer‐specific alpha‐synuclein antibodies (2008)

Aggregates of alpha-synuclein (a-syn) are present as Lewy bodies and Lewy neurites in the brains of patients suffering from dementia with Lewy bodies (DLB) and Parkinson′s disease (PD). Accumulating evidence suggests that oligomers, intermediately sized soluble species of the a-syn aggregation process, are primarily responsible for the neurotoxicity in these disorders. Our aim is to develop oligomer specific monoclonal antibodies as tools for studies on cell cultures and transgenic mice with a-syn pathology. Such antibodies might be useful for diagnostic purposes and for immunotherapy of DLB and PD. Mice were repeatedly immunized subcutaneously with preparations of oligomeric recombinant a-syn. Next, spleen cells were fused with mouse myeloma cells to generate antibody producing hybridomas. Finally, the generated clones were screened, using ELISA, for a-syn antibodies specifically binding to the oligomeric state. A total of five mice (Balb/c) were immunized with oligomeric a-syn preparations. All mice responded to the immunization and antibodies against monomeric, oligomeric and fibrillar a-syn forms were detected in plasma. After generation of hybridomas, some of the clones showed specificity to a-syn oligomers whereas others were more selective for a-syn monomers and fibrils. Ongoing subcloning aims at further isolating IgG-positive clones with a high degree of a-syn oligomer specificity. Preliminary results indicate that we have generated antibodies specific to a-syn oligomers. Further screening and characterization of these antibodies are ongoing.
A framework for approximating qubit unitaries (2016)

We present an algorithm for efficiently approximating of qubit unitaries over gate sets derived from totally definite quaternion algebras. It achieves ε-approximations using circuits of length O(log(1/ε)), which is asymptotically optimal. The algorithm achieves the same quality of approximation as previously-known algorithms for Clifford+T [arXiv:1212.6253], V-basis [arXiv:1303.1411] and Clifford+π/12 [arXiv:1409.3552], running on average in time polynomial in O(log(1/ε)) (conditional on a number-theoretic conjecture). Ours is the first such algorithm that works for a wide range of gate sets and provides insight into what should constitute a "good" gate set for a fault-tolerant quantum computer. Joint work with Alex Bocharov, Martin Roetteler, Jon Yard: http://arxiv.org/abs/1510.03888
Identification of frequent novel genetic alterations in small cell lung carcinoma. (1994)

We have performed a comprehensive analysis of the DNA copy number changes that occur in 18 small cell lung carcinoma cell lines using comparative genomic hybridization (Kallioniemi et al., Science (Washington DC). 258: 818-821, 1992). DNA copy number abnormalities detected in this study include previously identified increases at 1p22-32 (L-myc), 2p24-25 (N-myc), and 8q24 (c-myc) and decreases at 17p13 (p53), 13q14 (RB), and 3p. In addition, novel DNA copy number increases were detected at 5p, 1q24, and Xq26, and novel decreases were found at 22q12.1-13.1, 10q26, and 16p11.2. Many of the most common DNA copy number changes revealed are at loci not previously recognized to be important in small cell lung cancer. In addition, a number of the DNA copy number changes, including increases at 1p22-32, 2p24-25, and 3q22-25 and a decrease on 18p, were found to occur preferentially in small cell lung carcinoma lines of the "variant" phenotype. This correlation suggests that genes may reside at these loci whose overexpression or inactivation contributes to the radiation resistance or aggressive growth phenotypes characteristic of this subtype of small cell lung carcinoma.
Evidence for Papillomavirus Genus-Specific Antigens and DNA in Laryngeal Papilloma (1981)

Four juvenile laryngeal papillomas (JLPs) were examined for papillomavirus genus-specific structural antigens and polynucleotide sequences employing reagents derived from bovine papillomavirus type 1 (BPV-1). Three of four JLPs contained intranuclear antigens in the granular layer of differentiating epithelial cells of formalin-fixed, paraffin-embedded papillomas assayed by the peroxidase-antiperoxidase reaction using an antiserum prepared against purified detergent-disrupted BPV-1. Examination of these JLPs for viral sequences indicated two tumor DNA preparations contained polynucleotide sequences which hybridized to an in vitro labeled BPV-1 DNA probe under nonstringent conditions. These sequences were detectable after gel electrophoresis and immobilization of restriction-endonuclease-digested JLP DNAs onto nitrocellulose membranes. Specific hybridization of probe to digested JLP DNA was visualized as bands in autoradiograms coincidental with open circular and linearized papillomavirus DNA. Hybridization was extensively reduced when JLP DNA preparations were prehybridized to an unlabeled papillomavirus DNA heterologous to the probe. These results provide direct evidence for the association of a papillomavirus in JLP.