gebhart/patrepeval huggingface dataset:
Coupled Representation Learning for Domains, Intents and Slots in Spoken Language Understanding (2018)

Representation learning is an essential problem in a wide range of applications and it is important for performing downstream tasks successfully. In this paper, we propose a new model that learns coupled representations of domains, intents, and slots by taking advantage of their hierarchical dependency in a Spoken Language Understanding system. Our proposed model learns the vector representation of intents based on the slots tied to these intents by aggregating the representations of the slots. Similarly, the vector representation of a domain is learned by aggregating the representations of the intents tied to a specific domain. To the best of our knowledge, it is the first approach to jointly learning the representations of domains, intents, and slots using their hierarchical relationships. The experimental results demonstrate the effectiveness of the representations learned by our model, as evidenced by improved performance on the contextual cross-domain reranking task.
Colorimetric gold nanoparticles-based assay for direct detection of Clostridium difficile in clinical isolates from Qatar (2017)

Clostridium difficile infection (CDI) is a significant health problem worldwide. Control and prevention strategies of C. difficile horizontal transmission require assays with fast detection with high specificity and sensitivity. Conventional diagnostic methods are time consuming and costly for clinical field settings. This study aims to develop gold nanoparticles (AuNPs)-based assay for direct qualitative detection of the nucleic acid of C. difficile and its toxins. A colloidal solution of AuNPs with a diameter of 13±1 nm was prepared and characterized. The qualitative colorimetric AuNPs assay was developed for restricted genomic C. difficile DNA detection, and results were confirmed by PCR. One hundred and five positive C. difficile isolates were collected from patients with diarrheal diseases and tested using AuNPs based-assay. Ninety-six samples (91.4%) were detected positive using AuNPs based assay, as indicated by the color change from red to blue within 1 min. All ninety-six positive samples were positive for toxin B. In conclusion, nano-gold assay prototype was developed for direct and inexpensive detection of C. difficile. The developed prototypes are simple, sensitive, rapid and can substitute PCR-based detection. The developed assay may show potential in the clinical diagnosis of C. difficile, especially in developing countries as it is less costly as compared to the commercially available assays.
Abstract WP136: Grafted Human Neural Stem Cell-Secreted Matrilin-2 Improves Functional Recovery in Ischemic-Stroke Rats (2019)

Identifying the secretome of grafted stem cells is an important first step to elucidate how the graft communicates with the host brain, at the molecular level , to enhance post-stroke recovery. Here we use Translating Ribosome Affinity Purification (TRAP) to uncover the secretome of grafted human neural stem cells (hNSCs) and identify potential efficacious stem cell factors. Nude rats were subjected to permanent distal cerebral artery occlusion; 7d later hNSCs expressing GFP under a ribosomal-specific promoter were transplanted into the cortex of stroke (S) and naive (N) rats. The graft site was dissected 7d later and processed using TRAP to isolate ribosome-bound RNA from the grafted hNSCs. TRAP-isolated RNA was subjected to RNA sequencing and 479 differentially expressed genes were found between hNSC grafts in S and N brains. Of these, 21 genes encode secreted proteins, 14 of which were upregulated in hNSCs grafts in the stroke-injured brain. Pearson Correlation analysis revealed that the expression level of 9 of the 14 genes positively correlated with functional recovery. Gene Ontology (GO) analysis of the 14 genes identified the top enriched biological process as Response to Wounding which is related (i.e. a direct ancestor in the GO tree) to inflammatory response and axon injury. Three genes were present in this GO term: NOG, MATN2 and WNT1. MATN2 encodes matrilin-2, a protein known to be involved in axon regeneration and inflammation. In situ hybridization and immunohistochemistry showed high expression of matrilin-2 in grafted hNSCs. To test if matrilin-2 could affect post-stroke recovery we infused human recombinant matrilin-2 or vehicle into the cortex of stroke-injured rats. Seven days post-infusion, rats receiving matrilin-2 showed greater behavior recovery than the vehicle group. As matrilin-2 promotes axon outgrowth we investigated if it activated Rac-1 GTPase, which is associated with axon sprouting. Recombinant matrilin-2 increased activation of Rac-1 in primary mouse neural cultures, compared to the control. Our data show that grafted hNSCs in the stroke-injured brain express MATN2 and that secreted matrilin-2 may be involved in hNSC-induced stroke recovery potentially via activation of Rac-1 GTPase and axon sprouting.
Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands (2015)

Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP-regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP-competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2-phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first-generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules' effects on Hsp90 enzymatic, conformational, co-chaperone and client-binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary.
Spacious and mechanically flexible mesoporous silica thin film composed of an open network of interlinked nanoslabs (2011)

Transparent and smooth silica thin films with a very high porosity were prepared by linking zeolitic nanoslabs into open mesoporous networks. Calcined films characterized by ellipsometric porosimetry presented pore sizes in the range of 6–18 nm and porosities of 70–90% depending on the temperature of assembly of the nanoslabs in the presence of Pluronic P123 triblock copolymer. The films were disordered according to grazing incidence small angle X-ray scattering and transmission electron microscopy. The most spacious film had a very low refractive index of 1.08 (at 632.8 nm) and exhibited reversible shrinkage of up to 30% of its original thickness upon capillary condensation of adsorbate vapor. The mechanical flexibility of the film was confirmed by the low Young modulus of 0.9 GPa determined by nano-indentation. The full accessibility of the porosity and the convenience for chemical functionalization were demonstrated using Atomic Layer Deposition (ALD) of TiO2 monitored with Rutherford Backscattering Spectroscopy. Using ALD the porosity and mechanical flexibility of the film could be fine tuned.
Senescence‐associated vacuoles with intense proteolytic activity develop in leaves of Arabidopsis and soybean (2005)

Vacuolar compartments associated with leaf senescence and the subcellular localization of the senescence-specific cysteine-protease SAG12 (senescence-associated gene 12) were studied using specific fluorescent markers, the expression of reporter genes, and the analysis of high-pressure frozen/freeze-substituted samples. Senescence-associated vacuoles (SAVs) with intense proteolytic activity develop in the peripheral cytoplasm of mesophyll and guard cells in Arabidopsis and soybean. The vacuolar identity of these compartments was confirmed by immunolabeling with specific antibody markers. SAVs and the central vacuole differ in their acidity and tonoplast composition: SAVs are more acidic than the central vacuole and, whereas the tonoplast of central vacuoles is highly enriched in gamma-TIP (tonoplast intrinsic protein), the tonoplast of SAVs lacks this aquaporin. The expression of a SAG12-GFP fusion protein in transgenic Arabidopsis plants shows that SAG12 localizes to SAVs. The analysis of Pro(SAG12):GUS transgenic plants indicates that SAG12 expression in senescing leaves is restricted to SAV-containing cells, for example, mesophyll and guard cells. A homozygous sag12 Arabidopsis mutant develops SAVs and does not show any visually detectable phenotypical alteration during senescence, indicating that SAG12 is not required either for SAV formation or for progression of visual symptoms of senescence. The presence of two types of vacuoles in senescing leaves could provide different lytic compartments for the dismantling of specific cellular components. The possible origin and functions of SAVs during leaf senescence are discussed.
FLUID MECHANICS AND HOMELAND SECURITY (2005)

Homeland security involves many applications of fluid mechanics and offers many opportunities for research and development. This review explores a wide selection of fluids topics in counterterrorism and suggests future directions. Broad topics range from preparedness and deterrence of impending terrorist attacks to detection, response, and recovery. Specific topics include aircraft hardening, blast mitigation, sensors and sampling, explosive detection, microfluidics and labs-on-a-chip, chemical plume dispersal in urban settings, and building ventilation. Also discussed are vapor plumes and standoff detection, nonlethal weapons, airborne disease spread, personal protective equipment, and decontamination. Involvement in these applications requires fluid dynamicists to think across the traditional boundaries of the field and to work with related disciplines, especially chemistry, biology, aerosol science, and atmospheric science.
On the Incorporation of Public Attitudes Toward Administrative Options (1978)

As a mathematical economist, I work at the&#13;\nfoundations level of risk/benefit analysis, group&#13;\ndecision processes, polling, and related areas. The&#13;\nfoundations, however, are frequently removed from&#13;\nreal applications.
Exploring Resonance Levels and Nanostructuring in the PbTe−CdTe System and Enhancement of the Thermoelectric Figure of Merit (2010)

We explored the effect of Cd substitution on the thermoelectric properties of PbTe in an effort to test a theoretical hypothesis that Cd atoms on Pb sites of the rock salt lattice can increase the Seebeck coefficient via the formation of a resonance level in the density of states near the Fermi energy. We find that the solubility of Cd is less than previously reported, and CdTe precipitation occurs to create nanostructuring, which strongly suppresses the lattice thermal conductivity. We present detailed characterization including structural and spectroscopic data, transmission electron microscopy, and thermoelectric transport properties of samples of PbTe-x% CdTe-0.055% PbI(2) (x = 1, 3, 5, 7, 10), PbTe-1% CdTe-y% PbI(2) (y = 0.03, 0.045, 0.055, 0.08, 0.1, 0.2), PbTe-5% CdTe-y% PbI(2) (y = 0.01, 0.03, 0.055, 0.08), and PbTe-1% CdTe-z% Sb (z = 0.3, 0.5, 1, 1.5, 2, 3, 4, 5, 6). All samples follow the Pisarenko relationship, and no enhancement of the Seebeck coefficient was observed that could be attributed to a resonance level or a distortion in the density of states. A maximum ZT of approximately 1.2 at approximately 720 K was achieved for the PbTe-1% CdTe-0.055% PbI(2) sample arising from a high power factor of approximately 17 microW/(cm K(2)) and a very low lattice thermal conductivity of approximately 0.5 W/(m K) at approximately 720 K.
Colloidal Crystal Films with Narrow Reflection Bands by Hot-Pressing of Polymer-Grafted Silica Particles (2022)

Previous reports have shown that colloidal crystal (CC) films with visible Bragg reflection characteristics can be fabricated by the surface modification of monodisperse silica particles (SiPs) with poly(methyl methacrylate) (PMMA) chains, followed by hot-pressing at 150 °C. However, the reflection bands of the CC films were very broad due to their relative disordering of SiPs. In this report, we attempted to fabricate the CC films using SiPs surface-modified with poly(<i>n</i>-octyl acrylate) (POA) chains by hot-pressing. When the cast films of POA-grafted SiPs were prepared by hot-pressing at 100 °C, the reflection bands were narrow rather than those of CC films of PMMA-grafted SiPs. This can be ascribed to easy disentanglement of POA chains during the hot-pressing process, thereby enabling the formation of well-ordered CC structures. Moreover, the reflection colors of CC films could be easily tuned by controlling the molecular weight of POA chains grafted on the SiP surface.
Optimized via-hole structure in GaN-based vertical-injection light-emitting diodes (2016)

This study examined the electrical and the optical characteristics of GaN-based vertical-injection light-emitting diodes (VI-LEDs) with various numbers of via holes. As the number of via holes was increased from 1 to 11, the operating voltage at 350 mA of the VI-LEDs decreased from 5.4 to 3.7 V, and the light output power increased greatly from 150 to 233 mW. A further increase in the number of via holes up to 23, however, decreased the light output power due to a decrease in the active area, which resulted in an increase in the efficiency droop at high current injection. The light intensity distributions were characterized by using beam profile measurements to assess the current crowding phenomenon of the VI-LEDs according to the number of via holes. The VI-LEDs with 1 and 5 via holes exhibited a non-uniform light intensity distribution whereas the VI-LEDs with 11 via holes displayed a uniform light intensity distribution and an improved efficiency droop due to the current being uniformity spread by the adequate number of via holes, which suggests that in this study, the VI-LEDs with 11 via holes are optimized via the hole structures.
A Self-Contained, Flow-Powered Microgenerator System (2005)

Abstract : This paper reports the development of a fully functional self-contained microgenerator system which can power various portable electronics using only compressed gas. The system incorporates a previously reported axial-flux. permanent-magnet micromachine. an off-the-shelf air-turbine assembly. and self-powered electronics into a compact, standalone device. The purpose is to demonstrate the migration of a MEMS-based microgenerator from a bench-top laboratory experiment to a self- contained prototype for practical applications.
Abstract 1716: Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation (2015)

Abstract Approximately 70% of newly diagnosed breast cancers express high levels of estrogen receptor alpha (ERα). However, de novo and acquired drug resistance to anti-estrogen agents limit the treatment of such patients, requiring the use of cytotoxic chemotherapy; many such patients have a poor prognosis. Therefore, resistance to therapies targeting the estrogen pathway remains a challenge in the treatment of estrogen-receptor positive breast cancer. To address this challenge, a system biological approach by screening a library of siRNAs targeting an estrogen receptor- and aromatase-centered network, was used and identified 46 genes that are dispensable in estrogen-dependent MCF7 cells, but are selectively required for the survival of estrogen-independent MCF7-derived cells, and multiple additional estrogen-independent breast cancer cell lines. Integration of this information identified a tumor suppressor gene TOB1 as a critical determinant of estrogen-independent estrogen-receptor positive breast cell survival. Depletion of TOB1 selectively promoted G1 phase arrest and sensitivity to AKT and mTOR inhibitors in estrogen-independent cells but not estrogen-dependent cells. Phosphoproteomic profiles (results from reverse phase protein array, RPPA) under basal conditions and following TOB1 depletion identified significant signaling network reprogramming by TOB1 that differed in estrogen-sensitive and estrogen-resistant cell lines. These data support a novel function for TOB1 in mediating survival of estrogen-independent breast cancers. The translational significance of this new molecular mechanism of estrogen independence in human breast cancer will be fully determined when TOB1 inhibitors are developed to enable in vivo validation studies. These studies also provide evidence for combining TOB1 inhibition and AKT/mTOR inhibition as a therapeutic strategy, which have potential translational significance for the management of patients with estrogen receptor-positive breast cancers. Citation Format: Yong-Wei Zhang, Rochelle E. Nasto, Rency Varghese, Sandra A. Jablonski, Ilya G. Serebriiskii, Rishi Surana, Valerie S. Calvert, Ionut Bebu, Joseph Murray, Lu Jin, Michael Johnson, Rebecca Riggins, Habtom Ressom, Emmanuel Petricoin III, Robert Clarke, Erica A. Golemis, Louis M. Weiner. Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1716. doi:10.1158/1538-7445.AM2015-1716
Figure S6 from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine (2023)

&lt;p&gt;KDM5i and DAC do not synergize in MCF10A, nor alter cell cycle in MCF-7&lt;/p&gt;
Computing under occupation (2008)

Recent investigations have found a massively increasing professionalisation and organization of attacks executed on consumer computing systems. Simultaneously, the systems we are trying to defend are getting more and more complex and networked, while promising security technologies---such as trusted boot and strong process isolation---appear to have troubles finding their way into mainstream devices.
Prevalence of Learned Grapheme-Color Pairings in a Large Online Sample of Synesthetes (2015)

In this paper we estimate the minimum prevalence of grapheme-color synesthetes with letter-color matches learned from an external stimulus, by analyzing a large sample of English-speaking grapheme-color synesthetes. We find that at least 6% (400/6588 participants) of the total sample learned many of their matches from a widely available colored letter toy. Among those born in the decade after the toy began to be manufactured, the proportion of synesthetes with learned letter-color pairings approaches 15% for some 5-year periods. Among those born 5 years or more before it was manufactured, none have colors learned from the toy. Analysis of the letter-color matching data suggests the only difference between synesthetes with matches to the toy and those without is exposure to the stimulus. These data indicate learning of letter-color pairings from external contingencies can occur in a substantial fraction of synesthetes, and are consistent with the hypothesis that grapheme-color synesthesia is a kind of conditioned mental imagery.
Time Domain Reflectometer for measuring liquid waste levels in a septic system (2015)

A Time Domain Reflectometer (TDR) level measurement device capable of generating and receiving electromagnetic waves for the measurement of waste water is presented. The primary objective is to measure the height of waste water in a tank and design an efficient measuring device. The TDR is based on the reflection mechanism, in which the time delay between the transmitted and reflected signals helps to determine the distance from the source to the surface of water, which is later used to calculate the height of water in the tank. The TDR is built using a 74AC14 IC, which is capable of producing pulse signals with very low rising and falling times that provide greater accuracy. Thus, the generated pulse signals are transmitted into the probe inserted in a tank. The total time taken by the pulse to travel the path to and from is calculated, which in return helps in calculating the height of the liquid in the tank. The functioning of the proposed TDR circuit and the biaxial probe is also tested in the laboratory.
Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society (2020)

International audience
Insulin receptor expression and clinical outcome in node-negative breast cancer. (1997)

The insulin receptor (IR), a ligand-activated tyrosine kinase, is present in breast cancers, but its relationship to patient survival is unknown. The IR was measured in 584 tumor specimens from patients with node-negative breast carcinoma by frozen-section immunohistochemistry and light microscopy. The immunostaining signal was quantitated in relation to both the staining intensity and the proportion of positive malignant epithelial cells. Analyses indicated that patients with tumors with undetectable IR content in malignant epithelial cells (260 cases) had a relatively lower predicted 5-year disease-free survival (DFS) (69% +/- 3%) than did patients with tumors with detectable IR content (324 cases; DFS 76% +/- 3%, p = .032). The significance of IR content in these breast malignant epithelial cells was then analyzed along with patient age, tumor size, progesterone and estrogen receptor status, p53 accumulation, and S-phase. Multivariate analysis of these data revealed that after adjustment for these other variables, IR content was the strongest independent predictive factor for DFS (relative risk = 1.73, p = .005). Interestingly, in a small subset of patients with very high IR content (n = 62), DFS was decreased. These data indicate that IR content in node-negative breast cancers is a significant major predictor of reduced DFS. Moreover, they raise the possibility that the measurement of IR content might provide important information concerning breast cancer biology.
Electron Transfer from Hydrophobic Porphyrin to Hydrophilic Viologen via the Photoexcited Singlet State in Water (2009)

Abstract Viologen-linked porphyrins are a typical compound for photoinduced electron-transfer models via the photoexcited singlet state. The singlet-state electron transfer, however, does not occur in water, because solvent cage formation, which is motion of solvent molecules during electron transfer, is slow in the case of water. In order to boost the solvent cage formation of water and achieve the electron transfer via the singlet state in water, viologen-linked hydrophobic porphyrin was prepared.
Low-Temperature Imaging for Biological Applications of High-Voltage Electron Microscopy (1982)

The devices and methodology required for applying low-temperature imaging to biological problems have been under development during the last few years at the Boulder HVEM Facility. The present report describes briefly the characteristics and preliminary performance of this endeavor.