gebhart/patrepeval huggingface dataset:
LiST: Lite Prompted Self-training Makes Parameter-efficient Few-shot Learners (2022)

We present a new method LiST for efficient fine-tuning of large pre-trained language models (PLMs) in few-shot learning settings. LiST improves over recent methods that adopt prompt-based fine-tuning (FN) using two key techniques. The first is the use of self-training to leverage large amounts of unlabeled data for prompt-based FN in few-shot settings. We use self-training in conjunction with meta-learning for re-weighting noisy pseudo-prompt labels. Traditionally, self-training is expensive as it requires updating all the model parameters repetitively. Therefore, we use a second technique for light-weight fine-tuning where we introduce a small number of task-specific parameters that are fine-tuned during self-training while keeping the PLM encoder frozen. Our experiments show that LiST can effectively leverage unlabeled data to improve the model performance for few-shot learning. Additionally, the finetuning process is efficient as it only updates a small percentage of the parameters and the overall model footprint is reduced since several tasks can share a common PLM encoder as backbone. We present a comprehensive study on six NLU tasks to validate the effectiveness of LiST. The results show that LiST improves by 35% over classic fine-tuning methods and 6% over prompt-based FN with 96% reduction in number of trainable parameters when fine-tuned with no more than 30 labeled examples from each task. With only 14M tunable parameters, LiST outperforms GPT-3 in-context learning by 33% on few-shot NLU tasks
Supplemental Information from Efficacy of RG7787, a Next-Generation Mesothelin-Targeted Immunotoxin, against Triple-Negative Breast and Gastric Cancers (2023)

&lt;p&gt;Supplemental Information. Includes Supplementary Methods section and legends for Supplemental Figures&lt;/p&gt;
Comparison of the Ocular Distribution of a Model Oligonucleotide after Topical Instillation in Rabbits of Conventional and New Dosage Forms (1998)

The distribution of a model 16-mer oligothymidylate (pdT16) in several ocular tissues (cornea, conjunctiva, sclera, iris, lens, aqueous and vitreous humors) was determined after instillation in the eye of various dosage forms in a rabbit model. Radiolabelled pdT16 was applied as a simple solution, a 27% poloxamer 407 gel, a suspension of liposomes or liposomes dispersed within a 27% poloxamer 407 gel. pdT16 concentrations were measured in the tissues and fluids by radioactivity counting at time intervals of 10 min, 2 h and 24 h. When the pdT 16 solution was used, the highest concentrations were observed in the conjunctiva and the cornea, while a substantial amount of drug was also present in the sclera. Low concentrations were measured in the iris. Using the same treatment protocol, the two liposomal formulations (liposomes suspension or liposomes dispersed within the poloxamer gel) delivered low amounts of pdT16 to all ocular tissues, and particularly to the conjunctiva and the cornea. The poloxamer gel provided higher tissue concentrations of pdT16 than liposomes but lower than those observed with the solution except 10 min after administration in the iris where the amounts of pdT16 were higher when administered under the gel form. These findings indicate that liposomal forms may not be considered useful delivery systems for topical administration of oligonucleotides in superficial ocular diseases.
Phosphazene Bases:  A New Category of Organocatalysts for the Living Ring-Opening Polymerization of Cyclic Esters (2007)

We demonstrate that phosphazene bases, such as 2-tert-butylimino-2-diethylamino-1,3-dimethylperhydro-1,3,2-diazaphosphorine (BEMP) and N‘-tert-butyl-N,N,N‘,N‘,N‘ ‘,N‘ ‘-hexamethylphosphorimidic triamide (P1-t-Bu), are active organocatalysts for the living ring-opening polymerization (ROP) of cyclic esters. Polyesters prepared through this organocatalytic route possess predictable molecular weights, narrow polydispersities, and high end-group fidelity. Mechanistic studies suggest that the intermolecular hydrogen bonding of the alcohol initiator to phosphazene bases activates the alcohol for ROP of cyclic esters.
Hepcidin-Knockout Mäuse als Model der durch Eisenüberladung-induzierten Lebererkrankung (2011)

Störungen im Hepcidin-Regelkreis führen zu erblicher Hämochromatose und Eisen-Überladung bei chronischen Leber-Erkrankungen. Obwohl ein klarer Zusammenhang zwischen Eisenüberladung und Entwicklung einer Lebererkrankung besteht, sind die zugrunde liegenden Mechanismen unbekannt, nicht zuletzt deswegen, weil es an geeigneten Tiermodellen mangelt.
Conjugated Microporous Poly(aryleneethynylene) Networks (2008)

There was a small error in the second sentence on page 8576 of this Communication. This sentence should read: “The ratio of intensities of acetylene to aromatic peaks was calculated using variable-contact-time 1H–13C CP/MAS NMR spectra with the following results: CMP-1 0.27 (expected value 0.40); CMP-2 0.18 (expected value 0.25); CMP-3 0.10 (expected value 0.18).” The authors apologize for this error and wish to note that none of the interpretations in the paper are affected by this change. Dedicated to Colonel Joseph Hutchison on the occasion of his 70th birthday
Influence of Autothreshold Sensing and Sinus Rate on Mode Switching Algorithm Behavior (2000)

Mode switching is beneficial to pacemaker patients with paroxysmal atrial tachyarrhythmias. However, the optimal mode switching algorithm is still in evolution. Mode switching algorithms and atrial sensing circuitry can influence mode switching behavior. This study compared the mode switching behavior of four Medtronic, Inc. implantable devices: Thera DR model 7960 pacemaker, Kappa 700 model KDR701 pacemaker, Gem DR model 7271 dual chamber pacing defibrillator, and Jewel AF model 7250 dual chamber pacemaker atrial and ventricular defibrillator. The Thera and Gem DR use the same mean atrial rate mode switch algorithm. The Kappa and Jewel AF use four of seven short atrial intervals and an atrial fibrillation evidence counter algorithm, respectively. The Thera and Kappa devices use fixed gain sensing and the Gem DR and Jewel AF use autothreshold atrial sensing. Digitally recorded atrial electrograms from 52 episodes of human atrial fibrillation were fed into each device with differing simulated sinus rates before and after the atrial fibrillation. The percent of appropriate mode switching was highest for the Kappa 700 (94%) and lowest for the Thera (85%) (P = 0.046). The time to mode switching was significantly longer for the Thera and Gem DR compared to the Kappa 700 or Jewel AF (all P < 0.05). The time to mode switching was shorter for the Gem DR (9.0 +/- 1.6 s) using autothreshold atrial sensing than for the fixed gain Thera (11.1 +/- 2.1 s, P < 0.05). The mean atrial electrogram amplitude and cycle length were not correlated with the time to mode switching for any device. Faster sinus rates shortened the time to mode switching and prolonged the time to resynchronization in the two devices using the mean atrial interval algorithm. In conclusion, (1) mode switching function among these devices is influenced by algorithms and sensing circuitry, (2) the time to mode switching among these devices is influenced by the algorithm and use of autothreshold atrial sensing, and (3) the sinus rate before and after episodes of atrial fibrillation greatly influences the times to mode switching and resynchronization in devices using the mean atrial interval algorithm.
The synthesis and polymerization studies of some higher homologues of 9‐vinylcarbazole (1964)

Abstract 9‐Allylcarbazole, 9‐Δ 3 ‐butenylcarbazole, 9‐Δ 4 ‐pentenylcarbazole and 9‐Δ 5 −hexenylcarbazole were synthesized and their polymerization with Z IEGLER ‐N ATTA catalyst systems studied. 9‐Allylcarbazole could not be polymerized and 9‐Δ 3 ‐butenylcarbazole could only be polymerized with extreme difficulty. However, 9‐Δ 4 ‐pentylcarbazole and 9‐Δ 5 ‐hexenylcarbazole could be polymerized at conversions of about 55%. These results are interpreted in terms of steric hindrance about the vinyl group. No evidence of complexing due to the basic nitrogen atom was noted. Of the catalyst systems used only Et 2 AlClγTiCl 3 was found to be effective in the polymerization. As judged by X‐ray diffraction and insolubility the polymers were highly crystalline.
Partial discharge theory and technologies related to medium-voltage electrical equipment (2001)

Partial discharge (PD) monitoring is an effective online predictive maintenance test for medium-voltage (MV) motors, MV generators, and MV switchgear at 4160 V and above, as well as other electrical distribution equipment. The benefits of online testing allow for equipment analysis and diagnostics during normal production. Corrective actions can be planned and implemented, resulting in reduced unscheduled downtime. An understanding of the theory related to PD, and the relationship to early detection of insulation deterioration is required to properly evaluate this predictive maintenance tool. This paper presents a theory to promote the understanding of PD technology, as well as various implementation and measurement techniques that have evolved in the industry. Data interpretation, corrective actions, and application to electrical distribution equipment is also reviewed.
ChemInform Abstract: Metal‐Free Catalytic Enantioselective C—B Bond Formation: (Pinacolato)boron Conjugate Additions to α,β‐Unsaturated Ketones, Esters, Weinreb Amides, and Aldehydes Promoted by Chiral N‐Heterocyclic Carbenes. (2012)

Abstract Chiral imidazolium salts are transformed in situ to the catalytically active diastereo‐ and enantiomerically pure N‐heterocyclic carbenes by DBU.
Report of the Basic Energy Sciences Roundtable on Chemical Upcycling of Polymers (2019)

Plastics are ubiquitous in modern life. They are primarily made from synthetic carbon-based polymers— organic macromolecules made up of many repeating subunits called monomers—and are designed to be durable and resistant to degradation. Global plastics production has reached a rate of more than 400 million metric tons (MTs) per year, with more than 8 billion MTs produced in the past 50 years. Average production has increased by 36% in the past decade and is projected to grow to 700 million MTs in 2030—about 80 kg of plastics produced for every human on earth. Globally, 20% of discarded plastics are recycled (<10% in the United States), primarily using mechanical processes, and about 25% are incinerated for energy recovery. More than half are deposited into landfills or released into the environment. Thus, discarded plastics pose a long-term environmental challenge: For example, at the current rate of plastics production and disposal, the mass of plastics in the ocean is predicted to exceed the mass of fish by 2050. Current approaches to reducing unwanted plastics are insufficient to address the growing accumulation of discarded plastics. Although incineration eliminates unwanted plastics and recovers some of the energy used to make them, it uses up the potential resource and creates unwanted byproducts. Mechanical recycling—which involves shredding, heating, and remolding of the plastics—is more efficient than making them from petroleum products, using less than half as much energy to generate new plastics. However, mechanical recycling generally degrades, or downcycles, the polymers. Chemical recycling involves deconstruction of polymers by chemical processes to monomers for conversion back into polymers or to molecular intermediates that can be used as fuel or feedstock by the chemical industry. However, present methods (e.g., pyrolysis—high-temperature decomposition in the absence of oxygen), are energy-intensive and require further processing to make products. Chemical upcycling of polymers—the process of selectively converting discarded plastics into chemicals, fuels, or materials with higher value—holds the promise of changing the paradigm for discarded plastic from waste to valued resource. A significant opportunity exists for fundamental research to provide the foundational knowledge required to move toward a circular lifecycle for plastics, in which the chemical constituents of plastics are reformed into polymers or repurposed to give them another life. To identify the fundamental challenges and research opportunities that could accelerate the transformation of discarded plastics to higher-value fuels, chemicals, and materials, the US Department of Energy, Office of Science, Office of Basic Energy Sciences sponsored a Roundtable on Chemical Upcycling of Polymers, which was held near Washington, DC, on April 30–May 1, 2019. This roundtable identified four Priority Research Opportunities to address the complex chemical transformations and physical processes underlying the upcycling of discarded plastics.
Phosphorylation of the RitR DNA‐binding domain by a Ser–Thr phosphokinase: implications for global gene regulation in the streptococci (2008)

We report selective phosphorylation of the DNA-binding domain of the Streptococcus pneumoniae transcriptional regulator RitR. RitR is annotated as a two-component response regulator, but lacks a cognate His kinase as a neighbouring locus in the genome. In addition, Asn replaces Asp at the expected acceptor site. By the use of combinatorial phage display, we identified PhpP, a S. pneumoniae Ser-Thr eukaryotic-like PP2C phosphatase as an interacting partner of RitR. RitR interacts with the phage-displayed peptide VADGMGGR which forms a part of the active-site sequence of PhpP. RitR is phosphorylated in vitro by StkP, the presumed cognate kinase of PhpP, and the site on RitR that is phosphorylated has been localized to the RitR DNA-binding domain. PhpP together with its cognate kinase StkP appear to be necessary for Piu haem transporter expression. In vitro studies suggest that PhpP and StkP interact competitively with RitR in that RitR-PhpP-piu promoter ternary complexes are disrupted by StkP. Our findings indicate a regulatory link between RitR and Ser-Thr kinase-phosphatase-based bacterial signal transduction.
Rhodium(I)‐Catalyzed Enantioselective Activation of Cyclobutanols: Formation of Cyclohexane Derivatives with Quaternary Stereogenic Centers (2010)

The activation of carbon-carbon sigma bonds is a complementary method to access uncommon and difficult-to-prepare organometallic species. Herein, we describe the activation of tert-cyclobutanols through an enantioselective insertion of a chiral rhodium(I) complex into the C-C sigma bond of the cyclobutane, forming a quaternary stereogenic center and an alkyl-rhodium functionality that initiates ring-closure reactions. This technology provides access to a variety of substituted cyclohexane derivatives with quaternary stereogenic centers. The formation of different product families can be controlled by the employed set of reaction conditions and additives. In general, high yields and excellent enantioselectivities of up to 99% ee are obtained.
Single Molecule and Single Particle SERS (2010)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Richard P. Van Duyne; Single Molecule and Single Particle SERS. AIP Conf. Proc. 6 August 2010; 1267 (1): 57–58. https://doi.org/10.1063/1.3482687 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Abstract 4958: Fluorescent barcoding offers increased dimensionality in tracking tumor cells in vitro and in vivo (2014)

Abstract Fluorescent or luminescent imaging of tumors in animal models is a critical element in dynamic and longitudinal monitoring of tumor burden, tumor growth, and metastatic dissemination. Currently, most imaging strategies are limited to one or two different colors per animal. To improve utility of current imaging technologies, we have developed a library of fluorescent and luminescent tracking vectors designed to expand the color dimensions possible within a single model through a multi-label approach to fluorescent barcoding. The library was built using Multisite Gateway® Cloning technology, which offers a fast and simple recombination-based cloning approach that allows for efficient expression of several genes driven by one promoter on a single vector backbone. Our lentiviral-based vectors express firefly luciferase and one of seven spectrally unique fluorescent proteins covering the entire fluorescent protein color palette from blue to far-red. We have stably labeled bone-derived MDA-MB-231 cells with the vectors by viral transduction. Using these individually colored cell lines, we have demonstrated that the seven FPs are uniquely identifiable by spectral un-mixing with the Maestro Q Imaging System and by flow cytometry. The combination of luciferase and fluorescent labeling allows us to monitor tumor growth by luciferase activity and distinguish individual cell populations by their fluorescent label. We are currently verifying that the cells retain stable expression of the vectors in mouse models; preliminary results are promising. In the future, this system will be used to develop an elegant multi-label-based fluorescent barcoding strategy that will allow us to identify individual cell populations from a heterogeneous environment in vivo. By exploiting combinations of the seven fluorescent proteins, we could potentially create over 200 uniquely identifiable cells populations. This ability will not only reduce the number of animals necessary per experiment (as control and several experimental populations can be individually analyzed in a single mouse); but will also allow us to mimic the heterogeneous environment common to all human tumors. Citation Format: Katie E. Hebron, Tatiana Ketova, Shanna Arnold, H. Charles Manning, Julie Sterling, Florent Elefteriou, Andries Zijsltra. Fluorescent barcoding offers increased dimensionality in tracking tumor cells in vitro and in vivo. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4958. doi:10.1158/1538-7445.AM2014-4958
Photonic Device Layout Within the Foundry CMOS Design Environment (2010)

A design methodology to layout photonic devices within standard electronic complementary metal-oxide-semiconductor (CMOS) foundry data preparation flows is described. This platform has enabled the fabrication of designs in three foundry scaled-CMOS processes from two semiconductor manufacturers.
Tissue Engineered Axon Tracts Serve as Living Scaffolds to Accelerate Axonal Regeneration and Functional Recovery Following Peripheral Nerve Injury in Rats (2020)

Strategies to accelerate the rate of axon regeneration would improve functional recovery following peripheral nerve injury, in particular for cases involving segmental nerve defects. We are advancing tissue engineered nerve grafts (TENGs) comprised of long, aligned, centimeter-scale axon tracts developed by the controlled process of axon "stretch-growth" in custom mechanobioreactors. The current study used a rat sciatic nerve model to investigate the mechanisms of axon regeneration across nerve gaps bridged by TENGs as well as the extent of functional recovery compared to nerve guidance tubes (NGT) or autografts. We established that host axon growth occurred directly along TENG axons, which mimicked the action of "pioneer" axons during development by providing directed cues for accelerated outgrowth. Indeed, axon regeneration rates across TENGs were 3-4 fold faster than NGTs and equivalent to autografts. The infiltration of host Schwann cells - traditional drivers of peripheral axon regeneration - was also accelerated and progressed directly along TENG axons. Moreover, TENG repairs resulted in functional recovery levels equivalent to autografts, with both several-fold superior to NGTs. These findings demonstrate that engineered axon tracts serve as "living scaffolds" to guide host axon outgrowth by a new mechanism - which we term "axon-facilitated axon regeneration" - that leads to enhanced functional recovery.
Clinical and Immunological Response Following hTERT/Survivin mRNA-Loaded Dendritic Cell Vaccination Combined With Ex-Vivo Expanded T Cell Transfer In Melanoma Patients (2013)

New immunotherapy strategies have recently been developed combining peptide or dendritic cell (DC) vaccination with infusion of vaccine-primed and ex vivo expanded T cells. The hypothesis is that adoptive transfer of ex vivo expanded tumor specific T cells can improve progression-free and overall survival by restoring anti-tumor immunity. In a phase I/II clinical trial on malignant melanomas stage IV patients received DC vaccination prior to transfer of ex vivo expanded T cells. Our strategy was to target hTERT and survivin since both is highly expressed in most cancers. The vaccine consisted of autologous DCs loaded with hTERT and survivin mRNA. Prior to each DC vaccination the patients received 5 days of Temozolomide treatment to reduce the number of regulatory T cells (Treg). Following 2 monthly DC vaccinations, blood samples were tested for immune response against hTERT and survivin overlapping peptides. Immune responders were offered injection of T cells. The Elutra fraction of T cells was depleted of Treg using Dynabeads CD25 prior to expansion with Dynabeads CD3/CD28 in a WAVE bioreactor. After 10 days the beads were removed and T cells were washed. 3x1010 expanded T cells were injected fresh and DC vaccination was continued. Prior to T cell infusion, the patients received non-myeloablative conditioning with Fludarabine and Cyclophosphamide Here we present the results from three patients receiving expanded T cells. Immune response against hTERT and survivin peptides were detected in blood samples from 7 to 11 weeks of DC vaccination. After 4-7 months of DC vaccination the T cells were expanded for 10 days prior to injection. DC vaccination was continued 1 day after T cell injection. Infused T cells expanded significantly in vivo and in two of the three patients currently tested both patients showed response against hTERT and survivin peptides. Blood samples taken monthly after T cell injection demonstrated immune response against the same peptides. In one of patients the number of Treg was high (&gt; 4%) before and during vaccination and returned to low numbers (&lt;1%) after T cell injection. Since these findings might explain the beneficial effect of the vaccination we are currently investigating if the number of Tregs in blood show the same profile in the two other patients. Progression free survival (PFS) in the three patients was 31,20 and 11 months respectively. Patients with the shortest PFS relapsed very shortly after the T-cell infusion in spite of an objective immunresponse following the last DC vaccine. Metastatic melanoma patients included in this study given DC vaccines without T-cells had a median PFS of 7 months (3-13). We therefore conclude that dendritic cell vaccination combined with ex-vivo expanded T cell transfer can be an efficient immunotherapy strategy in melanoma patients. Disclosures: No relevant conflicts of interest to declare.