gebhart/patrepeval huggingface dataset:
Abstract 5831: Biopolymer β-brachytherapy delivered concomitantly with systemic paclitaxel outperforms traditional x-ray radiation to induce complete regression in multiple pancreatic tumor xenograft models (2018)

Abstract Pancreatic tumors remain one of the deadliest manifestations of cancer in clinical oncology. Even when tumors are diagnosed early, remain loco-regionalized, and receive cutting-edge cancer treatment, the 5-year survival rate remains less than 27%. This high mortality rate arises from the significant biologic barriers that inhibit drug delivery effectiveness in pancreatic tumors, as well as their underlying genetic mutations that confer resistance to traditional radiation and chemotherapeutic standards of care. In this work, we hypothesized that a new form of radiation brachytherapy might prove highly synergistic for overcoming the resistance native to pancreatic tumors. Utilizing the thermally stabilized biopolymer ELP, 131iodine radionuclides can be delivered intratumorally to provide continuous, focalized, high-dose β-radiation to treat pancreatic cancer from the inside out. Dose-escalation studies revealed that the two important variables for improving outcomes were the 131I-ELP radioactivity dose and the duration of concurrent paclitaxel therapy. 100% tumor regression was achieved across multiple genotypic models of pancreatic cancer models: MIA PaCa-2, AsPc-1, and BxPc3 (both subcutaneous and orthotopic). The potent synergistic results of 131I-ELP brachytherapy were replicated using both a novel micelle formulation of paclitaxel and the clinical standard Abraxane. Multigroup analysis revealed true molecular synergy as assessed by the Bliss Independence framework (p &amp;lt; 0.01). External beam irradiation, when similarly employed as comparison, merely induced growth inhibition when combined with paclitaxel utilizing a 5Gy hypofractionation regimen. Immunohistochemical analysis of treated tumors revealed differential modulation of biomolecular components that regulate the effectiveness of drug delivery and radiotoxicity. Levels of PECAM, VE-cadherin, claudin-4, HIF-1α, and stromal collagen were all specifically investigated, while macroscopic analysis revealed significantly enhanced accumulation and retention of fluorescently tagged paclitaxel when tumors were treated with biopolymer brachytherapy. Standard x-ray therapy indicated little to no improvement. No signs of any toxic side effects were observed in serologic enzyme analysis and multiorgan biodistribution studies. Citation Format: Jeffrey L. Schaal, Jayanta Bhattacharyya, Xinghai Li, Samagya Banskota, Jeremy Brownstein, David Kirsch, Michael Zalutsky, Ashutosh Chilkoti. Biopolymer β-brachytherapy delivered concomitantly with systemic paclitaxel outperforms traditional x-ray radiation to induce complete regression in multiple pancreatic tumor xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5831.
Silicon micro-masonry using elastomeric stamps for three-dimensional microfabrication (2012)

We present a micromanufacturing method for constructing microsystems, which we term 'micro-masonry' based on individual manipulation, influenced by strategies for deterministic materials assembly using advanced forms of transfer printing. Analogous to masonry in construction sites, micro-masonry consists of the preparation, manipulation, and binding of microscale units to assemble microcomponents and microsystems. In this paper, for the purpose of demonstration, we used microtipped elastomeric stamps as manipulators and built three dimensional silicon microstructures. Silicon units of varied shapes were fabricated in a suspended format on donors, retrieved, delivered, and placed on a target location on a receiver using microtipped stamps. Annealing of the assembled silicon units permanently bound them and completed the micro-masonry procedure.
Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene with purification and characterization of its product, D-alanine:D-alanine ligase (ADP forming) (1988)

A gene coding for D-alanine:D-alanine (D-Ala-D-Ala) ligase (ADP forming) (EC 6.3.2.4) activity has been isolated from a lambda library of Salmonella typhimurium DNA. Insertion mutations in the gene indicate that the gene is not essential for growth of the bacterium. The encoded enzyme was purified from an overproducing strain of S. typhimurium. D-Ala-D-Ala ligase is a protein of 39,271 molecular weight and has a kcat of 644 min-1 at pH 7.2. A 2.4-kilobase SalI-SphI fragment containing the gene was sequenced, and the ddlA gene consists of 1092 nucleotides. The gene sequence was compared to the sequence of the ddl gene of Escherichia coli [Robinson, A. C., Kenan, D. J., Sweeney, J., & Donachie, W. D. (1986) J. Bacteriol. 167, 809-817]. Because of differences between the S. typhimurium gene and the E. coli ddl gene, the S. typhimurium gene has been named ddlA.
Biochemical regulation of isoprene emission (2003)

ABSTRACT Isoprene (C 5 H 8 ) is emitted from many plants and has a substantial effect on atmospheric chemistry. There are several models to estimate the rate of isoprene emission used to calculate the impact of isoprene on atmospheric processes. The rate of isoprene synthesis will depend either on the activity of isoprene synthase or the availability of its substrate dimethylallyl pyrophosphate (DMAPP). To investigate long‐term regulation of isoprene synthesis, the isoprene emission rate of 15 kudzu leaves was measured. The chloroplast DMAPP level of the five leaves with the highest emission rates and the five leaves with the lowest rates were determined by non‐aqueous fractionation of the bulked leaf samples. Leaves with high basal emission rates had low levels of DMAPP whereas leaves with low basal emission rates had high DMAPP levels in their chloroplasts indicating that the activity of isoprene synthase exerts primary control over the basal emission rate. To investigate short‐term regulation, isoprene precursors were fed to leaves. Feeding dideuterated deoxyxylulose (DOX‐d 2 ) to Eucalyptus leaves resulted in the emission of dideuterated isoprene. Results from DOX‐d 2 feeding experiments indicated that control of isoprene emission rate was shared between reactions upstream and downstream of the DOX entry into isoprene metabolism. In CO 2 ‐free air DOX always increased isoprene emission indicating that carbon availability was an important control factor. In N 2 , isoprene emission stopped and could not be recovered by adding DOX‐d 2 . Taken together, these results indicate that the regulation of isoprene emission is shared among several steps and the relative importance of the different steps in controlling isoprene emission varies with conditions.
State of the Art of the Wireless Security in OFDM(A)-Based Systems (2009)

Security in wireless networks has traditionally been considered to be an issue to be addressed at the higher layers of the network. However, with the emergence of ad hoc and other less centralized networking architectures, there has been an increase in interest in the potential of the wireless physical layer to provide communications security. Information theory provides a natural framework for the study of this issue, and consequently there has been a resurgence of interest in information-theoretic security in recent years, particularly for wireless channel models. This work has expanded on earlier ideas about secure broadcast, by examining multiple-access channels, fading, code design, source coding, authentication, network coding, and many other issues. This paper will review recent works in the field of wireless security specially taking into account the OFDM(A)-based systems, e.g, Long Term Evolution (LTE) and WiMAX.
Sequence of the S-layer gene of Thermus thermophilus HB8 and functionality of its promoter in Escherichia coli (1992)

The nucleotide sequence of the slpA gene, which is responsible for the synthesis of the S-layer protein of Thermus thermophilus HB8, is described. This gene is transcribed as a unit in which the coding region is preceded by a 127-base-long leader mRNA sequence. The promoter region is also recognized by the RNA polymerase of Escherichia coli because of the presence of homologous -35 and -10 boxes. Homologies with other promoters from Thermus spp. are also presented.
Knock everything down (2013)

If you spend any time with a baby or young child you will know just how much they enjoying knocking things down, especially towers of blocks, encouraging this will help to develop a wide range of skills.
Clonogenic analysis reveals reserve stem cells in postnatal mammals. II. Pluripotent epiblastic‐like stem cells (2004)

Undifferentiated cells have been identified in the prenatal blastocyst, inner cell mass, and gonadal ridges of rodents and primates, including humans. After isolation these cells express molecular and immunological markers for embryonic cells, capabilities for extended self-renewal, and telomerase activity. When allowed to differentiate, embryonic stem cells express phenotypic markers for tissues of ectodermal, mesodermal, and endodermal origin. When implanted in vivo, undifferentiated noninduced embryonic stem cells formed teratomas. In this report we describe a cell clone isolated from postnatal rat skeletal muscle and derived by repetitive single-cell clonogenic analysis. In the undifferentiated state it consists of very small cells having a high ratio of nucleus to cytoplasm. The clone expresses molecular and immunological markers for embryonic stem cells. It exhibits telomerase activity, which is consistent with its extended capability for self-renewal. When induced to differentiate, it expressed phenotypic markers for tissues of ectodermal, mesodermal, and endodermal origin. The clone was designated as a postnatal pluripotent epiblastic-like stem cell (PPELSC). The undifferentiated clone was transfected with a genomic marker and assayed for alterations in stem cell characteristics. No alterations were noted. The labeled clone, when implanted into heart after injury, incorporated into myocardial tissues undergoing repair. The labeled clone was subjected to directed lineage induction in vitro, resulting in the formation of islet-like structures (ILSs) that secreted insulin in response to a glucose challenge. This study suggests that embryonic-like stem cells are retained within postnatal mammals and have the potential for use in gene therapy and tissue engineering.
The specifics of small interfering RNA specificity (2003)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Characterization of aluminum hydroxide for use as an adjuvant in parenteral vaccines. (1984)

Aluminum hydroxide has a long history of use as an adjuvant in parenteral vaccines but the problem of inconsistent antibody production has been frequently noted. Although the mechanism of adjuvant action is not fully understood, it is likely that the surface area, surface charge, and morphology of the aluminum hydroxide are of prime importance. Current understanding of the structure of aluminum hydroxide suggests that controlling the presence of anions which coordinate with aluminum during the precipitation reaction and precipitation at a constant pH will produce an aluminum hydroxide with consistent properties. Techniques are described for determining the surface area of aluminum hydroxide in the unaltered liquid state and the surface charge. The importance of morphology is illustrated by electronmicrographs of two forms of aluminum hydroxide which have the same particle size but different porosity and surface accessibility. The adsorption mechanism of proteins by aluminum hydroxide is discussed using pepsin as a model. Infrared and desorption studies showed that pepsin is adsorbed by anionic ligand exchange with surface aluminum as well as by electrostatic attraction.
A discourse-based consultant for interactive environments (2003)

The authors present their automated consultant and describe its application to a practical domain, the Berkeley Unix mail system. They take advantage of previous work on discourse-based assistants that focuses on understanding the user's question and goal, and instead concentrate on the generation of suitable advice.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bottom-Up and Top-Down Attention for Image Captioning and Visual Question Answering (2018)

Top-down visual attention mechanisms have been used extensively in image captioning and visual question answering (VQA) to enable deeper image understanding through fine-grained analysis and even multiple steps of reasoning. In this work, we propose a combined bottom-up and top-down attention mechanism that enables attention to be calculated at the level of objects and other salient image regions. This is the natural basis for attention to be considered. Within our approach, the bottom-up mechanism (based on Faster R-CNN) proposes image regions, each with an associated feature vector, while the top-down mechanism determines feature weightings. Applying this approach to image captioning, our results on the MSCOCO test server establish a new state-of-the-art for the task, achieving CIDEr / SPICE / BLEU-4 scores of 117.9, 21.5 and 36.9, respectively. Demonstrating the broad applicability of the method, applying the same approach to VQA we obtain first place in the 2017 VQA Challenge.
V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations (2001)

Severe combined immunodeficiency (SCID) comprises a heterogeneous group of primary immunodeficiencies, a proportion of which are due to mutations in either of the 2 recombination activating genes (RAG)-1 and -2, which mediate the process of V(D)J recombination leading to the assembly of antigen receptor genes. It is reported here that the clinical and immunologic phenotypes of patients bearing mutations in RAGs are more diverse than previously thought and that this variability is related, in part, to the specific type of RAG mutation. By analyzing 44 such patients from 41 families, the following conclusions were reached: (1) null mutations on both alleles lead to the T-B-SCID phenotype; (2) patients manifesting classic Omenn syndrome (OS) have missense mutations on at least one allele and maintain partial V(D)J recombination activity, which accounts for the generation of residual, oligoclonal T-lymphocytes; (3) in a third group of patients, findings were only partially compatible with OS, and these patients, who also carried at least one missense mutation, may be considered to have atypical SCID/OS; (4) patients with engraftment of maternal T cells as a complication of a transplacental transfusion represented a fourth group, and these patients, who often presented with a clinical phenotype mimicking OS, may be observed regardless of the type of RAG gene mutation. Analysis of the RAG genes by direct sequencing is an effective way to provide accurate diagnosis of RAG-deficient as opposed to RAG-independent V(D)J recombination defects, a distinction that cannot be made based on clinical and immunologic phenotype alone.
Inhibition of the Differentiation of Dendritic Cells From CD34+ Progenitors by Tumor Cells: Role of Interleukin-6 and Macrophage Colony-Stimulating Factor (1998)

The escape of malignant cells from the immune response against the tumor may result from a defective differentiation or function of professional antigen-presenting cells (APC), ie, dendritic cells (DC). To test this hypothesis, the effect of human renal cell carcinoma cell lines (RCC) on the development of DC from CD34(+) progenitors was investigated in vitro. RCC cell lines were found to release soluble factors that inhibit the differentiation of CD34(+) cells into DC and trigger their commitment towards monocytic cells (CD14(+)CD64(+)CD1a-CD86(-)CD80(-)HLA-D Rlow) with a potent phagocytic capacity but lacking APC function. RCC CM were found to act on the two distinct subpopulations emerging in the culture at day 6 ([CD14(+)CD1a-] and [CD14(-)CD1a+]) by inhibiting the differentiation into DC of [CD14(+)CD1a-] precursors and blocking the acquisition of APC function of the [CD14(-)CD1a+] derived DC. Interleukin-6 (IL-6) and macrophage colony-stimulating factor (M-CSF) were found to be responsible for this phenomenon: antibodies against IL-6 and M-CSF abrogated the inhibitory effects of RCC CM; and recombinant IL-6 and/or M-CSF inhibited the differentiation of DC similarly to RCC CM. The inhibition of DC differentiation by RCC CM was preceeded by an induction of M-CSF receptor (M-CSFR; CD115) and a loss of granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR; CD116) expression at the surface of CD34(+) cells, two phenomenon reversed by anti-IL-6/IL-6R and anti-M-CSF antibodies, respectively. Finally, a panel of tumor cell lines producing IL-6 and M-CSF induced similar effects. Taken together, the results suggest that the inhibition of DC development could represent a frequent mechanism by which tumor cells will escape immune recognition.
How to Pay? Understanding and Using Incentives (2004)

Many countries have experimented with alternative ways of paying providers of health care services. This paper illustrates different methods, suggests some of the theoretic advantages and limitations of each, and provides a general theoretical framework for evaluating alternatives. Over the last two decades, new and more sophisticated payment systems have evolved, with a broadening of units of payment and setting of payments prospectively. The authors discuss the international experience of a number of payment systems, both traditional and more recently developed, including line-item budgeting, salary, fee-for-service, per diem, case-mix adjusted per episode, global budgets and capitation. The authors argue that no one set of incentives will address the multiple objectives of purchasers, providers, and patients. As a result, purchasers and policymakers must understand and address policy objectives explicitly. With more sophisticated systems, part or all of the financial risk is transferred from the purchaser back to the provider and patient. Most observers caution against full risk but encourage some supply-side cost sharing only, with purchaser and provider sharing in risk arrangements to address moral hazard issues. Imposing high copayments or user fees is an alternative, but in developing countries that quickly erodes financial protection. More sophisticated payment systems may also lead to higher transaction costs and necessitate a greater capacity to use information and management systems. Finally, the best planned and implemented payment incentives and systems may fail due to a variety of other and related factors in health care delivery. Unless these issues are addressed, impacts of change in resource allocation and purchasing will be diluted or neutralized. Technicians and policymakers will need to address these potential "chokepoints" in any process of implementation and refinement.
PACT: an experiment in integrating concurrent engineering systems (1993)

The Palo Alto Collaborative Testbed (PACT), a concurrent engineering infrastructure that encompasses multiple sites, subsystems, and disciplines, is discussed. The PACT systems include NVisage, a distributed knowledge-based integration environment for design tools; DME (Device Modeling Environment), a model formulation and simulation environment; Next-Cut, a mechanical design and process planning system; and Designworld, a digital electronics design, simulation, assembly, and testing system. The motivations for PACT and the significance of the approach for concurrent engineering is discussed. Initial experiments in distributed simulation and incremental redesign are reviewed, and PACT's agent-based architecture and lessons learned from the PACT experiments are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analysis of the RNA- and DNA-dependent DNA polymerase activities of point mutants of HIV-1 reverse transcriptase lacking ribonuclease H activity (1991)

The RNA- and DNA-dependent DNA polymerase activities of two point mutants of HIV-1 reverse transcriptase lacking ribonuclease H activity have been compared to the wild-type enzyme activities using substrates consisting of an oligodeoxynucleotide primer hybridized to either a RNA or a DNA template. The RNase H phenotype had a negligible effect on the steady-state kinetics and processivity of reverse transcription of a homopolymer template-primer [poly(A).oligo(dT)]. However, analysis of the distribution of DNA products indicated that the ability of the mutants to reverse-transcribe a specifically primed 345-nucleotide heteropolymeric RNA template derived from the gag region of HIV-1 was impaired relative to the wild-type enzyme. Although the wild-type and mutant enzymes shared the same pause sites of synthesis along the RNA template, certain prematurely terminated nascent primer chains were poorly extended by the mutant enzymes and hence accumulated, suggesting that a catalytically functional RNase domain facilitated reinitiation of DNA synthesis at specific pause sites along a heteropolymer template. In contrast, the processivity and product distribution of DNA synthesis directed by a heteropolymer gag DNA template of the same nucleotide sequence were not significantly influenced by the RNase H phenotype of the mutants.
Predicting automatic speech recognition performance using prosodic cues (2000)

In spoken dialogue systems, it is important for a system to know how likely a speech recognition hypothesis is to be correct, so it can reprompt for fresh input, or, in cases where many errors have occurred, change its interaction strategy or switch the caller to a human attendant. We have discovered prosodic features which more accurately predict when a recognition hypothesis contains a word error than the acoustic confidence score thresholds traditionally used in automatic speech recognition. We present analytic results indicating that there are significant prosodic differences between correctly and incorrectly recognized turns in the toot train information corpus. We then present machine learning results showing how the use of prosodic features to automatically predict correct versus incorrectly recognized turns improves over the use of acoustic confidence scores alone. 1 Introduction One of the central tasks of the dialogue manager in most current spoken dialogue systems (SDSs) i...
An Incremental Programming Environment (1981)

This paper describes an incremental programming environment (IPE) based on compilation technology, but providing facilities traditionally found only in interpretive systems. IPE provides a comfortable environment for a single programmer working on a single program.
Biological Activity of Anti-CD20 Multivalent HPMA Copolymer-Fab’ Conjugates (2012)

High-molecular-weight, branched N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers were synthesized and conjugated with Fab' fragments of the anti-CD20 antibody, 1F5. This produced multivalent conjugates with varying valency (amount of Fab' per macromolecule) targeted to the B-cell antigen CD20. The apoptotic activity of the conjugates was screened against several B-cell lymphomas with varied expression levels of CD20 (Raji, Daudi, Ramos, Namalwa, and DG-75). The multivalent conjugates had the strongest activity against cells that had the highest expression of CD20 and failed to demonstrate any measurable activity against lymphomas that did not express the antigen. Furthermore, there was an apparent dose-dependent response to treatment with multivalent conjugates. At optimal valence and concentration, the apoptotic activity of HPMA copolymer-Fab' conjugates superseded that of free anti-CD20 Ab that was hyper-cross-linked with a polyclonal, secondary Ab.