gebhart/patrepeval huggingface dataset:
Cross-linking of iodinated prolactin to rat liver nuclear protein. (1993)

The specific binding of prolactin (PRL) in rat liver nuclei have been examined. Following cross-linking with the use of 125I-rat prolactin and autoradiography the evidence is presented for the specific binding of PRL to a nuclear protein with low Mr of about 7000. This study shows that the PRL binder in rat liver nuclei is a small protein and probably differs from molecular form of the rat liver membrane prolactin receptor.
DES-SRAM IP-core: a SRAM embedding DES feature [secure SoC applications] (2004)

This paper proposes a DES-SRAM IP-core dedicated to secure SoCs. This core is an optimized hardware implementation of a DES (data encryption standard) secret key algorithm. The main idea was to implement a DES feature inside a basic SRAM in order to suppress data transfers during data encryption and thus to avoid a bus bottleneck as well as to increase SoC security. The DES capability only adds few percent hardware overhead, and our modified SRAM offers two operating modes: a basic SRAM mode and an encryption mode. The DES-SRAM self-encrypts each 64 bit block of its own data in 17 clock cycles.
Differential display of peptides induced during the immune response of <i>Drosophila</i> : A matrix-assisted laser desorption ionization time-of-flight mass spectrometry study (1998)

We have developed an approach based on a differential mass spectrometric analysis to detect molecules induced during the immune response of Drosophila, regardless of their biological activities. For this, we have applied directly matrix-assisted laser desorption/ionization MS to hemolymph samples from individual flies before and after an immune challenge. This method provided precise information on the molecular masses of immune-induced molecules and allowed the detection, in the molecular range of 1.5-11 kDa, of 24 Drosophila immune-induced molecules (DIMs). These molecules are all peptides, and four correspond to already characterized antimicrobial peptides. We have further analyzed the induction of the various peptides by immune challenge in wild-type flies and in mutants with a compromised antimicrobial response. We also describe a methodology combining matrix-assisted laser desorption ionization time-of-flight MS, HPLC, and Edman degradation, which yielded the peptide sequence of three of the DIMs. Finally, molecular cloning and Northern blot analyses revealed that one of the DIMs is produced as a prepropeptide and is inducible on a bacterial challenge.
The ultrasound brain helmet: new transducers and volume registration for in vivo simultaneous multi-transducer 3-D transcranial imaging (2011)

Because stroke remains an important and time-sensitive health concern in developed nations, we present a system capable of fusing 3-D transcranial ultrasound volumes acquired from two sides of the head. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging through both temporal acoustic windows, allowing for potential registration of multiple real-time 3-D scans of cerebral vasculature. We examine hardware considerations for new matrix arrays-transducer design and interconnects-in this application. Specifically, it is proposed that SNR may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented, showing cerebral arteries with and without the use of microbubble contrast agent; they have been registered and fused using a simple algorithm which maximizes normalized cross-correlation.
Latent inhibitors of aldehyde dehydrogenase as alcohol deterrent agents (1984)

A series of compounds structurally related to pargyline (N-methyl-N-propargylbenzylamine, 4) were synthesized with the propargyl group replaced by a cyclopropyl, allyl, or 2,2,2-trichloroethyl group and, additionally in several cases, with the methyl group replaced by H. The rationale for their preparation was based on the expectation that, like pargyline, which gives rise to propiolaldehyde, oxidative metabolism of the above compounds by the hepatic cytochrome P-450 enzymes would lead to the generation in vivo of the aldehyde dehydrogenase (AlDH) inhibitors, cyclopropanone, acrolein, or chloral. These compounds were evaluated for inhibition of liver AlDH in vivo by measuring the elevation of ethanol-derived blood acetaldehyde in rats and in vitro by the rate of oxidation of acetaldehyde by intact and osmotically disrupted liver mitochondria. Administration of N-methyl-N-cyclopropylbenzylamine (5) and its nor-methyl analogue (8) to rats raised blood acetaldehyde levels significantly over controls at 2 h. This effect was more pronounced at 9 h, with blood acetaldehyde levels reaching 19 to 27 times control values and approaching the values induced by pargyline. Other compounds elicited significant elevations in ethanol-derived blood acetaldehyde only at 9 h. We suggest that latent inhibitors of AlDH such as 5 or 8 might be useful as alcohol deterrent agents.
Identification of Allergens in <i>Dermatophagoides pteronyssinus</i> Mite Body Extract by Crossed Radioimmunoelectrophoresis with Two Different Rabbit Antibody Pools (1983)

An extract of purified Dermatophagoides pteronyssinus mite bodies was investigated by crossed radioimmunoelectrophoresis (CRIE), using sera from 29 mite-allergic patients. Two CRIE series consisting of rabbit antibodies to (1) whole mite culture and to (2) purified mite bodies were run simultaneously, showing 27 and 29 precipitates, respectively. Cases of major discrepancy between the two series were ascribed to absence of antibody to allergenic components and to artefactual radiostaining due to inclusion of allergen in precipitates representing other antigens. Carefully performed controls were necessary to establish the reliability of CRIE. Specific response patterns in the studied set of sera were found to several of the represented antigens. Two major allergens appeared in both CRIE systems. Two intermediate and several minor allergens were further identified.
Local components and reuse of legacy code in the CORBA component model (2003)

The CORBA component model (CCM) seemed to be a new powerful multi-language and multi-platform component development framework. First applications based on CCM have shown that there are some drawbacks in practical use. We present a new approach for the CCM component implementation which improves communication performance of components living in the same address space. At the same time we simplify the component development process and the reuse of legacy code within components. These extensions to CCM are possible without changing its specification.
The role of ontologies in autonomic computing systems (2004)

The goal of IBM's autonomic computing strategy is to deliver information technology environments with improved self-management capabilities, such as self-healing, self-protection, self-optimization, and self-configuration. Data correlation and inference technologies can be used as core components to build autonomic computing systems. They can also be used to perform automated and continuous analysis of enterprise-wide event data based upon user-defined configurable rules, such as those intended for detecting threats or system failures. Furthermore, they may trigger corrective actions for protecting or healing the system. In this paper, we discuss the use of ontologies as a high-level, expressive, conceptual modeling approach for describing the knowledge upon which the processing of a correlation engine is based. The introduction of explicit models of state-based information technology resources into the correlation technology approach allows the construction of autonomic computing systems that are capable of dealing with policy-based goals on a higher abstraction level. We demonstrate some of the benefits of this approach by applying it to a particular IBM implementation, the eAutomation correlation engine.
The guanosine nucleotide (p)ppGpp initiates development and A-factor production in Myxococcus xanthus (1998)

Guanosine 3'-di-5'-(tri)di-phosphate nucleotides [(p)ppGpp], synthesized in response to amino acid limitation, induce early gene expression leading to multicellular fruiting body formation in Myxococcus xanthus. A mutant (DK527) that fails to accumulate (p)ppGpp in response to starvation was found to be blocked in development prior to aggregation. By use of a series of developmentally regulated Tn5lac transcriptional fusion reporters, the time of developmental arrest in DK527 was narrowed to within the few hours of development, the period of starvation recognition. The mutant is also defective in the production of A-factor, an early extracellular cell-density signal. The relA gene from Escherichia coli, which encodes a ribosome-dependent (p)ppGpp synthetase, rescues this mutant. We also demonstrate that inactivation of the M. xanthus relA homolog blocks development and the accumulation of (p)ppGpp. Moreover, the wild-type allele of Myxococcus relA rescues DK527. These observations support a model in which accumulation of (p)ppGpp, in response to starvation, initiates the program of fruiting body development, including the production of A-factor.
Total Synthesis of (+)-Concanamycin F (2000)

The choice of protecting groups proved imperative for successful macrocyclization in the total synthesis of the 18-membered macrolide concanamycin F (1), which is a potent inhibitor of vacuolar (H+) ATPases. A C14 – C22 subunit was prepared with complete stereocontrol by using asymmetric, boron-mediated, aldol reactions with appropriate chiral ketones. Other key steps included a copper(I)-mediated, Liebeskind cross-coupling and a Mukaiyama aldol reaction for subunit assembly.
12‐2: 3D Pixel Configurations for Optical Out‐Coupling of OLED Displays — Part II: Experimental Validation (2019)

The light extraction efficiency of OLED is crucial for display performance and other issues such as power consumption, lifetime, and image sticking issue. Although lots of effort was adopted, the existing technologies are either too difficult/expensive to be utilized or only suitable for bottom‐emitting OLEDs. Here we proposed a novel 3D pixel configuration to have effective light out‐coupling for top‐emitting OLEDs. Comprehensive multi‐scale optical simulation indicates several‐fold of extraction enhancement and excellent viewing characteristics are simultaneously achievable by extending the bottom reflective electrode to bank slope of the pixel definition layer (PDL) and selectively filling the bank opening (concave area) with high‐index filler to form the optically reflective concave structure. This scheme is scalable and wavelength insensitive, and thus can be generally applied to all red, green, and blue pixel OLEDs in high‐resolution full‐color displays. In this paper, the experiment results of validation were reported with discussion.
Self-configuring object-to-relational mapping queries (2008)

Object-to-relational maps are nowadays routinely utilized in providing a persistency mechanism for object-oriented programs. We present how an object-to-relational mapper, such as Hibernate, provides transparent persistency to object-oriented programs. We then show how the existing approaches of eager and lazy fetching of associations are problematic under the face of program evolution. As an improvement, we present self-configuring components, which reflectively configure the persistency layer usage sites, thus leading to improved maintainability of software.
Transcription‐induced deletions in <i>Escherichia coli</i> plasmids (1995)

Characterization of functions that render DNA susceptible to rearrangement is important for a better understanding of genome instability. In a previous work, we showed that sequences located downstream of a strong promoter are particularly prone to deletion. In this paper, the parameters that influence transcription-induced deletions were studied. pBR322 derivatives carrying the M13 (+) replication origin and a PTac-dependent transcription region were used. Deletion formation was analysed in the presence of the replication protein of M13, which introduces a nick at the phage replication origin, and in a rep- strain to avoid M13-driven replication. Our study showed that: (i) 4 h after induction of transcription, a few per cent of the plasmids have experienced a deletion; (ii) these deletions result in joining of the M13 replication origin to a nucleotide located in or downstream of the transcribed region; (iii) deletion formation strongly depends on the orientation of transcription, on promoter strength and transcript length, but is independent of translation; (iv) formation of transcription-induced supercoiling domains does not induce deletion formation. We propose that deletions in the transcribed region result from collisions between converging replication and transcription machineries.
Active clustering of biological sequences (2012)

Given a point set S and an unknown metric d on S, we study the problem of efficiently partitioning S into k clusters while querying few distances between the points. In our model we assume that we have access to one versus all queries that given a point s∈S return the distances between s and all other points. We show that given a natural assumption about the structure of the instance, we can efficiently find an accurate clustering using only O(k) distance queries. Our algorithm uses an active selection strategy to choose a small set of points that we call landmarks, and considers only the distances between landmarks and other points to produce a clustering. We use our procedure to cluster proteins by sequence similarity. This setting nicely fits our model because we can use a fast sequence database search program to query a sequence against an entire data set. We conduct an empirical study that shows that even though we query a small fraction of the distances between the points, we produce clusterings that are close to a desired clustering given by manual classification.
In Vitro Digestion Rate of Forage Cell Wall Components (1971)

Linearity of the semilog plots of remaining digestible fiber on time and their correlations (r = .98 approximately) indicated first order digestion kinetics for each of the six forages even though composition and observed rates of fiber digestion were markedly different. Immature rye cell walls digested fastest (27.03 .81%/ hour, r 2 --.999) and mature timothy cell walls digested slowest (5.65 -~+ .31%/ hour, r 2 : .985). Similarity of lignin to cellulose ratios in theoretically indigestible residues from rye (.77), alfalfa (.79), orchardgrass (.79), and timothy (.63) suggest a dlgestion-extent-limiting role of ]ignin. Rates of cell wall digestion were positively (r --.77, P < .05) related to cell solubles content of the forage. Cell solubles do not directly contribute to faster rates of cell wall digestion.
Crystallization Behavior and Properties of BaO· Al2O3· 2SiO2 Glass Matrices (2008)

Glass of stoichiometric celsian composition, BaO · Al2O3 · SiO2 has density of 3.39 g/cm3, thermal expansion coefficient of 6.6 × 106/°C, glass-transition temperature of 910°C, and dilatometric softening point of 925°C. On heat treatment, only hexacelsian crystallized out on the surface, but both celsian and hexacelsian were present in the bulk. Effects of cold isostatic pressing (CIP), sintering, and hot-pressing, in the presence and absence of an additive, on the formation of celsian phase in the glass have been studied. CIP'd samples, after appropriate heat treatments, always crystallized out as celsian, whereas presence of 5–10 wt% of an additive was necessary for formation of celsian in sintered as well as hot-pressed specimens. Green density increased with CIP'ing pressure but had no effect on sintered density. Hot-pressing resulted in fully dense samples.
The Contribution of Logging Data to Sedimentology and Stratigraphy (1982)

Abstract Until recently, the lithology and sedimentology of formations penetrated by a well could be studied only through the analysis of cores. Now a technique has been developed using multivariate analysis of logging data to give a high-resolution sedimentological description of any sequence of formations. The number of different logs and their range allow determination of many of the physical characteristics of the rock. The definition of a lithofacies has been extended by introducing the concept of an electrofacies, constructed on the basis of all the logging data at any depth interval. Thus, each logging datum is considered a descriptor for purposes of establishing electrofacies in a logged interval. Once established, electrofacies then can be correlated with actual geologic facies, if the logged interval has been cored.
Filtration of methylene blue‐photooxidized plasma: influence on coagulation and cellular contamination (2001)

WBCs and MB can be eliminated from MB-treated plasma units by filtration. Differences in biocompatibility of the different filters, especially the influence on the contact phase of coagulation, must be taken into consideration.
Analytical Modeling of the Acoustic Field during a Direct Field Acoustic Test (2011)

The acoustic field generated during a Direct Field Acoustic Test (DFAT) has been analytically modeled in two space dimensions using a properly phased distribution of propagating plane waves. Both the pure-tone and broadband acoustic field were qualitatively and quantitatively compared to a diffuse acoustic field. The modeling indicates significant non-uniformity of sound pressure level for an empty (no test article) DFAT, specifically a center peak and concentric maxima/minima rings. This spatial variation is due to the equivalent phase among all propagating plane waves at each frequency. The excitation of a simply supported slender beam immersed within the acoustic fields was also analytically modeled. Results indicate that mid-span response is dependent upon location and orientation of the beam relative to the center of the DFAT acoustic field. For a diffuse acoustic field, due to its spatial uniformity, mid-span response sensitivity to location and orientation is nonexistent.
Effect of c-kit ligand on in vitro human megakaryocytopoiesis (1991)

An evaluation of the effects of a recombinant, soluble form of the c- kit ligand alone and in combination with either granulocyte-macrophage colony-stimulating factor (GM-CSF) or interleukin-3 (IL-3) on the regulation of human megakaryocytopoiesis was performed using a serum- depleted clonal assay system and a long-term bone marrow culture system. The effects of the c-kit ligand on the primitive megakaryocyte (MK) progenitor cell, the burst-forming unit-megakaryocyte (BFU-MK), and the more differentiated colony-forming unit-megakaryocyte (CFU-MK) were determined. The c-kit ligand alone had no megakaryocyte colony- stimulating activity (MK-CSA) but was capable of augmenting the MK-CSA of both GM-CSF and IL-3. The range of synergistic interactions of c-kit ligand varied with the class of MK progenitor cell assayed. In the case of the BFU-MK, the c-kit ligand synergistically augmented the numbers of colonies formed in the presence of IL-3, but not GM-CSF, but increased the size of BFU-MK-derived colonies cloned in the presence of both of these cytokines. However, at the level of the CFU-MK, c-kit ligand synergized with both GM-CSF and IL-3 by increasing both colony numbers and size. Although the c-kit ligand alone exhibited limited potential in sustaining long-term megakaryocytopoiesis in vitro, it synergistically augmented the ability of IL-3, but not GM-CSF, to promote long-term megakaryocytopoiesis. These data indicate that multiple cytokines are necessary to optimally stimulate the proliferation of both classes of MK progenitor cells and that the c-kit ligand plays a significant role in this process by amplifying the MK- CSA of both GM-CSF and IL-3.
Development and validation of PRE-DELIRIC (PREdiction of DELIRium in ICu patients) delirium prediction model for intensive care patients: observational multicentre study (2012)

The PRE-DELIRIC model for intensive care patients consists of 10 risk factors that are readily available within 24 hours after intensive care admission and has a high predictive value. Clinical prediction by nurses and physicians performed significantly worse. The model allows for early prediction of delirium and initiation of preventive measures. Trial registration Clinical trials NCT00604773 (development study) and NCT00961389 (validation study).
Azacitidine/Decitabine Synergism with the NEDD8-Activating Enzyme Inhibitor MLN4924 in Pre-Clinical AML Models (2011)

Abstract Abstract 578 MLN4924 is an investigational small molecule inhibitor of NEDD8-activating enzyme that has shown clinical activity in a Phase I clinical trial in Acute Myelogenous Leukemia (AML). To identify potential combination partners of MLN4924 we performed a high-throughput viability screen in AML cells with 40 approved and investigational agents. In vitro characterization of AML cell lines revealed two distinct cell cycle phenotypes suggesting alternate mechanism of action following MLN4924 inhibition of NAE. One group demonstrated moderate S-phase accumulation with greater than 4N DNA content consistent with DNA-rereplication as a result of CDT1 dysregulation. The second group demonstrated distinct and rapid accumulation of subG1 cells without S-phase accumulation or DNA re-replication suggesting induction of apoptosis and cell death. These observations led us to choose two cells lines representative of each mechanism to understand potential for synergy in AML cells. Two hypomethylating agents were included in the screen (decitabine and azacitidine) and were found to be synergistic with MLN4924 by Combination Index and Blending Synergy Analysis. These data were confirmed with a second NAE inhibitor that is structurally dissimilar to MLN4924. The combination of azacitidine and MLN4924 were shown to result in significantly increased DNA-damage and cell death compared to single agent alone as measured by Western Blotting and FACS analysis of cell cycle distributions. In vivo studies were performed in HL-60 and THP-1 xenografts using MLN4924 on a clinically relevant dosing schedule twice weekly. Single agent azacitidine at its Maximum Tolerated Dose (MTD) had minimal activity in the HL-60 model and was combined with a sub-optimal dose of MLN4924 that when combined induced complete and sustained tumor regressions. The mechanism for the apparent synthetic lethality in this in vivo model is currently under evaluation; however it is supported by a dramatic elevation in DNA damage and cleaved caspase-3 in vivo in the combination arm. A second xenograft model (THP-1) that was also insensitive to single agent azacitidine treatment underwent complete and sustained tumor regressions when combined with MLN4924. Thus MLN4924 and azacitidine can combine to produce synergistic antitumor activity in pre-clinical models of AML. Coupled with their non-overlapping clinical toxicities these data suggest the potential for future combination studies in clinical trials. Disclosures: Smith: Millennium Pharmaceuticals: Employment. Traore:Millennium Pharmaceuticals: Employment. Grossman:Millennium Pharmaceuticals: Employment. Narayanan:Millennium Pharmaceuticals: Employment. Carew:Millennium Pharmaceuticals: Research Funding. Lublinksky:Millennium Pharmaceuticals: Employment. Kuranda:Millennium Pharmaceuticals: Employment. Milhollen:Millennium Pharmaceuticals: Employment.