gebhart/patrepeval huggingface dataset:
Engineering of vault nanocapsules with enzymatic and fluorescent properties (2005)

One of the central issues facing the emerging field of nanotechnology is cellular compatibility. Nanoparticles have been proposed for diagnostic and therapeutic applications, including drug delivery, gene therapy, biological sensors, and controlled catalysis. Viruses, liposomes, peptides, and synthetic and natural polymers have been engineered for these applications, yet significant limitations continue to prevent their use. Avoidance of the body's natural immune system, lack of targeting specificity, and the inability to control packaging and release are remaining obstacles. We have explored the use of a naturally occurring cellular nanoparticle known as the vault, which is named for its morphology with multiple arches reminiscent of cathedral ceilings. Vaults are 13-MDa ribonucleoprotein particles with an internal cavity large enough to sequester hundreds of proteins. Here, we report a strategy to target and sequester biologically active materials within the vault cavity. Attachment of a vault-targeting peptide to two proteins, luciferase and a variant of GFP, resulted in their sequestration within the vault cavity. The targeted proteins confer enzymatic and fluorescent properties on the recombinant vaults, both of which can be detected by their emission of light. The modified vaults are compatible with living cells. The ability to engineer vault particles with designed properties and functionalities represents an important step toward development of a biocompatible nanocapsule.
Flash Memory Fabricated with Protein-Mediated PbSe Nanocrystal Assembly as Floating Gate (2007)

This work is based on our previously developed technique which used chaperonin protein as a template for NC assembly on MOS capacitors. Our study on floating gate flash memory fabricated with protein-mediated PbSe NCs applied to MOS transistors with greatly improved spatial uniformity will be presented in this paper. With these device characteristics, we expect PbSe NCs as floating gate to be promising for flash memories.
A Novel Pulse Based Ultrawide Band System Using Chaotic Spreading Sequences (2007)

This paper proposes a novel method of using chaotic binary sequence in pulse amplitude modulation based ultrawideband (UWB) system to suppress interference and hence to improve the Bit Error Rate (BER) performance in the presence of narrowband interference (NBI). It is one of the very important considerations in the UWB systems as the spectrum of UWB overlays with the existing narrowband wireless systems. In the proposed method, the chaotic binary sequence is used across the frames within one symbol duration. The performance of the proposed scheme is analyzed using the channel models proposed by IEEE 802.15.3a working group for short range, high data rate wireless communications. The simulation results show that the proposed system has better BER performance compared to the existing systems, in the presence of NBI. In addition to the suppression of NBI, the proposed scheme has an added level of security due to the chaotic spreading.
ISA, ISSAM and EAU recommendations for the investigation, treatment and monitoring of late-onset hypogonadism in males: Scientific background and rationale (2005)

Prescription sales for testosterone products have substantially increased over the last several years reflecting the growing awareness of physicians for the potential benefits of testosterone replacement therapy in men with hypogonadism. Indiscriminate administration of testosterone poses a risk and has to be deprecated. Testosterone supplementation to treat late-onset hypogonadism (LOH), a term for androgen deficiency in elderly men, is still controversially discussed mainly due to a lack of large, controlled clinical trials on efficacy and safety. To provide guidance for physicians primarily dealing with aging men, ISSAM is periodically updating and publishing its recommendations as new data become available [Morales A, Lunenfeld B. International Society for the Study of the Aging Male. Investigation, treatment and monitoring of late-onset hypogonadism in males. Official recommendations of ISSAM. International Society for the Study of the Aging Male. Aging Male 2002;5:74-86 and Morales A, Lunenfeld B. Androgen replacement therapy in aging men with secondary hypogonadism. Draft recommendations for endorsement by ISSAM. Aging Male 2001;4:1]. Following a panel discussion at the 4th ISSAM Congress in Prague in February 2004, the International Society of Andrology (ISA), the International Society for the Study of the Aging Male (ISSAM) and the European Association of Urology (EAU) revised existing recommendations on the definition, diagnosis and management of LOH. The recommendations are based on the currently available scientific data on androgen supplementation therapy and should be regarded as provisional until larger-scale, long-term studies are available. While certainly not intending to be exhaustive, this review will highlight some relevant background information and provide the underlying scientific rationale for the ISA, ISSAM and EAU recommendations on LOH published in this issue.
Point mutation analysis in a mammalian gene: rapid preparation of total RNA, PCR amplification of cDNA, and Taq sequencing by a novel method. (1989)

We have developed a very rapid procedure for DNA sequence analysis of induced mutations in a typically large mammalian gene. We are able to determine the nature of chemical carcinogen-induced point mutations in the 25 kb Chinese hamster ovary (CHO) cell dihydrofolate reductase gene within two days starting with 5 to 10 x 10(6) cells. The approach is based on the use of rapidly prepared total RNA from which a 730 bp dhfr cDNA is synthesized by reverse transcriptase and amplified by the polymerase chain reaction (PCR) procedure. Genomic DNA can simultaneously be prepared from the same cells. The amplified double-stranded cDNA is then sequenced directly by the dideoxy method using Taq polymerase in the Thermal Cycler (Perkin Elmer/Cetus). We have previously shown that nonsense codons in the dhfr coding sequence often result in greatly reduced steady-state levels of dhfr mRNA (2). The methods described are suitable for mutants of this type which contain only 1 to 2 copies of mRNA per cell. This approach is readily adaptable to other selectable genes and other cell types provided the necessary primers can be prepared.
Variants in the Glutamate-Cysteine-Ligase Gene Are Associated with Cystic Fibrosis Lung Disease (2006)

In patients with CF with a milder CFTR genotype, there is a strong association between functional polymorphisms of the GCLC gene and CF lung disease severity.
Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus (2002)

In a specialized cDNA library from the archaeon Archaeoglobus fulgidus we have identified a total of 86 different expressed RNA sequences potentially encoding previously uncharacterized small non-messenger RNA (snmRNA) species. Ten of these RNAs resemble eukaryotic small nucleolar RNAs, which guide rRNA 2'-O-methylations (C/D-box type) and pseudouridylations (H/ACA-box type). Thereby, we identified four candidates for H/ACA small RNAs in an archaeal species that are predicted to guide a total of six rRNA pseudouridylations. Furthermore, we have verified the presence of the six predicted pseudouridines experimentally. We demonstrate that 22 snmRNAs are transcribed from a family of short tandem repeats conserved in most archaeal genomes and shown previously to be potentially involved in replicon partitioning. In addition, four snmRNAs derived from the rRNA operon of A. fulgidus were identified and shown to be generated by a splicing/processing pathway of pre-rRNAs. The remaining 50 RNAs could not be assigned to a known class of snmRNAs because of the lack of known structure and/or sequence motifs. Regarding their location on the genome, only nine were located in intergenic regions, whereas 33 were complementary to an ORF, five were overlapping an ORF, and three were derived from the sense orientation within an ORF. Our study further supports the importance of snmRNAs in all three domains of life.
Users, user interfaces, and objects: Envision, a digital library (1993)

Project Envision aims to build a “user-centered database from the computer science literature,” initially using the publications of the Association for Computing Machinery (ACM). Accordingly, we have interviewed potential users, as well as experts in library, information, and computer science—to understand their needs, to become aware of their perception of existing information systems, and to collect their recommendations. Design and formative usability evaluation of our interface have been based on those interviews, leading to innovative query formulation and search results screens that work well according to our usability testing. Our development of the Envision database, system software, and protocol for client-server communication builds upon work to identify and represent “objects” that will facilitate reuse and high-level communication of information from author to reader (user). All these efforts are leading not only to a usable prototype digital library but also to a set of nine principles for digital libraries, which we have tried to follow, covering issues of representation, architecture, and interfacing. © 1993 John Wiley & Sons, Inc.
Structure, expression, and activity of Tyro 3, a neural adhesion-related receptor tyrosine kinase. (1994)

We have isolated mouse cDNA clones encoding Tyro 3, a receptor protein-tyrosine kinase (PTK) of the mammalin central nervous system (CNS). Expression of the Tyro 3 gene is strongly up-regulated in neurons of the mouse neocortex, cerebellum, and hippocampus after the day of birth, during periods of active synaptogenesis, and high expression is maintained in the adult CNS. The sequence of Tyro 3 cDNAs predicts a glycoprotein receptor with similarity to neural cell recognition and adhesion molecules--the extracellular (ligand binding) region of this receptor is composed of two immunoglobulin-related domains followed by two fibronectin type III repeats. Immunoblot and immunoprecipitation analyses with anti-Tyro 3 antibodies indicate that the 125 kD Tyro 3 protein is abundantly expressed in CNS synaptosomes, and immunohistochemical analysis of cultured hippocampal cells demonstrates that Tyro 3 is a product of neurons. Rat-2 fibroblasts stably transfected with a Tyro 3 expression construct acquire the ability to grow in soft agar, suggesting that Tyro 3 is potentially oncogenic.
A novel canine leukointegrin, α d β 2, is expressed by specific macrophage subpopulations in tissue and a minor CD8+ lymphocyte subpopulation in peripheral blood (1995)

The beta 2 or leukointegrin family is comprised of three structurally related leukocyte surface heterodimers: LFA-1 (CD11a/CD18), Mac-1/Mo-1 (CD11b/CD18), and p150,95 (CD11c/CD18). In this work, we describe a novel canine beta 2 (CD18)-associated leukointegrin, designated alpha d. Expression of alpha d in tissues was prominent in macrophages in splenic red pulp, lymph node medullary regions, and bone marrow. In peripheral blood, alpha d expression was limited to a minor subpopulation of CD8+ T cells, which included small lymphocytes and large granular lymphocytes. A minor subpopulation of either CD8+ or CD4-CD8- splenic red pulp lymphocytes also expressed alpha d. Immunoprecipitation of alpha d from canine splenocytes revealed a heterodimer of 155 kDa and 95 kDa. Prior clearance of splenocyte extracts with an anti-CD18 mAb resulted in complete removal of alpha d. In addition, prior clearance of canine splenocyte extracts with anti-CD11a, anti-CD11b, or anti-CD11c mAb failed to clear alpha d. These immunoclearance data indicated that canine alpha d was antigenically distinct from the three known CD11 molecules, and occurred as an alpha d beta 2 heterodimer. Amino acid sequencing of canine alpha d affinity isolated from spleen further suggested that canine alpha d beta 2 probably represented a fourth member of the canine leukointegrin family via its homology to a subsequently discovered, novel human leukointegrin, alpha d beta 2, which further supported the uniqueness of the canine protein. The discovery of canine alpha d, and the demonstration of its highly restricted cell and tissue distribution, support a re-evaluation of leukointegrin-dependent inflammatory and immunologic interactions that involve cells now known to express alpha d.
Synthetics and theoretical seismology (1983)

In the near field, discrete‐finite wave number schemes are economic since they involve fewer wave numbers than most wave number integration schemes. The number of wave numbers is determined by the range and the location of artificial reflectors or fictitious sources inherent in discrete wave number techniques. The number and spacing of wave numbers in wave number integration schemes are determined by the desired accuracy. The vertical integration schemes used in the near field have been either spectral (Apsel, 1979, Bouchon, 1981) as in the regional techniques or finite‐element (Olson,1982) and finite‐difference in the time domain as in the Alexseev‐Mikhailenko method. The finite element schemes have the disadvantage in that the vertical step size is determined by the desired maximum frequency content, which in turn determines the time step required for stability. This time step is usually many times smaller than the time increment associated with the maximum frequency.
Formyl-methenyl-methylenetetrahydrofolate synthetase(combined) from yeast. Biochemical characterization of the protein from an ade3 mutant lacking the formyltetrahydrofolate synthetase function. (1980)

A protein from Saccharomyces cerevisiae mutant ade3-1050, a formyltetrahydrofolate synthetase-deficient mutant, has been purified to apparent homogeneity. The purified mutant enzyme shows both methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase activities, but lacks formyltetrahydrofolate synthetase activity. The biochemical characterization of the mutant protein described in this paper is consistent with genetic data which indicate that the 1050 mutation is a point mutation at the ade3 locus of chromosome VII of S. cerevisiae. The molecular weight of the native mutant protein (Mr = 227,000 by exclusion chromatography), as well as the number and size of its subunits are exactly the same as those of the trifunctional wild type enzyme. In addition, both proteins have the same sedimentation behavior in a glycerol density gradient (s20,w = 9.4 S), and their activities and structures are equally affected by exposure to mild tryptic degradation. ATP protects both enzymes from tryptic degradation, but NADP+ does not. Some of the kinetic properties of the activities of both enzymes were also determined and were essentially similar. Although both enzymes require the presence of metals for maximal synthetase and dehydrogenase activities, metals are not necessary to maintain their structures intact.
ATP Activates Ataxia-Telangiectasia Mutated (ATM) in Vitro (2003)

Ataxia-telangiectasia Mutated (ATM), mutated in the human disorder ataxia-telangiectasia, is rapidly activated by DNA double strand breaks. The mechanism of activation remains unresolved, and it is uncertain whether autophosphorylation contributes to activation. We describe an in vitro immunoprecipitation system demonstrating activation of ATM kinase from unirradiated extracts by preincubation with ATP. Activation is both time- and ATP concentration-dependent, other nucleotides fail to activate ATM, and DNA is not required. ATP activation is specific for ATM since it is not observed with kinase-dead ATM, it requires Mn2+, and it is inhibited by wortmannin. Exposure of activated ATM to phosphatase abrogates activity, and repeat cycles of ATP and phosphatase treatment reveal a requirement for autophosphorylation in the activation process. Phosphopeptide mapping revealed similarities between the patterns of autophosphorylation for irradiated and ATP-treated ATM. Caffeine inhibited ATM kinase activity for substrates but did not interfere with ATM autophosphorylation. ATP failed to activate either A-T and rad3-related protein (ATR) or DNA-dependent protein kinase under these conditions, supporting the specificity for ATM. These data demonstrate that ATP can specifically induce activation of ATM by a mechanism involving autophosphorylation. The relationship of this activation to DNA damage activation remains unclear but represents a useful model for understanding in vivo activation.
Performance of a Neural Network Trained to Make Third-molar Treatment-planning Decisions (1996)

The authors developed and tested 12 neural networks of different architectures to make lower-third-molar treatment-planning decisions, using a software-based neural network (Neudesk 1.2, Neural Computer Sciences, Southampton, UK). Network training was undertaken using clinical histories from 119 patients (with 238 lower third molars) referred for treatment planning (79 females and 40 males, mean age 25 years) together with output data consisting of actual treatments planned by a senior oral surgeon. Both the input clinical data and the consultant decisions were treated on a tooth-wise basis and were coded to numerical values. Binary data (e.g., present/absent) were coded to 1 and 0, while quantitative data (e.g., age) were scaled to fall between 0 and 1. A network based on the optimal architecture was trained and then interrogated with test data derived from a further 174 patients (119 females and 55 males, mean age 26 years) with 348 lower third molars. Network decisions were dichotomized with a threshold of 0.8. With no knowledge of the network decisions, the senior oral surgeon indicated his preferred treatments. The teeth were then assigned to "gold-standard" categories of indications present or absent based on National Institutes of Health consensus criteria. Against this, the network achieved a sensitivity of 0.78, which was slightly inferior to that of the oral surgeon (0.88), although this difference was not significant, and a specificity of 0.98, compared with 0.99 for the oral surgeon (p = NS). Agreement between the oral surgeon and network decisions was very high (kappa = 0.850). This study demonstrates that it is possible to train a neural network to provide reliable decision support for lower-third-molar treatment planning.
Two-Layer, Planar, Superconducting Multichip Module Technology (2000)

Given that the speed of integrated circuits (ICs) is projected to continue to increase at its present rate, the packaging of ICs may become a formidable task not too distant into the future. In fact, as circuit integration and IC switching speeds continue to increase, chip-to-chip interconnection becomes the limiting factor in realizing the system performance benefits of using faster ICs. Multichip modules (MCMs) offer a high performance alternative to conventional printed wiring boards (PWBs), and one of the more promising applications for high temperature superconductors (HTSCs) is as signal interconnects between bare ICs in MCMs. We report on the successful development and fabrication of a superconducting MCM packaging technology using a novel yttrium-barium-copper-oxide (YBCO)/yttrium-stabilized zirconia (YSZ)/silicon dioxide (SiO 2 )/yttrium-stabilized zirconia (YSZ)/yttrium-barium-copper-oxide (YBCO) multilayer substrate using either a chemical-mechanical planarization technique or a conventional lift-off process on a single-crystal YSZ substrate. To reduce the complexity of the processing required, the two-layer Interconnected Mesh Power System (IMPS) MCM topology was used. For demonstration purposes, a 100 MHZ ring oscillator multichip module using gallium arsenide technology was successfully fabricated.
Multicomponent AM-FM demodulation via periodicity-based algebraic separation and energy-based demodulation (2000)

Previously investigated multicomponent AM-FM demodulation techniques either assume that the individual component signals are spectrally isolated from each other or that the components can be isolated by linear time-invariant filtering techniques and, consequently, break down in the case where the components overlap spectrally or when one of the components is stronger than the other. In this paper, we present a nonlinear algorithm for the separation and demodulation of discrete-time multicomponent AM-FM signals. Our approach divides the demodulation problem into two independent tasks: algebraic separation of the components based on periodicity assumptions and then monocomponent demodulation of each component by instantaneously tracking and separating its source energy into its amplitude and frequency parts. The proposed new algorithm avoids the shortcomings of previous approaches and works well for extremely small spectral separations of the components and for a wide range of relative amplitude/power ratios. We present its theoretical analysis and experimental results and outline its application to demodulation of cochannel FM voice signals.
The Design and Application of Target-Focused Compound Libraries (2011)

Target-focused compound libraries are collections of compounds which are designed to interact with an individual protein target or, frequently, a family of related targets (such as kinases, voltage-gated ion channels, serine/cysteine proteases). They are used for screening against therapeutic targets in order to find hit compounds that might be further developed into drugs. The design of such libraries generally utilizes structural information about the target or family of interest. In the absence of such structural information, a chemogenomic model that incorporates sequence and mutagenesis data to predict the properties of the binding site can be employed. A third option, usually pursued when no structural data are available, utilizes knowledge of the ligands of the target from which focused libraries can be developed via scaffold hopping. Consequently, the methods used for the design of target-focused libraries vary according to the quantity and quality of structural or ligand data that is available for each target family. This article describes examples of each of these design approaches and illustrates them with case studies, which highlight some of the issues and successes observed when screening target-focused libraries.
Joseph Frank and his Criticism of the Financial Issues of the Croatian-Hungarian Agreement (2011)

Autor na temelju analize ranih radova Josipa Franka o financijskim aspektima Hrvatsko-ugarske Nagodbe i u njenoj usporedbi s Austro-Ugarskom nagodbom prikazuje osnovne probleme multiralnih odnosa u sklopu Dvojne Monarhije. Istaknut je kompleks hrvatske podređenosti u sklopu dualistickog i subdualistickog poretka u Monarhiji. Clanak donosi i uvid u kriticka promisljanja J. Franka o banovanju I. Mažuranica, kao i kriticke poglede druge stranke o nacinu Frankovih financijskih proracuna
The IBM token-ring network — A functional overview (1987)

The IBM token-ring network, which is based on a ring topology with token-access control, is described. In particular, a star-wired ring topology and the functions of several of the key physical components that compromise a token-ring network are examined. The token-access control protocol for regulating data flow on the ring is explained, including the data frame format and addressing structures, mechanisms for ensuring token integrity and fair token access to all attached nodes, and some token-ring performance attributes. The relationship between the token-ring architecture and systems network architecture (SNA) is also discussed. Some of the fault detection and isolation capabilities that are available with the token-ring LAN are also presented.