gebhart/patrepeval huggingface dataset:
Abolition of Cyclin-Dependent Kinase Inhibitor p16 Ink4a and p21 Cip1/Waf1 Functions Permits Ras-Induced Anchorage-Independent Growth in Telomerase-Immortalized Human Fibroblasts (2003)

Human cells are more resistant to both immortalization and malignant transformation than rodent cells. Recent studies have established the basic genetic requirements for the transformation of human cells, but much of this work relied on the expression of transforming proteins derived from DNA tumor viruses. We constructed an isogenic panel of human fibroblast cell lines using a combination of gene targeting and ectopic expression of dominantly acting mutants of cellular genes. Abolition of p21(Cip1/Waf1) and p16(Ink4a) functions prevented oncogenically activated Ras from inducing growth arrest and was sufficient for limited anchorage-independent growth but not tumorigenesis. Deletion of the tumor suppressor p53 combined with abolition of p16(Ink4a) function failed to mimic the introduction of simian virus 40 large T antigen, indicating that large T antigen may target additional cellular functions. Ha-Ras and Myc cooperated only to a limited extent, but in the absence of Ras, Myc cooperated strongly with the simian virus 40 small t antigen to elicit aggressive anchorage-independent growth. The experiments reported here further define specific components of human transformation pathways.
Purification of a mouse nuclear factor that binds to both the A and B cores of the polyomavirus enhancer (1990)

We have previously identified a protein factor, PEBP2 (polyomavirus enhancer-binding protein), in the nuclear extract from mouse NIH 3T3 cells which binds to the sequence motif, PEA2, located within the polyomavirus enhancer A element. Upon cellular transformation with activated oncogene c-Ha-ras, this factor frequently undergoes drastic molecular modifications into an altered form having a considerably reduced molecular size. In this study, the altered form, PEBP3, was purified to near homogeneity. The purified PEBP3 comprised two sets of families of polypeptides, alpha-1 to alpha-4 and beta-1 to beta-2, which were 30 to 35 kilodaltons and 20 to 25 kilodaltons in size, respectively. Both kinds of polypeptides possessed DNA-binding activities with exactly the same sequence specificity. Individual alpha or beta polypeptides complexed with DNA showed faster gel mobilities than did PEBP3. However, the original gel retardation pattern was restored when alpha and beta polypeptides were mixed together in any arbitrary pair. These observation along with the results of UV- and chemical-cross-linking studies led us to conclude that PEBP3 is a heterodimer of alpha and beta subunits, potentially having a divalent DNA-binding activity. Furthermore, PEBP3 was found to bind a second, hitherto-unnoticed site of the polyomavirus enhancer that is located within the B element and coincides with the sequence previously known as the simian virus 40 enhancer core homology. From comparison of this and the original binding sites, the consensus sequence for PEBP3 was defined to be PuACCPuCA. These findings provided new insights into the biological significance of PEBP3 and PEBP2.
Inflammatory and Mechanical Complications Associated With 3 Years of up to 30 Nights of Continuous Wear of Lotrafilcon A Silicone Hydrogel Lenses (2007)

These results show that the rate of contact lens adverse events occurring with lotrafilcon A is low in this cohort, with the highest likelihood occurring during the first 3 months of the study. There was a decrease in the rate of events during the later years of the study. Although clinicians should understand the likelihood of adverse inflammatory and mechanical events and their possible recurrence, the rate of these events may be lower in practice than previously reported.
Crystal Structure of Homo sapiens Kynureninase, (2007)

Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
Neurodevelopmental and Growth Impairment Among Extremely Low-Birth-Weight Infants With Neonatal Infection (2004)

This large cohort study suggests that neonatal infections among ELBW infants are associated with poor neurodevelopmental and growth outcomes in early childhood. Additional studies are needed to elucidate the pathogenesis of brain injury in infants with infection so that novel interventions to improve these outcomes can be explored.
Hardware synchronization for embedded multi-core processors (2011)

Multi-core processors are about to conquer embedded systems - it is not the question of whether they are coming but how the architectures of the microcontrollers should look with respect to the strict requirements in the field. We present the step from one to multiple cores in this paper, establishing coherence and consistency for different types of shared memory by hardware means. Also support for point-to-point synchronization between the processor cores is realized implementing different hardware barriers. The practical examinations focus on the logical first step from single- to dual-core systems, using an FPGA-development board with two hard PowerPC processor cores. Best and worst-case results, together with intensive bench- marking of all synchronization primitives implemented, show the expected superiority of the hardware solutions. It is also shown that dual-ported memory outperforms single-ported memory if the multiple cores use inherent parallelism by locking shared memory more intelligently using an address-sensitive method.
Prospective Trials of Intelligent Alarm Algorithms for Patient Monitoring. (2001)

“Intelligent” alarm algorithms have the potential to improve monitoring systems for critical care by safe reduction of false alarms and better integration of physiological signals. Evaluation is a key process in the development of these algorithms. This study explores a new evaluation approach: prospective trials in real time. Preliminary results indicate that this approach may allow better data correlation, collection of algorithm-specific information, and adaptive learning in real time.
Basic Mechanisms of Epilepsy: Targets for Therapeutic Intervention (1997)

Although a wide variety of drugs are available for treatment of epilepsy, many patients with epilepsy still experience uncontrolled seizures. In addition, there is a need for new drugs that can halt epileptogenesis after brain injury. Mechanisms that underlie seizure processes constitute potential target areas for the development of new antiepileptic drugs (AEDs). An understanding of the underlying mechanisms of interictal spike discharge and seizure spread is critical for the development of AEDs for treatment of partial seizures. Suppression of specific forms of voltage-dependent calcium currents and inhibition of GABA(B) receptor-mediated inhibition are two key target areas for new AEDs to treat primary generalized seizures. As researchers gain more understanding of the cellular, molecular, and genetic mechanisms underlying seizure propagation, we should be better able to develop therapeutic agents designed to suppress seizure-provoking mechanisms and to enhance the brain's natural protective mechanisms.
Regulation of chondrogenesis and chondrocyte differentiation by stress (2008)

Chondrogenesis and endochondral ossification are the cartilage differentiation processes that lead to skeletal formation and growth in the developing vertebrate as well as skeletal repair in the adult. The exquisite regulation of these processes, both in normal development and in pathologic situations, is impacted by a number of different types of stress. These include normal stressors such as mechanical loading and hypoxia as well pathologic stressors such as injury and/or inflammation and environmental toxins. This article provides an overview of the processes of chondrogenesis and endochondral ossification and their control at the molecular level. A summary of the influence of the most well-understood normal and pathologic stressors on the differentiation program is also presented.
gRmobile: A Framework for Touch and Accelerometer Gesture Recognition for Mobile Games (2009)

Mobile phone games are usually design to be able to play using the traditional number pads of the handsets. This is stressfully difficult for the user interaction and consequently for the game design. Because of that, one of the most desired features of a mobile games is the usage of few buttons as possible. Nowadays, with the evolution of the mobile phones, more types of user interaction are appearing, like touch and accelerometer input. With these features, game developers have new forms of exploring the user input, being necessary to adapt or create new kinds of game play. With mobile phones equipped with 3D accelerometers, developers can use the simple motion of the device to control the game or use complex accelerated gestures. And with mobile phones equipped with the touch feature, they can use a simple touch or a complex touch gesture recognitions. For the gesture to be recognized one can use different methods like simple brute force gestures, that only works well on simple gestures, or more complex pattern recognition techniques like hidden Markov fields, fuzzy logic and neural networks. This work presents a novel framework for touch/accelerometer gesture recognition that uses hidden Markov model for recognition of the gestures. This framework can also be used for the development of mobile application with the use of gestures.
Digital Image Processing Software (1985)

We examine and attempt to classify presently available image processing software products. Next, we suggest that the advent of extremely inexpensive image processing hardware puts new demands upon image processing software. These include ease of use, ease of adaptation to new tasks and transportability. Finally, we illustrate the discussion by presenting in some detail a system whose novelty is an unusually low cost, combined with surprising performance, ease of use and versatility.
Base excision repair intermediates are mutagenic in mammalian cells (2005)

Base excision repair (BER) is the main pathway for repair of DNA damage in mammalian cells. This pathway leads to the formation of DNA repair intermediates which, if still unsolved, cause cell lethality and mutagenesis. To characterize mutations induced by BER intermediates in mammalian cells, an SV-40 derived shuttle vector was constructed carrying a site-specific lesion within the recognition sequence of a restriction endonuclease. The mutation spectra of abasic (AP) sites, 5'-deoxyribose-5-phosphate (5'dRp) and 3'-[2,3-didehydro-2,3-dideoxy-ribose] (3'ddR5p) single-strand breaks (ssb) in mammalian cells was analysed by RFLP/PCR and mutation frequency was estimated by quantitative PCR. Point mutations were the predominant events occurring at all BER intermediates. The AP site-induced mutation spectrum supports evidence for the 'A-rule' and is also consistent with the use of the 5' neighbouring base to instruct nucleotide incorporation (5'-rule). Preferential adenine insertion was also observed after in vivo replication of 5'dRp or 3'ddR5p ssb. We provide original evidence that not only the abasic site but also its derivatives 'faceless' BER intermediates are mutagenic, with a similar mutation frequency, in mammalian cells. Our findings support the hypothesis that unattended BER intermediates could be a constant threat for genome integrity as well as a spontaneous source of mutations.
Bounds for DNA Codes with Constant GC-Content (2003)

We derive theoretical upper and lower bounds on the maximum size of DNA codes of length $n$ with constant GC-content $w$ and minimum Hamming distance $d$, both with and without the additional constraint that the minimum Hamming distance between any codeword and the reverse-complement of any codeword be at least $d$. We also explicitly construct codes that are larger than the best previously-published codes for many choices of the parameters $n$, $d$ and $w$.
Kinetics of fibrin oligomer formation observed by electron microscopy (1983)

Fibrin oligomers, obtained by interrupting the polymerization of fibrinogen at early stages with a thrombin inhibitor, were examined by electron microscopy. The lengths of the various oligomers were determined and histograms were constructed to show their distribution. The length distribution agreed with a theory based on the assumption that thrombin releases the second A peptide more rapidly than the first, with a ratio of the release rates for the two peptides which is qualitatively in agreement with that deduced from oligomer size distributions obtained by agarose gel electrophoresis.
Time-resolved fluorimetric detection of terbium-labelled deoxyribonucleic acid separated by gel electrophoresis (1989)

Deoxyribonucleic acid (DNA) was reacted with a strong chelating agent and labelled with terbium, yielding a highly fluorescent conjugate with a lifetime of 1.5 ms. When a pulsed source and gated detection electronics were employed, the long-lived decay allowed effective discrimination against background fluorescence and scattered excitation. Detection limits should therefore be significantly improved in comparison with covalent labels with fluorescence lifetimes in the nanosecond regime or stains such as ethidium bromide. The conjugate is very stable, remaining fluorescent on dilution and in an electric field at elevated temperatures (60 degrees C), conditions typically encountered during polyacrylamide gel electrophoresis. As an enhancement solution is not required to develop the fluorescence, this system could be utilised in situations where on-line detection is desirable. Although only DNA was labelled, the method is equally applicable to ribonucleic acid.
Graphite Epoxide (2008)

Oxidation of graphite may be carried out by reaction with meta-chloroperoxybenzoic acid to yield graphite epoxide. Scanning tunneling microscopy (STM) showed that the functionalization occurs at the edges rather than on the basal plane of the graphite. Quantification of the epoxide content is possible through the deepoxidation reaction using MeReO3/PPh3.
A Cell Proliferation and Chromosomal Instability Signature in Anaplastic Thyroid Carcinoma (2007)

Here, we show that the anaplastic thyroid carcinoma (ATC) features the up-regulation of a set of genes involved in the control of cell cycle progression and chromosome segregation. This phenotype differentiates ATC from normal tissue and from well-differentiated papillary thyroid carcinoma. Transcriptional promoters of the ATC up-regulated genes are characterized by a modular organization featuring binding sites for E2F and NF-Y transcription factors and cell cycle-dependent element (CDE)/cell cycle gene homology region (CHR) cis-regulatory elements. Two protein kinases involved in cell cycle regulation, namely, Polo-like kinase 1 (PLK1) and T cell tyrosine kinase (TTK), are part of the gene set that is up-regulated in ATC. Adoptive overexpression of p53, p21 (CIP1/WAF1), and E2F4 down-regulated transcription from the PLK1 and TTK promoters in ATC cells, suggesting that these genes might be under the negative control of tumor suppressors of the p53 and pRB families. ATC, but not normal thyroid, cells depended on PLK1 for survival. RNAi-mediated PLK1 knockdown caused cell cycle arrest associated with 4N DNA content and massive mitotic cell death. Thus, thyroid cell anaplastic transformation is accompanied by the overexpression of a cell proliferation/genetic instability-related gene cluster that includes PLK1 kinase, which is a potential molecular target for ATC treatment.
Delayed microsurgical reconstruction of the extremities for complex soft-tissue injuries (2005)

The treatment of severe wounds of the extremities, characterized by large posttraumatic tissue loss, represents a clinical problem difficult to resolve, especially when the lesion is surrounded by large areas of ischemic distrophic tissue which progressively aggravate and extend the initial lesion, with frequent exposure of bone and joint structures making the amputation of the limb an inevitable outcome. The authors present their experience based on combined treatments by medical support methods such as hyperbaric oxygen (HBO) and vacuum-assisted closure therapy (VAC) and microsurgical reconstruction of the limbs, within a precise therapeutic protocol. The use of this protocol in appropriate times and ways allowed us to successfully treat severe posttraumatic sequelae of the limbs, avoiding the delayed healing typical of these pathologies, both on the donor site of the flap and on the repaired area, and avoiding unsuitable microsurgical reconstruction of limbs, allowing satisfactory morpho-functional restoration and a reduction of the hospitalization period.
IL-17 is increased in asthmatic airways and induces human bronchial fibroblasts to produce cytokines (2001)

Our results, which demonstrate for the first time that eosinophils are a potential source of IL-17 within asthmatic airways, suggest that IL-17 might have the potential to amplify inflammatory responses through the release of proinflammatory mediators such as alpha-chemokines.
Biophysical Attributes of CpG Presentation Control TLR9 Signaling to Differentially Polarize Systemic Immune Responses (2017)

It is currently unknown whether and how mammalian pathogen recognition receptors (PRRs) respond to biophysical patterns of pathogen-associated molecular danger signals. Using synthetic pathogen-like particles (PLPs) that mimic physical properties of bacteria or large viruses, we have discovered that the quality and quantity of Toll-like receptor 9 (TLR9) signaling by CpG in mouse dendritic cells (mDCs) are uniquely dependent on biophysical attributes; specifically, the surface density of CpG and size of the presenting PLP. These physical patterns control DC programming by regulating the kinetics and magnitude of MyD88-IRAK4 signaling, NF-κB-driven responses, and STAT3 phosphorylation, which, in turn, controls differential T cell responses and in vivo immune polarization, especially T helper 1 (Th1) versus T helper 2 (Th2) antibody responses. Our findings suggest that innate immune cells can sense and respond not only to molecular but also pathogen-associated physical patterns (PAPPs), broadening the tools for modulating immunity and helping to better understand innate response mechanisms to pathogens and develop improved vaccines.
Development of SNP Assays for Marker‐Assisted Selection of Two Southern Root‐Knot Nematode Resistance QTL in Soybean (2007)

The identification of single nucleotide polymorphism (SNP) markers tightly linked to soybean [ Glycine max (L.) Merr.] quantitative trait loci (QTL) conditioning resistance to southern root‐knot nematode ( Meloidogyne incognita ) (Mi) would enhance the efficiency and cost effectiveness of marker‐assisted selection (MAS) for this trait. Bacterial artificial chromosome (BAC) ends and simple sequence repeat (SSR)‐containing genomic DNA clones were used to develop SNP markers linked to two soybean Mi resistance QTL on Linkage Group O (LG‐O) and LG‐G. A total of 14 BAC‐end sequences and seven SSR flanking regions were used to design primers to amplify genomic fragments of PI 96354 (Mi resistant) and ‘Bossier’ (Mi susceptible). We discovered three SNPs in Satt358 source‐sequences located near a major Mi‐resistant QTL on LG‐O and three SNPs in Satt199 source‐sequences located near a minor Mi‐resistant QTL on LG‐G. Using a direct hybridization SNP assay detected on a Luminex 100 flow cytometer, the SNP358 genotypes of 94 F 2:3 lines from a cross of PI 96354 × Bossier were congruent with the genotypes of the SSR marker Satt358. The genotypes of SNP199 marker which targets a SNP in Satt199 source‐sequence also showed 100% congruence with the genotypes of the SSR marker Satt199. SNP genotyping of 24 known Mi‐resistant or Mi‐susceptible cultivars showed that SNP358 and SNP199 markers should be highly effective in MAS for the Mi‐resistance QTL on LG‐O and LG‐G.
The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance (2008)

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor composed of three distinct subunits (NF-YA, NF-YB, and NF-YC). We found that the Arabidopsis thaliana NFYA5 transcript is strongly induced by drought stress in an abscisic acid (ABA)-dependent manner. Promoter:beta-glucuronidase analyses showed that NFYA5 was highly expressed in vascular tissues and guard cells and that part of the induction by drought was transcriptional. NFYA5 contains a target site for miR169, which targets mRNAs for cleavage or translational repression. We found that miR169 was downregulated by drought stress through an ABA-dependent pathway. Analysis of the expression of miR169 precursors showed that miR169a and miR169c were substantially downregulated by drought stress. Coexpression of miR169 and NFYA5 suggested that miR169a was more efficient than miR169c at repressing the NFYA5 mRNA level. nfya5 knockout plants and plants overexpressing miR169a showed enhanced leaf water loss and were more sensitive to drought stress than wild-type plants. By contrast, transgenic Arabidopsis plants overexpressing NFYA5 displayed reduced leaf water loss and were more resistant to drought stress than the wild type. Microarray analysis indicated that NFYA5 is crucial for the expression of a number of drought stress-responsive genes. Thus, NFYA5 is important for drought resistance, and its induction by drought stress occurs at both the transcriptional and posttranscriptional levels.
Assessing document relevance with run-time reconfigurable machines (1996)

Free text database searching is a natural candidate for acceleration by run time reconfigurable custom computing machines. We describe a fully pipelined search machine architecture for scoring the relevance of textual documents against approximately 100 relevant target words, with provision for limited regular expression matching and error tolerance. An implementation on the SPACE custom computing platform indicates that throughput in the order of 20 megabytes per second is achievable on ALgotronix FPGAs if a locally synchronous design style is adopted and global communications minimized. Partial reconfiguration of the datapath at run time, in around 3 seconds, serves to maximize the density of data storage on the machine and correspondingly avoid costly input from the environment.