gebhart/patrepeval huggingface dataset:
Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems (1999)

Arabidopsis thaliana floral meristems are determinate structures that produce a defined number of organs, after which cell division ceases. A new recessive mutant, carpel factory (caf), converts the floral meristems to an indeterminate state. They produce extra whorls of stamens, and an indefinite number of carpels. Thus, CAF appears to suppress cell division in floral meristems. The function of CAF is partially redundant with the function of the CLAVATA (CLV) and SUPERMAN (SUP) genes, as caf clv and caf sup double mutants show dramatically enhanced floral meristem over-proliferation. caf mutant plants also show other defects, including absence of axillary inflorescence meristems, and abnormally shaped leaves and floral organs. The CAF gene was cloned and found to encode a putative protein of 1909 amino acids containing an N-terminal DExH/DEAD-box type RNA helicase domain attached to a C-terminal RNaseIII-like domain. A very similar protein of unknown function is encoded by a fungal and an animal genome. Helicase proteins are involved in a number of processes, including specific mRNA localization and mRNA splicing. RNase III proteins are involved in the processing of rRNA and some mRNA molecules. Thus CAF may act through some type of RNA processing event(s). CAF gives rise to two major transcripts of 2.5 and 6.2 kb. In situ hybridization experiments show that CAF RNA is expressed throughout all shoot tissues.
Spore Germination and Germ Tube Growth of a Vesicular-Arbuscular Mycorrhizal Fungusin Vitro (1982)

The effects of mineral nutrients, thiamine, pH, and organic substrates on germination and germ tube growth of a vesicular-arbuscular mycorrhizal fungus were examined. Surfacesterilized azygospores of Gigaspora margarita were plated on 1% water agar containing different components and incubated at 28 C up to 30 da. Maximum germination and germ tube growth occurred when 20 mg 1-1 CaH2PO4 was used, whereas 24 mg 1-1 NH4NO3 did not affect germination and depressed germ tube growth by 55%. Potassium or concentrations of soluble nutrient salts as high as those used to grow seedlings axenically had no effect on spore germination or germ tube growth. Thiamine at 0.1 mg 1-1 increased germination, and maximum germ tube growth occurred at 0.01 mg 1-1. The interaction between medium pH and medium composition was significant. Spore germination was not enhanced by any of the organic substrates. Low concentrations (4 g 1-1) of sucrose favored germ tube growth. Relation of these results to nutrition and root-colonizing ability of VA mycorrhizal spores is discussed.
Variable Markov Oracle: A Novel Sequential Data Points Clustering Algorithm with Application to 3D Gesture Query-Matching (2014)

In this paper a new method, Variable Markov Oracle, for clustering time series data points is proposed. Variable Markov Oracle is based on previous results of Audio Oracle, a method of fast indexing repeating sub-clips in an audio stream. The proposed method is capable of discovering natural clusters with temporal relations without specifying the number of clusters. The discovery of inherent clusters in time series data points allows the devising of an efficient algorithm for time series query-matching. The ability of discovering clusters is demonstrated with a synthetic audio example, and an application of querying 3D skeletal gesture using the query-matching algorithm based on the proposed method is experimented with comparable result to state of the art.
Long-Term Persistence of Resistant Enterococcus Species after Antibiotics To Eradicate Helicobacter pylori (2003)

A common H. pylori treatment selects for highly resistant enterococci that can persist for at least 3 years without further selection.
Two-dimensional silicon photonic crystal based biosensing platform for protein detection (2007)

We theoretically and experimentally demonstrate an ultrasensitive two-dimensional photonic crystal microcavity biosensor. The device is fabricated on a silicon-on-insulator wafer and operates near its resonance at 1.58 microm. Coating the sensor internal surface with proteins of different sizes produces a different amount of resonance redshift. The present device can detect a molecule monolayer with a total mass as small as 2.5 fg. The device performance is verified by measuring the redshift corresponding to the binding of glutaraldehyde and bovine serum albumin (BSA). The experimental results are in good agreement with theory and with ellipsometric measurements performed on a flat oxidized silicon wafer surface.
Interferon-alpha, zidovudine, and granulocyte-macrophage colony-stimulating factor: a phase I AIDS Clinical Trials Group study in patients with Kaposi's sarcoma associated with AIDS. (1992)

GM-CSF prevents neutropenia induced by the IFN-alpha and zidovudine combination and induced no adverse effects on immune function or HIV activity. However, nonhematologic toxicity precluded a major increase in the maximum-tolerated doses of IFN-alpha and zidovudine.
High efficiency error suppression for accurate detection of low-frequency variants (2019)

Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to technical artefacts that can limit the accuracy for calling low-allele-frequency mutations. State-of-the-art methods to improve detection of low-frequency mutations often employ unique molecular identifiers (UMIs) for error suppression; however, these methods are highly inefficient as they depend on redundant sequencing to assemble consensus sequences. Here, we present a novel strategy to enhance the efficiency of UMI-based error suppression by retaining single reads (singletons) that can participate in consensus assembly. This 'Singleton Correction' methodology outperformed other UMI-based strategies in efficiency, leading to greater sensitivity with high specificity in a cell line dilution series. Significant benefits were seen with Singleton Correction at sequencing depths ≤16 000×. We validated the utility and generalizability of this approach in a cohort of >300 individuals whose peripheral blood DNA was subjected to hybrid capture sequencing at ∼5000× depth. Singleton Correction can be incorporated into existing UMI-based error suppression workflows to boost mutation detection accuracy, thus improving the cost-effectiveness and clinical impact of NGS.
Detection of Ductal Carcinoma In Situ in Women Undergoing Screening Mammography (2002)

Overall, approximately 1 in every 1300 screening mammography examinations leads to a diagnosis of DCIS. Given uncertainty about the natural history of DCIS, the clinical significance of screen-detected DCIS needs further investigation.
Adaptive bit-rate control for Region-of-Interest Scalable Video Coding (2010)

In this work, we present a novel approach for providing an adaptive bit-rate control for the Region-of-Interest (ROI) Scalable Video Coding (SVC). Recently, much of the attention in the field of video adaptation has been directed to the SVC, which is the extension of the H.264/AVC standard. The need for the scalability mainly arises from the need for spatial formats, bit rates or power. To fulfill these requirements, it would be beneficial to simultaneously transmit or store video in variety of spatial/temporal resolutions and qualities, leading to the video bit-stream scalability. The ROI coding is a desirable feature in future SVC applications. For those SVC applications, users at the decoder side usually wish to receive a high-quality decoded video stream, containing the desired ROI, which should be adaptively selected from the pre-encoded scalable bit-stream. By implementing the proposed adaptive bit-rate control for the ROI SVC, smaller quantization parameters can be used, while obtaining the same compression rate, especially, in order to optimally employ the decoder computational resources and in order to achieve optimal video presentation quality. As a result, the SVC visual presentation quality at the decoder side will be significantly improved even for the decoders with very limited computational resources, which can be very useful for various mobile devices, such as cellular phones. Further, the proposed adaptive bit-rate control scheme is especially useful for future Internet and 4G applications with limited computational resources and/or with a limited channel bandwidth, such as video conferencing (between two or more mobile device users), video transrating, video transcoding between video coding standards, and many other applications.
Heterogeneous Integration of Compound Semiconductors (2010)

The ability to tailor compound semiconductors and to integrate them onto foreign substrates can lead to superior or novel functionalities with a potential impact on various areas in electronics, optoelectronics, spintronics, biosensing, and photovoltaics. This review provides a brief description of different approaches to achieve this heterogeneous integration, with an emphasis on the ion-cut process, also known commercially as the Smart-Cut ™ process. This process combines semiconductor wafer bonding and undercutting using defect engineering by light ion implantation. Bulk-quality heterostructures frequently unattainable by direct epitaxial growth can be produced, provided that a list of technical criteria is fulfilled, thus offering an additional degree of freedom in the design and fabrication of heterogeneous and flexible devices. Ion cutting is a generic process that can be employed to split and transfer fine monocrystalline layers from various crystals. Materials and engineering issues as well as our current understanding of the underlying physics involved in its application to cleaving thin layers from freestanding GaN, InP, and GaAs wafers are presented.
Host microenvironment in breast cancer development: Extracellular matrix–stromal cell contribution to neoplastic phenotype of epithelial cells in the breast (2003)

Epithelial-mesenchymal interactions play an important role both in normal mammary gland development and during neoplastic transformation. Perturbations in the production, deposition and degradation of the extracellular matrix occurring during neoplastic transformation and progression have been implicated to arise from alterations in the stromal response. These changes in the stroma exhibit a dominant regulatory role, via microenvironmental epigenetic effectors, to contribute to the development of the tumorigenic epithelial phenotype. The role of stromally derived microenvironmental epigenetic effectors in modulating epithelial growth, hormonal response, morphogenesis and epithelial plasticity is discussed.
The chemotherapy of rodent malaria, XXII. The value of drug-resistant strains of P. berghei in screening for blood schizontocidal activity. (1975)

Data are provided on the activity of a variety of antimalarial drugs against drug-sensitive and drug-resistant lines of Plasmodium berghei in albino mice. Parallel data for the response of the drug-sensitive parasites to these compounds in vitro indicate whether the drugs have a chloroquine-like or quinine-like type of action, or neither. The value of this test system for drug evaluation is debated. It is concluded that the in vivo tests do provide a valuable indication of the potential use of a compound against drug-resistant malaria parasites of man. The tests may also provide a good indication of the future value of new compounds against strains of parasites that are already resistant to chloroquine. Where necessary, steps should be taken to protect promising new compounds.
Sterically stabilized liposomes in cancer therapy and gene delivery. (1999)

The introduction of colloidally stable liposomes with low drug leakage rates resulted in a renaissance in liposome applications in cancer therapy. Furthermore, a platform of sterically stabilized liposomes also allows the construction of new generations of drug delivery vehicles. These include targeted liposomes and targeted nucleic acid delivery vehicles, based either on cationic sterically stabilized liposomes or pre-condensed DNA encapsulated in neutral or negatively charged liposomes.
The toxicity of three second‐generation rodenticides to Barn Owls (1994)

Abstract The toxicity of three second‐generation rodenticides to Barn Owls ( Tyto alba Scop.) has been investigated. Brodifacoum, difenacoum and flocoumafen were separately fed to owls over a period of 15 days via rodenticide‐fed mice to simulate the potential route of exposure in the wild. The owls survived a cumulative dose of each rodenticide of at least 1.9 mg kg −1 owl body weight over 15 days. This is equivalent to the consumption of two 25 g mice with a rodenticide residue of 1 mg kg −1 each day for 15 days. Residue analysis confirmed that the liver is the organ which retains the largest residue of ingested rodenticide.
The Effect of Heat Shock on Gene Expression in Drosophila melanogaster (1978)

When Drosophila melanogaster is exposed to 37°C, a series of specific genes is activated, whereas most of the other genes, active at 25°C before this heat shock, appear to be repressed.
Robust adaptive beamforming via target tracking (1996)

The proposed robust beamformer adaptively self-corrects and tracks desired-source location errors or variations regardless of the eigenstructure of the input correlation matrix, of the array shape and nature of the noise. It only requires an order of computations of the sensors number and performs nearly as well as MUSIC in localization.
Recent advances in the treatment of ARDS (1995)

Despite more than 25 years of extensive research the mortality of ARDS patients remains high. Besides the often deleterious course of the underlying disease, another reason for this high mortality lies in the aggressive ventilatory regimen which is required to maintain arterial blood gases in a more or less normal range. Therapeutic methods which are used to reduce iatrogenic damage to the lungs are pressure controlled ventilation with permissive hypercapnia, differential lung ventilation, positioning therapy, dehydration, and extracorporeal gas exchange with membrane lungs. Nevertheless, many of these patients still die following hypoxaemia or multiple organ failure. Therefore, the need remains to develop new therapeutic strategies and to investigate their influence on the morbidity and mortality of this life-threatening disease. First experiences with nitric oxide (NO) inhalation, intravenous application of antioxidants, intratracheal instillation of surfactant, tracheal gas insufflation and combined fluid/gas ventilation with perfluorocarbon are presented. All these new methods have proved their efficacy, at least in animal studies, however, they should still be regarded as experimental.
Induction of Direct Antimicrobial Activity Through Mammalian Toll-Like Receptors (2001)

The mammalian innate immune system retains from Drosophila a family of homologous Toll-like receptors (TLRs) that mediate responses to microbial ligands. Here, we show that TLR2 activation leads to killing of intracellular Mycobacterium tuberculosis in both mouse and human macrophages, through distinct mechanisms. In mouse macrophages, bacterial lipoprotein activation of TLR2 leads to a nitric oxide-dependent killing of intracellular tubercle bacilli, but in human monocytes and alveolar macrophages, this pathway was nitric oxide-independent. Thus, mammalian TLRs respond (as Drosophila Toll receptors do) to microbial ligands and also have the ability to activate antimicrobial effector pathways at the site of infection.
The design and performance of a neural network for predicting turbo decoding error with application to hybrid ARQ protocols (2000)

It is shown that a neural network can be trained to observe the cross entropy of the outputs of component decoders in a turbo error control system and to accurately predict the presence of errors in the decoded data. The neural network can be used as a trigger for retransmission requests at either the beginning or the conclusion of the decoding process, providing improved reliability and throughput performance at a lower average decoding complexity than turbo decoding with cyclic redundancy check error detection.
Investigation into the 5‐hydroxytryptamine receptor mediating smooth muscle relaxation in the rat oesophagus (1991)

1. An investigation has been made into the 5-hydroxytryptamine (5-HT) receptor mediating relaxation of rat oesophagus in preparations precontracted with carbachol. 2. In tissues treated with pargyline (100 microM) and in the presence of corticosterone (30 microM) and cocaine (30 microM) the potency of 5-HT and 5-methoxytyramine (5-MeOT) was not changed but the maximum response to these agonists was reduced. Thus there was no evidence of metabolism and/or uptake through an amine depleting mechanism. 3. The relaxant concentration-effect curves to 5-HT were shifted to the left in a concentration-related manner by isobutylmethylxanthine (1 and 10 microM), suggesting the involvement of adenosine 3':5'-cyclic monophosphate in these responses. 4. 5-HT produced concentration-related relaxations of rat oesophagus with an EC50 value of 0.24 microM. Several indole agonists were tested and the following rank order of potency of key agonists obtained: 5-HT greater than alpha-methyl-5-hydroxytryptamine = 5-carboxamidotryptamine (5-CT) greater than 5-MeOT. In contrast, 2-methyl-5-hydroxytryptamine, sumatriptan and 8-hydroxy-2-(di-n-propylamino) tetralin were weak or inactive. 5. The substituted benzamides, metoclopramide, cisapride, renzapride and R,S-zacopride acted as partial agonists, producing 60-70% of the 5-HT maximum. 6. The relaxation responses to 5-HT were neither inhibited by antagonists selective for 5-HT1 or 5-HT2 receptors nor by the 5-HT3 receptor antagonists, ondansetron, granisetron or MDL 72222. 7. The relaxation responses induced by 5-HT, 5-CT, 5-MeOT and renzapride were selectively inhibited by high concentrations of ICS 205-930 with pKB values of approximately 6. 8. The 5-HT receptor mediating relaxation in rat oesophagus cannot be designated 5-HT1, 5-HT2 or 5-HT3 under the current 5-HT classification, but the observed effects are consistent with stimulation of the putative 5-HT4 receptor.
Comparative study of the impact of chronic urticaria, psoriasis and atopic dermatitis on the quality of life (2005)

The comparison shows that CU, PSO and AD are characterized by completely different qualitative profiles of impact on HRQL, which are influenced by their clinical characteristics and usual treatment options. It underlines the severe impairment of CU which is often underestimated.
Targeted Drug Delivery Systems Mediated by a Novel Peptide in Breast Cancer Therapy and Imaging (2013)

Targeted delivery of drugs to tumors represents a significant advance in cancer diagnosis and therapy. Therefore, development of novel tumor-specific ligands or pharmaceutical nanocarriers is highly desirable. In this study, we utilized phage display to identify a new targeting peptide, SP90, which specifically binds to breast cancer cells, and recognizes tumor tissues from breast cancer patients. We used confocal and electron microscopy to reveal that conjugation of SP90 with liposomes enables efficient delivery of drugs into cancer cells through endocytosis. Furthermore, in vivo fluorescent imaging demonstrated that SP90-conjugated quantum dots possess tumor-targeting properties. In tumor xenograft and orthotopic models, SP90-conjugated liposomal doxorubicin was found to improve the therapeutic index of the chemotherapeutic drug by selectively increasing its accumulation in tumors. We conclude that the targeting peptide SP90 has significant potential in improving the clinical benefits of chemotherapy in the treatment and the diagnosis of breast cancer.
The Importance of Hydrochemical Investigations in Sustainable Groundwater Resource Management in Irrigated Catchments (2003)

The continuing demand for water to support agricultural practices in irrigated catchments has placed significant pressures on groundwater systems and raised questions pertaining , to the long-term sustainability of these resources. The stress placed on groundwater systems threatens not only the sustainability of the agriculture itself, but also the continual access to potable water, and environmental flow needs. The impacts of irrigated agriculture affect not only the hydrodynamics of groundwater systems but the chemistry and quality of the groundwater and these impacts have been witnessed in many groundwater systems in both Australia and internationally. It is only in recent years that resource managers and farmers alike have recognised the need for hydrochemical investigations of groundwater systems to assess the impacts of irrigation on water quality and the threat to groundwater sustainability. In the Lower Namoi River catchment, northern New South Wales, Australia, overexploitation of groundwater resources to support irrigated agriculture over the last 35 years, has not only caused groundwater level declines of up to 35m, but has significantly altered the hydrochemistry and quality of groundwater in the multilayered alluvial aquifer system. Pumping from productive aquifers for irrigation has led to the reversal of natural vertical hydraulic gradients and has allowed the mixing of groundwater of different chemical composition and quality. In the southeast of the catchment, pumping activities have enhanced the upward leakage of Na-HC03-rich groundwater from the Great Artesian Basin into the overlying alluvial aquifers and degraded the quality of the groundwater for irrigation. This paper focuses on the hydrochemical investigation undertaken by the University of New South Wales to delineate the impact of overexploitation on groundwater chemistry. It will discuss the methodology of the investigation, the interpretation and conclusions drawn from analytical data and how the information gained from this investigation can be utilised by resource managers.
Studies on the Specificity and Site of Action of α-Cyclopropyl-α-[p-methoxyphenyl]-5-pyrimidine Methyl Alcohol (Ancymidol), a Plant Growth Regulator (1978)

alpha-Cyclopropyl-alpha-[p-methoxyphenyl]-5-pyrimidine methyl alcohol (ancymidol) is an inhibitor of ent-kaur-16-ene oxidation in microsomal preparations from the liquid endosperm of immature Marah macrocarpus seeds. The K(i) for this inhibitor is about 2 x 10(-9)m. Ancymidol also blocks ent-kaur-16-en-19-ol and ent-kaur-16-en-19-al oxidation by the same preparations with a similar efficiency, but does not significantly inhibit ent-kaur-16-en-19-oic acid oxidation. Ancymidol appears to be specific for this series of oxidations in higher plant tissues. It does not inhibit the oxidation of kaurene nor kaurenoic acid in rat liver microsomes and has no significant effect on the oxidation of cinnamic acid in microsomal preparations from Sorghum bicolor seedlings. Ancymidol also does not inhibit kaurene oxidation in vitro nor in vivo in cultures of the fungus Fusarium moniliforme. The presence of ancymidol did not significantly alter the activities of NADPH-cytochrome c reductase, NADH-cytochrome c reductase, or NADH-cytochrome b(5) reductase. The addition of ancymidol to suspensions of oxidized M. macrocarpus endosperm led to a difference spectrum with an absorption maximum at 427 nm and a minimum at 410 nm.