gebhart/patrepeval huggingface dataset:
Stearoyl-CoA desaturase 1 (Scd1) gene overexpression is associated with genetic predisposition to hepatocarcinogenesis in mice and rats (2002)

The stearoyl-CoA desaturase 1 (Scd1) gene is involved in the synthesis and regulation of unsaturated fatty acids. Its expression is increased by several treatments/conditions that are associated with hepatocarcinogenesis (peroxisome proliferators, iron overload, dichloroacetic acid). We found that the Scd1 gene is differentially expressed, showing >10-fold higher mRNA levels in the normal liver tissue of C3H/He mice, which are genetically susceptible to hepatocarcinogenesis, than of BALB/c mice, which are resistant. Similarly, Scd1 mRNA expression was approximately 4-fold higher in the normal liver of F344 rats, which are susceptible to hepatocarcinogenesis, than in Brown Norway (BN) rats, which are resistant. The chromosomal location of the Scd1 locus, both in mice and rats, excludes Scd1 candidacy as a hepatocellular tumor-modifier gene, as the Scd1 locus did not show allele-specific effects in a BALB/cxC3H/He intercross or in a BNxF344 backcross and intercross. No Scd1 coding polymorphisms were detected in the mouse and the rat strains showing elevated Scd1 expression. These results suggest that the Scd1 gene represents a downstream target of hepatocellular tumor-modifier loci in two rodent species.
Bioapplications of hyperbranched polymers (2014)

Hyperbranched polymers (HBPs), an important subclass of dendritic macromolecules, are highly branched, three-dimensional globular nanopolymeric architectures. Attractive features like highly branched topological structures, adequate spatial cavities, numerous terminal functional groups and convenient synthetic procedures distinguish them from the available polymers (the linear, branched, and crosslinking polymers). Due to their unique physical/chemical properties, applications of HBPs have been explored in a large variety of fields. In particular, HBPs exhibit unique advantages in the biological and biomedical systems and devices. Firstly, the way to prepare HBPs usually only involves simple one-pot reactions and avoids the complicated synthesis and purification procedures, which makes the manufacturing process more convenient, thus reducing production costs. Secondly, the large number of end-groups of HBPs provides a platform for conjugation of the functional moieties and can also be employed to tailor-make the properties of HBPs, enhancing their versatility in biological applications. Thirdly, HBPs possess excellent biocompatibility and biodegradability, controlled responsive nature, and ability to incorporate a multiple array of guest molecules through covalent or noncovalent approaches. All of these features of HBPs are of great significance for designing and producing biomaterials. To date, significant progress has been made for the HBPs in solving some of the fundamental and technical questions toward their bioapplications. The present review highlights the contribution of HBPs to biological and biomedical fields with intent to aid the researchers in exploring HBPs for bioapplications.
Just Click It: Undergraduate Procedures for the Copper(I)-Catalyzed Formation of 1,2,3-Triazoles from Azides and Terminal Acetylenes (2005)

A procedure for copper(I)-catalyzed triazole synthesis using azides and terminal acetylenes introduces undergraduate organic students to the growing world of click chemistry. The reaction is ideal for the undergraduate laboratory as, in keeping with the defining aspects of click chemistry, it is high-yielding, requires no chromatography, is easily monitored by TLC, and displays distinct peaks in both IR and 1H-NMR. Virtually all products precipitate, and with just a few different starting blocks every student, or pair of lab partners, can produce a unique "clicked" compound. Additionally, general procedures for in situ azide synthesis and phenol propargylation provide a vehicle for chemical discovery and creativity well beyond the mini-libraries presented.
Sustainedex vivoexpansion of hematopoietic stem cells mediated by thrombopoietin (1999)

The hematopoietic stem cell (HSC) is defined as a cell that can either self-replicate or generate daughter cells that are destined to commit to mature cells of different specific lineages. Self-replication of the most primitive HSC produces daughter cells that possess a long (possibly unlimited) clonal lifespan, whereas differentiation of HSC produces daughter cells that demonstrate a progressive reduction of their clonal lifespan, a loss of multilineage potential, and lineage commitment. Previous studies indicated that the proliferation of HSC ex vivo favors differentiation at the expense of self-replication, eventually resulting in a complete loss of HSC. In contrast, transplantation studies have shown that a single HSC can repopulate the marrow of a lethally irradiated mouse, demonstrating that self-renewal of HSC occurs in vivo. Thrombopoietin (TPO) has been shown to function both as a proliferative and differentiative factor for megakaryocytes and as a survival and weakly proliferative factor for HSC. Our studies focused on the effects of exogenous TPO on HSC in mouse long-term bone marrow cultures (LTBMC). Previous results indicate that HSC decline in LTBMC in the absence of TPO. In contrast, the continuous presence of TPO resulted in the generation of both long- and short-term repopulating HSC as detected by an in vivo competitive repopulation assay. HSC were generated over a 4-month period at concentrations similar to normal bone marrow. Our results demonstrate that TPO can mediate the self-replication of HSC in LTBMC, and provide proof that HSC can self-replicate ex vivo.
Direct-qPCR Assay for Coupled Identification and Antimicrobial Susceptibility Testing of Neisseria gonorrhoeae (2018)

Multidrug-resistant gonorrhea has become an urgent issue for global public health. As the causative agent of gonorrhea, Neisseria gonorrhoeae, has been progressively developing resistance to nearly all prescribed antimicrobial drugs, monitoring its antimicrobial resistance on a broader scale has become a crucial agenda for effective antibiotic stewardship. Unfortunately, gold standard antimicrobial susceptibility testing (AST) relies on time and labor-intensive phenotypic assays, which lag behind the current diagnostic workflow for N. gonorrhoeae identification based on nucleic acid amplification tests (NAAT). Newer assay technologies based on NAAT can rapidly identify N. gonorrhoeae from clinical specimen but fundamentally lack the capacity to provide phenotypic AST information. Herein, we propose a direct-quantitative PCR (direct-qPCR) assay that enables pathogen-specific identification and phenotypic AST via quantitative measurement of N. gonorrhoeae growth directly from a liquid medium without any sample preprocessing. The assay has an analytical sensitivity of 10<sup>2</sup> CFU/mL and is highly specific to N. gonorrhoeae in the presence of urogenital flora and clinical swab eluent. We tested seven N. gonorrhoeae strains against three antibiotic agents, penicillin, tetracycline, and ciprofloxacin, and achieved 95.2% category agreement and 85.7% essential agreement with the FDA-approved E-test. The assay presented in this work has the unique ability to identify N. gonorrhoeae and provide phenotypic AST directly from the liquid medium with cell densities as low as 10<sup>2</sup> CFU/mL, demonstrating an accelerated, sensitive, and scalable workflow for performing both identification and AST of N. gonorrhoeae.
Detection of static and dynamic activities using uniaxial accelerometers (1996)

Rehabilitation treatment may be improved by objective analysis of activities of daily living. For this reason, the feasibility of distinguishing several static and dynamic activities (standing, sitting, lying, walking, ascending stairs, descending stairs, cycling) using a small set of two or three uniaxial accelerometers signals can be measured with a portable data acquisition system, which potentially makes it possible to perform online detection of static and dynamic activities in the home environment. However, the procedures described in this paper have yet to be evaluated in the home environment. Experiments were conducted on ten healthy subjects, with accelerometers mounted on several positions and orientations on the body, performing static and dynamic activities according to a fixed protocol. Specifically, accelerometers on the sternum and thigh were evaluated. These accelerometers were oriented in the sagittal plane, perpendicular to the long axis of the segment (tangential), or along this axis (radial). First, discrimination between the static or dynamic character of activities was investigated. This appeared to be feasible using an rms-detector applied on the signal of one sensor tangentially mounted on the thigh. Second, the distinction between static activities was investigated. Standing, sitting, lying supine, on a side and prone could be distinguished by observing the static signals of two accelerometers, one mounted tangentially on the thigh, and the second mounted radially on the sternum. Third, the distinction between the cyclical dynamic activities walking, stair ascent, stair descent and cycling was investigated. The discriminating potentials of several features of the accelerometer signals were assessed: the mean value, the standard deviation, the cycle time and the morphology. Signal morphology was expressed by the maximal cross-correlation coefficients with template signals for the different dynamic activities. The mean signal values and signal morphology of accelerometers mounted tangentially on the thigh and the sternum appeared to contribute to the discrimination of dynamic activities with varying detection performances. The standard deviation of the signal and the cycle time were primarily related to the speed of the dynamic activities, and did not contribute to the discrimination of the activities. Therefore, discrimination of dynamic activities on the basis of the combined evaluation of the mean signal value and signal morphology is proposed.
Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices (2011)

Appropriately-placed hydrogen bond surrogates have been demonstrated to efficiently nucleate helical conformations. Herein we describe an efficient method for the synthesis of thioether-based hydrogen bond surrogate (teHBS) helices. A teHBS helix is shown to adopt a stable conformation and target its cognate protein receptor with high affinity.
A Pharmacodynamic Study of Rapamycin in Men with Intermediate- to High-Risk Localized Prostate Cancer (2010)

At 3 mg daily, rapamycin successfully and safely inhibited prostate cancer S6 phosphorylation and achieved relatively high prostate tissue concentrations. No effect on AKT phosphorylation, tumor proliferation, or apoptosis was observed.
Detection of somatic quantitative genetic alterations by multiplex polymerase chain reaction for the prediction of outcome in diffuse large B-cell lymphomas (2008)

QMPSF is a reliable and flexible method for detecting somatic quantitative genetic alterations in diffuse large B-cell lymphomas and could be integrated in future prognostic predictive models.
High-power, diffraction-limited-beam operation from phase-locked diode-laser arrays of closely spaced ‘‘leaky’’ waveguides (antiguides) (1988)

A novel type of phase-locked diode-laser array is demonstrated: an array of closely spaced index depressions (antiguides). The arrays are ten-element AlGaAs/GaAs devices fabricated by metalorganic chemical vapor deposition and liquid phase epitaxy over a patterned substrate. The fundamental and highest-order modes of the array of antiguides have negligible radiation loss: 20–30 times less than that for a single antiguide. The modal-gain differentials between adjacent array modes are at least an order of magnitude larger than those for evanescently coupled arrays of positive-index guides. Fundamental-array-mode operation in a virtually diffraction-limited-beam (1.4°) pattern is obtained to 200 mW. Out-of-phase-mode operation in a virtually diffraction-limited-beam (1.2°) pattern is achieved to 110 mW/uncoated facet. The inherent array-mode stability of antiguided arrays is discussed.
Drug targeting in magnetic resonance imaging. (1992)

This review summarizes the attempts of drug targeting in the field of magnetic resonance imaging. Although the field is young and most work is performed in nonspecific lanthanide chelates, it is obvious that target selectivity and receptor and/or antigen specificity is the most important issue if functional magnetic resonance imaging is to establish itself in the next decade. Recent advances in biochemical engineering and magnetic resonance research have made targeting of diagnostic drugs a credible alternative to conventional drug use in magnetic resonance imaging.
DNA Double-Strand Break Repair: All's Well that Ends Well (2006)

Breaks in both DNA strands are a particularly dangerous threat to genome stability. At a DNA double-strand break (DSB), potentially lost sequence information cannot be recovered from the same DNA molecule. However, simple repair by joining two broken ends, though inherently error prone, is preferable to leaving ends broken and capable of causing genome rearrangements. To avoid DSB-induced genetic disinformation and disruption of vital processes, such as replication and transcription, cells possess robust mechanisms to repair DSBs. Because all breaks are not created equal, the particular repair mechanism used depends largely on what is possible and needed based on the structure of the broken DNA. We argue that although categorizing different DSB repair mechanisms along pathways and subpathways can be conceptually useful, in cells flexible and reversible interactions among DSB repair factors form a web from which a nonpredetermined path to repair for any number of different DNA breaks will emerge.
Diffuse sclerosing variant of papillary thyroid carcinoma: major genetic alterations and prognostic implications (2015)

Taken together, RET/PTC rearrangement was the major genetic alteration seen in patients with DSV-PTC, and the RET/PTC3 rearrangement was associated with advanced stage at diagnosis and poor clinical outcome.
Three-dimensional structure of vaccinia virus-produced human papillomavirus type 1 capsids (1994)

The capsid proteins of papillomavirus self-assemble to form empty capsids or virus-like particles that appear quite similar to naturally occurring virions by conventional electron microscopy. To characterize such virus-like particles more fully, cryoelectron microscopy and image analysis techniques were used to generate three-dimensional reconstructions of capsids produced by vaccinia virus recombinants (V capsids) that expressed human papillomavirus type 1 L1 protein only or both L1 and L2 proteins. All V capsids had 72 pentameric capsomers arranged on a T = 7 icosahedral lattice. Each particle (approximately 60 nm in diameter) consisted of an approximately 2-nm-thick shell of protein with a radius of 22 nm with capsomers that extend approximately 6 nm from the shell. At a resolution of 3.5 nm, both V capsid structures appear identical to the capsid structure of native human papillomavirus type 1 (T. S. Baker, W. W. Newcomb, N. H. Olson, L. M. Cowsert, C. Olson, and J. C. Brown, Biophys. J. 60:1445-1456, 1991), thus implying that expressed and native capsids are structurally equivalent.
Ultraviolet C light with wavelength of 222 nm inactivates a wide spectrum of microbial pathogens (2020)

The 222-nm UVC is able to inactivate a wide spectrum of microbial pathogens. In comparison with the conventional 254-nm UVC, the germicidal effect of 222-nm UVC to the fungal hyphae and spores is low, but the 222-nm UVC exhibits strong germicidal effect to the bacterial endospores.
Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families. (1991)

Several types of domain occur in beta-1, 4-glycanases. The best characterized of these are the catalytic domains and the cellulose-binding domains. The domains may be joined by linker sequences rich in proline or hydroxyamino acids or both. Some of the enzymes contain repeated sequences up to 150 amino acids in length. The enzymes can be grouped into families on the basis of sequence similarities between the catalytic domains. There are sequence similarities between the cellulose-binding domains, of which two types have been identified, and also between some domains of unknown function. The beta-1, 4-glycanases appear to have arisen by the shuffling of a relatively small number of progenitor sequences.
The essential WD-repeat protein Rsa4p is required for rRNA processing and intra-nuclear transport of 60S ribosomal subunits (2005)

We report the characterization of a novel factor, Rsa4p (Ycr072cp), which is essential for the synthesis of 60S ribosomal subunits. Rsa4p is a conserved WD-repeat protein that seems to localize in the nucleolus. In vivo depletion of Rsa4p results in a deficit of 60S ribosomal subunits and the appearance of half-mer polysomes. Northern hybridization and primer extension analyses of pre-rRNA and mature rRNAs show that depletion of Rsa4p leads to the accumulation of the 27S, 25.5S and 7S pre-rRNAs, resulting in a reduction of the mature 25S and 5.8S rRNAs. Pulse-chase analyses of pre-rRNA processing reveal that, at least, this is due to a strong delay in the maturation of 27S pre-rRNA intermediates to mature 25S rRNA. Furthermore, depletion of Rsa4p inhibited the release of the pre-60S ribosomal particles from the nucleolus to the nucleoplasm, as judged by the predominantly nucleolar accumulation of the large subunit Rpl25-eGFP reporter construct. We propose that Rsa4p associates early with pre-60S ribosomal particles and provides a platform of interaction for correct processing of rRNA precursors and nucleolar release of 60S ribosomal subunits.
TEL2, an ETS Factor Expressed in Human Leukemia, Regulates Monocytic Differentiation of U937 Cells and Blocks the Inhibitory Effect of TEL1 on Ras-Induced Cellular Transformation (2004)

TEL2 is a member of the ETS family of transcription factors, which is highly similar to TEL1/ETV6. It binds to DNA via the ETS domain and interacts with itself or TEL1 via the pointed domain. The expression of TEL2 in normal and leukemic hematopoietic cells suggests a role in hematopoietic development. In this article, we describe the role of TEL2 in hematopoietic differentiation and cellular transformation. Quantitative reverse transcription-PCR showed that the expression of TEL2 mRNA was down-regulated during monocytic differentiation of U937 and HL60 induced by 1,25-(OH)2 vitamin D3 and 12-O-tetradecanoylphorbol 13-acetate, respectively. Overexpression of TEL2 in U937 cells inhibited differentiation induced by vitamin D3. In contrast, overexpression of a TEL2 mutant lacking either the pointed domain or a functional ETS domain induced both differentiation of U937 cells and inhibited their growth in vitro and in vivo. In addition, these mutants blocked TEL2-mediated transcriptional repression of a synthetic promoter containing TEL2 binding sites. These data suggest that dominant-negative inhibition of TEL2 might cause differentiation. Quantitative reverse transcription-PCR demonstrated that TEL2 is expressed at higher level in some primary human leukemia samples than in normal bone marrow. Furthermore, overexpression of TEL2 in NIH3T3-UCLA cells blocked the inhibitory effect of TEL1 on Ras-induced cellular transformation. These results suggest that TEL2 may play an important role in hematopoiesis and oncogenesis.
FRMD7 mutations in Chinese families with X-linked congenital motor nystagmus. (2007)

Our results provide additional evidence for mutations in FRMD7 as a common cause of XL-CMN and expand its mutation spectrum. CMN in a Chinese family with pure X-linked recessive pattern, previously mapped to Xq23-q27, is associated with the c.41-43delAGA mutation in FRMD7.
Interpreting face images using active appearance models (2002)

We demonstrate a fast, robust method of interpreting face images using an Active Appearance Model (AAM). An AAM contains a statistical model of shape and grey level appearance which can generalise to almost any face. Matching to an image involves finding model parameters which minimise the difference between the image and a synthesised face. We observe that displacing each model parameter from the correct value induces a particular pattern in the residuals. In a training phase, the AAM learns a linear model of the correlation between parameter displacements and the induced residuals. During search it measures the residuals and uses this model to correct the current parameters, leading to a better fit. A good overall match is obtained in a few iterations, even from poor starting estimates. We describe the technique in detail and show it matching to new face images.
Delivery of electronic news: a broadband application (1994)

This paper describes an ongoing research program for the development of an electronic news delivery system that exploits the promised high-bandwidth, switched, interactive communication facilities of the information highway. The research program is in a preliminary stage and will investigate the design and organization of the news sources, client/server architecture, and user interfaces leading to a prototype model electronic news delivery system. Initially based on a newspaper metaphor, the system will exploit communication and multimedia technologies to integrate other news sources, such as newscasts and video clips, with the text backbone. The system will provide selective content delivery based on individual and group profiles, hypertext links into archival and external data, continuous coverage of news stories, interactive objects, and smart advertising.An initial prototype client has been developed using data that include video clips and news and photos from the Halifax newspaper, The Chronicle-Herald. An abstract data representation was developed for the integration of layout, syntactic, and semantic information from a variety of sources for the dynamic presentation and manipulation of the news items. This prototype allows us to explore the potential of the medium for supporting user interfaces that cope with a potentially large number of news items in a very restricted screen space and the potential for innovative advertising unlike any advertising we currently experience.
A novel 16k micro-nail CMOS-chip for in-vitro single-cell recording, stimulation and impedance measurements (2010)

In neurophysiological and pharmaceutical research, parallel and individual access to a dense population of in-vitro cultured neurons is a key feature for analyzing networks of neurons. This paper presents a 0.18µm CMOS chip containing a dense array of micro-nail electrodes, a 128×128 sensor/actuator matrix with in-situ differential amplification circuits, pico-Ampere current stimulation, and impedance measurement circuits. Measurements on packaged chips show successful impedance measurements matching the simulation model and electrical recordings of in-vitro cultured cardiomyocytes, correlated with recorded changes in intra-cellular calcium concentrations. This system is a first step towards a high-throughput neuron/chip interface.