gebhart/patrepeval huggingface dataset:
miR-122, a Mammalian Liver-Specific microRNA, is Processed from hcr mRNA and MayDownregulate the High Affinity Cationic Amino Acid Transporter CAT-1 (2004)

These studies show that miR-122, a 22-nucleotide microRNA, is derived from a liver-specific noncoding polyadenylated RNA transcribed from the gene hcr. The exact sequence of miR-122 as well as the adjacent secondary structure within the hcr mRNA are conserved from mammalian species back to fish. Levels of miR-122 in the mouse liver increase to half maximal values around day 17 of embryogenesis, and reach near maximal levels of 50,000 copies per average cell before birth. Lewis et al. (2003) predicted the cationic amino acid transporter (CAT-1 or SLC7A1) as a miR-122 target. CAT-1 protein and its mRNA are expressed in all mammalian tissues but with lower levels in adult liver. Furthermore, during mouse liver development CAT-1 mRNA decreases in an almost inverse correlation with miR-122. Eight potential miR-122 target sites were predicted within the human CAT-1 mRNA, with six in the 3'-untranslated region. Using a reporter construct it was found that just three of the predicted sites, linked in a 400-nucleotide sequence from human CAT-1, acted with synergy and were sufficient to strongly inhibit protein synthesis and reduce mRNA levels. In summary, these studies followed the accumulation during development of miR-122 from its mRNA precursor, hcr, through to identification of what may be a specific mRNA target, CAT-1.
Targeted ablation of α-crystalIin-synthesizing cells produces lens-deficient eyes in transgenic mice (1989)

Genetic ablation techniques were used to study the role of the lens in mammalian eye development. Ablation was accomplished by microinjecting murine eggs with chimeric DNA constructs in which the alpha A-crystallin gene regulatory sequence (-366 to +46) was fused to the highly cytotoxic diphtheria toxin gene coding sequence. For genetic ablation to be successful the promoter regulating expression should be specific and completely silent in cells necessary for normal mouse development. In this report, we describe the generation and analysis of transgenic mice with this readily discernible phenotype: aphakia or eyes without lens. Of the 109 live-born pups, eight carried the transgene and could be grouped according to the apparent severity of eye malformations. Lines 4, 5 and 6 founder (F0) mice had the most severe phenotype. Histological analysis revealed: marked reduction in eye size, total absence of lens, increased retinal cell density and extensive whorling of the retinal fibre layers. The line 1 F0 mouse displayed a distinct lens opacity and lines 2, 3 and 8 F0 mice were mosaics with a relatively mild, but most unusual phenotype. Their eyes contained a small, highly vacuolated lens. The progeny of these mosaics that inherited the transgene, however, again exhibited the severe phenotype. The aberrant structures of the eyes in which complete genetic ablation of the lens has been achieved suggest that the lens plays a pivotal role in the development of multiple components of the murine eye.
Down-Regulation of Rad51 and Decreased Homologous Recombination in Hypoxic Cancer Cells (2004)

There is an emerging concept that acquired genetic instability in cancer cells can arise from the dysregulation of critical DNA repair pathways due to cell stresses such as inflammation and hypoxia. Here we report that hypoxia specifically down-regulates the expression of RAD51, a key mediator of homologous recombination in mammalian cells. Decreased levels of Rad51 were observed in multiple cancer cell types during hypoxic exposure and were not associated with the cell cycle profile or with expression of hypoxia-inducible factor. Analyses of RAD51 gene promoter activity, as well as mRNA and protein stability, indicate that the hypoxia-mediated regulation of this gene occurs via transcriptional repression. Decreased expression of Rad51 was also observed to persist in posthypoxic cells for as long as 48 h following reoxygenation. Correspondingly, we found reduced levels of homologous recombination in both hypoxic and posthypoxic cells, suggesting that the hypoxia-associated reduction in Rad51 expression has functional consequences for DNA repair. In addition, hypoxia-mediated down-regulation of Rad51 was confirmed in vivo via immunofluorescent image analysis of experimental tumors in mice. Based on these findings, we propose a novel mechanism of genetic instability in the tumor microenvironment mediated by hypoxia-induced suppression of the homologous recombination pathway in cancer cells. The aberrant regulation of Rad51 expression may also create heterogeneity in the DNA damage response among cells within tumors, with implications for the response to cancer therapies.
Hydrothermal Growth of Mesoporous SBA-15 Silica in the Presence of PVP-Stabilized Pt Nanoparticles:  Synthesis, Characterization, and Catalytic Properties (2006)

A novel high surface area heterogeneous catalyst based on solution phase colloidal nanoparticle chemistry has been developed. Monodisperse platinum nanoparticles of 1.7-7.1 nm have been synthesized by alcohol reduction methods and incorporated into mesoporous SBA-15 silica during hydrothermal synthesis. Characterization of the Pt/SBA-15 catalysts suggests that Pt particles are located within the surfactant micelles during silica formation leading to their dispersion throughout the silica structure. After removal of the templating polymer from the nanoparticle surface, Pt particle sizes were determined from monolayer gas adsorption measurements. Infrared studies of CO adsorption revealed that CO exclusively adsorbs to atop sites and red-shifts as the particle size decreases suggesting surface roughness increases with decreasing particle size. Ethylene hydrogenation rates were invariant with particle size and consistent with a clean Pt surface. Ethane hydrogenolysis displayed significant structure sensitivity over the size range of 1-7 nm, while the apparent activation energy increased linearly up to a Pt particle size of approximately 4 nm and then remained constant. The observed rate dependence with particle size is attributed to a higher reactivity of coordinatively unsaturated surface atoms in small particles compared to low-index surface atoms prevalent in large particles. The most reactive of these unsaturated surface atoms are responsible for ethane decomposition to surface carbon. The ability to design catalytic structures with tunable properties by rational synthetic methods is a major advance in the field of catalyst synthesis and for the development of accurate structure-function relationships in heterogeneous reaction kinetics.
Automatic 3D registration of dynamic stress and rest 82Rb and flurpiridaz F 18 myocardial perfusion PET data for patient motion detection and correction (2011)

Fully automatic motion correction of dynamic PET frames can be performed accurately, potentially allowing improved image quantification of cardiac PET data.
Immunosenescence and germinal center reaction (1997)

Dysfunction of the immune system in aged individuals includes at least two important factors: accumulation of immunocytes with reduced function and accumulation of lymphocyte clones with self-reactive potential. Coincidently, there is a profound reduction of the germinal center reaction in the aged. While this reduction is likely the result of age-associated impairment in lymphocyte function (e.g. diminished response to costimulus, altered lymphokine production etc.), the reduction of germinal centers may itself make an important contribution to further immunological dysfunction.
Calcium homeostasis in plants (1993)

ABSTRACT Many aspects of Ca2+ homeostasis in plants are similar to those in animals and fungi (Poovaiah and Reddy, 1989), but an understanding of how Ca2+ transport and function are integrated from the level of the whole plant to the sub-cellular level remains elusive. At the whole-plant level, a constant supply of Ca2+ in the range 1-10 mM is required to maintain normal growth and development (Epstein, 1972; Clarkson and Hanson, 1980). Calcium uptake by roots leads to millimolar concentrations of Ca2+ in plant tissues, and in most plants Ca is the second most abundant metal and the fifth most abundant element, after C, H, O and K (Epstein, 1972). At the subcellular level, certain organelles, such as the large central vacuole, may have similarly high Ca concentrations, but cytoplasmic Ca2+ levels are three to four orders of magnitude lower. Despite the abundance of Ca in plant tissues and the small amounts required for most cellular processes, the supply of Ca to the plant must be uninterrupted. Removal of Ca from the nutrient supply results in rapid death of cells in the apical meristem and a cessation of growth (Epstein, 1972). Just why this calcium starvation occurs when Ca levels in the plant are so high is not fully understood, but the low mobility of Ca within the plant body must be at least partially responsible.
Lentiviral Vector Delivery of Human Interleukin-7 (hIL-7) to Human Immune System (HIS) Mice Expands T Lymphocyte Populations (2010)

Genetically modified mice carrying engrafted human tissues provide useful models to study human cell biology in physiologically relevant contexts. However, there remain several obstacles limiting the compatibility of human cells within their mouse hosts. Among these is inadequate cross-reactvitiy between certain mouse cytokines and human cellular receptors, depriving the graft of important survival and growth signals. To circumvent this problem, we utilized a lentivirus-based delivery system to express physiologically relevant levels of human interleukin-7 (hIL-7) in Rag2-/-gammac-/- mice following a single intravenous injection. hIL-7 promoted homeostatic proliferation of both adoptively transferred and endogenously generated T-cells in Rag2-/-gammac-/- Human Immune System (HIS) mice. Interestingly, we found that hIL-7 increased T lymphocyte numbers in the spleens of HIV infected HIS mice without affecting viral load. Taken together, our study unveils a versatile approach to deliver human cytokines to HIS mice, to both improve engraftment and determine the impact of cytokines on human diseases.
Escherichia coli rna gene encoding RNase I: cloning, overexpression, subcellular distribution of the enzyme, and use of an rna deletion to identify additional RNases (1990)

The cloning and overexpression of the Escherichia coli rna gene encoding RNase I are described. Only a single copy of the rna gene is present on the E. coli chromosome. Although cells with as much as a 100-fold increase in RNase I activity were constructed, little effect on cell growth was observed. Overexpressed RNase I was found in the periplasmic space to the same degree (approximately 85%) as wild-type enzyme, suggesting no limitation in RNase I transport. The rna clone was used to identify a deletion strain totally lacking the rna gene. The normal growth of this strain showed that RNase I is not essential for cell viability. Extracts from the RNase I deletion strain still retained a low level of RNase activity in the presence of EDTA, conclusively demonstrating the existence of additional EDTA-active RNases in E. coli. The possibility of a RNase I inhibitor is also discussed.
Functionally Distinct Subsets of CD1d-restricted Natural Killer T Cells Revealed by CD1d Tetramer Staining (2002)

CD1d-restricted natural killer (NK)T cells are known to potently secrete T helper (Th)1 and Th2 cytokines and to mediate cytolysis, but it is unclear how these contrasting functional activities are regulated. Using lipid antigen-loaded CD1d tetramers, we have distinguished two subsets of CD1d-restricted T cells in fresh peripheral blood that differ in cytokine production and cytotoxic activation. One subset, which was CD4(-), selectively produced the Th1 cytokines interferon gamma and tumor necrosis factor alpha, and expressed NKG2d, a marker associated with cytolysis of microbially infected and neoplastic cells. This subset up-regulated perforin after exposure to interleukin (IL)-2 or IL-12. In contrast, CD4(+) CD1d-restricted NKT cells potently produced both Th1 and Th2 cytokines, up-regulated perforin in response to stimulation by phorbol myristate acetate and ionomycin but not IL-2 or IL-12, and could be induced to express CD95L. Further, for both CD1d-restricted NKT cell subsets, we found that antigenic stimulation induced cytokine production but not perforin expression, whereas exposure to inflammatory factors enhanced perforin expression but did not stimulate cytokine production. These results show that the various activities of CD1d-restricted T cells in tumor rejection, autoimmune disease, and microbial infections could result from activation of functionally distinct subsets, and that inflammatory and antigenic stimuli may influence different effector functions.
ERFNet: Efficient Residual Factorized ConvNet for Real-Time Semantic Segmentation (2017)

Semantic segmentation is a challenging task that addresses most of the perception needs of intelligent vehicles (IVs) in an unified way. Deep neural networks excel at this task, as they can be trained end-to-end to accurately classify multiple object categories in an image at pixel level. However, a good tradeoff between high quality and computational resources is yet not present in the state-of-the-art semantic segmentation approaches, limiting their application in real vehicles. In this paper, we propose a deep architecture that is able to run in real time while providing accurate semantic segmentation. The core of our architecture is a novel layer that uses residual connections and factorized convolutions in order to remain efficient while retaining remarkable accuracy. Our approach is able to run at over 83 FPS in a single Titan X, and 7 FPS in a Jetson TX1 (embedded device). A comprehensive set of experiments on the publicly available Cityscapes data set demonstrates that our system achieves an accuracy that is similar to the state of the art, while being orders of magnitude faster to compute than other architectures that achieve top precision. The resulting tradeoff makes our model an ideal approach for scene understanding in IV applications. The code is publicly available at: https://github.com/Eromera/erfnet.
Fatty acids in bovine milk fat (2008)

Milk fat contains approximately 400 different fatty acid, which make it the most complex of all natural fats. The milk fatty acids are derived almost equally from two sources, the feed and the microbial activity in the rumen of the cow and the lipids in bovine milk are mainly present in globules as an oil-in-water emulsion. Almost 70% of the fat in Swedish milk is saturated of which around 11% comprises short-chain fatty acids, almost half of which is butyric acid. Approximately 25% of the fatty acids in milk are mono-unsaturated and 2.3% are poly-unsaturated with omega-6/omega-3 ratio around 2.3. Approximately 2.7% are trans fatty acids.
An Efficient Memetic Algorithm for Dynamic Flexible Job Shop Scheduling with Random Job Arrivals (2013)

Much of the research on flexible job shop scheduling problem has ignored dynamic events in dynamic environment where there are complex constraints and a variety of unexpected disruptions. This paper proposes an efficient memetic algorithm to solve the flexible job shop scheduling problem with random job arrivals. Firstly, a periodic policy is presented to update the problem condition and generate the rescheduling point. Secondly, the efficient memetic algorithm with a new local search procedure is proposed to optimize the problem at each rescheduling point. Five kinds of neighborhood structures are presented in the local search. Moreover, the performance measures investigated respectively are: minimization of the makespan and minimization of the mean tardiness. Finally, several experiments have been designed to test and evaluated the performance of the memetic algorithm. The experimental results show that the proposed algorithm is efficient to solve the flexible job shop scheduling problem in dynamic environment.
Comparing the Refolding and Reoxidation of Recombinant Porcine Growth Hormone from a Urea Denatured State and from Escherichia coli Inclusion Bodies (1995)

Overexpression of cloned genes in bacteria often leads to insoluble refractile body formation requiring solubilization and refolding to obtain biologically active proteins. A refolding pathway was established for a model protein, porcine growth hormone (PGH), yielding an appreciably high recovery of 85%. The conditions include the dilution of a urea, beta-mercaptoethanol (beta-ME) denatured PGH solution in a refolding environment containing 3.5 M urea and 10 mM beta-ME/HED at a 10:1 ratio at pH 9.1 and 0.5 mg/mL PGH. The intrinsic fluorescence-detected transition of PGH in urea gives 3.8 kcal/mol for the free energy of denaturation (delta GH2O) of PGH. The native-like conformation of PGH is dependent on disulfide bonds because reduced and carboxymethylated PGH is devoid of tertiary structure as assessed by intrinsic tryptophan fluorescence. Physical analysis of C-terminally truncated recombinant PGH indicated no significant difference in the free energy of denaturation of P-band in urea as full-length PGH. This suggests that the first disulfide, forming the large loop domain of PGH, provides a significantly greater contribution to the conformational stability of PGH than the second disulfide, which forms the carboxy-terminal small loop domain. The rate of formation of native structure during refolding was biphasic, with native structure identified by intrinsic fluorescence and hydrophobicity spectroscopy prior to disulfide bond formation. Thus "framework" intermediates are prerequisites for correct disulfide formation and tertiary folding of PGH. This study shows how a protein refolds, forms disulfides, and self-associates, which may be useful for examining the refolding of other recombinant proteins.
Trends in primary androgen depletion therapy for patients with localized and locally advanced prostate cancer: Japanese perspective (2006)

It has been conventionally accepted that primary androgen depletion therapy (PADT) is effective only as a palliative treatment against localized prostate cancer (LPC) and locally advanced prostate cancer (LAPC), like its effect against advanced (metastatic) prostate cancer. In Japan, however, PADT has long been the treatment of choice for LPC and LAPC. The frequency of PADT being chosen to treat LPC and LAPC is also on the rise in clinical practice in the USA. Very little evidence to support this trend has so far been available. A study on the outcomes of endocrine therapy is currently being conducted in Japan by the Japanese Prostate Cancer Surveillance Group. Results of several domestic and overseas randomized trials have recently been published, and evidence for the efficacy of PADT in LPC and LAPC has been accumulating. The effectiveness of PADT in LAPC, in particular, is worthy of attention. There is a possibility that therapeutic strategies for LPC and LAPC may change dramatically in the near future.
TDP-43 Is a Developmentally Regulated Protein Essential for Early Embryonic Development (2009)

TDP-43 is a DNA/RNA-binding protein implicated in multiple steps of transcriptional and post-transcriptional regulation of gene expression. Alteration of this multifunctional protein is associated with a number of neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin positive inclusions. Whereas a pathological link to neurodegenerative disorders has been established, the cellular and physiological functions of TDP-43 remain unknown. In this study, we show that TDP-43 is a nuclear protein with persistent high-level expression during embryonic development and with progressively decreased protein levels during postnatal development. In mice where the TDP-43 gene (Tardbp) was disrupted using a gene trap that carries a beta-galactosidase marker gene, heterozygous (Tardbp(+/-)) mice are fertile and healthy, but intercrosses of Tardbp(+/-) mice yielded no viable homozygotic null (Tardbp(-/-)) mice. Indeed, Tardbp(-/-) embryos die between 3.5 and 8.5 days of development. Tardbp(-/-) blastocysts grown in cell culture display abnormal expansion of their inner cell mass. The pattern of beta-galactosidase staining at E9.5 Tardbp(+/-) embryos is predominantly restricted to the neuroepithelium and remains prominent in neural progenitors at E10.5-12.5. TDP-43 is detected in spinal cord progenitors and in differentiated motor neurons as well as in the dorsal root ganglia at E12.5. Beta-galactosidase staining of tissues from adult Tardbp(+/-) mice shows widespread expression of TDP-43, including prominent levels in various regions of the central nervous system afflicted in neurodegenerative disorders. These results indicate that TDP-43 is developmentally regulated and indispensible for early embryonic development.
Nonthermal irreversible electroporation for intracranial surgical applications (2010)

The authors' results reveal that NTIRE at selected voltages can be safely administered in normal canine brain and that the volume of ablated tissue correlates with the voltage of the applied pulses. This preliminary study is the first step toward using NTIRE as a brain cancer treatment.
New advances in the understanding of sporadic inclusion-body myositis and hereditary inclusion-body myopathies (1995)

This review emphasizes new advances in seeking the pathogenic mechanisms of sporadic inclusion-body myositis and hereditary inclusion-body myopathy syndromes. Clinical and pathologic similarities and differences between sporadic and hereditary forms are described. Hypotheses are presented regarding the possible causes and consequences of abnormally accumulated intramyofiber beta-amyloid precursor protein (beta APP) (including beta-amyloid protein and C- and N-terminal epitopes), hyperphosphorylated tau, alpha 1-antichymotrypsin, apolipoprotein E, prion protein, ubiquitin, nicotinic acetylcholine receptor and its 43-kD associated protein, fibroblast growth factor, and transforming growth factor-beta. Also increased are beta APP mRNA and prion protein mRNA. Striking similarities between the pathology of muscle specimens from sporadic inclusion-body myositis and samples from the brains of patients with Alzheimer's disease in regard to Congo red positivity and accumulations of several proteins are discussed. Because most of the proteins that pathologically accumulate throughout the abnormal muscle fibers also accumulate focally at normal human neuromuscular junctions, the possible "junctionalization" of nonjunctional nuclei as a pathogenic mechanism in the muscle fiber is discussed.