gebhart/patrepeval huggingface dataset:
MMAC1/PTEN mutations in primary tumor specimens and tumor cell lines. (1997)

A candidate tumor suppressor gene, MMAC1/PTEN, located in human chromosome band 10q23, was recently identified based on sequence alterations observed in several glioma, breast, prostate, and kidney tumor specimens or cell lines. To further investigate the mutational profile of this gene in human cancers, we examined a large set of human tumor specimens and cancer cell lines of many types for 10q23 allelic losses and MMAC1 sequence alterations. Loss of heterozygosity (LOH) at the MMAC1 locus was observed in approximately one-half of the samples examined, consistent with the high frequency of 10q allelic loss reported for many cancers. Of 124 tumor specimens exhibiting LOH that have been screened for MMAC1 alterations to date, we have detected variants in 13 (approximately 10%) of these primary tumors; the highest frequency of variants was found in glioblastoma specimens (approximately 23%). Novel alterations identified in this gene include a missense variant in a melanoma sample and a splicing variant and a nonsense mutation in pediatric glioblastomas. Of 76 tumor cell lines prescreened for probable LOH, microsequence alterations of MMAC1 were detected in 12 (approximately 16%) of the lines, including those derived from astrocytoma, leukemia, and melanoma tumors, as well as bladder, breast, lung, prostate, submaxillary gland, and testis carcinomas. In addition, in this set of tumor cell lines, we detected 11 (approximately 14%) homozygous deletions that eliminated coding portions of MMAC1, a class of abnormality not detected by our methods in primary tumors. These data support the occurrence of inactivating MMAC1 alterations in multiple human cancer types. In addition, we report the discovery of a putative pseudogene of MMAC1 localized on chromosome 9.
Comparing algorithm for dynamic speed-setting of a low-power CPU (1995)

Article Comparing algorithm for dynamic speed-setting of a low-power CPU Share on Authors: Kinshuk Govil Computer Science Division, University of California, Berkeley, CA Computer Science Division, University of California, Berkeley, CAView Profile , Edwin Chan Computer Science Division, University of California, Berkeley, CA Computer Science Division, University of California, Berkeley, CAView Profile , Hal Wasserman Computer Science Division, University of California, Berkeley, CA Computer Science Division, University of California, Berkeley, CAView Profile Authors Info & Claims MobiCom '95: Proceedings of the 1st annual international conference on Mobile computing and networkingDecember 1995 Pages 13–25https://doi.org/10.1145/215530.215546Online:01 December 1995Publication History 309citation1,647DownloadsMetricsTotal Citations309Total Downloads1,647Last 12 Months29Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Spatiotemporal and geometric optimization of sensor arrays for detecting analytes fluids (2023)

Sensor arrays and sensor array systems for detecting analytes in fluids. Sensors configured to generate a response upon introduction of a fluid containing one or more analytes can be located on one or more surfaces relative to one or more fluid channels in an array. Fluid channels can take the form of pores or holes in a substrate material. Fluid channels can be formed between one or more substrate plates. Sensor can be fabricated with substantially optimized sensor volumes to generate a response having a substantially maximized signal to noise ratio upon introduction of a fluid containing one or more target analytes. Methods of fabricating and using such sensor arrays and systems are also disclosed.
Isolation, Structure Determination, and Biological Activity of a Novel Alkaloid, Perophoramidine, from the Philippine Ascidian Perophora namei (2002)

Chemical investigation of the Philippine ascidian Perophora namei has resulted in the isolation of a novel polycyclic alkaloid, perophoramidine (1). The structure of 1 was determined by the interpretation of 1D/2D NMR and MS data. Dehalogenation of perophoramidine (1) by ammonium formate catalyzed transfer hydrogenation confirmed the type and number of halogen atoms present in 1.
Inhibition of DLX-7 homeobox gene causes decreased expression of GATA-1 and c- myc genes and apoptosis (1997)

The DLX gene family is a family of divergent homeobox genes which are related to the Drosophila distal-less (Dll) gene and has been reported to be expressed primarily in the forebrain and craniofacial structures. We have previously identified a new member of this family, DLX-7. We now report that this gene is expressed in normal hematopoietic cells and leukemia cell lines with erythroid characteristics. We used an antisense oligonucleotide targeted against the translation start site of DLX-7 mRNA to inhibit its expression in a human erythroleukemia cell line K562, which expresses DLX-7 at a high level. The antisense oligonucleotide efficiently reduced the DLX-7 mRNA, while control oligonucleotides, including a mutant oligonucleotide identical to the antisense sequence except for four nucleotide mismatches, had no effect on DLX-7 mRNA level. Inhibition of DLX-7 expression decreased the plating efficiency by approximately 70% compared with control. The antisense treatment caused apoptosis, as shown by the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-digoxigenin nick end labeling (TUNEL) method. Down-regulation of DLX-7 expression by antisense treatment was associated with a reduction in GATA-1 and c-myc mRNA levels. Thus, we conclude that DLX-7 is expressed in hematopoietic cells and that the inhibition of its expression results in the decreased levels of GATA-1 and c-myc genes, with an accompanying induction of apoptosis.
Transformation of an Australian Cotton Cultivar: Prospects for Cotton Improvement Through Genetic Engineering (1991)

Somatic embryogenesis and regeneration of whole plants is a highly genotype-dependent process in cotton. We have identified at least one highly regenerable Australian cultivar, Siokra 1-3, which is a sister line to the current major variety being grown in Australia. A number of plants have been regenerated and although some are showing abnormal pollen development, most can produce fertile seed when selfed or crossed with a normal pollen donor. Agrobacterium tumefaciens has been used to efficiently produce fertile transgenic Siokra 1-3 plants expressing novel genes such as the bacterial neomycin phosphotransferase or the β-glucuronidase. This is the first example of the transformation of an elite commercial cultivar. Critical factors in the transformation are the use of a supervirulent disarmed Ti-plasmid with a binary transformation vector, and a highly regenerable genotype of cotton. Bacterial concentration at the time of infection, tissue age, kanamycin selection regime, and co-cultivation support and media composition all have an influence on transformation efficiency and were optimised in our protocol. The ability to transform an elite Australian cultivar of cotton paves the way for agronomic improvements through genetic engineering. We have concentrated on increasing the tolerance of Australian cotton to the herbicide 2,4-D (to protect it from spray drift damage from adjacent cereal crops), and increasing its tolerance to insect pests, such as Helicoverpa armigera, using BT-toxin genes, protease inhibitors and other novel insect resistance genes.
Benefits of Epidural Methylprednisolone in a Unilateral Lumbar Discectomy (1990)

The effects of instilling methylprednisolone acetate (MP) (Depo-Medrol) onto the exposed nerve root during a unilateral lumbar laminotomy (either L4 or L5) for disc excision was studied in 43 patients (primary: 35; repeated procedure: 8). The results were compared with two similarly matched control groups without the steroid drug. All 86 patients preoperatively experienced radicular pain to the calf, and were operated on by one surgeon. Four parameters, studied during the postoperative hospital stay, were compared between the control and MP series. The MP (primary/repeat) groups' (a) stay was reduced by 37/40%, respectively; (b) need for strong narcotic drugs was decreased by 64/70%; (c) need for milder pain medication was decreased by 49/72%; and (d) need for spasm medication was reduced by 77/59%. The paired t test indicated that there is a statistical difference between the MP and control groups' results because of the use of MP, with confidence levels of 0.9927-0.9999 in the primary group, and 0.9806-0.9913 for three of the four parameters in the repeat group. Intraoperative application of epidural steroid drugs such as MP, in a unilateral low-lumbar discectomy, leads to a shorter hospital stay because of less pain and spasm.
On the recognition of occluded shapes and generic faces using multiple-template expansion matching (2002)

An approach for template matching by signal expansion into a set of nonorthogonal template-similar basis functions and its generalization to multiple templates is described. The single-template method is proven to be equivalent to restoration of undergraded images using the Wiener filter and optimizes a practically defined matching criterion called discriminative signal-to-noise ratio (DSNR). Compared to the matched filtering approach which optimizes the SNR, expansion matching is more robust in conditions of noise, superposition, and severe occlusion. The multiple-template expansion filter presented is generalized to match more than one template. It is also optimal in terms of DSNR. It can be designed to elicit any desired response for each of the templates.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Real-Time Brain Oscillation Detection and Phase-Locked Stimulation Using Autoregressive Spectral Estimation and Time-Series Forward Prediction (2011)

Neural oscillations are important features in a working central nervous system, facilitating efficient communication across large networks of neurons. They are implicated in a diverse range of processes such as synchronization and synaptic plasticity, and can be seen in a variety of cognitive processes. For example, hippocampal theta oscillations are thought to be a crucial component of memory encoding and retrieval. To better study the role of these oscillations in various cognitive processes, and to be able to build clinical applications around them, accurate and precise estimations of the instantaneous frequency and phase are required. Here, we present methodology based on autoregressive modeling to accomplish this in real time. This allows the targeting of stimulation to a specific phase of a detected oscillation. We first assess performance of the algorithm on two signals where the exact phase and frequency are known. Then, using intracranial EEG recorded from two patients performing a Sternberg memory task, we characterize our algorithm's phase-locking performance on physiologic theta oscillations: optimizing algorithm parameters on the first patient using a genetic algorithm, we carried out cross-validation procedures on subsequent trials and electrodes within the same patient, as well as on data recorded from the second patient.
Enterocyte TLR4 Mediates Phagocytosis and Translocation of Bacteria Across the Intestinal Barrier (2006)

Translocation of bacteria across the intestinal barrier is important in the pathogenesis of systemic sepsis, although the mechanisms by which bacterial translocation occurs remain largely unknown. We hypothesized that bacterial translocation across the intact barrier occurs after internalization of the bacteria by enterocytes in a process resembling phagocytosis and that TLR4 is required for this process. We now show that FcgammaRIIa-transfected enterocytes can internalize IgG-opsonized erythrocytes into actin-rich cups, confirming that these enterocytes have the molecular machinery required for phagocytosis. We further show that enterocytes can internalize Escherichia coli into phagosomes, that the bacteria remain viable intracellularly, and that TLR4 is required for this process to occur. TLR4 signaling was found to be necessary and sufficient for phagocytosis by epithelial cells, because IEC-6 intestinal epithelial cells were able to internalize LPS-coated, but not uncoated, latex particles and because MD2/TLR4-transfected human endothelial kidney (HEK)-293 cells acquired the capacity to internalize E. coli, whereas nontransfected HEK-293 cells and HEK-293 cells transfected with dominant-negative TLR4 bearing a P712H mutation did not. LPS did not induce membrane ruffling or macropinocytosis in enterocytes, excluding their role in bacterial internalization. Strikingly, the internalization of Gram-negative bacteria into enterocytes in vivo and the translocation of bacteria across the intestinal epithelium to mesenteric lymph nodes were significantly greater in wild-type mice as compared with mice having mutations in TLR4. These data suggest a novel mechanism by which bacterial translocation occurs and suggest a critical role for TLR4 in the phagocytosis of bacteria by enterocytes in this process.
Activated T cells from umbilical cord blood armed with anti‐CD3 × anti‐CD20 bispecific antibody mediate specific cytotoxicity against CD20+ targets with minimal allogeneic reactivity: a strategy for providing antitumor effects after cord blood transplants (2011)

We showed that armed CBATCs mediate specific cytotoxicity, secrete low levels of cytokines and chemokines, and demonstrate attenuated response to alloantigens.
The accessibility of thiophosphorylated groups in DNA fragments to the enzymatic activity of ligases and restriction endonuclease Bbs I. (1995)

The aim of this paper was to test the possibility to ligate and hydrolyse DNA sequences containing thiomodified ends and bonds. T4 DNA ligase was shown to ligate DNA fragments regardless of whether it contains phosphorylated or thiophosphorylated 5'-end. But the cleavage of an internally thiomodified phosphodiester bond was found to be totally inhibited when using the non-palindromic restrictase Bbs I. The special properties of this restriction endonuclease should allow the development of an oriented cloning strategy when combined with T4 ligase and a thiophosphorylation of DNA fragments.
Immunogenicity against Human Papillomavirus Type 16 Virus-Like Particles Is Strongly Enhanced by the PhoPcPhenotype inSalmonella entericaSerovar Typhimurium (2004)

Recombinant Salmonella strains have been widely used to deliver heterologous antigens and induce immune responses in vaccinated animals and humans. It remains to be established, however, how these bacteria mount an immune response; this has prevented the rational design of vaccines. Here we report for the first time that a particular genetic program, PhoPc, is necessary for recombinant Salmonella strains to induce an antibody response to a heterologous antigen, the human papillomaviruses type 16 (HPV16) virus-like particle (VLP). The PhoPc phenotype results from a point mutation in phoQ, the gene encoding the sensor component of a two-component regulatory system (PhoP-PhoQ) that controls the expression of a number of virulence factors in Salmonellae. To demonstrate that immunogenicity of the viral antigen expressed by the bacterial vector was dependent on the PhoPc phenotype, we have expressed the phoQ mutant gene (phoQ24) in two differently attenuated Salmonella enterica serovar Typhimurium strains. Our data show extrachromosomal phoQ24 to be dominant over the chromosomal copy of the phoQ gene, conferring the PhoPc phenotype on the recipient strains. In addition, activation of PhoPQ-regulated genes by the plasmid-encoded PhoQ24 did not alter bacterial survival and conferred immunogenicity to the HPV16 VLP expressed in the two S. enterica serovar Typhimurium backgrounds, inducing the production of HPV-specific antibodies in mice. This strongly suggests that at least one of the PhoP-regulated genes is necessary for mounting an efficient antibody response to HPV16 VLP. This finding sets the stage for further development of a Salmonella-based vaccine against HPV infection and cervical cancer.
Unreeling netflix: Understanding and improving multi-CDN movie delivery (2012)

Netflix is the leading provider of on-demand Internet video streaming in the US and Canada, accounting for 29.7% of the peak downstream traffic in US. Understanding the Netflix architecture and its performance can shed light on how to best optimize its design as well as on the design of similar on-demand streaming services. In this paper, we perform a measurement study of Netflix to uncover its architecture and service strategy. We find that Netflix employs a blend of data centers and Content Delivery Networks (CDNs) for content distribution. We also perform active measurements of the three CDNs employed by Netflix to quantify the video delivery bandwidth available to users across the US. Finally, as improvements to Netflix's current CDN assignment strategy, we propose a measurement-based adaptive CDN selection strategy and a multiple-CDN-based video delivery strategy, and demonstrate their potentials in significantly increasing user's average bandwidth.
Sparse Subspace Clustering: Algorithm, Theory, and Applications (2013)

Many real-world problems deal with collections of high-dimensional data, such as images, videos, text, and web documents, DNA microarray data, and more. Often, such high-dimensional data lie close to low-dimensional structures corresponding to several classes or categories to which the data belong. In this paper, we propose and study an algorithm, called sparse subspace clustering, to cluster data points that lie in a union of low-dimensional subspaces. The key idea is that, among the infinitely many possible representations of a data point in terms of other points, a sparse representation corresponds to selecting a few points from the same subspace. This motivates solving a sparse optimization program whose solution is used in a spectral clustering framework to infer the clustering of the data into subspaces. Since solving the sparse optimization program is in general NP-hard, we consider a convex relaxation and show that, under appropriate conditions on the arrangement of the subspaces and the distribution of the data, the proposed minimization program succeeds in recovering the desired sparse representations. The proposed algorithm is efficient and can handle data points near the intersections of subspaces. Another key advantage of the proposed algorithm with respect to the state of the art is that it can deal directly with data nuisances, such as noise, sparse outlying entries, and missing entries, by incorporating the model of the data into the sparse optimization program. We demonstrate the effectiveness of the proposed algorithm through experiments on synthetic data as well as the two real-world problems of motion segmentation and face clustering.
A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1 (2004)

Lv1 restriction of HIV-1 in the cells of Old World monkeys is associated with the expression of the Trim5 gene. Uniquely, in owl monkey kidney cells, HIV-1 restriction is dependent on the ability of incoming viral capsid protein to bind cyclophilin A (CypA). Cloning of the owl monkey Trim5 gene now reveals the presence of an inserted CypA pseudogene within intron 7 of the Trim5 gene. This insertion results in the formation of a chimeric Trim5-CypA transcript. Transfer of a cDNA corresponding to this transcript into human cells confers cyclosporin A-sensitive resistance to HIV-1 infection. The restriction factor appears to be a chimeric protein created by retrotransposon-mediated exon shuffling.
Physical and Functional Interactions between Lyn and p34 Kinases in Irradiated Human B-cell Precursors (1996)

Exposure of human B-cell precursors (BCP) to ionizing radiation results in cell cycle arrest at the G2-M checkpoint as a result of inhibitory tyrosine phosphorylation of p34cdc2 . Here, we show that ionizing radiation promotes physical interactions between p34cdc2 and the Src family protein-tyrosine kinase Lyn in the cytoplasm of human BCP leading to tyrosine phosphorylation of p34cdc2. Lyn kinase immunoprecipitated from lysates of irradiated BCP as well as a full-length glutathione S-transferase (GST)-Lyn fusion protein-phosphorylated recombinant human p34cdc2 on tyrosine 15. Furthermore, Lyn kinase physically associated with and tyrosine-phosphorylated p34cdc2 kinase in vivo when co-expressed in COS-7 cells. Binding experiments with truncated GST-Lyn fusion proteins suggested a functional role for the SH3 rather than the SH2 domain of Lyn in Lyn-p34cdc2 interactions in BCP. The first 27 residues of the unique amino-terminal domain of Lyn were also essential for the ability of GST-Lyn fusion proteins to bind to p34cdc2 from BCP lysates. Ionizing radiation failed to cause tyrosine phosphorylation of p34cdc2 or G2 arrest in Lyn kinase-deficient BCP, supporting an important role of Lyn kinase in radiation-induced G2 phase-specific cell cycle arrest. Our findings implicate Lyn as an important cytoplasmic suppressor of p34cdc2 function.
Standards and monitoring treatment (2012)

Accuracy and reproducibility of laboratory measurements are important in the diagnosis and treatment of bleeding disorders. This article describes the process of establishment of international standards and some of the problems that have arisen in standardization of these measurements.
Exact inference for categorical data: recent advances and continuing controversies (2001)

Methods for exact small-sample analyses with categorical data have been increasingly well developed in recent years. A variety of exact methods exist, primarily using the approach that eliminates unknown parameters by conditioning on their sufficient statistics. In addition, a variety of algorithms now exist for implementing the methods. This paper briefly summarizes the exact approaches and describes recent developments. Controversy continues about the appropriateness of some exact methods, primarily relating to their conservative nature because of discreteness. This issue is examined for two simple problems in which discreteness can be severe--interval estimation of a proportion and the odds ratio. In general, adjusted exact methods based on the mid-P-value seem a reasonable way of reducing the severity of this problem.
Bleeding and mortality outcomes in ITP clinical trials: A review of thrombopoietin mimetics data (2012)

Patients with ITP may have severe thrombocytopenia, putting them at risk for serious bleeding. ITP trials of new treatments must allow use of standard-of-care therapies to prevent serious bleeding. Thrombopoietin mimetic trials used platelet counts and rescue/concomitant medication use as endpoints. These trials were of insufficient size and duration to measure mortality or serious bleeding, which are infrequent with appropriate treatment. A recent Cochrane review criticized the thrombopoietin mimetic registrational trials for inadequately assessing bleeding and survival. We discuss how these endpoints are difficult to measure in clinical trials designed to improve platelet counts and minimize bleeding, in accordance with ethical trial design.
Single Photon Emission Computed Tomography Demonstrated Efficacy of 17β-Estradiol Therapy in Male Rats After Trauma-Hemorrhage and Extended Hypotension (2010)

The significantly larger blood volume maintained in heart, kidney, and liver of rats after E2 therapy compared with control supports the notion that E2 produces salutary effects on the cardiovascular system after trauma-hemorrhage and even extended periods of severe hypotension.