gebhart/patrepeval huggingface dataset:
Joint analysis of gene expression levels and histological images identifies genes associated with tissue morphology (2018)

Histological images are used to identify and to characterize complex phenotypes such as tumor stage. Our goal is to associate histological image phenotypes with high-dimensional genomic markers; the limitations to incorporating histological image phenotypes in genomic studies are that the relevant image features are difficult to identify and extract in an automated way, and confounders are difficult to control in this high-dimensional setting. In this paper, we use convolutional autoencoders and sparse canonical correlation analysis (CCA) on histological images and gene expression levels from paired samples to find subsets of genes whose expression values in a tissue sample correlate with subsets of morphological features from the corresponding sample image. We apply our approach, ImageCCA, to three data sets, two from TCGA and one from GTEx v6, and we find three types of biological associations. In TCGA, we find gene sets associated with the structure of the extracellular matrix and cell wall infrastructure, implicating uncharacterized genes in extracellular processes. Across studies, we find sets of genes associated with specific cell types, including muscle tissue and neuronal cells, and with cell type proportions in heterogeneous tissues. In the GTEx v6 data, we find image features that capture population variation in thyroid and in colon tissues associated with genetic variants, suggesting that genetic variation regulates population variation in tissue morphological traits. The software is publicly available at: https://github.com/daniel-munro/imageCCA .
Lymphoma Thy-1 glycoprotein is linked to the cytoskeleton via a 4.1-like protein. (1986)

In this study we have found that the phosphoprotein doublet of 68,000 and 65,000 daltons (68/65 kD) in mouse T-lymphoma cells shares several structural and functional similarities with erythrocyte band 4.1. Our evidence for identifying the 68/65-kD doublet as a lymphoma 4.1-like protein is as follows: it displays an immunological cross-reactivity with anti-erythrocyte band 4.1 antibody; it exhibits a Svedberg unit of sedimentation coefficient of 4 S; it is phosphorylated in the presence of phorbol ester (phorbol-12-O-tetradecanoylphorbol-13-acetate) and its phosphorylation requires Ca2+; it is phosphorylated primarily at serine residues; and it can bind directly to fodrin (a spectrin-like actin-binding protein). In addition, this lymphoma 4.1-like protein can be both colocalized and coisolated with the major T-lymphocyte-specific glycoprotein, Thy-1 (gp 25). Therefore, all of these results strongly suggest that the lymphoma 4.1-like protein (68/65-kD doublet) may play a pivotal role in linking the Thy-1 (gp 25) glycoprotein to fodrin which, in turn, binds to the actin filaments that are responsible for recruiting Thy-1 antigens into cap structures.
Enantioselective Addition of Diethylzinc to Aldehydes Using 1,1′-Bi-2-naphthol-3,3′-dicarboxamide as a Chiral Auxiliary (1996)

Abstract A highly enantioselective addition of diethylzinc to a wide range of aldehydes was achieved by using N,N,N′,N′-tetraalkyl-1,1′-bi-2-naphthol-3,3′-dicarboxamides as chiral auxiliaries.
What’s More Dangerous, Your Aspirin Or Your Car? Thinking Rationally About Drug Risks (And Benefits) (2007)

We compare mortality risks of several common drugs with risks related to work, transportation, and recreation. Comparing risks can provide a more intuitive sense of the magnitude of drug risks than stand-alone estimates can, to help inform policy discussions. The drug risks we quantify generally exceed the magnitude of risks for other domains (although aspirin and cars are similarly "risky" under the definition of risk used here). Nonetheless, these comparisons underscore a crucial point: that risks should not be evaluated without considering attendant benefits. We discuss the need for the Food and Drug Administration to compare risks and benefits quantitatively, consistently, and explicitly.
ColoGuideEx: a robust gene classifier specific for stage II colorectal cancer prognosis (2012)

This study presents the development and validation of a 13-gene expression classifier, ColoGuideEx, for prognosis prediction specific to patients with stage II CRC. The robustness was shown across patient series, populations and different microarray versions.
Early Allelic Selection in Maize as Revealed by Ancient DNA (2003)

Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.
The Use of the Near-bit Vibration Sensor While Drilling Leads to Optimized Rotary-Steerable Drilling in Push- and Point-the-Bit Configurations (2008)

Abstract In an extended-reach and horizontal well drilling environment, stick-slip becomes increasingly problematic with smaller-diameter and longer drillstring. Surface detection of the bottom-hole assembly stick-slip and vibration becomes ever more difficult. A Real-time Stick-slip and Vibration Detection (RSVD) system was incorporated into a rotary-steerable system (RSS), to increase drilling efficiency in deep wells and to protect the RSS and the MWD/LWD tools from harmful vibrations. Bit/BHA instability often results in excessive vibration and stick-slip problems, which lead to BHA component failure, poor directional results and excessive wear/damage to bits. This system is a unique near-bit vibration sensor integrated into the RSS, featuring detection of the three principal modes of drillstring vibration: torsional, lateral and axial. The sensor system sends the detected stick-slip severity to the surface in real time so that operators can change drilling parameters if harmful downhole conditions are detected. Additionally the real-time drilling data were remotely available to a multi-disciplinary drilling optimization team consisting of engineers and researchers. This sensor system has been extensively tested and proved to be effective with the 8 ½-in.-hole-size RSS in various wells, including vertical and horizontal, both onshore and offshore. This paper reviews the harmful stick-slip and vibration conditions in smaller-hole-size wells and how the RSVD system improved penetration rate and prolonged the optimum performance of the drill bit, bottom-hole assembly (BHA), MWD/LWD, and RSS in various situations. Through the integrated sensor and team approach, the ability to detect poor borehole conditions and/or BHA instability due to vibration allows RSS operators to take timely remedial action before downhole RSS failure occurs. As a result, the performance and survivability of the RSS has been remarkably improved.
Analysis of enhancing effect of sand fly saliva on Leishmania infection in mice (1991)

Salivary gland lysates of the sand fly Lutzomyia longipalpis markedly enhance the course of infection with Leishmania major in mice. Here we examine various parameters of this phenomenon. The exacerbative effect of L. longipalpis salivary gland lysates occurred in five different mouse strains; however, the character of the effect varied from one strain to another. Consistent exacerbation of infection was achieved with as little as 1/10 of a gland. The exacerbative effect applied to more than one Leishmania species and to more than one species of sand fly, since salivary gland lysates of L. longipalpis enhanced infection with L. mexicana amazonensis and salivary gland lysates of Phlebotomus papatasi enhanced infection with L. major. A synthetic rat calcitonin gene-related peptide was also found to exacerbate infection with L. major but was found to be approximately 100-fold less potent than saliva in mediating this effect. In addition, lesions induced at skin sites at which L. longipalpis had probed for a blood meal exhibited an exacerbated course of infection similar to that seen when parasites were injected with sand fly salivary gland lysates.
Cardiac Cell Therapy — Mixed Results from Mixed Cells (2006)

Despite substantial advances in treatment, ischemic cardiac injury and the ventricular dysfunction it can provoke remain major causes of morbidity and mortality throughout the world. The endogenous regenerative capacity of the heart appears inadequate to repair injured myocardium, leading to the cumulative loss of cardiomyocytes over the lifetime of a patient. This may contribute to the prevalence of heart failure as a diagnosis at hospital admission — particularly among the elderly.For these reasons, experiments in animals suggesting that the transfer of cells derived from bone marrow (BMC) could dramatically improve cardiac function after infarction through regeneration of the myocardium . . .
A novel isolation-scaling technology for NAND EEPROMs with the minimized program disturbance (2002)

This paper describes the key technology to realize a scaled NAND EEPROM with the minimized program disturbance. It has been clarified for the first time that the program disturbance caused by neighboring cells is drastically improved by reducing the field implantation dose. The limitation of conventional LOGOS width is estimated to be about 0.56 /spl mu/m. Moreover, a careful device design and an optimization of the bottom implantation are essential in an advanced STI cell.
Calibration of a multichannel MEG system based on the Signal Space Separation method (2012)

For an efficient use of multichannel MEG systems, an accurate sensor calibration is extremely important. This includes the knowledge of both channel sensitivities and channel arrangement, which can deviate from original system plans, e.g., because of thermal stresses. In this paper, we propose a new solution to the calibration of a multichannel MEG sensor array based on the signal space separation (SSS) method. It has been shown that an inaccurate knowledge of sensor calibration limits the performances of the SSS method, resulting in a mismatch between the measured neuromagnetic field and its SSS reconstruction. Given a set of known magnetic sources, we show that an objective function, which strongly depends on sensor geometry, can be derived from the principal angle between the measured vector signal and the SSS basis. Hence, the MEG sensor array calibration is carried out by minimizing the objective function through a standard large-scale optimization technique. Details on the magnetic sources and calibration process are presented here. Finally, an application to the calibration of the 153-channel whole-head MEG system installed at the University of Chieti is discussed.
Subcutaneous Ghrelin Enhances Acute Food Intake in Malnourished Patients Who Receive Maintenance Peritoneal Dialysis (2005)

Anorexia and malnutrition confer significant morbidity and mortality to patients with end-stage kidney disease but are resistant to therapy. The aim of this study was to determine whether subcutaneous administration of ghrelin, an appetite-stimulating gut hormone, could enhance food intake in patients who are receiving maintenance peritoneal dialysis and have evidence of malnutrition. The principal outcome measure was energy intake during a measured study meal. Secondary outcome measures were BP and heart rate and 3-d food intake after intervention. Nine peritoneal dialysis patients with mild to moderate malnutrition (mean serum albumin 28.6 +/- 5.0 g/L, total cholesterol 4.4 +/- 0.6 mmol/L, subjective global assessment score of 5.7 +/- 1.7) were given subcutaneous ghrelin (3.6 nmol/kg) and saline placebo in a randomized, double-blind, crossover protocol. Administration of subcutaneous ghrelin significantly increased the group mean absolute energy intake, compared with placebo, during the study meal (690 +/- 190 versus 440 +/- 250 kcal; P = 0.0062). When expressed as proportional energy increase for each individual, ghrelin administration resulted in immediate doubling of energy intake (204 +/- 120 versus 100%; P = 0.0319). Administration of ghrelin maintained a nonsignificant increase in energy intake over 24 h after intervention (2009 +/- 669 versus 1579 +/- 330 kcal) and was not followed by subsequent underswing (1790 +/- 370 versus 1670 +/- 530 and 1880 +/- 390 versus 1830 +/- 530 kcal on days 2 and 3, respectively). Ghrelin administration resulted in a significant fall in mean arterial BP (P = 0.0030 by ANOVA). There were no significant adverse events during the study. Subcutaneous ghrelin administration enhances short-term food intake in dialysis patients with mild to moderate malnutrition.
Cloning, sequencing, expression, and functional studies of a 15,000-molecular-weight Haemophilus somnus antigen similar to Escherichia coli ribosomal protein S9 (1992)

Haemophilus somnus is a gram-negative bacterium capable of causing a number of disease syndromes in cattle. This article describes the cloning and characterization of a gene coding for a 15,000-molecular-weight (15K) polypeptide which reacts strongly with antiserum against H. somnus. Analysis of plasmid-encoded polypeptides by polyacrylamide gel electrophoresis showed that the corresponding gene is the second in a transcriptional unit. The first gene codes for a protein with a molecular weight of approximately 17,000. Using antiserum against the two recombinant proteins, we could show that the natural proteins are predominantly present in purified ribosomes from H. somnus. The nucleotide sequence of both genes and flanking regions has been determined, and the deduced amino acid sequence of the two polypeptides was used to search for sequence homology in the GenBank data base. The 15K polypeptide showed 89% similarity to the Escherichia coli ribosomal protein S9, and the 17K polypeptide showed 94% similarity to the E. coli ribosomal protein L13. In E. coli, the corresponding genes constitute a bicistronic operon, with the same gene order as that found in H. somnus. A plasmid expressing the 15K protein was found to complement an E. coli rpsI mutation. When a frameshift mutation was introduced into the 15K protein gene, the resulting plasmid failed to complement this rpsI mutation, demonstrating functional homology between the 15K protein and S9 from E. coli. Downstream from the 15K protein gene is located another open reading frame, which could code for a polypeptide with a predicted molecular weight of 24,427. A protein with a similar molecular weight was detected in minicells containing the recombinant clone. This polypeptide is 69% similar to the stringent starvation protein (Ssp) of E. coli.
Electroluminescence efficiency of 1.3 μm wavelength InGaAs/GaAs quantum dots (1998)

Data are presented characterizing the spectral emission and the electroluminescence efficiency dependence on growth conditions of 1.3 μm wavelength InGaAs/GaAs quantum dots. We show that highly efficient 1.3 μm room temperature electroluminescence can be achieved with only ten total deposited monolayers with an averaged In content of 50%. Atomic force microscopy shows that the 1.3 μm wavelength quantum dots form with a density of ∼1.3×1010 cm−2.
Capromab Pendetide Imaging of Prostate Cancer (2000)

Capromab Pendetide imaging illustrates the successful translation of monoclonal antibody technology from the laboratory to the clinic. It provides a means of identifying otherwise occult soft tissue metastases in patients with adenocarcinoma of the prostate. When utilized with other clinical, pathological and laboratory findings, Capromab Pendetide imaging enables more accurate disease staging and monitoring than is afforded by other imaging modalities such as CT and MRI. In the primary disease setting Capromab Pendetide imaging should be reserved for use in patients with negative bone scans who are at high risk for metastatic disease based on such factors as advanced clinical stage, high Gleason score and significantly elevated serum PSA or alkaline phosphatase. Due to low sensitivity for small-volume disease, a negative Mab scan may not eliminate the need for a staging lymph node dissection but should encourage further consideration of local treatment options. Capromab Pendetide should be used with caution in patients at low risk for metastatic disease. Positive scan findings in low risk patients should be confirmed before altering the treatment plan since some false positive scans should be anticipated in a population with low disease prevalence. Capromab Pendetide imaging has not been shown to be reliable in determining the local extent of the primary tumor but new techniques involving co-registration of SPECT and CT images show promise in this regard. In the patient with recurrent disease following primary therapy, the predictive value of Capromab Pendetide imaging of the prostate or prostate fossa is limited, particularly following RT. Its more important role in this setting is to identify lymph node metastases in the high risk patient with a negative bone scan who might otherwise be a candidate for local salvage therapy. A large prospective study is needed for confirmation, but preliminary data suggest that Capromab Pendetide imaging is helpful in identifying those patients with PSA elevation after radical prostatectomy who are most likely to benefit from salvage RT. As with any imaging technique, Capromab Pendetide has strengths and weaknesses that must be understood to maximize patient benefit by utilizing the scan in clinical settings where it is most likely to be useful and least likely to be misleading. Capromab Pendetide is a technically demanding procedure best performed and interpreted at sites with experience and expertise.
Replication-Defective Canarypox (ALVAC) Vectors Effectively Activate Anti–Human Immunodeficiency Virus-1 Cytotoxic T Lymphocytes Present in Infected Patients: Implications for Antigen-Specific Immunotherapy (1997)

In the attempt to develop immunotherapeutic strategies for acquired immunodeficiency syndrome capable of activating effector cells in an antigen-specific manner while maintaining the broadest possible T-cell repertoire, we evaluated two canarypox (ALVAC)-based vectors for their capacity to induce ex vivo activation/expansion of human immunodeficiency virus (HIV)-specific CD8+ cytotoxic lymphocyte precursors (CTLp) obtained from HIV-1-infected donors. These two vectors, vCP205 encoding HIV-1 gp120 + TM (28 amino acid transmembrane anchor sequence) in addition to Gag/protease and vCP300 encoding gp120 + Gag/protease as well as Nef and Pol CTL determinants, are pancytotropic but replication incompetent in mammalian cells. Bulk peripheral blood mononuclear cells (PBMCs) or enriched CD8+ T cells were stimulated for 10 days with autologous ALVAC-infected PBMCs in the presence of different cytokine combinations (interleukin-2 [IL-2], IL-4, IL-7, and IL-12). Activation by ALVAC constructs was highly antigen-specific, because vCP205 elicited only Env and Gag CTL, whereas vCP300 elicited broader reactivities against Env, Gag, Pol, and Nef determinants. The ALVAC activation of CTLp was IL-2 dependent and enhanced by the addition of IL-7, whereas IL-4 and IL-12 failed to augment cytotoxic reactivities elicited by these constructs. The expansion of enriched CD8+ T cells after activation with vCP300 was higher in patients with CD4 counts greater than 400 cells/microL. Two rounds of in vitro stimulation (IVS) with vCP300 resulted in nearly an eightfold expansion of CD8+ lymphocytes over a 25-day period. After the second IVS, an average 3.2-fold increase among the different antigen-specific CTL frequencies was achieved. These studies clearly show that HIV-recombinant ALVAC vectors represent powerful polyvalent antigenic stimuli for activation and expansion of the CD8 lymphocyte response that occurs as a result of HIV infection.
Interlaboratory Study on Thermal Cycler Performance in Controlled PCR and Random Amplified Polymorphic DNA Analyses (2001)

Irrespective of the make and model of thermal cycler, temperature-calibrated instruments consistently generated more repeatable RAPD data than noncalibrated instruments. Guidelines are offered on optimizing and monitoring thermal cycler performance.
Resource location in very large networks (2002)

Networks such as the Internet and the telephone system are examples of ubiquitous large networks. While such networks are quite common, what is not so common is completely scalable, non-hierarchical naming that is independent of the entities location or affiliations. The problem of providing a unique, logical name for each nameable entity that can be kept immutant over the lifetime of the entity has been studied in many contexts. However, most results are not scalable for really large worldwide networks. We first motivate the need for such naming schemes and then explore the possible name translation solutions. We develop a set of pragmatic criteria that a solution has to provide. The scenario we use is a hypothetical, but desirable naming scheme for telephony. In our scheme, each resource (human, telephone or computer) has a unique name that is neither mutable, nor dependent on any hierarchy of domains or geographical boundaries. We then provide an engineering solution for resolving the location of a resource given its name. This solution has to be efficient scalable and fault-tolerant. The solution uses several disjoint techniques such as caching, physically hierarchical servers and hashing. We show how the scheme meets our goals and argue its feasibility.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Robust feature space adaptation for telephony speech recognition (2006)

Speaker adaptation is critical for modern speech recognition systems. Due to the computational and multi-channel model sharing considerations, the use of model adaptation techniques is limited in telephony speech recognition systems. On the other hand, feature space adaptation methods such as feature space maximum likelihood linear regression (fMLLR) are efficient approaches suitable for telephony systems. In this work, we first describe techniques for efficient implementation of online fMLLR adaptation. Then feature space maximum a posteriori linear regression (fMAPLR) is proposed to incorporate prior knowledge for the feature transform estimation and improve the robustness of the conventional fMLLR approach. Experiments on telephony data indicate that fMAPLR is significantly more robust than fMLLR, and outperforms fMLLR especially when the adaptation data is very limited.