gebhart/patrepeval huggingface dataset:
The Sucrose Synthase Gene Is Predominantly Expressed in the Root Nodule Tissue of<i>Vicia faba</i> (1993)

To analyze nodule-specific gene expression in broadbean, we have isolated and sequenced sucrose synthase (SUCS) cDNAs from a broadbean nodule-specific cDNA library. The most 5' sequences identified from these partial cDNAs were used as a molecular probe to isolate a full-length sucrose synthase transcript sequence from a cDNA library derived from broadbean nodule mRNA. This cDNA (VfSUCS) contained a reading frame of 2,418 bp, coding for a protein of 806 amino acids with a deduced molecular weight of 92.5 kDa. The DNA as well as the deduced amino acid sequence displayed substantial homologies (68-95%) to other plant SUCS sequences. Northern and RNA dot blot experiments demonstrated that this gene is strongly expressed in the broadbean nodule tissue. An at least 10-fold lower VfSUCS expression could be detected in the uninfected root, hypocotyl, stem, and flower tissues of broadbean, whereas only traces of VfSUCS transcripts were recognizable in the broadbean leaf tissues. VfSUCS transcripts could not be detected in mature seeds of broadbean. Because of this significantly nodule-amplified type of expression, we refer to VfSUCS as a nodulin gene and propose to designate it VfNOD93 (Nuf-93) for the sucrose synthase enzyme).
Theoretical limitations in the immunodiagnostic imaging of cancer with computed tomography and nuclear scanning. (1980)

In order to help assess the feasibility of using immunologically tagged agents to render tumors detectable with current computed tomographic and nuclear scanners, mathematical formulations were developed to determine the theoretical limits of tumor detection relative to size and depth of the lesions. The results of our analysis suggest that visualization with computed tomography of a tiny tumor (1 sq mm, cross-sectional area) would require binding in the order of 2 x 10(5) iodine atoms/antigenic site, while imaging of a very large (900-sq mm) tumor would require approximately 10(4) atoms/site. Very low energy scanners might reduce these discouraging estimates by an order of 10(2). The immunological imaging of tumors with nuclear scanning appears quite feasible from our formulations, as has been demonstrated by others clinically. Small (1-sq cm) and deep (greater than or equal to 5-cm) tumors appear detectable with uptake ratios of the order of 5 or higher, which seem to be attainable currently. Smaller and deeper tumors require much higher uptake ratios to be detected.
Proposed Cardiac Pacemaker System Combining Unipolar Stimulation with Bipolar Sensing (1979)

Present cardiac pacemaker designs use either unipolar or bipolar electrode systems. Advantages of unipolar electrodes for stimulation are listed; then arguments in favor of bipolar electrodes for sensing are cited. A proposed system combines unipolar stimulation with bipolar sensing and may be implemented by adding a differential-input stage to the sensing amplifier.
Effect of treatment with estrogen conjugates on endogenous plasma steroids. (1977)

President Roosevelt received Arthur F. Estabrook's letter from Senator Hoar. He didn't choose one of the officials from Puerto Rico because it would cause too much jealousy among them. Instead, Roosevelt chose Beekman Winthrop, a man he holds in high regard.
<i>Ex Vivo</i> Gene Therapy of Familial Hypercholesterolemia. Howard Hughes Medical Institute, University of Michigan (1992)

Familial hypercholesterolemia (FH) is an autosomal dominant disorder caused by a deficiency in the receptor that clears low density lipoprotein (LDL) from the serum (reviewed in Ref. 1 and 2). Patients with one abnormal LDL receptor allele have moderate elevations in plasma LDL and suffer premature coronary artery disease (CAD). Approximately 5% of all patients under 45 who have had a myocardial infarction carry this trait. Patients with two abnormal LDL receptor genes (homozygous deficient patients) have severe hypercholesterolemia and life-threatening coronary artery disease in childhood. Strategies for treating patients with FH are directed at lowering the plasma level of LDL. In heterozygotes, this is accomplished through the administration of drugs that stimulate the expression of LDL receptor from the normal allele (2). This therapeutic approach is not effective in the treatment of homozygous deficient patients, especially those that retain less than 2% of residual LDL receptor activity. Partial amelioration of hyperlipidemia has been achieved in some homozygous deficient patients by diverting the portal circulation through a portacaval anastomosis (3) and by chronic plasmapheresis therapy (4). A more direct approach has been to correct the deficiency of hepatic LDL receptor by transplanting a liver that expresses normal levels of LDL receptor. Three patients that survived this procedure normalized their serum LDL-cholesterol (5-9). We have used an authentic animal model for FH, the Watanabe Heritable Hyperlipidemic rabbit (WHHL), to develop gene therapies for the homozygous form of FH (10-13). The WHHL rabbit has a mutation in its LDL receptor gene which renders the receptor completely dysfunctional (12) leading to severe hypercholesterolemia, diffuse atherosclerosis, and premature death. The potential efficacy of gene therapy for FH is supported by a series of studies we have performed in the WHHL rabbit in which we have achieved metabolic improvement (14-18). Liver tissue was removed from WHHL rabbits and used to isolate hepatocytes and establish primary cultures. A functional rabbit LDL receptor gene was transduced into a high proportion of hepatocytes using recombinant retroviruses, and the genetically corrected cells were transplanted into the animal from which they were derived. Transplantation of the genetically corrected, autologous hepatocytes was associated with a 30-40% decrease in serum cholesterol that persisted for the duration of the experiment (4 months, Ref. 18). Recombinant derived LDL receptor RNA was detected in liver for at least 6 months. There was no apparent immunological response to the recombinant derived LDL receptor.(ABSTRACT TRUNCATED AT 400 WORDS)
A locality preserving one-sided binary tree - Crossbar switch wiring design algorithm (2015)

One-sided crossbar switches allow for a simple implementation of complete K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> graphs. However, designing these circuits is a cumbersome process and can be automated. We present an algorithm that allows designing automatic one-sided binary tree - crossbar switches which do not exceed ⌊n/2⌋ columns, and achieves K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> graph without connecting any wires between any three adjacent blocks, thus preserving locality in connections.
Predicting response or progression of human leukemia by premature chromosome condensation of bone marrow cells. (1978)

Abstract The object of this study was to apply the phenomenon of premature chromosome condensation to the prediction of the future course of the disease in leukemic patients during chemotherapy and to the forecasting of relapse if they are in complete remission. The proliferative potential index (PPI) of bone marrows from leukemic patients was compared with that of solid tumor patients with no bone marrow involvement. This technique involves the fusion of bone marrow cells with mitotic Chinese hamster ovary cells with the use of UV-inactivated Sendal virus. The morphology of the prematurely condensed chromosomes (PCC) of the bone marrow cells reflects their position in the cell cycle, i.e. , G 1 , S, or G 2 . In addition, the G 1 PCC exhibited a wide range of variability in their degree of condensation and were arbitrarily ranked on a scale of 1 to 6. The value of 6 represents the most decondensed and extended G 1 PCC. The PPI of a bone marrow was defined as a percentage of highly extended G 1 PCC (belonging to Classes 4 to 6) among the total number of G 1 PCC scored (Classes 1 to 6). The average PPI values are: 11.7% for solid tumor patients; 27.5% for untreated leukemic patients; 22.0 to 24.5% for leukemic patients responding to chemotherapy; and 39.0% for those not responding to therapy. Among the 13 leukemic patients in complete remission at the time of the bone marrow sample, 4 patients had PPI values greater than 35%, of which 3 relapsed within 6 months. Of the remaining nine patients who exhibited low PPI values, only one relapsed within the same time interval. These data suggest a correlation between the PPI values of the bone marrow cells and the prognosis of the disease. A lower PPI value is indicative of a good prognosis, i.e. , impending or continued remission with therapy. A high PPI value during active phase of the disease or during remission, on the other hand, is indicative of continued progression or impending relapse.
IRF5:RelA Interaction Targets Inflammatory Genes in Macrophages (2014)

Interferon Regulatory Factor 5 (IRF5) plays a major role in setting up an inflammatory macrophage phenotype, but the molecular basis of its transcriptional activity is not fully understood. In this study, we conduct a comprehensive genome-wide analysis of IRF5 recruitment in macrophages stimulated with bacterial lipopolysaccharide and discover that IRF5 binds to regulatory elements of highly transcribed genes. Analysis of protein:DNA microarrays demonstrates that IRF5 recognizes the canonical IRF-binding (interferon-stimulated response element [ISRE]) motif in vitro. However, IRF5 binding in vivo appears to rely on its interactions with other proteins. IRF5 binds to a noncanonical composite PU.1:ISRE motif, and its recruitment is aided by RelA. Global gene expression analysis in macrophages deficient in IRF5 and RelA highlights the direct role of the RelA:IRF5 cistrome in regulation of a subset of key inflammatory genes. We map the RelA:IRF5 interaction domain and suggest that interfering with it would offer selective targeting of macrophage inflammatory activities.
A parallel luma-chroma filtering architecture for H.264/AVC deblocking filter (2015)

A novel architecture for the H.264/AVC deblocking filter is proposed. It includes three filtering units to filter in parallel the luma and chroma components. Also, a proper two dimensional filtering order for the luma edges and a one-dimensional filtering order for the chroma edges are presented. The architecture achieves 750 MHz in 560 MHz in 90nm and 130 nm, respectively, and requires 76 cycles to filter each MB. Compared to existing architectures, it outperforms them in frequency and throughput, while it is the only one that achieves over 60 Fps in 8K-UHD resolution.
A Multiplexable, Microfluidic Platform for the Rapid Quantitation of a Biomarker Panel for Early Ovarian Cancer Detection at the Point-of-Care (2014)

Point-of-care (POC) diagnostic platforms have the potential to enable low-cost, large-scale screening. As no single biomarker is shed by all ovarian cancers, multiplexed biomarker panels promise improved sensitivity and specificity to address the unmet need for early detection of ovarian cancer. We have configured the programmable bio-nano-chip (p-BNC)-a multiplexable, microfluidic, modular platform-to quantify a novel multi-marker panel comprising CA125, HE4, MMP-7, and CA72-4. The p-BNC is a bead-based immunoanalyzer system with a credit-card-sized footprint that integrates automated sample metering, bubble and debris removal, reagent storage and waste disposal, permitting POC analysis. Multiplexed p-BNC immunoassays demonstrated high specificity, low cross-reactivity, low limits of detection suitable for early detection, and a short analysis time of 43 minutes. Day-to-day variability, a critical factor for longitudinally monitoring biomarkers, ranged between 5.4% and 10.5%, well below the biologic variation for all four markers. Biomarker concentrations for 31 late-stage sera correlated well (R(2) = 0.71 to 0.93 for various biomarkers) with values obtained on the Luminex platform. In a 31 patient cohort encompassing early- and late-stage ovarian cancers along with benign and healthy controls, the multiplexed p-BNC panel was able to distinguish cases from controls with 68.7% sensitivity at 80% specificity. Utility for longitudinal biomarker monitoring was demonstrated with prediagnostic plasma from 2 cases and 4 controls. Taken together, the p-BNC shows strong promise as a diagnostic tool for large-scale screening that takes advantage of faster results and lower costs while leveraging possible improvement in sensitivity and specificity from biomarker panels.
Method for the Synthesis of Phenothiazines via a Domino Iron-Catalyzed C–S/C–N Cross-Coupling Reaction (2015)

An environmentally benign and efficient method has been developed for the synthesis of phenothiazines via a tandem iron-catalyzed C-S/C-N cross-coupling reaction. Some of the issues typically encountered during the synthesis of phenothiazines in the presence of palladium and copper catalysts, including poor substrate scope, long reaction times and poor regioselectivity, have been addressed using this newly developed iron-catalyzed method.
Analysis of p53 Gene Mutations in Keloids Using Polymerase Chain Reaction–Based Single-Strand Conformational Polymorphism and DNA Sequencing (1998)

Focal mutations in p53 may increase cell proliferation and decrease cell death in the dysregulated growth patterns that have been clinically documented. An understanding of the pattern of all growth dysregulation related to keloids may lead to new therapeutic strategies.
Tele-nanorobotics using an atomic force microscope as a nanorobot and sensor (1998)

In this paper, a tele-nanorobotic system using an atomic force microscope (AFM) as the nanorobot and sensor has been proposed. Modeling and control of the AFM cantilever, and modeling of nanometer scale forces have been realized for telemanipulation applications. In addition to three-dimensional virtual reality visual feedback in the user interface, a 1 d.o.f. haptic device has been constructed for nano-scale haptic sensing. For feeling the nano forces, a bilateral teleoperation control system with virtual impedance approach has been introduced. Initial experiments and simulations on the AFM and teleoperation system show that the system can be utilized for different telenanomanipulation applications such as two-dimensional nano particle assembly or biological object manipulation.
Parallel and SIMD Optimization of Image Feature Extraction (2011)

Image feature extraction is widely used in content-based image retrieval(CBIR), computer version and all kinds of image processing applications. In this paper, we introduce some parallel and SIMD optimizations of image-feature extraction to overcome the disadvantages of original methods. We mainly use both thread-parallel optimization and Single Instruction Multiple Data (SIMD) optimizations. And especially, for some hot point, we use SIMD logical operations to eliminate the random conditional branches which cannot be effectively predicted by CPU Branch Prediction. We experimented our optimized implementation on multi-core systems, and various images were used to test the image-feature extraction results and performance. All the parallel and SIMD optimizations work out a good cumulative performance speedup.
The Amidation of Carboxylic Acid with Amine over Hydrous Zirconium(IV) Oxide (1989)

Abstract The reaction of a carboxylic acid or an ester with an amine to give the corresponding amide was carried out efficiently over hydrous zirconium(IV) oxide, whether in the vapor phase or in the liquid phase.
Effect of coordinated therapeutic assays using <i>C. parvum</i>, interferon and arginine butyrate on spontaneous disease and survival of AKR mice (1983)

AKR mice, known to develop spontaneous leukemia in almost 100% of cases, were studied throughout their life-span. Different treatments combining a potent immune stimulator, Corynebacterium parvum (CP), with interferon (IFN) and arginine butyrate were initiated at the 15th week of life. In a preliminary series of experiments, CP (200 micrograms), IFN (20,000 units) and butyrate 50 mM) were employed in a well-defined chronological order. In controls, the mean survival time (MST) was 35.17 +/- 1.67 weeks and the final survival rates was 0/50 mice for all experiments. Only CP associated with arginine butyrate significantly augmented the MST (42.5 +/- 3.66 weeks) and final survival rate (9/35 mice). In an adjusted set of experiments, reducing the IFN concentration to 10,000 and 5,000 units and that of butyrate to 6 mM greatly improved the results. The MST was substantially increased with the combinations of CP + IFN + butyrate (41.4 +/- 1.86 weeks), CP + IFN (42.73 +/- 3.29 weeks) and butyrate + IFN (41 +/- 2.34 weeks), as well as the final survival rates (8/15, 10/15 and 6/15 mice respectively). An important finding was that when CP and IFN were used separately, they were ineffective.
Case History – World's First Slim Open Hole Smart MRC Wells (2009)

Abstract Smart Maximum Reservoir Contact (MRC) wells have been successfully utilized extensively across Saudi Aramco to increase reservoir contact, well productivity and total oil recovery. This concept has primarily been used in newly drilled wells. It requires larger than conventional hole and casing sizes to achieve the dimensions required for the Intelligent Well System. Converting an existing well to an MRC poses a new challenge. This paper presents a case history of two old existing dead wells in Saudi Aramco that were successfully converted into the first Slim Open Hole MRC Wells in the world. The two wells were originally drilled as vertical producing wells with 7" 23# liner set above the top of the target zone and extending to surface. To access more reserves from the field, the decision was made to sidetrack the wells to a new location and drill an MRC wells to achieve maximum productivity from those wells. The wells were planned to be a three lateral wells with a total of 12,000' of reservoir contact in each well. To maximize the long term productivity of the wells, it was decided to run Intelligent Well Systems that enables remote monitoring and control of each lateral throughout the life of the two wells. The final success of these converted slim open hole smart MRC wells are supported by more than expected production gain.
FairFed: Enabling Group Fairness in Federated Learning (2021)

Training ML models which are fair across different demographic groups is of critical importance due to the increased integration of ML in crucial decision-making scenarios such as healthcare and recruitment. Federated learning has been viewed as a promising solution for collaboratively training machine learning models among multiple parties while maintaining the privacy of their local data. However, federated learning also poses new challenges in mitigating the potential bias against certain populations (e.g., demographic groups), as this typically requires centralized access to the sensitive information (e.g., race, gender) of each datapoint. Motivated by the importance and challenges of group fairness in federated learning, in this work, we propose FairFed, a novel algorithm for fairness-aware aggregation to enhance group fairness in federated learning. Our proposed approach is server-side and agnostic to the applied local debiasing thus allowing for flexible use of different local debiasing methods across clients. We evaluate FairFed empirically versus common baselines for fair ML and federated learning, and demonstrate that it provides fairer models particularly under highly heterogeneous data distributions across clients. We also demonstrate the benefits of FairFed in scenarios involving naturally distributed real-life data collected from different geographical locations or departments within an organization.
MicroRNA heterogeneity in endometrial cancer cell lines revealed by deep sequencing (2015)

The aim of the present study was to obtain comprehensive microRNA (miRNA) profiles of type I [Ishikawa (ISK)] and type II (HEC-1B) human endometrial adenocarcinoma cell lines, utilizing the latest high-throughput sequencing techniques. RNA was extracted from ISK and HEC-1B cell lines. Sequencing results were obtained from a next-generation sequencing platform. Using the miRBase database and a series of software pipelines, miRNA expression was analyzed in the ISK and HEC-1B cell lines. It was revealed that the type and quantity of miRNAs in the two cell types varied significantly; 34 miRNAs were upregulated and 105 miRNAs were downregulated in HEC-1B cells compared with those of ISK cells. Furthermore, it was observed that the expression pattern of the miRNA (miR)-17-92 cluster differed between the two cell types, and the expression levels of the miR-200 family in ISK cells were markedly increased compared with those of HEC-1B cells. The present study therefore identified potential novel biomarkers, which may be useful in the differentiation between type I and type II endometrial cancer, and also revealed miRNA alterations that may be associated with endometrial cancer and its underlying pathogenic mechanisms.
The Recent Progress in Quantitative Medical Image Analysis for Computer Aided Diagnosis Systems (2011)

Computer-aided diagnosis (CAD) has become one of the major research subjects in medical imaging and diagnostic radiology. Many different CAD schemes are being developed for use in the detection and/or characterization of various lesions found through various types of medical imaging. These imaging technologies employ conventional projection radiography, computed tomography, magnetic resonance imaging, ultrasonography, etc. In order to achieve a high performance level for a computerized diagnosis, it is important to employ effective image analysis techniques in the major steps of a CAD scheme. The main objective of this review is to attempt to introduce the diverse methods used for quantitative image analysis, and to provide a guide for clinicians.
Diagnostic expert system for the B1B (1988)

A description is given of CEPS (CITS Expert Parameter System), one of the first large-scale applications of an expert system to upgrade a major weapon system, the B-1B strategic aircraft. CEPS is a ground-based system that augments the onboard CITS (central integrated test system) as a maintenance aid for both organizational and intermediate level technicians. Phase I of CEPS successfully demonstrated the utilization of expert system techniques for the isolation of fault ambiguities, and analysis and reduction of retest okays. Phase II consists of implementation of a prototype, including a five month period of usage by personnel at Dyess Air Force Base. Phase III will be the actual implementation of CEPS at all B-1B main operating bases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>