gebhart/patrepeval huggingface dataset:
Gene Expression Profiles of Normal Human Fibroblasts after Exposure to Ionizing Radiation: A Comparative Study of Low and High Doses (2005)

Several types of cellular responses to ionizing radiation, such as the adaptive response or the bystander effect, suggest that low-dose radiation may possess characteristics that distinguish it from its high-dose counterpart. Accumulated evidence also implies that the biological effects of low-dose and high-dose ionizing radiation are not linearly distributed. We have investigated, for the first time, global gene expression changes induced by ionizing radiation at doses as low as 2 cGy and have compared this to expression changes at 4 Gy. We applied cDNA microarray analyses to G1-arrested normal human skin fibroblasts subjected to X irradiation. Our data suggest that both qualitative and quantitative differences exist between gene expression profiles induced by 2 cGy and 4 Gy. The predominant functional groups responding to low-dose radiation are those involved in cell-cell signaling, signal transduction, development and DNA damage responses. At high dose, the responding genes are involved in apoptosis and cell proliferation. Interestingly, several genes, such as cytoskeleton components ANLN and KRT15 and cell-cell signaling genes GRAP2 and GPR51, were found to respond to low-dose radiation but not to high-dose radiation. Pathways that are specifically activated by low-dose radiation were also evident. These quantitative and qualitative differences in gene expression changes may help explain the non-linear correlation of biological effects of ionizing radiation from low dose to high dose.
Phosphorylation of p40AUF1 Regulates Binding to A + U-rich mRNA-destabilizing Elements and Protein-induced Changes in Ribonucleoprotein Structure (2003)

Messenger RNA turnover directed by A + U-rich elements (AREs) involves selected ARE-binding proteins. Whereas several signaling systems may modulate ARE-directed mRNA decay and/or post-translationally modify specific trans-acting factors, it is unclear how these mechanisms are linked. In THP-1 monocytic leukemia cells, phorbol ester-induced stabilization of some mRNAs containing AREs was accompanied by dephosphorylation of Ser83 and Ser87 of polysome-associated p40AUF1. Here, we report that phosphorylation of p40AUF1 influences its ARE-binding affinity as well as the RNA conformational dynamics and global structure of the p40AUF1-ARE ribonucleoprotein complex. Most notably, association of unphosphorylated p40AUF1 induces a condensed RNA conformation upon ARE substrates. By contrast, phosphorylation of p40AUF1 at Ser83 and Ser87 inhibits this RNA structural transition. These data indicate that selective AUF1 phosphorylation may regulate ARE-directed mRNA turnover by remodeling local RNA structures, thus potentially altering the presentation of RNA and/or protein determinants involved in subsequent trans-factor recruitment.
Intelligent prediction of execution times (2013)

It is a major challenge in software engineering to statically analyze in advance the expectable run-time behavior of applications. The most needed information is the expected execution time of a function to determine its computational cost. In this paper, we present a sophisticated approach that solves this problem by utilizing Machine Learning (ML) techniques based on regression modeling to automatically derive precise predictions for this information. This enables to focus optimization efforts on the parts that are relevant for the resulting performance and to predict execution times of functions on different processing elements of a heterogeneous architecture. Among others, our approach eliminates the need for manual annotations of run-time information, which automates and facilitates the development of complex software, thus improving the software engineering process. For our experiments that demonstrate the accuracy of our approach, we have used a considerable number of programs from various benchmark suites which encompass different realworld application domains. This shows on the one hand the general applicability and on the other hand the high scalability of our ML techniques.
INCORPORATING CONTENT ADDRESSABLE ARRAY PROCESSORS INTO COMPUTER VISION SYSTEMS (1983)

121-133
Blood flow in the normal human retina. (1989)

The laser Doppler technique was used to measure the blood flow rate in 41 major vessels in ten eyes of healthy volunteer subjects. The specific relationship between blood flow rate, F, and vessel diameter, D, was determined for both retinal arteries and retinal veins. On average, F increased with increasing D at a power of 4.1, consistent with the presence of Poiseuille flow. In six eyes of six subjects, measurements on individual vessels were combined to yield the total retinal blood flow rate. The mean and standard deviation of the total retinal blood flow was 80 +/- 12 microliter/min. The blood flow rate per unit mass of retinal tissue was calculated and found to be in good agreement with that reported for macaque monkeys. Blood flow to the temporal side of the retina was approximately three times larger than to the nasal side. There was no significant difference between blood flow to the superior and the inferior retina.
Maternal transfer of the 6-MBOA chemical signal in <i>Microtus montanus</i> during gestation and lactation (1993)

A study was undertaken to determine how reproductive information from the plant metabolite 6-methoxybenzoxazolinone (6-MBOA) is transferred maternally to offspring in the montane vole, Microtus montanus. Adult female M. montanus were implanted with 10- or 20-mm Silastic capsules containing 6-MBOA (experimental) or empty capsules (control). Females were paired with males and monitored daily for births. On the day of birth, the offspring were either cross-fostered to other mated pairs, or maintained in the natal nest. Six groups were formed based on whether the litter was transferred to a female of the same treatment, to a female of the opposite treatment, or left in the cage of birth until weaning. The offspring were reared in the nest until 18 days and sacrificed 8 days after weaning. Data were collected on weight, total length, paired-testes weight (males), and uterine weight (females). The data indicate that offspring receiving 6-MBOA information demonstrate significantly increased growth and increased gonadal size compared with offspring receiving no 6-MBOA information, and that the 6-MBOA information is transferred maternally during both gestation and lactation.
Evaluation of several commercial biochemical and immunologic methods for rapid identification of gram-positive cocci directly from blood cultures (1988)

To develop laboratory methods for the rapid identification of gram-positive cocci from blood cultures, several commercial immunological and biochemical tests for identifying staphylococci and streptococci from two different blood culture systems (Thiol/TSB, Difco Laboratories; BACTEC, Johnston Laboratories, Inc.) were evaluated and compared with conventional identification methods. A total of 44 cultures contained Staphylococcus aureus as determined by conventional methods. Commercial immunological methods (six tested) ranged in overall sensitivity from 38.6 (Staphyloslide; BBL Microbiology Systems) to 77.3% (Staphaurex; Wellcome Diagnostics). All methods tested had 100% specificity. A total of 30 isolates of group D streptococci were tested with immunological and biochemical identification systems. The overall sensitivity ranged from 14.2% (Phadebact Group D; Pharmacia Diagnostics) to 100% with Streptex (Wellcome; immunological) and Identicult A-E (Scott Laboratories, Inc.; biochemical). The results of this study suggest that some reagents can be used to provide rapid identification of gram-positive cocci from blood cultures 24 h earlier than standard methods.
Persistent fatigue following SARS-CoV-2 infection is common and independent of severity of initial infection (2020)

Fatigue is a common symptom in those presenting with symptomatic COVID-19 infection. However, it is unknown if COVID-19 results in persistent fatigue in those recovered from acute infection. We examined the prevalence of fatigue in individuals recovered from the acute phase of COVID-19 illness using the Chalder Fatigue Score (CFQ-11). We further examined potential predictors of fatigue following COVID-19 infection, evaluating indicators of COVID-19 severity, markers of peripheral immune activation and circulating pro-inflammatory cytokines. Of 128 participants (49.5 ± 15 years; 54% female), more than half reported persistent fatigue (67/128; 52.3%) at median of 10 weeks after initial COVID-19 symptoms. There was no association between COVID-19 severity (need for inpatient admission, supplemental oxygen or critical care) and fatigue following COVID-19. Additionally, there was no association between routine laboratory markers of inflammation and cell turnover (leukocyte, neutrophil or lymphocyte counts, neutrophil-to-lymphocyte ratio, lactate dehydrogenase, C-reactive protein) or pro-inflammatory molecules (IL-6 or sCD25) and fatigue post COVID-19. Female gender and those with a pre-existing diagnosis of depression/anxiety were over-represented in those with fatigue. Our findings demonstrate a significant burden of post-viral fatigue in individuals with previous SARS-CoV-2 infection after the acute phase of COVID-19 illness. This study highlights the importance of assessing those recovering from COVID-19 for symptoms of severe fatigue, irrespective of severity of initial illness, and may identify a group worthy of further study and early intervention.
Monolithic High-Voltage GaN MOSFET/Schottky Pair with Reverse Blocking Capability (2007)

We report on a high voltage, reverse blocking GaN MOS-gated transistor switch which integrates a n-channel lateral GaN MOSFET with a Schottky diode. The device, with RESURF lengths up to 18μm, exhibits good DC characteristics with forward and reverse blocking voltages as high as 770V and 1050V respectively.
Semi-automated location identification of catheters in digital chest radiographs (2007)

Localization of catheter tips is the most common task in intensive care unit imaging. In this work, catheters appearing in digital chest radiographs acquired by portable chest x-rays were tracked using a semi-automatic method. Due to the fact that catheters are synthetic objects, its profile does not vary drastically over its length. Therefore, we use forward looking registration with normalized cross-correlation in order to take advantage of a priori information of the catheter profile. The registration is accomplished with a two-dimensional template representative of the catheter to be tracked generated using two seed points given by the user. To validate catheter tracking with this method, we look at two metrics: accuracy and precision. The algorithms results are compared to a ground truth established by catheter midlines marked by expert radiologists. Using 12 objects of interest comprised of naso-gastric, endo-tracheal tubes, and chest tubes, and PICC and central venous catheters, we find that our algorithm can fully track 75% of the objects of interest, with a average tracking accuracy and precision of 85.0%, 93.6% respectively using the above metrics. Such a technique would be useful for physicians wishing to verify the positioning of catheter tips using chest radiographs.
A Two-Dimensional Pretilt Angle Distribution Measurement of Twisted Nematic Liquid Crystal Cells Using Stokes Parameters at Plural Wavelengths (2004)

We propose a Stokes parameter method for determining two-dimensional (2D) cell parameter distributions such as a pretilt angle in addition to the cell thickness and the twist angle of the twisted nematic liquid crystal display (TNLCD) by measuring Stokes parameters at plural wavelengths including a near-infrared region. The cell thickness and twist angle can be determined simultaneously by measurements of Stokes parameters at only one wavelength. The 2D cell parameter distributions of full-color LCDs can be obtained using near-infrared light. The pretilt angle can also be determined using at least two wavelengths. Measurement fluctuations or errors in cell parameters decrease with increasing wavelengths and are discussed in detail.
The effect of intermittent preventive treatment using sulphadoxine pyrimethamine in the control of malaria in pregnancy: A cross-sectional study in the Offinso district of Ghana (2010)

Malaria infection during pregnancy causes maternal anaemia and placental parasitaemia both of which pose substantial risks to the mother, the foetus and the newborn. This study assessed the effects of intermittent preventive treatment (IPTp) using sulphadoxine-pyrimethamine (SP) to control malaria in pregnancy in the Offinso district, Ghana. Pregnant women attending antenatal clinics (ANC) between October 2005 and June 2006 in five health facilities in the District were studied. The effects of SP on parasitaemia, haemoglobin level and adverse effects on pregnant women were assessed. Of the 444 pregnant women studied, 190 (43%) took SP. The influence of SP intake on malaria infection was insignificant (r = 0.0008, p = 0.986). However, there was a tendency towards reduced parasitaemia as number of SP doses increased; one dose: 29/82 (35%), two doses: 18/57 (32%) and three doses: 11/57 (22%). The mean Hb level (10.4 ± 1.69 g/dl) for the SP group (all doses combined) was significantly higher than that (9.9 ± 1.64 g/dl) in the no SP group (p = 0.002). Further, there was a significant association between IPTp using SP and haemoglobin level (p = 0.01) with a dose-response relationship. SP usage had no significant adverse effects on the pregnant women. Effective implementation of IPTp using SP is an evidence-based measure for control of malaria-related anaemia in pregnancy. 
	
	Key words: Malaria, intermittent preventive treatment, pregnant women, sulphadoxine-pyrimethamine.
Metabolic functions of duplicate genes in <i>Saccharomyces cerevisiae</i> (2005)

The roles of duplicate genes and their contribution to the phenomenon of enzyme dispensability are a central issue in molecular and genome evolution. A comprehensive classification of the mechanisms that may have led to their preservation, however, is currently lacking. In a systems biology approach, we classify here back-up, regulatory, and gene dosage functions for the 105 duplicate gene families of Saccharomyces cerevisiae metabolism. The key tool was the reconciled genome-scale metabolic model iLL672, which was based on the older iFF708. Computational predictions of all metabolic gene knockouts were validated with the experimentally determined phenotypes of the entire singleton yeast library of 4658 mutants under five environmental conditions. iLL672 correctly identified 96%-98% and 73%-80% of the viable and lethal singleton phenotypes, respectively. Functional roles for each duplicate family were identified by integrating the iLL672-predicted in silico duplicate knockout phenotypes, genome-scale carbon-flux distributions, singleton mutant phenotypes, and network topology analysis. The results provide no evidence for a particular dominant function that maintains duplicate genes in the genome. In particular, the back-up function is not favored by evolutionary selection because duplicates do not occur more frequently in essential reactions than singleton genes. Instead of a prevailing role, multigene-encoded enzymes cover different functions. Thus, at least for metabolism, persistence of the paralog fraction in the genome can be better explained with an array of different, often overlapping functional roles.
Detection of visible and latent fingerprints by micro-X-ray fluorescence (2006)

Numerous methods are available to forensic scientists for detecting fingerprints in which the prints are treated with various agents to enhance the visual contrast between the print and the surface. In the present work, the spatial elemental imaging capabilities of micro-X-ray fluorescence (MXRF) were used to visualize fingerprint patterns based on inorganic elements present in the prints. A major advantage of using MXRF is that the prints are left unaltered for other analyses, such as deoxyribonucleic acid extraction or for archiving. Most of the fingerprints which were examined were imaged from the potassium and chlorine present in the print residue. Among the various prints studied, lower count rates were also observed in the elemental maps of Ca, Al, Na, Mg, Si, P, S, and the X-ray source scatter. A sebaceous oily fingerprint left by one subject was successfully imaged by MXRF, but sebaceous prints left by a different person were undetectable, indicating that print elemental composition may be person and/or diet dependent. Prints containing substances that might be found in real-world cases were also visualized including sweat, lotion, saliva, and sunscreen.
<sup>68</sup> Ga-Radiolabeled AGuIX Nanoparticles as Dual-Modality Imaging Agents for PET/MRI-Guided Radiation Therapy (2017)

This study demonstrates that <sup>68</sup>Ga-AGuIX@NODAGA can be used as a dual-modality PET/MR imaging agent with passive accumulation in the diseased area, thus showing great potential for PET/MR image-guided radiation therapy.
An Alkane-Responsive Expression System for the Production of Fine Chemicals (1999)

Membrane-located monooxygenase systems, such as the Pseudomonas putida mt-2-derived xylene oxygenase, are attractive for challenging transformations of apolar compounds, including enantiospecific epoxidations, but are difficult to synthesize at levels that are useful for application to biotechnological processes. In order to construct efficient biocatalysis strains, we utilized the alkane-responsive regulatory system of the OCT plasmid-located alk genes of Pseudomonas oleovorans GPo1, a very attractive system for recombinant biotransformation processes. Determination of the nucleotide sequence of alkS, whose activated gene product positively regulates the transcription of the structural genes alkBFGHJKL, on a 3.7-kb SalI-HpaI OCT plasmid fragment was completed, and the N-terminal amino acid sequence of an AlkS-LacZ fusion protein was found to be consistent with the predicted DNA sequence. The alkS gene and the alkBp promoter were assembled into a convenient alkane-responsive genetic expression cassette which allowed expression of the xylene oxygenase genes in a recombinant Escherichia coli strain at a specific activity of 91 U per g (dry weight) of cells when styrene was the substrate. This biocatalyst was used to produce (S)-styrene oxide in two-liquid-phase cultures. Volumetric productivities of more than 2 g of styrene oxide per h per liter of aqueous phase were obtained; these values represented a fivefold improvement compared with previous results.
A Facile Route to Bimetallic Ruthenium Dipyridophenazine Complexes (2003)

Using achiral coordinatively unsaturated metal complex building-blocks, the two step synthesis of a bimetallic complex containing independent [Ru(II)dppz] units tethered together by a linking 4,4'dipyridyl-1,5-pentane ligand is reported. Photophysical studies on this prototype system indicate that the characteristic luminescence of the [Ru(II)dppz] moieties is perturbed by self-quenching processes. Preliminary binding studies on the complex with natural and synthetic duplex DNA is reported. Luminescence and calorimetric titrations reveal that the complex does not show enhanced binding affinity with respect to analogous monometallic complexes. This result is interpreted by a consideration of the length and rigidity of the linker employed in the complex.
Adeno-associated viral vectors: background and technical aspects. (1998)

There are several obstacles that prevent the successful clinical application of gene therapy. Some of these challenges are unique to the particular disease and organ that is being targeted. Desirable characteristics of approaches aimed at delivery of a therapeutic gene to the kidney ideally will require a vector that is safe, that efficiently transduces nondividing cells, and that can lead to long-term gene expression. Viral vectors that are derived from the small replication-deficient parvovirus, adeno-associated virus, offer many potential advantages. The wild-type virus is nonpathogenic and can site specifically integrate at a single location on chromosome 19, a process that offers the hope that this characteristic could be engineered into recombinant vectors as well. Recombinant adeno-associated virus can also efficiently integrate into the host genome, can transduce nondividing cells, and does not induce an immune response which destroys the transduced cells. Efforts focused both on gaining a more complete understanding of the virus life cycle as well on the efficient production of high-titer virus should bring this vector closer to clinical application.
Column-Oriented Database Systems (Tutorial) (2009)

Column-oriented database systems (column-stores) have attracted a lot of attention in the past few years. Column-stores, in a nutshell, store each database table column separately, with attribute values belonging to the same column stored contiguously, compressed, and densely packed, as opposed to traditional database systems that store entire records (rows) one after the other. Reading a subset of a table’s columns becomes faster, at the potential expense of excessive disk-head seeking from column to column for scattered reads or updates. After several dozens of research papers and at least a dozen of new column-store start-ups, several questions remain. Are these a new breed of systems or simply old wine in new bottles? How easily can a major row-based system achieve column-store performance? Are column-stores the answer to effortlessly support large-scale data-intensive applications? What are the new, exciting system research problems to tackle? What are the new applications that can be potentially enabled by column-stores? In this tutorial, we present an overview of column-oriented database system technology and address these and other related questions.
Efficient <scp>TALEN</scp> construction and evaluation methods for human cell and animal applications (2013)

Transcription activator-like effector nucleases (TALENs) have recently arisen as effective tools for targeted genome engineering. Here, we report streamlined methods for the construction and evaluation of TALENs based on the 'Golden Gate TALEN and TAL Effector Kit' (Addgene). We diminished array vector requirements and increased assembly rates using six-module concatemerization. We altered the architecture of the native TALEN protein to increase nuclease activity and replaced the final destination vector with a mammalian expression/in vitro transcription vector bearing both CMV and T7 promoters. Using our methods, the whole process, from initiating construction to completing evaluation directly in mammalian cells, requires only 1 week. Furthermore, TALENs constructed in this manner may be directly applied to transfection of cultured cells or mRNA synthesis for use in animals and embryos. In this article, we show genomic modification of HEK293T cells, human induced pluripotent stem cells, Drosophila melanogaster, Danio rerio and Xenopus laevis, using custom-made TALENs constructed and evaluated with our protocol. Our methods are more time efficient compared with conventional yeast-based evaluation methods and provide a more accessible and effective protocol for the application of TALENs in various model organisms.