gebhart/patrepeval huggingface dataset:
Pageserver: High-Performance SSD-Based Checkpointing of Transactional Distributed Memory (2010)

The Rainbow cluster operating system provides fault tolerance by storing incremental checkpoints on a solid state disk (SSD) drive. As the access characteristics of SSD drives differ substantially from those of traditional magnetic hard disk drives (HDDs) new interesting techniques of storing checkpoints in an elegant object-oriented fashion can be applied. The usage of transactional distributed memory (TDM) simplifies the distributed checkpointing algorithm as it automatically guarantees consistent checkpoints of the entire Rainbow cluster without additional coordination overhead.
Prediction of second-order statistics in motion-compensated video coding (2002)

Motion-compensated prediction is widely used in video coding. In current coders, it only predicts the first-order statistics (mean value). However, we show in this paper that the variance of each individual pixel in the residual field can be predicted too, by relating it to the gradient magnitude computed from the previous frame. This relationship leads to designing the residual field coder such that optimal Karhunen-Loeve transforms can be computed for each block. Furthermore, no matter what transform is used, the variance of each individual transform coefficient is known to both ends of the coding process, and hence conditional entropy coding can be implemented.
An HF-1a/ HF-1b/MEF-2 combinatorial element confers cardiac ventricular specificity and establishes an anterior-posterior gradient of expression (1996)

The molecular determinants that direct gene expression to the ventricles of the heart are for the most part unknown. Additionally, little data is available on how the anterior/posterior axis of the heart tube is determined and whether the left and right atrial and ventricular chambers are assigned as part of this process. Utilizing myosin light chain-2 ventricular promoter/beta-galactosidase reporter transgenes, we have determined the minimal cis-acting sequences required for ventricular-specific gene expression. In multiple independent transgenic mouse lines, we found that both a 250 base pair myosin light chain-2 ventricular promoter fragment, as well as a dimerized 28 bp sub-element (HF-1) containing binding sites for HF1a and HF1b/MEF2 factors, directed ventricular-specific reporter expression from as early as the endogenous gene, at day 7.5-8.0 post coitum. While the endogenous gene is expressed uniformly throughout both ventricles, the transgenes were expressed in a right ventricular/conotruncal dominant fashion, suggesting that they contain only a subset of the elements which respond to positional information in the developing heart tube. Expression of the transgene was cell autonomous and its temporospatial characteristics not affected by mouse strain/methylation state of the genome. To determine whether ventricular-specific expression of the transgene was dependent upon regulatory genes required for correct ventricular differentiation, the 250 base pair transgene was bred into both retinoid X receptoralpha and Nkx2-5 null backgrounds. The transgene was expressed in both mutant backgrounds, despite the absence of endogenous myosin light chain-2 ventricular transcript in Nkx2-5 null embryos. Ventricular specification, as judged by transgene expression, appeared to occur normally in both mutants. Thus, the HF-1 element, directs chamber-specific transcription of a transgene reporter independently of retinoid X receptoralpha and Nkx2-5, and defines a minimal combinatorial pathway for ventricular chamber gene expression. The patterned expression of this transgene may provide a model system in which to investigate the cues that dictate anterior-posterior (right ventricle/left ventricle) gradients during mammalian heart development.
Effects of a high‐fat diet on the electrical properties of porcine atria (2015)

The shorter ERPs for the PV observed in response to the HFD increased vulnerability to AF, and these electrophysiological characteristics may underlie obesity-related AF.
Multiresolution network flow phase unwrapping (2002)

Phase unwrapping is a key step in deriving topographic information from interferometric SAR. Several recent methods are based on a minimum cost network flow approach. The authors develop a new, computationally efficient, "divide-and-conquer" strategy for phase unwrapping.
The third subunit of protein phosphatase 2A (PP2A), a 55-kilodalton protein which is apparently substituted for by T antigens in complexes with the 36- and 63-kilodalton PP2A subunits, bears little resemblance to T antigens (1992)

The small and middle T (tumor) antigens of polyomavirus have been shown previously to associate with the 36-kDa catalytic subunit and the 63-kDa regulatory subunit of protein phosphatase type 2A, apparently substituting for a normal third 55-kDa regulatory subunit (D.C. Pallas, L.K. Shahrik, B.L. Martin, S. Jaspers, T.B. Miller, D.L. Brautigan, and T.M. Roberts, Cell 60:167-176, 1990). To facilitate a comparison of the normal regulatory subunit and T antigens, we isolated a 2.14-kb cDNA clone encoding this 55-kDa subunit from a rat liver library. Using a probe from the coding region of this gene, we detected a major 2.4-kb mRNA transcript in liver and muscle RNAs. The 55-kDa protein phosphatase 2A subunit purified from rat skeletal muscle generates multiple species when analyzed on two-dimensional gels. Transcription and translation of the clone in vitro produced a full-length protein that comigrated precisely on two-dimensional gels with three of these species, indicating that the 55-kDa protein is apparently modified similarly in vivo and in reticulocyte lysates. Additional species in the purified preparation were not found in the translate, suggesting that there are probably two or more isoforms of this protein in rat muscle. Somewhat surprisingly, there was no clear homology with T-antigen amino acid sequences.
A protective monoclonal antibody recognizes an epitope in the carboxyl-terminal cysteine-rich domain in the precursor of the major merozoite surface antigen of the rodent malarial parasite, Plasmodium yoelii. (1989)

The 195-kDa major merozoite surface antigen of Plasmodium falciparum (Pf PMMSA) is a potential candidate for the development of a blood-stage malarial vaccine. We have focused on an analogous 230-kDa Ag of the rodent malarial parasite, Plasmodium yoelii, in an effort to study this protein in an experimental model system. Previously we reported the cloning and sequencing of a 2.1-kb portion of the gene encoding the carboxyl-terminal 77 kDa of the Py PMMSA. This region contained the B cell epitope recognized by mAb 302, a mAb shown to protect mice passively against P. yoelii challenge infection. To localize this B cell epitope, we have inserted various restriction fragments of the cloned Py PMMSA sequence into the bacterial expression vector pMG27NSTerm. Recombinant peptides of 74, 40, 34, 17, and 10 kDa have been produced which bear the epitope recognized by mAb 302. The results demonstrate that this B cell epitope is located within the most carboxyl-region of the Py PMMSA which contains a series of ten cysteine residues, also found in the PMMSA of P. falciparum. Further analysis showed that the reduction of disulfide bonds as well as the deletion of CYS-607 of the cloned sequence, resulted in the loss of the expression of this epitope. It is of interest that this epitope does not appear to be a dominant B cell determinant of the Py PMMSA molecule during infection. Inasmuch as this cysteine-rich domain of Py PMMSA displays considerable homology with that of Pf PMMSA, our data suggest that this region of the Pf PMMSA should be considered for inclusion in the development of a blood-stage vaccine.
Cervical Pedicle Screws: Conventional Versus Computer-Assisted Placement of Cannulated Screws (2005)

Transpedicular screws in the cervical spine and cervicothoracic junction can be applied safely and with high accuracy in a conventional technique. Cannulated screws and the use of separate stab incisions from C3-C6 with a trocar system allow for reduced screw misplacement rates. The CAS system leads to significantly reduced screw misplacement rates. Therefore, because of the potential risk of injury to the vertebral artery and neural elements, the use of a CAS system seems to be beneficial, especially for pedicle instrumentation C3-C6.
Unprimed spleen cell populations recognize macrophage-bound antigen with opposite net electric charge. (1977)

Previous studies have demonstrated an inverse charge relationship between the net electrical charge of antigen and the responding cells. In the present study we attempted to establish whether this phenomenon holds also for the primary recognition phase of cell-mediated immunity, when the involvement of the macrophage in presenting antigen is obligatory. Normal spleen cells were fractionated over negatively and positively charged columns. The fractionated cell populations, as well as the original cells, were sensitized in vitro on macrophage monolayers that were pulsed either with the basic encephalitogenic protein of myelin or with the acidic copolymer poly(Glu50,Tyr50). Cells eluted from glass bead columns(i.e., the more negative cells) could be sensitized only with the basic antigen, while cells eluted from poly(L-lysine)-glass bead columns (i.e., more positive cells) could be sensitized only to the acidic antigen. Thus, in delayed type hypersensitivity the inverse charge relationship prevails also for the primary immunological recognition of antigen bound to macrophages.
Characterisation of blood-derived exosomal hTERT mRNA secretion in cancer patients: a potential pan-cancer marker (2017)

Human telomerase reverse transcriptase mRNA levels may reflect the tumour burden and the clinical status of the patient. In patients with detectable levels, this assay may potentially serve as a diagnostic and follow-up 'pan-cancer' marker. Owing to the large variety of patients and small sample size in each diagnosis, the statistical power is limited and will be explored further in larger groups.
A biomarker of n−3 compliance in patients taking fish oil for rheumatoid arthritis (2003)

Dietary fish oil supplements have been shown to have benefits in rheumatoid arthritis (RA), other inflammatory diseases, and in cardiovascular disease. As with any medical advice, variability will exist with regard to adherence and consequent biochemical or pharmacophysiologic effects. The aim was to explore the utility of plasma phospholipid EPA as a measure of n-3 PUFA intake and response to standardized therapeutic advice given in an outpatient or office practice setting, to increase dietary n-3 PUFA, including a fish oil supplement. Patients with early RA were given verbal and written advice to alter their dietary n-3 PUFA intake, including ingestion of 20 mL of bottled fish oil on juice daily. The advice included instructions to increase n-3 PUFA and to avoid foods rich in n-6 PUFA. Every 3 mon, blood samples were obtained for analysis of plasma phospholipid FA. Plasma phospholipid EPA was used as the primary index of n-3 PUFA intake. A diverse response was seen, with about one-third of patients achieving a substantial elevation of plasma phospholipid EPA over the 12-mon study period. A third had little change, with the remainder achieving intermediate levels. Data obtained longitudinally from individual patients indicated that substantial elevations of EPA (> 5% total plasma phospholipid FA) could be maintained for more than 3 yr. Plasma phospholipid EPA is a convenient measure of adherence to advice to take a dietary n-3 PUFA-rich fish oil supplement This measure may prove a useful adjunct to intention to treat analyses in determining the effect of dietary fish oil supplements on long-term outcomes in arthritis and other chronic inflammatory diseases. It may also provide a guide to the effectiveness of therapeutic and preventive messages designed to increase n-3 PUFA intake.
Copper deterioration in a water distribution system of a county hospital in Germany caused by microbially induced corrosion – I. Description of the problem (1992)

Abstract A severe copper corrosion process in the water distribution system of a County Hospital has been detected in the cold and warm water sections shortly after the opening of the Hospital. The damaged copper pipes showed pitting corrosion phenomena that could not be attributed to known types of pitting. The results of a first sampling revealed the same kind of corrosion in all installation areas. A thorough examination of the samples (perforations and hole depths) proved an influence of design and operating conditions on the extent of corrosion. The analysis of the corrosion products showed that some products could be attributed to microbial activities in the copper pipes. A polymeric layer, the so‐called “biofi”, could be detected beneath the corrosion products. The presence of a biofilm indicates microbially induced corrosion. First countermeasures are being taken in the County Hospital to prevent further damages.
Disintegration of Solid Foods in Human Stomach (2008)

Knowledge of the disintegration of solid foods in human stomach is essential to assess the bioavailability of nutrients in the gastrointestinal (GI) tract. A comprehensive review of food gastric digestion, focusing on disintegration of solid foods, is presented. Most of the research reviewed in this paper is contained in the medical, pharmaceutical, food, and nutritional literature. Stomach physiology is briefly introduced, including composition and rheological properties of gastric contents, stomach wall motility in fed/fasted states, and hydrodynamic and mechanical forces that act on the ingested food. In vivo and in vitro methods used for studying food and drug digestion in GI are summarized. Stomach emptying rate, which controls the rate of absorption of nutrients, is highly related to the disintegration of foods. This topic is highlighted with focus on the important mechanisms and the influence of chemical and physical properties of foods. Future research in this area is identified to increase our fundamental understanding of the food digestion process in the stomach as related to the food composition, material properties such as texture and microstructure, and chemical characteristics. This information is necessary to develop new guidelines for seeking innovative processing methods to manufacture foods specifically targeted for health.
METLIN (2005)

Endogenous metabolites have gained increasing interest over the past 5 years largely for their implications in diagnostic and pharmaceutical biomarker discovery. METLIN (http://metlin.scripps.edu), a freely accessible web-based data repository, has been developed to assist in a broad array of metabolite research and to facilitate metabolite identification through mass analysis. METLINincludes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrometry (MS/MS) spectra, and LC/MS data.
Poly(ethylene glycol) Carbodiimide Coupling Reagents for the Biological and Chemical Functionalization of Water-Soluble Nanoparticles (2009)

Many types of metal and semiconductor nanoparticles (NPs) are created via colloidal synthetic methods, which renders the materials hydrophobic. Such NPs are dispersed in water through surface organic cap exchange or by amphiphilic polymer encapsulation; often, water solubility is achieved via the presence of carboxylic acid functionalities on the solubilizing agents. While this renders the material water-soluble, subsequent functionalization of the systems can be very difficult. The most obvious method to derivatize carboxylic acid coated NPs is to conjugate chemical and biological moieties containing amine functionality to the NP surface using the water-soluble activator 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC). However, the excess use of this reagent appears to cause complete and permanent precipitation of the NPs. We report here our method on the chemical and biological functionalization of a variety of semiconductor nanoparticle systems using novel carbodiimide reagents. These reagents do not cause precipitation even at high loading levels and can be used to efficiently functionalize carboxylic acid coated NPs.
Another Unusual Type of Citric Acid Cycle Enzyme in Helicobacter pylori : the Malate:Quinone Oxidoreductase (2000)

The only enzyme of the citric acid cycle for which no open reading frame (ORF) was found in the Helicobacter pylori genome is the NAD-dependent malate dehydrogenase. Here, it is shown that in this organism the oxidation of malate to oxaloacetate is catalyzed by a malate:quinone oxidoreductase (MQO). This flavin adenine dinucleotide-dependent membrane-associated enzyme donates electrons to quinones of the electron transfer chain. Similar to succinate dehydrogenase, it is part of both the electron transfer chain and the citric acid cycle. MQO activity was demonstrated in isolated membranes of H. pylori. The enzyme is encoded by the ORF HP0086, which is shown by the fact that expression of the HP0086 sequence from a plasmid induces high MQO activity in mqo deletion mutants of Escherichia coli or Corynebacterium glutamicum. Furthermore, this plasmid was able to complement the phenotype of the C. glutamicum mqo deletion mutant. Interestingly, the protein predicted to be encoded by this ORF is only distantly related to known or postulated MQO sequences from other bacteria. The presence of an MQO shown here and the previously demonstrated presence of a 2-ketoglutarate:ferredoxin oxidoreductase and a succinyl-coenzyme A (CoA):acetoacetyl-CoA transferase indicate that H. pylori possesses a complete citric acid cycle, but one which deviates from the standard textbook example in three steps.
Isolation of Human Induced Pluripotent Stem Cell-Derived Dopaminergic Progenitors by Cell Sorting for Successful Transplantation (2014)

Human induced pluripotent stem cells (iPSCs) can provide a promising source of midbrain dopaminergic (DA) neurons for cell replacement therapy for Parkinson's disease. However, iPSC-derived donor cells inevitably contain tumorigenic or inappropriate cells. Here, we show that human iPSC-derived DA progenitor cells can be efficiently isolated by cell sorting using a floor plate marker, CORIN. We induced DA neurons using scalable culture conditions on human laminin fragment, and the sorted CORIN(+) cells expressed the midbrain DA progenitor markers, FOXA2 and LMX1A. When transplanted into 6-OHDA-lesioned rats, the CORIN(+) cells survived and differentiated into midbrain DA neurons in vivo, resulting in significant improvement of the motor behavior, without tumor formation. In particular, the CORIN(+) cells in a NURR1(+) cell-dominant stage exhibited the best survival and function as DA neurons. Our method is a favorable strategy in terms of scalability, safety, and efficiency and may be advantageous for clinical application.
Mutations affecting the cardiovascular system and other internal organs in zebrafish (1996)

In a screen for early developmental mutants of the zebrafish, we have identified mutations specifically affecting the internal organs. We identified 53 mutations affecting the cardiovascular system. Nine of them affect specific landmarks of heart morphogenesis. Mutations in four genes cause a failure in the fusion of the bilateral heart primordia, resulting in cardia bifida. In lonely atrium, no heart venticle is visible and the atrium is directly fused to the outflow tract. In the overlooped mutant, the relative position of the two heart chambers is distorted. The heart is enormously enlarged in the santa mutant. In two mutants, scotch tape and superglue, the cardiac jelly between the two layers of the heart is significantly reduced. We also identified a number of mutations affecting the function of the heart. The mutations affecting heart function can be subdivided into two groups, one affecting heart contraction and another affecting the rhythm of the heart beat. Among the contractility group of mutants are 5 with no heart beat at all and 15 with a reduced heart beat of one or both chambers. 6 mutations are in the rhythmicity group and specifically affect the beating pattern of the heart. Mutations in two genes, bypass and kurzschluss, cause specific defects in the circulatory system. In addition to the heart mutants, we identified 23 mutations affecting the integrity of the liver, the intestine or the kidney. In this report, we demonstrate that it is feasible to screen for genes specific for the patterning or function of certain internal organs in the zebrafish. The mutations presented here could serve as an entry point to the establishment of a genetic hierarchy underlying organogenesis.
How and why do root apices sense light under the soil surface? (2015)

Light can penetrate several centimeters below the soil surface. Growth, development and behavior of plant roots are markedly affected by light despite their underground lifestyle. Early studies provided contrasting information on the spatial and temporal distribution of light-sensing cells in the apical region of root apex and discussed the physiological roles of plant hormones in root responses to light. Recent biological and microscopic advances have improved our understanding of the processes involved in the sensing and transduction of light signals, resulting in subsequent physiological and behavioral responses in growing root apices. Here, we review current knowledge of cellular distributions of photoreceptors and their signal transduction pathways in diverse root tissues and root apex zones. We are discussing also the roles of auxin transporters in roots exposed to light, as well as interactions of light signal perceptions with sensing of other environmental factors relevant to plant roots.
Inhibition of HIV-1 replication and reactivation from latency by tat transdominant negative mutants in the cysteine rich region. (1996)

Tat mutants (tat22, tat37 and tat22/37) were constructed in the transactivation domain, where cysteines at positions 22 or/and 37 were substituted with glycine and serine, respectively. These mutants were expressed either in a BK virus episomal vector or in the retroviral vector LXSN. Constitutive production of tat22 by Jurkat T cells in the context of both vectors blocked HIV-1 replication during lytic infection. Conversely, the tat37 mutant did not show any inhibitory activity and tat22/37 displayed a mild effect on HIV-1 infection only when expressed by the recombinant retrovirus. However, constitutive production of tat22/37 by the BK virus vector in Jurkat T cells chronically infected by HIV-1 was effective in blocking reactivation of viral replication induced by tumor necrosis factor-alpha or human herpesvirus-6. These results suggest that mutants in the transactivation domain of tat may be considered in designing alternative strategies to control HIV-1 replication and reactivation from latency during different phases of infection.