gebhart/patrepeval huggingface dataset:
Effect of distance between decaying <sup>125</sup> I and DNA on Auger-electron induced double-strand break yield (2012)

These results suggest that at a critical distance between the (125)I atom and the DNA helix, DSB production switches from an 'all' direct to an 'all' indirect mechanism, the latter situation being comparable to the decay of (125)I free in solution. These experimental findings were correlated with theoretical expectations based on microdosimetry.
Retooling the Ethanol Industry: Thermophilic Anaerobic Digestion of Thin Stillage for Methane Production and Pollution Prevention (2008)

Anaerobic digestion of corn ethanol thin stillage was tested at thermophilic temperature (55 degrees C) with two completely stirred tank reactors. The thin stillage wastestream was organically concentrated with 100 g/L total chemical oxygen demand and 60 g/L volatiles solids and a low pH of approximately 4.0. Steady-state was achieved at 30-, 20-, and 15-day hydraulic retention times (HRTs) and digester failure at a 12-day HRT. Significant reduction of volatile solids was achieved, with a maximum reduction (89.8%) at the 20-day HRT. Methane yield ranged from 0.6 to 0.7 L methane/g volatile solids removed during steady-state operation. Effluent volatile fatty acids below 200 mg/L as acetic acid were achieved at 20- and 30-day HRTs. Ultrasonic pretreatment was used for one digester, although no significant improvement was observed. Ethanol plant natural gas consumption could be reduced 43 to 59% with the methane produced, while saving an estimated $7 to $17 million ($10 million likely) for a facility producing 360 million L ethanol/y.
Altered Expression of Diabetes-Related Genes in Alzheimer's Disease Brains: The Hisayama Study (2013)

Diabetes mellitus (DM) is considered to be a risk factor for dementia including Alzheimer's disease (AD). However, the molecular mechanism underlying this risk is not well understood. We examined gene expression profiles in postmortem human brains donated for the Hisayama study. Three-way analysis of variance of microarray data from frontal cortex, temporal cortex, and hippocampus was performed with the presence/absence of AD and vascular dementia, and sex, as factors. Comparative analyses of expression changes in the brains of AD patients and a mouse model of AD were also performed. Relevant changes in gene expression identified by microarray analysis were validated by quantitative real-time reverse-transcription polymerase chain reaction and western blotting. The hippocampi of AD brains showed the most significant alteration in gene expression profile. Genes involved in noninsulin-dependent DM and obesity were significantly altered in both AD brains and the AD mouse model, as were genes related to psychiatric disorders and AD. The alterations in the expression profiles of DM-related genes in AD brains were independent of peripheral DM-related abnormalities. These results indicate that altered expression of genes related to DM in AD brains is a result of AD pathology, which may thereby be exacerbated by peripheral insulin resistance or DM.
Degradation of lipoproteins by human monocyte-derived macrophages. Evidence for two distinct processes for the degradation of abnormal very-low-density lipoprotein from subjects with type III hyperlipidaemia (1984)

Human blood monocyte-derived macrophages that had been cultured in medium containing human serum for 7 days degraded the abnormal very-low-density lipoproteins (VLDL) from the plasma of subjects with type III hyperlipoproteinaemia by two distinct saturable processes. One process was stimulated when cells from normal subjects were preincubated with lipoprotein-free medium, was inhibited by excess unlabelled low-density lipoproteins (LDL) and was absent from cells from subjects with homozygous familial hypercholesterolaemia; on these criteria it was identified as an LDL-receptor-dependent process. Degradation by the second process was of equal magnitude in both cell types and was unaffected by excess unlabelled LDL or acetylated LDL. The activity of this process was reduced when the cells were preincubated in lipoprotein-free medium. The abnormal VLDL from the plasma of cholesterol-fed rabbits were also degraded by this process, which was similar to that in mouse peritoneal macrophages mediated by the receptor for VLDL of beta-electrophoretic mobility [Goldstein, Ho, Brown, Innerarity & Mahley (1980) J. Biol. Chem. 255, 1839-1848].
Active Surveillance Using Dynamic Background Subtraction (1996)

A prototype active surveillance system is presented. The system has two cameras, one of which is rigidly fixed &amp; has a wide angle lenses while the other is mounted on a pan-tilt head &amp; has a zoomed lenses. The images from the wide angle camera are analyzed using dynamic background subtraction together with normalized cross correlation in order to identify moving people within the scene. An approximate mapping is determined (off-line) between the pan-tilt angles and the position of the zoomed image within the wide-angle view. This mapping is improved (for each frame) through 1-D image based correlation and hence moving people are located in the zoomed view. The system has been tested on a difficult real-world scene and image sequences from both cameras are presented. The potential of the system as an `intelligent&apos; security device and the power of the dynamic background subtration &amp; correlation mechanism are clearly demonstrated. Keywords: Active vision, Surveillance, Motion tracking A...
CARM1 Is an Important Determinant of ERα-Dependent Breast Cancer Cell Differentiation and Proliferation in Breast Cancer Cells (2011)

Breast cancers with estrogen receptor α (ERα) expression are often more differentiated histologically than ERα-negative tumors, but the reasons for this difference are poorly understood. One possible explanation is that transcriptional cofactors associated with ERα determine the expression of genes which promote a more differentiated phenotype. In this study, we identify one such cofactor as coactivator-associated arginine methyltransferase 1 (CARM1), a unique coactivator of ERα that can simultaneously block cell proliferation and induce differentiation through global regulation of ERα-regulated genes. CARM1 was evidenced as an ERα coactivator in cell-based assays, gene expression microarrays, and mouse xenograft models. In human breast tumors, CARM1 expression positively correlated with ERα levels in ER-positive tumors but was inversely correlated with tumor grade. Our findings suggest that coexpression of CARM1 and ERα may provide a better biomarker of well-differentiated breast cancer. Furthermore, our findings define an important functional role of this histone arginine methyltransferase in reprogramming ERα-regulated cellular processes, implicating CARM1 as a putative epigenetic target in ER-positive breast cancers.
Tunneling of Dirac electrons through spatial regions of finite mass (2008)

We study the tunneling of chiral electrons in graphene through a region where the electronic spectrum changes from the usual linear dispersion to a hyperbolic dispersion, due to the presence of a gap. It is shown that contrary to the tunneling through a potential barrier, the transmission of electrons is, in this case, smaller than one for normal incidence. This mechanism may be useful for designing electronic devices made of graphene.
Feasibility of Intelligent Control Strategies to Reduce Cooling System Size (2001)

<div class="htmlview paragraph">As specific engine power output increases so does the heat rejected to the coolant. The resulting need to increase radiator size is counter-productive due to the lack of package space, and a strong desire to reduce, not increase, vehicle drag. Current tendency is to size the radiator to reject sufficient heat at extreme operating conditions (full engine power, high ambient). However, this “oversized” cooling system may only be needed by a small number of vehicles. A better approach could be to size the radiator for the majority, but not all, operational conditions and manage the coolant temperature by actively controlling coolant flow and engine output. This will need to be done without compromising durability or driveability. This approach sounds highly beneficial in principle, but how sound would it be in practice ? The authors have investigated the feasibility of active control by considering the details of radiator performance and engine heat rejection. A simulation model representing a minivan type vehicle has been created. This model is capable of analyzing the effect of active control on coolant temperature under different vehicle operating conditions. The paper shows that there is indeed merit in deploying active control of the cooling system.</div>
Comparative genomic hybridization detects novel deletions and amplifications in head and neck squamous cell carcinomas. (1995)

To gain a better understanding of genetic changes in squamous cell carcinomas of the head and neck we used comparative genomic hybridization for the analysis of 13 primary tumors. Copy number increases were most frequently observed on chromosomes 3q (10 cases) and 5p (8 cases) and less frequently on 1q (4 cases), 2 (1 case), 7 (2 cases), 8q (2 cases), 9 (1 case), 10p (2 cases), 13q (2 cases), 14q (1 case), 16 (1 case), 17 (2 cases), 20p (2 cases), 21q (1 case) and 22q (1 case). Copy number decreases occurred most frequently at 3p (5 cases), 5q (4 cases), 19p (6 cases), and 19q (5 cases). Copy number decreases also were observed on 1p (2 cases), 2q (2 cases), 4p (2 cases), 4q (2 cases), 7q (2 cases), 8p (1 case), 10q (1 case), 11p (2 cases), 11q (3 cases), 13q (3 cases), 14q (1 case), 16p (1 case), 17p (3 cases), 17q (1 case), 18q (1 case), and 22 (2 cases). Eight sites exhibiting significant sequence amplification were mapped to 3q26-->qter (3 cases), 11q13 (2 cases), 12p (2 cases), 2q33-36 (1 case), 7q21-22 (1 case), 7q33-->qter (1 case), 9p (1 case), and 13q32-->qter (1 case). Our data suggest that the regions 3q26-->qter and 5p may harbor oncogenes important for initiation or progression of squamous cell carcinomas of the head and neck. In addition, comparative genomic hybridization defines a subgroup of tumors with 11q13 involvement, the location of the PRAD1/(CCND1)/cyclin D1 gene.
Three-dimensional simulation for urban warming in Tokyo and proposal of an environmental index for urban outdoor comfort (2002)

According to a computer simulation for urban warming in the Tokyo metro area in 2031, the maximum ambient temperature in the evening (18:00) at Otemachi will exceed 42/spl deg/C. In contrast to the interior thermal comfort in residential and office buildings, the urban outdoor comfort is strongly affected by intense thermal radiation coming from the surface of the structures, as well as solar radiation. Motivated by the above facts, we propose a new standard effective temperature index (USET*), which is applicable to evaluate urban thermal comfort. By using this thermal comfort index, assessment of the urban environment can be made for both present Tokyo and Tokyo around 2030. Furthermore, it is suggested that a comprehensive urban environmental index (UEI), which includes pollutants and ultraviolet rays, might be adopted for the future urban environment.
Cavity wound management (1993)

A guide to patient assessment, wound classification and dressing choice in the management of cavity wounds.
Crystal Structure of the Rat Liver Fructose-2,6-bisphosphatase Based on Selenomethionine Multiwavelength Anomalous Dispersion Phases<sup>,</sup> (1996)

The crystal structure of the recombinant fructose-2,6-bisphosphatase domain, which covers the residues between 251 and 440 of the rat liver bifunctional enzyme, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, was determined by multiwavelength anomalous dispersion phasing and refined at 2.5 A resolution. The selenomethionine-substituted protein was induced in the methionine auxotroph, Escherichia coli DL41DE3, purified, and crystallized in a manner similar to that of the native protein. Phase information was calculated using the multiwavelength anomalous dispersion data collected at the X-ray wavelengths near the absorption edge of the K-shell alpha electrons of selenium. The fructose-2,6-bisphosphatase domain has a core alpha/beta structure which consists of six stacked beta-strands, four parallel and two antiparallel. The core beta-sheet is surrounded by nine alpha-helices. The catalytic site, as defined by a bound phosphate ion, is positioned near the C-terminal end of the beta-sheet and close to the N-terminal end of an alpha-helix. The active site pocket is funnel-shaped. The narrow opening of the funnel is wide enough for a water molecule to pass. The key catalytic residues, including His7, His141, and Glu76, are near each other at the active site and probably function as general acids and/or bases during a catalytic cycle. The inorganic phosphate molecule is bound to an anion trap formed by Arg6, His7, Arg56, and His141. The core structure of the Fru-2,6-P2ase is similar to that of the yeast phosphoglycerate mutase and the rat prostatic acid phosphatase. However, the structure of one of the loops near the active site is completely different from the other family members, perhaps reflecting functional differences and the nanomolar range affinity of Fru-2,6-P2ase for its substrate. The imidazole rings of the two key catalytic residues, His7 and His141, are not parallel as in the yeast phosphoglycerate mutase. The crystal structure is used to interpret the existing chemical data already available for the bisphosphatase domain. In addition, the crystal structure is compared with two other proteins that belong to the histidine phosphatase family.
Heat Dissipation, Gas Exchange and Acid-Base Status in the Land Snail<i>Oreoheux</i>During Short-Term Estivation (1990)

ABSTRACT Within 4 days following entry into estivation, heat dissipation and oxygen consumption by the land snail Oreohelix spp. decreased by 83% compared to standard non-estivating rates. During both non-estivating and estivating conditions, the quantity of heat dissipated per mole of O2 consumed was indicative of a completely aerobic metabolism. This calorimetric-respirometric (C/R) ratio was –461 ±12 kJ mol−1O2 (S.E.M., N=5) under standard non-estivating conditions and –464±26kJmol−1O2 (N=4) during estivation. Respiratory exchange ratios reflected a primary dependence upon carbohydrate as a metabolic substrate during both states. Carbon dioxide retention occurred during the first 36h of estivation, resulting in an increase in hemolymph and a decrease in pH. The respiratory acidosis during short-term estivation was not compensated by elevation of hemolymph [HCO3−] above levels predicted from the in vitro non-bicarbonate buffer value of hemolymph. A brief period of rapid CO2 release, which caused hemolymph and pH to return to pre-estivation values, preceded the increase in O2 consumption during arousal. Exposure of nonestivating snails to 4.67 kPa (1 kPa=7.5mmHg) caused a rapid and fully reversible 50% suppression of respiration rate. The temporal nature of CO2 retention and release during entry into and arousal from estivation, and the suppression of O2 consumption by artificial hypercapnia, support the hypothesis that elevated or the resultant acidosis may contribute to metabolic suppression during estivation by land snails.
Optimizing Order Consolidation with Simulation Optimization (2017)

In this work we study the order consolidation process of an e-retailing warehouse using real data. Order consolidation is a process that follows the picking operation in a warehouse. After stock keeping units (SKUs) of an order are picked into possibly multiple totes, they are sorted and the SKUs are consolidated back into orders to be packed and shipped to customers. There are two main operations in order consolidation: wave sortation and putting. Wave sortation involves tote sequencing which is a major driver of how smooth the system runs. First, totes should be sequenced so that the work load is balanced. Second, totes that carry SKUs of the same order should be close in sequence in order to reduce order processing times, and to reduce resource utilization. At the same time, orders should be assigned to operators for putting in order to balance operator workload and to avoid recirculation. The assignment and sequencing of totes, when assuming known and constant tote induction times and when the goal is total completion time, is a problem similar to parallel machine scheduling. However, the goal from order consolidation is minimizing order, as opposed to tote, consolidation times. Order consolidation also depends on the putting operation. Moreover, processing times are uncertain and may vary because of different sizes and weights of SKUs and because of variations in manual and automatic processes. In order to reflect a realistic system performance accurately, we need to take randomness into account when evaluating measures like order completion time, resource utilization, and congestion. In this thesis, we first build a simulation model for the consolidation process using a given tote assignment and sequencing. We use the empirical distributions derived from the data to run the simulation. Second, we develop a simulated annealing heuristic and apply it to solve the deterministic tote sequencing problem with the goal of minimizing order completion time or order processing time. Third, we develop a stochastic simulated annealing algorithm to optimize the whole consolidation process. The algorithm decides on tote assignment and sequencing and evaluates the sequences using the simulation model. We experimented with optimizing order completion times and SKU wait times for putting. Our approach is then a simulation optimization to optimize the consolidation process using different metrics. We report on numerical tests using real instances.
CXCL10 and its receptor CXCR3 regulate synovial fibroblast invasion in rheumatoid arthritis (2011)

We describe and characterize a new autocrine/paracrine role of CXCL10/CXCR3 in the regulation of FLS invasion in rats with arthritis and in RA patients. These observations suggest that the CXCL10/CXCR3 axis is a potential new target for therapies aimed at reducing FLS invasion and its associated joint damage and pannus invasion and destruction in RA.
Analog implementations of sampling detectors (1991)

The motivation for pursuing analog implementations of sampling detectors is presented. Two implementations, a Viterbi detector and a decision feedback equalizer, are described in detail at the block-diagram level. The issues of importance in the design of analog sampling detectors are discussed, and some circuit designs are presented. The concomitant problems of analog equalization and timing recovery are briefly addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Trans-signaling by cytokine and growth factor receptors (1996)

Although ligand-induced dimerization or oligomerization of receptors is a well established mechanism of growth factor signaling, increasing evidence indicates that biological responses are often mediated by receptor trans-signaling mechanisms involving two or more receptor systems. These include G protein-coupled receptors, cytokine, growth factor and trophic factor receptors. Greater responsiveness and inhibitory signaling responses are provided when different signaling pathways merge through receptor trans-signaling.
A new concept in the design of the LHC beam dump (2002)

Recent Monte Carlo cascade simulations have shown that a reduction in the maximum of deposited energy density can be obtained by applying a uniform magnetic field over a front part of the graphite core of the LHC dump. This paper shows the effect of field strength on spatial distributions of absorbed energy and temperatures, and discusses problems to be solved when designing a suitable magnet.
Neurodynamic control of the heart of freely moving spiny lobster (Panulirus japonicus) (2010)

The heart of the crustaceans has its own pacemaker neurons inside the heart, which are composed of 9 neurons. The neurons receive innervations of only three kinds of axons originated from the central nervous system; one pair of inhibitory and two pairs of acceleratory axons. Thus, in terms of the neural cardiac control from higher center, this system may have much more simplistic operation comparing to our hearts, because those vertebrate hearts receive hundreds of central nerve fibers so called the autonomic nervous system; sympathetic and parasympathetic nerves. This simplicity of the crustacean hearts may have a great advantage for physiological and physical understanding for the essential mechanism of the heartbeat control. Thus, we performed time series analysis of ECG data of Japanese spiny lobster, Panulirus japonicus. The ECGs were recorded in three conditions of the heart. The isolated hearts, which are obviously disconnected from the center but are well maintained at a steady condition, and the intact hearts, heartbeats of which were recorded at either a freely moving condition or a stressful condition receiving severe immobilizing stress. DFA (Detrended Fluctuation Analysis) revealed a difference of operation of the CNS. The three conditions of the hearts were found to have different scaling properties. Focusing on the difference between the scaling exponents of the isolated heart and the stressful heart, both of which had, intriguingly, almost identical power spectra, we will discuss the possibility to index the CNS operation by means of the scaling exponents.
Prospects and challenges of the development of lipoprotein-based formulations for anti-cancer drugs (2007)

This review evaluates drug delivery systems that involve intact plasma lipoproteins or some of their components. These complex macromolecules transport highly water-insoluble compounds (cholesteryl esters and triacylglycerols) in their natural environment - a property that renders them ideal carriers of hydrophobic drugs. Particular emphasis is placed on the application of lipoproteins as drug delivery agents in cancer chemotherapy. The history and present activity regarding lipoprotein-based formulations are reviewed, with the primary focus on the smaller sized (low and high density) lipoprotein-based formulations and their potential clinical and commercial value. The use of both native and synthetic lipoproteins as drug delivery agents are discussed from the standpoint of therapeutic efficacy, as well as commercial feasibility. The advantages of lipoprotein-based drug delivery formulations are compared with other drug delivery models, with the primary focus on liposomal preparations. Finally, an expert opinion is provided, regarding the potential use of lipoprotein-based formulations in cancer treatment, taking into consideration the major advantages (biocompatibility, safety, drug solubility) and the barriers (manufacturing protein components, financial interest, investments) to their commercial development.
Cloning and DNA Sequencing of the Genes Encoding <i>Clostridium josui</i> Scaffolding Protein CipA and Cellulase CelD and Identification of Their Gene Products as Major Components of the Cellulosome (1998)

The Clostridium josui cipA and celD genes, encoding a scaffolding-like protein (CipA) and a putative cellulase (CelD), respectively, have been cloned and sequenced. CipA, with an estimated molecular weight of 120,227, consists of an N-terminal signal peptide, a cellulose-binding domain of family III, and six successive cohesin domains. The molecular architecture of C. josui CipA is similar to those of the scaffolding proteins reported so far, such as Clostridium thermocellum CipA, Clostridium cellulovorans CbpA, and Clostridium cellulolyticum CipC, but C. josui CipA is considerably smaller than the other scaffolding proteins. CelD consists of an N-terminal signal peptide, a family 48 catalytic domain of glycosyl hydrolase, and a dockerin domain. N-terminal amino acid sequence analysis of the C. josui cellulosomal proteins indicates that both CipA and CelD are major components of the cellulosome.