gebhart/patrepeval huggingface dataset:
LOCALIZATION OF ANTIGEN IN TISSUE CELLS (1950)

The cytological distribution of the pneumococcal polysaccharides, types II and III, was followed in the tissues of the mouse. The most constant and striking concentrations of these polysaccharides were found in the cells of the reticulo-endothelial system, the ordinary capillary endothelium, and fibroblasts throughout the body. In addition, polysaccharide was detected in monocytes and lymphocytes, hepatic cells, cardiac and smooth muscle cells, uterine epithelium, and in steroid-forming cells in the adrenal cortex, testis, and ovary. Studies of the persistence of polysaccharide, type III, in the tissues were carried out after an injection of 4.0 mg. The polysaccharide remained for at least 75 days in the macrophages of lymphoid organs, the Kupffer cells of the liver, the interstitial macrophages in the myocardium, the lung septal cells, the capillary endothelium, and the renal glomerulus. After a single injection of 8 mg., it persisted for at least 6 months in the macrophages of the spleen, liver, and heart and in the endothelium of peritubular capillaries in the kidney. The smallest dose of polysaccharide which produced detectable amounts in any cells 24 hours after injection was 0.03 mg. The distribution of polysaccharide is compared with that of acid vital dyes and suspensoids, and the significance of its fixation in relation to its antigenicity and possible toxicity in mice is discussed.
DNA sequence‐specific adducts of adriamycin and mitomycin C (1989)

Adriamycin and mitomycin C were reduced by xanthine oxidase/NADH in the presence of a DNA template comprising a stable initiated ternary transcription complex derived from the lac UV5 promoter. Subsequent elongation of the transcription complex treated with mitomycin C revealed high levels of terminated transcripts one nucleotide prior to G residues on the coding strand (i.e. at X of XpC sequences of the non-coding strand). Lower levels of termination occurred with adriamycin, and these were also one nucleotide prior to G residues of the coding strand, but with greater sequence specificity since they were observed mainly at G of GpC sequences of the non-coding strand. The same sites were also observed with adriamycin in the absence of reducing conditions and the level of termination at these sites was enhanced up to 10-fold by Fe2+ and Fe3+, but not by Cu2+, Zn2+, Co2+ or Ni2+. These results suggest that an iron-adriamycin complex with DNA is highly sequence-specific and results in adducts, similar to those of mitomycin C, which can terminate the transcription process. Such a mechanism offers new insights into the possible mode of action of anthracyclines.
Expression of Prohibitin in Rat Seminiferous Epithelium1 (1993)

Subtractive hybridization was used to isolate cDNAs highly expressed in stages IX-XI of the cycle of the seminiferous epithelium in the rat. One of the cloned cDNAs was sequenced and shown to be homologous to a previously described cDNA encoding rat prohibitin. Northern blot analyses showed that 1.9- and 1.2-kb transcripts were present in Sertoli cells whereas 1.5-, 1.2-, and 0.7-kb transcripts were expressed in germ cells. Western blot analyses with anti-peptide antibody to prohibitin revealed only a single 30-kDa protein in testis. Immunocytochemistry demonstrated that prohibitin protein was expressed constitutively in adult Leydig cells and Sertoli cells at all stages. Immunoreactivity of prohibition was very low in preleptotene spermatocytes, very high in leptotene spermatocytes, and very low in zygotene spermatocytes. In pachytene spermatocytes, immunoreactivity was very high in stages VII-XI and was minimal during stages XII and XIV. No protein was detected in spermatogonia and spermatocytes undergoing mitotic and meiotic divisions, respectively. These studies show that the prohibitin gene is expressed differentially in testis. The expression pattern of the prohibitin gene in rat testis appears to correlate with a proposed antiproliferative role of prohibitin.
CO2 Capture by Means of an Enzyme‐Based Reactor (2003)

We report a means for efficient and selective extraction of carbon dioxide (CO(2)) at low to medium concentration from mixed gas streams. CO(2) capture was accomplished by use of a novel enzyme-based, facilitated transport contained liquid membrane (EBCLM) reactor. The parametric studies we report explore both structural and operational parameters of this design. The structural parameters include carbonic anhydrase (CA) concentration, buffer concentration and pH, and liquid membrane thickness. The operational parameters are temperature, humidity of the inlet gas stream, and CO(2) concentration in the feed stream. The data show that this system effectively captures CO(2) over the range 400 ppm to at least 100,000 ppm, at or around ambient temperature and pressure. In a single pass across this homogeneous catalyst design, given a feed of 0.1% CO(2), the selectivity of CO(2) versus N(2) is 1,090 : 1 and CO(2) versus O(2) is 790 :1. CO(2) permeance is 4.71 x 10(-8) molm(-2) Pa(-1) sec(-1). The CLM design results in a system that is very stable even in the presence of dry feed and sweep gases.
NH2-terminal arm of phage lambda repressor contributes energy and specificity to repressor binding and determines the effects of operator mutations. (1985)

Several lines of evidence indicate that the phage lambda repressor recognizes its operator by using, in part, an alpha helix (the "recognition helix"), which it inserts into the major groove of DNA. In addition to its recognition helix, lambda repressor has an "arm," consisting of the first six amino acids, that wraps around the DNA helix. We constructed plasmids that, in Escherichia coli, direct the expression of derivatives of lambda repressor that lack the NH2-terminal one, three, six, or seven amino acids. We studied these modified proteins in vivo and in vitro, and from our results we argue that the arm: contributes a large portion of the binding energy; helps to determine sequence specificity of binding and, in particular, the relative affinities for two wild-type binding sites; determines entirely repressor's response to one operator mutation (a "back-side" mutation); magnifies repressor's response to other operator mutations ("front-side" mutations); and increases the sensitivity of repressor binding to salt concentration and temperature.
Clamped-Clamped Beam Micro-Mechanical Resonators in Thick-Film Epitaxial Polysilicon Technology (2002)

This paper presents design and test results of clampedclamped beam resonators fabricated in thick-film epitaxial polysilicon technology. A new technique is used to achieve a 0.2 μm sensing electrod-to-resonator lateral gap in a structural polysilicon layer of 15 μm thickness. The frequencies of the designed resonators belong to the range of 2.3-16.4 MHz, the measured quality factors are of 450-15500 for different resonance frequencies.
Prostate cancer update: 2007 (2008)

The data of the present year have important implications in the diagnosis and management of prostate cancer by urologists, radiation oncologists, and medical oncologists.
Smart-NICs: Power Proxying for Reduced Power Consumption in Network Edge Devices (2008)

The number of edge devices connected to the Internet is increasing at a rapid rate. To maintain network connectivity, the majority of these devices remain completely powered on when idle, wasting unnecessary energy. A novel idea to conserve energy while maintaining network connectivity is to place the computer in standby mode during idle periods and delegate the packet-handling functions to its network interface card (NIC). The NIC, acting as a liaison for the host, can proxy a variety of network protocols, increasing the standby time of the host without compromising its active connections. In this paper, we analyze the requirements of such a packet classifier and design a low-power hardware-based packet classification technique, which, compared to a software-based packet classification technique, consumes 59% less energy with a 9x speedup.
Research on Antiviral Agents. 5. Lithiation of 6-Methyluracil as a New and Efficient Entry to C(6)-Substituted Uracils (1996)

Synthesis of numerous C(6)-substituted untcils can be effected by lithiation of N(1).N(3)-substihlted dmethyluracils ( 1) and (4) with LiHMDS, followed by the reaction of the resulting lithio derivatives with carbon, sulfur, and selenium elecmphiles.The unexpected migration of the N(1)-benzoyl group in the metalation-alkylation and the high stemselectivity obtained in the reaction with substituted cyclohexanones are also reported In spite of s e v e d syntheses described in literature2 for the preparation of uracil derivatives, little attention has been paid to the synthesis and the chemistry of 6-substituted uracils, mainly because of the following reasons: i) 6-substituted uracils are not good substrates towards N-1 glycosylation procedures to obtain 6substituted nucleosides;3 ii) 6-substituted uracils are not substrates for the enzymes involved in neoplastic diseases?and iii) 6-substituted uracils are not prepared in good yields using the general methods reported for other uracil derivative^.^Recently the chemistry of 6-substituted uracils has been subjected to renewed interest, due to the unexpected antiviral activity shown by some of these compounds; as for example, 142-
Expression of insulin-like growth factor II mRNA-binding protein 3 predicts early recurrence and poor prognosis in intrahepatic cholangiocarcinoma (2012)

IMP3 expression can serve as a novel maker for ETR and prognostic prediction, and may be a target for adjuvant therapy of patients with ICC after tumor resection.
Nonlinearity of Heart Rate in the Neonate (1995)

The relationship between heart rate variability and level of illness was examined. Fifteen patients (10 male and 5 female), gestational ages 25 to 42 weeks, postnatal ages 1 to 42 days, birthweights 545 to 4375 g receiving care in the neonatal intensive care nursery were randomly selected. Data from each infant was transferred from the bedside physiologic monitor to a microcomputer for analysis. A severity of illness index (the Children's Hospital Illness Score [CHILLS]) correlated with heart rate variability. Four patterns of heart rate variability were identified: (1) infants whose CHILLS score indicated that they were cardiovascularly normal demonstrated a modest amount of variability; (2) infants with a CHILLS score indicating a moderate amount of illness had heart rates and heart rate variability greater than the normal infants; (3) three infants exhibited bimodality (period doubling) in their heart rates; each of these infants had a CHILLS score that indicated that they were less ill than the most critically ill patients, but sicker than those moderately ill infants without period doubling; and (4) heart rate decreased in the most critically ill infants identified by the CHILLS, but it remained above the heart rate of a healthy newborn; heart rate variability collapsed below that of a healthy newborn. Our data suggest that the variability of heart rate may increase as an infant becomes sicker. When the infant becomes critically ill and unstable, heart rate variability is less than the normal infant. Nonlinear dynamics theory may be a potential model for fitting the data.
A meta-analysis of association between acne vulgaris and Demodex infestation (2012)

Until now, etiology of acne vulgaris is still uncertain. Although clinicians usually deny the association between Demodex infestation and acne vulgaris, it has been proved in some clinical practices. To confirm the association between Demodex infestation and acne vulgaris, a meta-analysis was conducted. Predefined selection criteria were applied to search all published papers that analyzed the association between Demodex infestation and acne vulgaris (January 1950 to August 2011) in ISI Web of Knowledge, MEDLINE, and China National Knowledge Infrastructure (CNKI) databases. A meta-analysis was performed to calculate odds ratios (ORs) and 95% confidence intervals (CIs) based on fixed effects models or random effects models. We enrolled the 60 Chinese and 3 English papers in this meta-analysis, which covered Turkey and 25 different provinces/municipalities in China and 42130 participants including students and residents, aged from 1 to 78 years. The pooled OR in random effects models is 2.80 (95% CI, 2.34-3.36). Stability is robust according to sensitivity analysis. The fail-safe number is 18477, suggesting that at least 18477 articles with negative conclusions would be needed to reverse the conclusion that acne vulgaris was related to Demodex infestation. So the effect of publication bias was insignificant and could be ignored. It was concluded that acne vulgaris is associated with Demodex infestation. This indicates that when regular treatments for acne vulgaris are ineffective, examination of Demodex mites and necessary acaricidal therapies should be considered.
Ion beam assisted coating and surface modification with plasma source ion implantation (1990)

Plasma source ion implantation (PSII) is a non-line-of-sight technique which is being developed as an alternative to beamline accelerator technology for ion implantation. The initial development phase of PSII concentrated on implantation of ion species which are gaseous at room temperature (primarily nitrogen ions) and employed a cylindrical vacuum chamber 16 in. high and 14 in. in diameter. A second generation PSII system is being constructed to extend the PSII process to ion beam mixing and ion beam assisted coating modes of operation. The new, larger system (with dimensions 36×36×36 in.) will feature multiple-array sources for sputter deposition concurrent with ion bombardment.
Role of Saccharomyces cerevisiae ISA1 and ISA2 in Iron Homeostasis (2000)

The budding yeast Saccharomyces cerevisiae contains two homologues of bacterial IscA proteins, designated Isa1p and Isa2p. Bacterial IscA is a product of the isc (iron-sulfur cluster) operon and has been suggested to participate in Fe-S cluster formation or repair. To test the function of yeast Isa1p and Isa2p, single or combinatorial disruptions were introduced in ISA1 and ISA2. The resultant isaDelta mutants were viable but exhibited a dependency on lysine and glutamate for growth and a respiratory deficiency due to an accumulation of mutations in mitochondrial DNA. As with other yeast genes proposed to function in Fe-S cluster assembly, mitochondrial iron concentration was significantly elevated in the isa mutants, and the activities of the Fe-S cluster-containing enzymes aconitase and succinate dehydrogenase were dramatically reduced. An inspection of Isa-like proteins from bacteria to mammals revealed three invariant cysteine residues, which in the case of Isa1p and Isa2p are essential for function and may be involved in iron binding. As predicted, Isa1p is targeted to the mitochondrial matrix. However, Isa2p is present within the intermembrane space of the mitochondria. Our deletion analyses revealed that Isa2p harbors a bipartite N-terminal leader sequence containing a mitochondrial import signal linked to a second sequence that targets Isa2p to the intermembrane space. Both signals are needed for Isa2p function. A model for the nonredundant roles of Isa1p and Isa2p in delivering iron to sites of the Fe-S cluster assembly is discussed.
Specific Labeling of Polypeptides at Amino-Terminal Cysteine Residues Using Cy5-benzyl Thioester (2002)

Even for moderately sized proteins, the multiple occurrence of cysteine and lysine residues often prevents the specific labeling of polypeptides with a single probe. To increase specificity, a method was developed to convert the commonly available succinimidyl esters of fluorescent dyes into benzyl thioesters via trimethyl aluminum-activated benzyl mercaptan. The thioester can then be reacted very specifically with polypeptides containing an N-terminal cysteine residue, forming a stable amide bond, analogous to the native chemical ligation of peptide fragments. Both reaction steps are easy to perform and proceed to high yields. The practicability of the approach was demonstrated using the popular cyanine dye Cy5 and a soluble peptide, and it is expected to be applicable to a wide range of succinimidyl esters and both chemically and recombinantly synthesized proteins. The method should dramatically facilitate the preparation of proteins for experiments requiring exact positioning of labels, for instance, Förster resonance energy transfer studies.
Sequence γ377−395(P2), but Not γ190−202(P1), Is the Binding Site for the αMI-Domain of Integrin αMβ2 in the γC-Domain of Fibrinogen (2003)

The interaction between the leukocyte integrin alpha(M)beta(2) (CD11b/CD18, Mac-1, CR3) and fibrinogen mediates the recruitment of phagocytes during the inflammatory response. Previous studies demonstrated that peptides P2 and P1, duplicating gamma 377-395 and gamma 190-202 sequences in the gamma C domain of fibrinogen, respectively, blocked the fibrinogen-binding function of alpha(M)beta(2), implicating these sequences as possible binding sites for alpha(M)beta(2). To determine the role of these sequences in integrin binding, recombinant wild-type and mutant gamma C domains were prepared, and their interactions with the alpha(M)I-domain, a ligand recognition domain within alpha(M)beta(2), were tested. Deletion of gamma 383-411 (P2-C) and gamma 377-411 produced gamma C mutants which were defective in binding to the alpha(M)I-domain. In contrast, alanine mutations of several residues in P1 did not affect alpha(M)I-domain binding, and simultaneous mutations in P1 and deletion of P2 did not decrease the binding function of gamma C further. Verifying the significance of P2, inserting P2-C and the entire P2 into the homologous position of the beta C-domain of fibrinogen imparted the higher alpha(M)I-domain binding ability to the chimeric proteins. To further define the molecular requirements for the P2-C activity, synthetic peptides derived from P2-C and a peptide array covering P2-C have been analyzed, and a minimal recognition motif was localized to gamma(390)NRLTIG(395). Confirming a critical role of this sequence, the cyclic peptide NRLTIG retained full activity inherent to P2-C, with Arg and Leu being important residues. Thus, these data demonstrate the essential role of the P2, but not P1, sequence for binding of gamma C by the alpha(M)I-domain and suggest that the adhesive function of P2 depends on the minimal recognition motif NRLTIG.
Physical linkage of the constant region genes for immunoglobulins lambda I and lambda III. (1981)

During differentiation from a stem cell to an antibody-secreting cell, the immunoglobulin genes within a B cell undergo a rearrangement that juxtaposes a variable region gene to a constant region gene. To analyze the genetic organization of an immunoglobulin gene family in nonrearranged, germ-line DNA, we have constructed a recombinant DNA library from randomly cleaved mouse kidney DNA fragments. From this library, we have isolated three overlapping recombinant clones containing the constant region gene for lambda I light chains (C lambda I). These clones spanned 24.9 kilobases of mouse DNA and contained no variable region sequences. Hybridization of these clones with lambda II cDNA demonstrated the presence of an additional constant region gene and a joining region 3.2 kilobases 5' of C lambda I. This gene was tentatively identified as C lambda III by the absence of an Ava I endonuclease site, which is present within C lambda II. The C lambda III amino acid sequence has recently been reported [Azuma, T., Steiner, L. A. & Eisen, H. N. (1981) Proc. Natl. Acad. Sci. USA 78, 569-573] and is very closely related to the C lambda II amino acid sequence.
Effect of growth hormone on osteoblasts and demonstration of somatomedin-C/IGF I in bone organ culture (1984)

Bone organ culture makes it possible to observe the direct influence of hormones on bone cells. We studied the effect of growth hormone in vitro on embryonal rat tibiae during culture for 7 days, functionally by measuring the levels of alkaline phosphatase in the culture medium, and morphologically by means of semi-thin sections and electron microscopic examination. Since growth hormone (GH) is supposed to exert an indirect effect on bone cells, somatomedin-C/insulin-like growth factor I (SM-C/IGF I) as a possible mediator was also measured radioimmunologically in the culture medium. In the controls alkaline phosphatase levels showed a continuous increase up to the 7th day which was significantly higher in the presence of GH. There was also a significantly enhanced increase of SM-C/IGF I in the presence of GH during culture in comparison to the controls. Evidently IGF I is produced locally in bone and mediates the effect of GH on bone formation.
Stereopsis-guided brain shift compensation (2005)

Brain deformation models have proven to be a powerful tool in compensating for soft tissue deformation during image-guided neurosurgery. The accuracy of these models can be improved by incorporating intraoperative measurements of brain motion. We have designed and implemented a passive intraoperative stereo vision system capable of estimating the three-dimensional shape of the surgical scene in near real-time. This intraoperative shape is compared with the cortical surface in the co-registered preoperative magnetic resonance (MR) volume for the estimation of the cortical motion resulting from the open cranial surgery. The estimated cortical motion is then used to guide a full brain model, which updates a preoperative MR volume. We have found that the stereo vision system is accurate to within approximately 1 mm. Based on data from two representative clinical cases, we show that stereopsis guidance improves the accuracy of brain shift compensation both at and below the cortical surface.
Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic (1999)

Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.