gebhart/patrepeval huggingface dataset:
Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts (2015)

SeqFF is a robust and direct method to determine fetal DNA fraction. Furthermore, the method is applicable to both male and female pregnancies and can greatly improve the accuracy of noninvasive prenatal testing for fetal copy number variation.
Pentameric complex of viral glycoprotein H is the primary target for potent neutralization by a human cytomegalovirus vaccine (2013)

Human cytomegalovirus (HCMV) can cause serious morbidity/mortality in transplant patients, and congenital HCMV infection can lead to birth defects. Developing an effective HCMV vaccine is a high medical priority. One of the challenges to the efforts has been our limited understanding of the viral antigens important for protective antibodies. Receptor-mediated viral entry to endothelial/epithelial cells requires a glycoprotein H (gH) complex comprising five viral proteins (gH, gL, UL128, UL130, and UL131). This gH complex is notably missing from HCMV laboratory strains as well as HCMV vaccines previously evaluated in the clinic. To support a unique vaccine concept based on the pentameric gH complex, we established a panel of 45 monoclonal antibodies (mAbs) from a rabbit immunized with an experimental vaccine virus in which the expression of the pentameric gH complex was restored. Over one-half (25 of 45) of the mAbs have neutralizing activity. Interestingly, affinity for an antibody to bind virions was not correlated with its ability to neutralize the virus. Genetic analysis of the 45 mAbs based on their heavy- and light-chain sequences identified at least 26 B-cell linage groups characterized by distinct binding or neutralizing properties. Moreover, neutralizing antibodies possessed longer complementarity-determining region 3 for both heavy and light chains than those with no neutralizing activity. Importantly, potent neutralizing mAbs reacted to the pentameric gH complex but not to gB. Thus, the pentameric gH complex is the primary target for antiviral antibodies by vaccination.
Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method (1997)

A new, simple method for predicting transmembrane segments in integral membrane proteins has been developed. It is based on low-stringency dot-plots of the query sequence against a collection of non-homologous membrane proteins using a previously derived scoring matrix [Cserzö et al., 1994, J. Mol. Biol., 243, 388-396]. This so-called dense alignment surface (DAS) method is shown to perform on par with earlier methods that require extra information in the form of multiple sequence alignments or the distribution of positively charged residues outside the transmembrane segments, and thus improves prediction abilities when only single-sequence information is available or for classes of membrane proteins that do not follow the 'positive inside' rule.
Differential Response to Chlorpromazine, Imipramine, and Placebo (1970)

A MAJOR aim of the present study was to examine the differential effects of chlorpromazine and imipramine among various depression subgroups. Tests were made of differential drug effects among Overall et al's<sup>1</sup>three empirically derived depressive subtypes, ie, anxious, hostile, and withdrawn-retarded depressives. These investigators found a tranquilizer, thioridazine, best for their anxious depressives and imipramine best for the withdrawn-retarded depressives. An examination was also made of differential drug effects among psychotic depressives, neurotic depressives, and schizophrenics with depression. As there is a tendency in this country to equate psychotic depression with endogenous depression, study findings may have some relevance for the endogenous-neurotic distinction. Proponents of this distinction have reported that imipramine is especially efficacious for endogenous depression and of little value in neurotic depressions.<sup>2-12</sup> Finally, tests were made of differential drug effects among depressed patients categorized on the basis of sex and age (below 40 and 40 and
Altered frequency and migration capacity of CD4+CD25+ regulatory T cells in systemic lupus erythematosus (2008)

These results suggest that altered frequency of Tregs and CCR4(+) Tregs(bright) and decreased migratory capacity of Tregs might be involved in the pathogenesis of SLE and indicate that targeting the Tregs can be a new therapeutic strategy in SLE.
Branched and Linear Poly(Ethylene Glycol): Influence of the Polymer Structure on Enzymological, Pharmacokinetic, and Immunological Properties of Protein Conjugates (1997)

Linear and branched poly(ethylene glycol)s, with similar molecular weights, were conjugated with uricase and asparaginase, and an investigation of enzymological, immunological, and pharmacokinetic properties of the conjugates was carried out. It was found that the steric hindrance of the branched polymer has a relevant role in determining the biological properties of the conjugates. Conjugations with branched polymers inactivate the enzyme less than the linear ones. Compared to the native and the linear polymer conjugate counterparts the branched polymer derivatives: (1) are more stable to proteolysis by elastase, pronase, and trypsin, (2) stay longer in the blood with increased systemic availability after intravenous administration in mice, and (3) give rise to lower levels of antinative enzyme antibodies after immunization. These data are consistent with a greater surface area of protein covered by the branched PEG.
The Java class libraries : an annotated reference (1996)

From the Publisher:
This example-driven, annotated reference guide to the Java class libraries from two leading Java developers is an essential resource for both beginner and experienced Java programmers. You will find complete and detailed coverage of all the class libraries, including the Core Packages (java.io, java net, java.util, and java.lang) as well as the Window Toolkit and Applet packages (java.awt, java.awt.image, java.awt.peer, and java.applet), including more than 600 examples and more than 20,000 lines of code. The book has been specifically designed to make it possible to find information on any class or member quickly and easily. Each class description includes a class hierarchy diagram showing its connection to related classes, a detailed overview describing its purpose and key concepts, a convenient member summary which briefly describes each member and arranges the members into related groups, an example demonstrating the class in a real-world context, and comprehensive descriptions and examples for each of its members.
The preparation and some reactions of 2-(arylsulfonyl)vinamidinium salts (1991)

The preparation of novel 2-(arylsulfonyl)vinamidinium salts is described. The reactions of these materials with amidines, hydrazine, hydroxylamine, sodium borohydride, and Grignard reagents are presented along with an evaluation of their chemical behavior as compared to the 2-arylvinamidinium salts. © 1991, American Chemical Society. All rights reserved.
Angular micropositioner for disk drives (2002)

Rotary electrostatic microactuators suitable for use in a two-stage servo system for magnetic disk drives have been fabricated using the HexSil process. A 2.6 mm diameter device is shown to be capable of producing 0.17 mN-mm of output torque, corresponding to a predicted actuation bandwidth of 1.6 kHz. The structures are formed from LPCVD polysilicon deposited into deep trenches etched into a silicon mold wafer. Upon release, these structures are transferred to a target wafer using a solder bond. The solder bonding process will provide easy integration of mechanical structures with integrated circuits, allowing separate optimization of the circuit and structure fabrication processes. An advantage of HexSil is that once the mold wafer has undergone the initial plasma etching, it may be re-used for subsequent polysilicon depositions, amortizing the cost of the deep trench etching over many structural runs and thereby significantly reducing the cost of finished actuators. Further, 100 /spl mu/m high structures may be made from a 3 /spl mu/m deposition of polysilicon, increasing overall fabrication speed.
A New Homobifunctional p-Nitro Phenyl Ester Coupling Reagent for the Preparation of Neoglycoproteins (2004)

A new linker system has been designed and applied to neoglycoprotein synthesis. Reaction of oligosaccharide omega-aminoalkyl glycosides with homobifunctional adipic acid p-nitrophenyl diesters in dry DMF gave the corresponding amide half ester in good yields and of sufficient stability to permit chromatographic purification. Subsequent conjugation with bovine serum albumin under very mild conditions afforded the corresponding neoglycoproteins with good efficiency. The method is well suited for the coupling of very small amounts (mg) of oligosaccharide and protein. [structure: see text]
Leucocyte typing VII : white cell differentiation antigens : proceedings of the seventh international workshop and conference held in Harrogate, United Kingdom (2002)

PART 1: ADHESION STRUCTURES PART 2: APOPTOSIS AND CELL FATE PART 3: B CELLS PART 4: CARBOHYDRATES AND LECTINS PART 5: CLINICAL ASPECTS OF LEUCOCYTE MOLECULES PART 6: CYTOKINE/CHEMOKINE RECEPTORS PART 7: DENDRITIC CELLS PART 8: ENDOTHELIAL CELLS PART 9: MYELOID CELLS PART 10: NEW TECHNOLOGIES PART 11: NATURAL KILLER CELLS PART 12: NON-LINEAGE ANTIGENS PART 13: PLATELETS PART 14: RED CELLS PART 15: STEM/PROGENITOR CELLS PART 16: STRUCTURAL/FUNCTIONAL ASEPECTS OF LEUCOCYTE MOLECULES PART 17: T CELLS
A novel cyclic D/A converter (2002)

A new cyclic digital-to-analog converter using integrator-type sample and hold (S/H) circuits is described. The converter is capable of achieving very high-resolution and very-high accuracy conversion without requiring a precision weighted network. It does not suffer from the problems of stability, switch charge injection, etc. If a high degree of linearity is desired, trimming is necessary. The trimming process is as simple as in the case of gain error or zero error trimming.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Feasibility Study Evaluating the Functional Diffusion Map as a Predictive Imaging Biomarker for Detection of Treatment Response in a Patient with Metastatic Prostate Cancer to the Bone (2007)

Prostate cancer (PCa) is the most commonly diagnosed cancer in American men with a subset inevitably presenting with metastatic disease to the bone. A well-recognized limitation in evaluating new treatments for metastatic PCa is the inability to use imaging to objectively assess response therapy. In this study, we evaluated the feasibility of clinically translating the functional diffusion map (fDM) imaging biomarker for quantifying the spatiotemporal effects of bone tumor response in a patient treated for metastatic PCa with bone metastases. A patient beginning therapy was scanned using MRI before treatment and again at 2 and 8 weeks post-treatment initiation to quantify changes in tumor diffusion values. Three metastatic lesions were identified for fDM analysis, all of which all demonstrated an early increase in diffusion values at 2 weeks, which increased further at 8 weeks post-treatment initiation. This finding correlated with a decrease in the patient's prostate-specific antigen (PSA) levels suggestive of patient response. CT, bone scans, and anatomic MRI images obtained posttreatment were found to be uninformative for the assessment of treatment effectiveness. This study presents the feasibility of fDM-measurements in osseous lesions over time and shows that changes in fDM values were consistent with therapeutic response. Thus, the fDM imaging biomarker may provide a quantifiable therapeutic endpoint to assess response in patients with metastatic bone cancer.
Palladium-Catalyzed Direct Oxidation of Alkenes with Molecular Oxygen: General and Practical Methods for the Preparation of 1,2-Diols, Aldehydes, and Ketones (2010)

1,2-Diols, aldehydes, and ketones are important intermediates in chemical synthesis, and alkenes are possible precursors for 1,2-diols, aldehydes, and ketones. Herein, novel and environmentally benign methods for palladium-catalyzed dihydroxylation and oxidative cleavage of olefins with oxygen as sole oxidant are presented. The cleavage reactions were performed with acid as additive in aqueous solution, whereas 1,2-diols were formed in the presence of base. A broad substrate scope has been demonstrated allowing monosubstituted aromatic and aliphatic terminal alkenes, 1,2-disubstituted, and 1,1-disubstituted olefins. The cleavage reactions of dioxo-Pd(II) complexes implicate 1,2-diol might act as a key intermediate of olefin cleavage.
A blind carrier frequency offset estimation scheme for OFDM systems with constant modulus signaling (2008)

This paper presents a new blind carrier frequency offset (CFO) estimation scheme for orthogonal frequency division multiplexing (OFDM) systems with constant modulus (CM) signaling. Both single-input single-output (SISO) systems and multiple-input multiple-output (MIMO) systems with orthogonal space-time block coding are considered. The proposed scheme is based on the reasonable assumption that the channel frequency response changes slowly in the frequency domain, which implies that the channel frequency response on two consecutive sub- carriers is approximately the same. Based on this assumption, cost functions are derived in closed-form, which minimize the difference between the signal power of two neighboring subcarriers. The identifiability of the proposed scheme is mathematically proved, which implies that minimizing the derived cost function gives an approximate estimate of the CFO. We demonstrate that the proposed scheme provides an excellent trade-off between complexity and performance as compared to prominent existing estimation schemes.
Structural Correlates of Antibacterial and Membrane-Permeabilizing Activities in Acylpolyamines (2006)

A homologous series of mono- and bis-acyl polyamines with varying acyl chain lengths originally synthesized for the purpose of sequestering lipopolysaccharide were evaluated for antimicrobial activity to test the hypothesis that these bis-cationic amphipathic compounds may also bind to and permeabilize intact gram-negative bacterial membranes. Some compounds were found to possess significant antimicrobial activity, mediated via permeabilization of bacterial membranes. Structure-activity relationship studies revealed a strong dependence of the acyl chain length on antimicrobial potency and permeabilization activity. Homologated spermine, bis-acylated with C8 or C9 chains, was found to profoundly sensitize Escherichia coli to hydrophobic antibiotics such as rifampin. Nonspecific cytotoxicity is a potential drawback of these membranophilic compounds. However, the surface activity of these cationic amphipaths is strongly attenuated under physiological conditions via binding to serum albumin. Significant antibacterial activity is still retained in the presence of physiological concentrations of human serum albumin, suggesting that these compounds may serve as leads in the development of novel adjuncts to conventional antimicrobial chemotherapy.
The Pavlodar chemical weapons plant in Kazakhstan: History and legacy (2000)

(2000). The Pavlodar chemical weapons plant in Kazakhstan: History and legacy. The Nonproliferation Review: Vol. 7, No. 2, pp. 136-145.
Cellular Logic-in-Memory Arrays (1969)

As a direct consequence of large-scale integration, many advantages in the design, fabrication, testing, and use of digital circuitry can be achieved if the circuits can be arranged in a two-dimensional iterative, or cellular, array of identical elementary networks, or cells. When a small amount of storage is included in each cell, the same array may be regarded either as a logically enhanced memory array, or as a logic array whose elementary gates and connections can be "programmed" to realize a desired logical behavior.
UDP-N-acetylgalactosamine:globoside alpha-3-N-acetylgalactosaminyltransferase. Purification, characterization, and some properties. (1982)

A UDP-N-acetylgalactosamine:globoside alpha-3-N-acetylgalactosaminyltransferase has been purified over 3500-fold in 4% yield from a Triton X-100 extract of canine spleen microsomes by affinity chromatography on globoside acid-agarose. Sodium dodecyl sulfate gel electrophoresis of the purified enzyme revealed two major bands with molecular weights of 66,000 and 56,000. Judging from the molecular weight of 120,000 estimated by Sephadex gel filtration in Triton X-100 and the above electrophoretic result, the enzyme presumably exists normally as a dimer. It required Mn2+ for its activity and had a pH optimum at 6.7-6.9. The enzyme catalyzes the transfer of N-acetylgalactosamine in alpha 1 leads to 3 linkage to globoside. Neither Fuc alpha 1 leads to 2Gal beta 1 leads to 4Glc nor H blood group substance nor deglycosylated mucin were acceptors. This indicates that the enzyme was distinct from both the N-acetylgalactosaminyltransferases converting the H to the A blood group substance and catalyzing synthesis of the Ser(Thr)-GalNAc linkage. Studies on substrate specificities indicate that the preferred substrates have the general structure GalNAc beta 1 leads to 3Gal-OR in which the nature of the R moiety has relatively little effect on activity. Kinetic analysis indicates UDP is a competitive inhibitor with respect to UDP-N-acetylgalactosamine and a noncompetitive inhibitor with respect to globoside. These studies demonstrate the first report of the properties of a purified enzyme catalyzing the transfer of sugar residues to glycolipids.
Anion activation of angiotensin converting enzyme: dependence on nature of substrate (1983)

Anion activation of pulmonary angiotensin converting enzyme has been examined by using 23 furanacryloyl- and 3 benzoyl-tripeptides as substrates. Chloride stimulates hydrolysis of all substrates at least 24-fold. However, the kinetic mechanism, the amount of chloride required, and the effect of pH on activation, plus the relative activating potencies of various anions, are all strongly dependent on the substrate employed. Three substrate classes have been identified. Class I substrates appear to be hydrolyzed at pH 7.5 by an ordered bireactant mechanism in which anion must bind before substrate. The apparent activation constant (KA') for Cl- ranges from 75 to 150 mM at pH 7.5, doubles at pH 9.0, and decreases to about 3 mM at pH 6.0. Class II substrates, in contrast, are hydrolyzed by a nonessential activator mechanism. The kinetically determined KA' for Cl- at pH 7.5 ranges from 2.9 to 5.0 mM and changes only slightly with pH. Class III substrates are also hydrolyzed by a nonessential kinetic mechanism but one different from that followed by class II peptides. KA' values for Cl- at pH 7.5 measured with class III substrates are 18-30 mM. Class II substrates have Arg or Lys at the ultimate or penultimate position. The features distinguishing class I and III peptides are less clear, although all class III substrates identified have penultimate alanine residues. Possible explanations for this substrate dependence are offered.
Mannose receptor induces T-cell tolerance via inhibition of CD45 and up-regulation of CTLA-4 (2016)

The mannose receptor (MR) is an endocytic receptor involved in serum homeostasis and antigen presentation. Here, we identify the MR as a direct regulator of CD8(+) T-cell activity. We demonstrate that MR expression on dendritic cells (DCs) impaired T-cell cytotoxicity in vitro and in vivo. This regulatory effect of the MR was mediated by a direct interaction with CD45 on the T cell, inhibiting its phosphatase activity, which resulted in up-regulation of cytotoxic T-lymphocyte-associated Protein 4 (CTLA-4) and the induction of T-cell tolerance. Inhibition of CD45 prevented expression of B-cell lymphoma 6 (Bcl-6), a transcriptional inhibitor that directly bound the CTLA-4 promoter and regulated its activity. These data demonstrate that endocytic receptors expressed on DCs contribute to the regulation of T-cell functionality.
EWOD-driven droplet microfluidic device integrated with optoelectronic tweezers as an automated platform for cellular isolation and analysis (2009)

We report the integration of two technologies: droplet microfluidics using electrowetting-on-dielectric (EWOD) and individual particle manipulation using optoelectronic tweezers (OET)-in one microfluidic device. The integrated device successfully demonstrates a sequence involving both EWOD and OET operations. We encountered various challenges during integration of the two different technologies and present how they are addressed. To show the applicability of the device in cellular biology, live HeLa cells are used in the experiments. The unique advantages of EWOD and OET make their integration a significant step towards a powerful tool for many applications, such as single cell studies involving multiplexed environmental stimuli.
Implementation of floating-point operations for 3D graphics on a coarse-grained reconfigurable architecture (2007)

With the increasing requirements for more flexibility and higher performance in embedded systems design, reconfigurable computing has become more popular. There have been many coarse-grained reconfigurable architectures proposed and/or commercialized. But most of the existing architectures cannot be used for applications that require floating-point operations, since they have only integer units. In this paper, we present how we can perform various floating-point operations on a coarse-grained reconfigurable array of integer processing elements. We demonstrate the effectiveness of our approach through the implementation of various floating-point operations for 3D graphics and their performance analysis.
The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation (2002)

Stably integrated transgenes flanked by the chicken beta-globin HS4 insulator are protected against chromosomal position effects and gradual extinction of expression during long-term propagation in culture. To investigate the mechanism of action of this insulator, we used bisulfite genomic sequencing to examine the methylation of individual CpG sites within insulated transgenes, and compared this with patterns of histone acetylation. Surprisingly, although the histones of the entire insulated transgene are highly acetylated, only a specific region in the promoter, containing binding sites for erythroid-specific transcription factors, is highly protected from DNA methylation. This critical region is methylated in noninsulated and inactive lines. MBD3 and Mi-2, subunits of the Mi-2/NuRD repressor complex, are bound in vivo to these silenced noninsulated transgenes. In contrast, insulated cell lines do not show any enrichment of Mi-2/NuRD proteins very late in culture. In addition to the high levels of histone acetylation observed across the entire insulated transgene, significant peaks of H3 acetylation are present over the HS4 insulator elements. Targeted histone acetylation by the chicken beta-globin insulator occurs independently of gene transcription and does not require the presence of a functional enhancer. We suggest that this acetylation is in turn responsible for the maintenance of a region of unmethylated DNA over the promoter. Whereas DNA methylation often leads to histone deacetylation, here acetylation appears to prevent methylation.