gebhart/patrepeval huggingface dataset:
Optimal input states and feedback for interferometric phase estimation (2001)

We derive optimal N-photon two-mode input states for interferometric phase measurements. Under canonical measurements the phase variance scales as ${N}^{\ensuremath{-}2}$ for these states, as compared to ${N}^{\ensuremath{-}1}$ or ${N}^{\ensuremath{-}1/2}$ for states considered by previous authors. We prove that it is not possible to realize the canonical measurement by counting photons in the outputs of the interferometer, even if an adjustable auxiliary phase shift is allowed in the interferometer. However, we introduce a feedback algorithm based on Bayesian inference to control this auxiliary phase shift. This makes the measurement close to a canonical one, with a phase variance scaling slightly above ${N}^{\ensuremath{-}2}.$ With no feedback, the best result (given that the phase to be measured is completely unknown) is a scaling of ${N}^{\ensuremath{-}1}.$ For optimal input states having up to four photons, our feedback scheme is the best possible one, but for higher photon numbers more complicated schemes perform marginally better.
Postfractionation for Enhanced Proteomic Analyses:  Routine Electrophoretic Methods Increase the Resolution of Standard 2D-PAGE (2005)

Here we have addressed common issues of resolution in two-dimensional polyacrylamide gel electrophoresis (2DE) experiments including proteins 'stacked' at pH extremes, unresolved peptides migrating at the front of separation, and areas of the 2D gel obscured by high abundance proteins. Postfractionation, by selective application of well-established electrophoretic separations immediately following standard 2DE, yields markedly improved resolution in these traditional problem areas using no more specialized equipment or techniques than SDS-PAGE itself.
Evaluating Real-Time Anomaly Detection Algorithms -- The Numenta Anomaly Benchmark (2015)

Much of the world's data is streaming, time-series data, where anomalies give significant information in critical situations, examples abound in domains such as finance, IT, security, medical, and energy. Yet detecting anomalies in streaming data is a difficult task, requiring detectors to process data in real-time, not batches, and learn while simultaneously making predictions. There are no benchmarks to adequately test and score the efficacy of real-time anomaly detectors. Here we propose the Numenta Anomaly Benchmark (NAB), which attempts to provide a controlled and repeatable environment of open-source tools to test and measure anomaly detection algorithms on streaming data. The perfect detector would detect all anomalies as soon as possible, trigger no false alarms, work with real-world time-series data across a variety of domains, and automatically adapt to changing statistics. Rewarding these characteristics is formalized in NAB, using a scoring algorithm designed for streaming data. NAB evaluates detectors on a benchmark dataset with labeled, real-world time-series data. We present these components, and give results and analyses for several open source, commercially-used algorithms. The goal for NAB is to provide a standard, open source framework with which the research community can compare and evaluate different algorithms for detecting anomalies in streaming data.
Observing Lysozyme’s Closing and Opening Motions by High-Resolution Single-Molecule Enzymology (2015)

Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the resolution to observe the underlying transition pathway or intermediate conformational dynamics. We have used a 1 MHz bandwidth carbon nanotube transistor to electronically monitor single molecules of the enzyme T4 lysozyme as it processes substrate. An experimental resolution of 2 μs allowed the direct recording of lysozyme's opening and closing transitions. Unexpectedly, both motions required 37 μs, on average. The distribution of transition durations was also independent of the enzyme's state: either catalytic or nonproductive. The observation of smooth, continuous transitions suggests a concerted mechanism for glycoside hydrolysis with lysozyme's two domains closing upon the polysaccharide substrate in its active site. We distinguish these smooth motions from a nonconcerted mechanism, observed in approximately 10% of lysozyme openings and closings, in which the enzyme pauses for an additional 40-140 μs in an intermediate, partially closed conformation. During intermediate forming events, the number of rate-limiting steps observed increases to four, consistent with four steps required in the stepwise, arrow-pushing mechanism. The formation of such intermediate conformations was again independent of the enzyme's state. Taken together, the results suggest lysozyme operates as a Brownian motor. In this model, the enzyme traces a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. The observed symmetry in enzyme opening and closing thus suggests that substrate translocation occurs while the enzyme is closed.
Probing the Intracellular Redox Status of Tumors with Magnetic Resonance Imaging and Redox-Sensitive Contrast Agents (2006)

Nitroxide radicals are paramagnetic contrast agents, used in magnetic resonance imaging (MRI), that also exert antioxidant effects. Participating in cellular redox reactions, they lose their ability to provide contrast as a function of time after administration. In this study, the rate of contrast loss was correlated to the reducing power of the tissue or the "redox status." The preferential reduction of nitroxides in tumors compared with normal tissue was observed by MRI. The influence of the structure of the nitroxide on the reduction rate was investigated by MRI using two cell-permeable nitroxides, 4-hydroxy-2,2,6,6,-tetramethyl-1-piperidynyloxyl (Tempol) and 3-carbamoyl-2,2,5,5-tetramethylpyrrolidine-1-oxyl (3CP), and one cell-impermeable nitroxide, 3-carboxy-2,2,5,5,5-tetramethylpyrrolidine-1-oxyl (3CxP). Pharmacokinetic images of these nitroxides in normal tissue, tumor, kidney, and artery regions in mice were simultaneously obtained using MRI. The decay of Tempol and 3CP in tumor tissue was significantly faster than in normal tissue. No significant change in the total nitroxide (oxidized + reduced forms) was noted from tissue extracts, suggesting that the loss in contrast as a function of time is a result of intracellular bioreduction. However, in the case of 3CxP (membrane impermeable), there was no difference in the reduction rates between normal and tumor tissue. The time course of T(1) enhancement by 3CxP and the total amount of 3CxP (oxidized + reduced) in the femoral region showed similar pharmacokinetics. These results show that the differential bioreduction of cell-permeable nitroxides in tumor and normal tissue is supported by intracellular processes and the reduction rates are a means by which the intracellular redox status can be assessed noninvasively.
Gene expression signature of estrogen receptor α status in breast cancer (2005)

The integration of the breast cancer comparative transcriptome analysis based on ERalpha status coupled to the genome-wide identification of high-affinity EREs and GO over-representation analysis, provide useful information for validation and discovery of signaling networks related to estrogen response in this malignancy.
Structure-function relationships in lactose synthase. Structural requirements of the UDP-galactose binding site (1982)

The structural requirements for the donor pyranosyl moiety of UDP-Gal in either galactosyl transfer or "lactose" biosynthesis have been determined. The 4"-deoxy analogue, UDP-4"-deoxyglucose, was synthesized and fully characterized as a donor substrate for galactosyltransferase. The relative rate of deoxyglucosyl transfer to glucose or GlcNAc acceptors was 5.5 +/- 0.6% of that of UDP-Gal as the substrate, with Km values in the same range as that for UDP-Gal or UDP-Glc. Several conclusions may be drawn as to the detailed structural requirements of the UDP-Gal binding site: an axial 4"-hydroxyl group on the pyranosyl moiety is necessary for precise substrate alignment as is also an equatorial 6"-CH2OH moiety. Where one or the other moiety was lacking (UDP-dGlc or UDP-Arab), the maximal rate of glycosyl transfer was ca. 1/20th that of UDP-Gal.
DO11.10 and OT-II T Cells Recognize a C-Terminal Ovalbumin 323–339 Epitope (2000)

The OVA323-339 epitope recognized by DO11.10 (H-2d) and OT-II (H-2b) T cells was investigated using amino- and carboxy-terminal truncations to locate the approximate ends of the epitopes and single amino acid substitutions of OVA323-339 to identify critical TCR contact residues of the OVA323-339 peptide. DO11.10 and OT-II T cells are both specific for a C-terminal epitope whose core encompasses amino acids 329-337. Amino acid 333 was identified as the primary TCR contact residue for both cells, and amino acid 331 was found to be an important secondary TCR contact residue; however, the importance of other secondary TCR contact residues and peptide flanking residues differ between the cells. Additional OVA323-339-specific clones were generated that recognized epitopes found in the N-terminal end or in the center of the peptide. These findings indicate that OVA323-339 can be presented by I-Ad in at least three binding registers. This study highlights some of the complexities of peptide Ags such as OVA323-339, which contain a nested set of overlapping T cell epitopes and MHC binding registers.
Validation of Egg Yolk Antibody Testing as a Method to Determine Influenza Status in White Leghorn Hens (2003)

Determination of the avian influenza (AI) status of a flock has traditionally been done by detection of serum antibodies. However, for many diseases, detection of antibodies in egg yolk has been effective in monitoring the disease status of laying flocks. This study compared the utility of egg yolk vs. serum for determining AI status in laying hen flocks. Specific-pathogen-free white leghorn hens were inoculated via the respiratory tract with a low-pathogenic H7N2 AI virus or sterile allantoic fluid or subcutaneously with an inactivated oil emulsion vaccine produced from the same AI virus or normal allantoic fluid. Antibody levels were determined by the agar gel immunodiffusion (AGID) test, the hemagglutination-inhibition (HI) test, and the enzyme-linked immunosorbent assay (ELISA). Anti-influenza antibodies were detected in sera of all live virus-inoculated hens by day 7 postinoculation (PI) (AGID and ELISA tests), but detection of antibodies in egg yolk was delayed by a few days, with all being positive by day 14 PI. Sera from all vaccinated hens were positive by day 14 PI (AGID and ELISA tests), and egg yolk was positive by day 18 PI. The HI test was less sensitive than the ELISA and AGID tests in detecting anti-influenza antibodies in both sera and yolk. Serum and yolk from all control birds remained negative throughout the study. These studies show that currently used serologic tests can detect antibodies in serum and yolk samples from hens exposed to live AI virus or from those that have been vaccinated. Antibody is detected earlier in the serum than in the yolk and antibody is detected earlier from birds exposed to a live infection compared to birds vaccinated with an inactivated oil emulsion vaccine.
Nanoparticle-induced pulmonary toxicity (2010)

In recent decades, advances in nanotechnology engineering have given rise to the rapid development of many novel applications in the biomedical field. However, studies into the health and safety of these nanomaterials are still lacking. The main concerns are the adverse effects to health caused by acute or chronic exposure to nanoparticles (NPs), especially in the workplace environment. The lung is one of the main routes of entry for NPs into the body and, hence, a likely site for accumulation of NPs. Once NPs enter the interstitial air spaces and are quickly taken up by alveolar cells, they are likely to induce toxic effects. In this review, we highlight the different aspects of lung toxicity resulting from NP exposure, such as generation of oxidative stress, DNA damage and inflammation leading to fibrosis and pneumoconiosis, and the underlying mechanisms causing pulmonary toxicity.
Two types of astrocytes in cultures of developing rat white matter: differences in morphology, surface gangliosides, and growth characteristics (1983)

Two types of glial fibrillary acidic protein-positive (GFAP+) astrocytes were found in cultures of developing rat optic nerve. Type 1 astrocytes had a fibroblast-like morphology, did not bind tetanus toxin or the monoclonal antibody A2B5 (both of which bind to specific polysialogangliosides), and were stimulated to divide by an extract of bovine pituitary and by epidermal growth factor (EGF). Type 2 astrocytes had a neuron-like morphology, bound tetanus toxin and A2B5 antibody, and were not stimulated to divide by bovine pituitary extract or by EGF. Although both types of astrocytes were present in cultures of white matter, only type 1 astrocytes were found in cultures of gray matter. Astrocytes did not convert from one type to the other in culture: while many type 1 astrocytes adopted a neuron-like morphology when exposed to dibutyryl cyclic adenosine 3':5'-monophosphate, or pituitary or brain extracts, especially in serum-free medium, such morphologically altered cells did not bind tetanus toxin or A2B5 antibody. Although small numbers of tetanus toxin-binding, A2B5+, GFAP+ cells were present in suspensions of freshly dissected, neonatal optic nerves, most of the type 2 astrocytes in cultures of such optic nerves developed from tetanus toxin-binding, A2B5+, GFAP- cells, which were induced to express GFAP by the culture conditions. Since type 2 astrocytes have a neuron-like morphology and bind tetanus toxin and A2B5 antibody, these ligands cannot be used on their own as neuron-specific markers in central nervous system cultures.
Human immunodeficiency virus reverse transcriptase: steady-state and pre-steady-state kinetics of nucleotide incorporation (1992)

Steady-state and pre-steady-state kinetic constants were determined for reverse transcriptase catalyzed incorporation of nucleotides and nucleotide analogues into defined-sequence DNA primed-RNA templates. 3'-Azido-3'-deoxythymidine 5'-triphosphate (AZTTP) was almost as efficient a substrate (kcat/Km) as dTTP for the enzyme. In contrast, the four 2',3'-dideoxynucleoside 5'-triphosphates and 3'-deoxy-2',3'-didehydrothymidine 5'-triphosphate (d4TTP) were 6-30-fold less efficient substrates of the enzyme. The kcat values for all nucleotide analogues were similar, consistent with a kinetic model in which the steady-state rate-limiting step was dissociation of the template-primer from the enzyme [Reardon, J. E., & Miller, W. H. (1990) J. Biol. Chem. 265, 20302-20307]. The pre-steady-state kinetics of single-nucleotide incorporation were consistent with the kinetic model: [formula: see text] where E, TP, and dNTP represent reverse transcriptase, a defined-sequence DNA primed-RNA template, and 2'-deoxynucleoside 5'-triphosphate (or analogue), respectively. The dissociation constant (Kd1) for template-primer binding was 10 nM, and the estimated rate constants for association and dissociation of the enzyme.template-primer complex were 4 x 10(6) M-1 s-1 and 0.04 s-1, respectively. The dissociation constants (Kd2) for dTTP, AZTTP, and 3'-deoxythymidine 5'-triphosphate (ddTTP) were 9, 11, and 4.6 microM, respectively. Thus, the differences in steady-state Km values were not due to differences in binding of the nucleotide analogues to the enzyme. In contrast, the rate-limiting step during single-nucleotide incorporation (kp) was sensitive to the structure of the nucleotide substrate.(ABSTRACT TRUNCATED AT 250 WORDS)
Low-birefringence lens design for polarization sensitive optical systems (2006)

Polarization sensitive optical systems may contain optical components that are considered non-polarization optics, such as multi-element collection/illumination lenses, relay lenses and focusing/imaging lenses. With conventional optical design and optomechanical software tools to design these lenses, special consideration is required in choosing glass materials, coatings, and optomechanical design for low intrinsic and stress-induced birefringence and thermal stability. Optical design parameters are discussed to achieve overall minimum birefringence, by optimizing with low intrinsic birefringence glass material, applying phase-controlled (balanced) coating design, and low stress mechanical design approaches. Also discussed are options for matching thermal expansion coefficient (CTE) of the system components. Analysis on transmissive phase retardation of a microbjective at its pupil plane, as well as its birefringence measurement data, will be presented. It is shown that it is critical to design and optimize at multiple positions across the lens pupil to achieve better polarization performance.
Clarification of the functional significance of human folate-binding protein-alpha, peptide 191-199, based on a correct GenBank sequence and on other FBP (191-199) sequences. (2007)

It has been brought to our attention that one of the folate binding protein (FBP) peptides, which we reported first as antigenic and immunogenic in cancer patients, the FBP 191-199, is "off by one amino acid from the amino acid sequence that is listed in GenBank". We searched the published information on FBP and found that the FBP 191-199, which we reported contains threonine 197 instead of the GenBank tyrosine 197. In addition, we found mutations in the FBP (191-199) in other positions, as well as in the flanking residues which direct processing. The potential significance of these changes for cancer vaccines is discussed. It is highly recommended that future human studies with FBP will analyze both GenBank and published sequences in the literature. The large number of mutations in immunogenic FBP-tumor antigens, reported more recently, should be considered during preclinical testing for vaccine and gene therapy in human cancers.
Algorithm-driven optimization of cryopreservation protocols for transfusion model cell types including Jurkat cells and mesenchymal stem cells (2016)

This investigation describes the use of a differential evolution (DE) algorithm to optimize cryopreservation solution compositions and cooling rates for specific cell types. Jurkat cells (a lymphocyte model cell type) and mesenchymal stem cells (MSCs) were combined with non-DMSO solutions at concentrations dictated by a DE algorithm. The cells were then frozen in 96-well plates at DE algorithm-dictated cooling rates in the range 0.5-10°C/min. The DE algorithm was iterated until convergence resulted in identification of an optimum solution composition and cooling rate, which occurred within six to nine generations (seven to 10 experiments) for both cell types. The optimal composition for cryopreserving Jurkat cells included 300 mm trehalose, 10% glycerol and 0.01% ectoine (TGE) at 10°C/min. The optimal composition for cryopreserving MSCs included 300 mm ethylene glycol, 1 mm taurine and 1% ectoine (SEGA) at 1°C/min. High-throughput concentration studies verified the optimum identified by the DE algorithm. Vial freezing experiments showed that experimental solutions of TGE at 10°C/min resulted in significantly higher viability for Jurkat cells than DMSO at 1°C/min, while experimental solutions of SEGA at 10°C/min resulted in significantly higher recovery for MSCs than DMSO at 1°C/min; these results were solution- and cell type-specific. Implementation of the DE algorithm permits optimization of multicomponent freezing solutions in a rational, accelerated fashion. This technique can be applied to optimize freezing conditions, which vary by cell type, with significantly fewer experiments than traditional methods. Copyright © 2016 John Wiley & Sons, Ltd.
Energy-efficient data scrambling on memory-processor interfaces (2003)

Crypto-processors are prone to security attacks based on the observation of their power consumption profile. We propose new techniques for increasing the non-determinism of such profile, which rely on the idea of introducing randomness in the bus data transfers. This is achieved by combining data scrambling with energy-efficient bus encoding, thus providing high information protection at no energy cost.Results on a set of bus traces originated by real-life applications demonstrate the applicability of the proposed solution.
Central role of tumour necrosis factor, GM‐CSF, and interleukin 1 in the pathogenesis of juvenile chronic myelogenous leukaemia (1992)

In previous studies on patients with juvenile chronic myelogenous leukaemia (JCML), we found excessive proliferation of malignant monocyte-macrophage elements in the absence of exogenous growth factor, and impaired growth of normal haematopoietic progenitors. In the current study, six newly-diagnosed JCML patients were investigated to characterize the disease further. In co-cultures, JCML cell culture supernatant as well as patient plasma obtained at diagnosis produced a striking reduction in numbers of control marrow BFU-E, CFU-GM, CFU-Meg and CFU-GEMM colonies. Monoclonal anti-tumour necrosis factor alpha neutralizing antibodies (anti-TNF-alpha Ab) abolished these inhibitory properties. In sharp contrast, JCML supernatants exerted a marked growth-promoting effect on autologous JCML cells cultured in clonogenic assays. Anti-TNF-alpha Ab and anti-granulocyte-macrophage colony-stimulating factor neutralizing antibodies (anti-GM-CSF Ab) both reversed the stimulating effect. Recombinant GM-CSF and recombinant TNF alpha produced a profound increase in JCML colonies when tested individually and anti-GM-CSF Ab reversed the TNF-alpha effect. Expression studies of TNF-alpha and TNF-alpha receptor genes of cultured JCML cells demonstrated mRNAs for both. Further, TNF-alpha activity was assayed in a wide variety of cell culture supernatants and in normal and patients' plasma, and only the JCML specimens showed increased TNF-alpha values. Recombinant interleukin-1 alpha (IL-1 alpha) also stimulated JCML colony growth, but polyclonal anti-IL-1 neutralizing antibodies did not suppress JCML colony numbers nor did it reverse the effects of TNF-alpha or GM-CSF. The evidence indicated that the JCML monokine which inhibits normal haematopoiesis is TNF-alpha and that the endogenously-produced TNF-alpha and GM-CSF from JCML cells play an important role in the pathogenesis of the disease by acting as autocrine growth factors. IL-1 alpha also stimulates JCML cell proliferation as an accessory factor and augments the effect of GM-CSF, TNF-alpha or both.
Comparison of Starch Granule Size Distribution Between Hard and Soft Wheat Cultivars in Eastern China (2008)

小麦淀粉的小粒尺寸分发是能影响它的化学组成和功能的一个重要特征。小麦栽培变种的二种类型，难并且软质小麦栽培变种，在山东农业大学的 Tai'an 试验性的车站成年， Taian，山东，中国，在这研究被检验。在小麦谷物的小粒尺寸分发和直链淀粉内容被学习并且比较，并且在性质之间的关系被识别。小粒尺寸的形式的分发在所有小麦栽培变种被给看的一个清楚的双性人。淀粉小粒的卷分发分别地在 5.6-6.1 μ m 和 20.7-24.9 μ m 的范围给与山峰值形式的典型双性人看。另外，小粒表面区域分发分别地是与在 2.4-3.2 μ m 和 20.7-24.9 μ m 的范围的山峰价值形式的双性人。小粒的数字分发是有在 0.54-1.05 μ m 的范围的山峰价值的一张典型人口。从小粒 < 的贡献到全部的体积的 9.9 μ m 在 94.2-95.1% 的范围和总数的 99.7-99.9% 的 2.8 μ m 和 < 分别地数。为软质小麦的 2.8 μ m， 2.8-9.9 μ m， 9.9-22.8 μ m，和 22.8-42.8 μ m 在为硬质小麦的 12.9-14.3% ， 28.4-31.1% ， 33.5-35.6% ，和 19.7-22.7% 的范围的小粒 < 的比例，和 10.3-13.9% ， 26.6-28.1% ， 32.7-34.6% ，和 24.2-27% 。硬质小麦有更大的 B 类型小粒(< 9.9 μ m ) ，并且比软质小麦有 22.8-42.8 μ m 的更少小粒。直链淀粉内容是断然与小粒 22.8-42.8 μ m 的体积百分比有关，并且否定地与小粒 2.8-22.8 μ m 的体积百分比有关。