gebhart/patrepeval huggingface dataset:
Highly Sensitive and Multiplexed In-Situ Protein Profiling with Cleavable Fluorescent Streptavidin (2020)

The ability to perform highly sensitive and multiplexed in-situ protein analysis is crucial to advance our understanding of normal physiology and disease pathogenesis. To achieve this goal, we here develop an approach using cleavable biotin-conjugated antibodies and cleavable fluorescent streptavidin (CFS). In this approach, protein targets are first recognized by the cleavable biotin-labeled antibodies. Subsequently, CFS is applied to stain the protein targets. Though layer-by-layer signal amplification using cleavable biotin-conjugated orthogonal antibodies and CSF, the protein detection sensitivity can be enhanced at least 10-fold, compared with the current in-situ proteomics methods. After imaging, the fluorophore and the biotin unbound to streptavidin are removed by chemical cleavage. The leftover streptavidin is blocked by biotin. Upon reiterative analysis cycles, a large number of different proteins with a wide range of expression levels can be profiled in individual cells at the optical resolution. Applying this approach, we have demonstrated that multiple proteins are unambiguously detected in the same set of cells, regardless of the protein analysis order. We have also shown that this method can be successfully applied to quantify proteins in formalin-fixed paraffin-embedded (FFPE) tissues.
Staphylococcal Surface Display of Immunoglobulin A (IgA)- and IgE-Specific In Vitro-Selected Binding Proteins (Affibodies) Based on Staphylococcus aureus Protein A (1999)

An expression system designed for cell surface display of hybrid proteins on Staphylococcus carnosus has been evaluated for the display of Staphylococcus aureus protein A (SpA) domains, normally binding to immunoglobulin G (IgG) Fc but here engineered by combinatorial protein chemistry to yield SpA domains, denoted affibodies, with new binding specificities. Such affibodies, with human IgA or IgE binding activity, have previously been selected from a phage library, based on an SpA domain. In this study, these affibodies have been genetically introduced in monomeric or dimeric forms into chimeric proteins expressed on the surface of S. carnosus by using translocation signals from a Staphylococcus hyicus lipase construct together with surface-anchoring regions of SpA. The recombinant surface proteins, containing the IgA- or IgE-specific affibodies, were demonstrated to be expressed as full-length proteins, localized and properly exposed at the cell surface of S. carnosus. Furthermore, these chimeric receptors were found to be functional, since recombinant S. carnosus cells were shown to have gained IgA and IgE binding capacity, respectively. In addition, a positive effect in terms of IgA and IgE reactivity was observed when dimeric versions of the affibodies were present. Potential applications for recombinant bacteria with redirected binding specificity in their surface proteins are discussed.
Virtual machines, managed code and component technology (2005)

Abstract machines have been used as an implementation mechanism for programming languages for more than thirty years. In their latest incarnation execution engines based on virtual machines offer "managed execution ". The implications of this change go far beyond the superficial advantages of platform portability and go to the heart of software reliability. In this paper it is argued that managed execution platforms such as the .NET common language runtime and the Java virtual machine form the only reasonable basis for trustworthy component software. There is also an overview of current research in this field, including the vexed question of version evolution.
The synthesis and reactivity of novel azetidinyl enediynes (1996)

A. Basak, U. K. Khamrai and U. Mallik, Chem. Commun., 1996, 749 DOI: 10.1039/CC9960000749
Experimental Campylobacter diarrhea in chickens (1981)

An animal model for Campylobacter fetus subsp. jejuni enteritis was developed in 3-day-old chickens. Diarrhea was induced in 88% (22 of 25) of chickens inoculated with 9 X 10(7) bacteria given orally. The mean incubation time was 45 h (range, 24 to 72 h). Considerable weight loss was observed in the experimental group compared with the control group. Ninety bacteria was the minimal infective dose capable of inducing diarrhea in 90% of the chickens. Overall mortality was 32% (8 of 25). Light microscopy, immunofluorescence, and electron microscopy of the gastrointestinal tract of serially sacrificed chickens were performed in control and experimental groups. A moderate infiltration of mononuclear cells was observed in ileum and cecum in the experimental group, with no disruption of intestinal mucosa. By immunofluorescence and electron microscopy, campylobacter was located within the epithelial cells and phagocytosed to a greater degree by mononuclear cells of the lamina propria.
Production of 6-Methylsalicylic Acid by Expression of a Fungal Polyketide Synthase Activates Disease Resistance in Tobacco (2001)

Nasser Yalpani, Daniel J. Altier, Eric Barbour, Amy L. Cigan, Christopher J. Scelonge, Production of 6-Methylsalicylic Acid by Expression of a Fungal Polyketide Synthase Activates Disease Resistance in Tobacco, The Plant Cell, Vol. 13, No. 6 (Jun., 2001), pp. 1401-1409
Wideband speech coder employing T-codes and reversible variable length codes (2003)

The performance of speech coders, such as the ITU-T G.722.1 wideband speech coder, that employ nonself-synchronizing variable length codes is greatly affected when the received bit stream is in error. This paper studies the use of T-codes and reversible variable length codes (RVLC) to replace the Huffman codes recommended in the G.722.1 coder in order to improve its robustness when bit errors occur. Preliminary simulation results show significant improvement in coder performance with the proposed schemes.
A novel shape complementarity scoring function for protein‐protein docking (2003)

Shape complementarity is the most basic ingredient of the scoring functions for protein-protein docking. Most grid-based docking algorithms use the total number of grid points at the binding interface to quantify shape complementarity. We have developed a novel Pairwise Shape Complementarity (PSC) function that is conceptually simple and rapid to compute. The favorable component of PSC is the total number of atom pairs between the receptor and the ligand within a distance cutoff. When applied to a benchmark of 49 test cases, PSC consistently ranks near-native structures higher and produces more near-native structures than the traditional grid-based function, and the improvement was seen across all prediction levels and in all categories of the benchmark. Without any post-processing or biological information about the binding site except the complementarity-determining region of antibodies, PSC predicts the complex structure correctly for 6 test cases, and ranks at least one near-native structure in the top 20 predictions for 18 test cases. Our docking program ZDOCK has been parallelized and the average computing time is 4 minutes using sixteen IBM SP3 processors. Both ZDOCK and the benchmark are freely available to academic users (http://zlab.bu.edu/~ rong/dock).
A neural system for behavioral conditioning of mobile robots (1990)

A control system for mobile robots which is reminiscent of the modular distributed architecture of the brain is proposed. This system is motivated by the various neural network models of S. Grossberg (1982, 1988) and M. Seibert and A.M. Waxman (1989). The approach takes the point of view that the robot must be adaptive to its environment and learn from experience. The system utilizes neural networks for learning and performance at all stages, from visual object recognition to behavioral conditioning. The system includes networks for early visual perception, pattern learning and recognition, object associations, emotional states, behavioral actions, and motor control. These networks are interconnected by a variety of adaptive pathways. The system demonstrates self-organizing, teacher-controlled, and reinforcement learning paradigms, and it integrates these into a system in which external events interact with internal emotional states. The system has been implemented on a mobile robot, MAVIN (mobile adaptive visual navigator), and a variety of behavioral conditioning paradigms are demonstrated
Algorithms for association rule mining — a general survey and comparison (2000)

Today there are several efficient algorithms that cope with the popular and computationally expensive task of association rule mining. Actually, these algorithms are more or less described on their own. In this paper we explain the fundamentals of association rule mining and moreover derive a general framework. Based on this we describe today's approaches in context by pointing out common aspects and differences. After that we thoroughly investigate their strengths and weaknesses and carry out several runtime experiments. It turns out that the runtime behavior of the algorithms is much more similar as to be expected.
HMM-based Error Detection of Dance Step Selection for Dance Partner Robot -MS DanceR- (2006)

We have proposed a dance partner robot, which has been developed as a platform for realizing the effective human-robot coordination with physical interactions. In the previous research, we have improved an estimation system for dance steps, which estimates the next dance step intended by a human. Although estimating the intended step is important for realizing the human-robot coordination, the cases that the estimation is failed and that the robot selects an incorrect step are not considered. Such cases have to be discussed carefully for realizing the effective human-robot coordination. In this paper, a method for error detections of dance step selections are proposed, which is designed using hidden Markov models. Experimental results illustrate the validity of the proposed method
CXCL12 (SDF-1α) suppresses ongoing experimental autoimmune encephalomyelitis by selecting antigen-specific regulatory T cells (2008)

Experimental autoimmune encephalomyelitis (EAE) is a T cell-mediated autoimmune disease of the central nervous system induced by antigen-specific effector Th17 and Th1 cells. We show that a key chemokine, CXCL12 (stromal cell-derived factor 1alpha), redirects the polarization of effector Th1 cells into CD4(+)CD25(-)Foxp3(-)interleukin (IL) 10(high) antigen-specific regulatory T cells in a CXCR4-dependent manner, and by doing so acts as a regulatory mediator restraining the autoimmune inflammatory process. In an attempt to explore the therapeutic implication of these findings, we have generated a CXCL12-immunoglobulin (Ig) fusion protein that, when administered during ongoing EAE, rapidly suppresses the disease in wild-type but not IL-10-deficient mice. Anti-IL-10 neutralizing antibodies could reverse this suppression. The beneficial effect included selection of antigen-specific T cells that were CD4(+)CD25(-)Foxp3(-)IL-10(high), which could adoptively transfer disease resistance, and suppression of Th17 selection. However, in vitro functional analysis of these cells suggested that, even though CXCL12-Ig-induced tolerance is IL-10 dependent, IL-10-independent mechanisms may also contribute to their regulatory function. Collectively, our results not only demonstrate, for the first time, that a chemokine functions as a regulatory mediator, but also suggest a novel way for treating multiple sclerosis and possibly other inflammatory autoimmune diseases.
Interleukin-3-Induced Phosphorylation of BAD Through the Protein Kinase Akt (1997)

BAD is a distant member of the Bcl-2 family that promotes cell death. Phosphorylation of BAD prevents this. BAD phosphorylation induced by interleukin-3 (IL-3) was inhibited by specific inhibitors of phosphoinositide 3-kinase (PI 3-kinase). Akt, a survival-promoting serine-threonine protein kinase, was activated by IL-3 in a PI 3-kinase-dependent manner. Active, but not inactive, forms of Akt were found to phosphorylate BAD in vivo and in vitro at the same residues that are phosphorylated in response to IL-3. Thus, the proapoptotic function of BAD is regulated by the PI 3-kinase-Akt pathway.
CD66b, CD66c and carcinoembryonic antigen (CEA) are independently regulated markers in sera of tumor patients (1995)

Non-specific cross-reacting antigens (NCA-95 = CD66b and NCA-50/90 = CD66c) are members of the CEA (carcinoembryonic antigen = CD66e) family. Analysis of mRNA levels of CD66c in colon tumors suggests that this antigen is strongly up-regulated compared to its normal counterpart and could, therefore, be of clinical interest. CD66c is also expressed in normal lung and spleen tissues and, above all, on granulocytes. The appearance of CD66b in serum, the only strictly granulocyte-specific antigen, could point to the involvement of granulocytes in disease. Specific sandwich ELISAs have been established to determine CEA, CD66b and CD66c levels in serum. Controls have been carried out by testing sera from patients with benign tumors or inflammatory diseases and from healthy individuals. In sera of most patients suffering from solid tumors, sensitivities for CD66c are comparable to or lower than those for CEA. CD66c showed a much higher sensitivity in early colon tumor stages. Sensitivities over 40% have been determined for CD66b in sera of patients with uterine and kidney carcinomas. CML patients revealed sensitivities of 84% for CD66c and 47% for CD66b. Investigations of sera from patients with inflammatory colon diseases which are negative for CEA showed high sensitivity for CD66c but not for the granulocyte-specific CD66b. Patients with mastopathy revealed sensitivities of over 40% for both CD66c and CD66b. CD66b, CD66c and CEA are independently regulated proteins in a high percentage of patients. The simultaneous determination of CEA and CD66b/c can increase the sensitivities for malignant tumors but high sensitivities of CD66b/c for benign diseases limit their usefulness as tumor markers. CD66b may be interesting as a marker for kidney and corpus carcinomas, for which good markers are not yet available.
Two Regions in the CD80 Cytoplasmic Tail Regulate CD80 Redistribution and T Cell Costimulation (1998)

CD28 is a major T cell costimulatory molecule, delivering signals distinct from those of the CD3/TCR complex, which regulate cytokine and cytokine receptor expression, cell proliferation, and cell viability. CD28 needs to be cross-linked to initiate signals, yet both of its ligands, CD80 and CD86, are expressed as monomers. Previously, we determined the cytoplasmic tail of CD80 is required for CD28-mediated costimulation and subcellular relocalization of CD80 in lymphocytes. In this study, we report that Reh B cell transfectants expressing CD80 with mutations in the cytoplasmic tail region either at 275-278 (RRNE-->AAAA, CD80/4A) or serine 284 (S-->A, CD80/SA) can bind ligand similar to transfectants expressing wild-type CD80, yet are unable to costimulate T cell proliferation. These mutant CD80 molecules are expressed on the surface of the Reh cells in small clusters or foci indistinguishable from those of wild-type CD80 molecules. However, mutant CD80 molecules unlike wild-type CD80 cannot be readily induced by ligand into caps. Thus, small clusters of CD80 found on APC are insufficient to initiate CD28-mediated signals, and the formation of CD80 caps appears to be a critical factor regulating the initiation of T cell costimulation. A 30-kDa phosphoprotein that associates with the cytoplasmic tail of CD80 in activated cells may play a role in CD80 redistribution and thus CD28-mediated costimulation. These results indicate two distinct regions of the CD80 cytoplasmic tail regulate its costimulatory function, and both regions are required for CD80 function.
CONNEXIN EXPRESSION IN HUNTINGTON'S DISEASED HUMAN BRAIN (1998)

In Huntington's diseased human brain, it is in the caudate nucleus (CN) and globus pallidus (GP) of the basal ganglia where nerve cell death is seen most dramatically. The distribution of five gap junction proteins (connexins 26, 32, 40, 43 and 50) has been examined in these areas in normal and Huntington's diseased human brain using immunohistochemical techniques. There was no Cx50 expression observed and Cx40 was localized in the endothelial cells of blood vessels, with the Huntington's diseased brains having more numerous and smaller blood vessels than normal tissue. Cx26 and Cx32 revealed a similar distribution pattern to each other in both normal and diseased brains with little labelling in the CN but clear labelling in the GP. Cx43, expressed by astrocytes, was the most abundant connexin type of those studied. In both normal and diseased brains Cx43 in the GP was homogeneously distributed in the neuropil. In the CN, however, Cx43 density was both increased with Huntington's disease and became located in patches. Glial fibrillary acidic protein(GFAP) staining of astrocytes was also highly increased in the CN compared with normal brains. These labelling patterns indicate a reactive astrocytosis around degenerating neurons with an increased expression of astrocytic gap junctions. The enhanced coupling state between astrocytes, assuming the junctions are functional, could provide an increased spatial buffering capacity by the astrocytes in an attempt to maintain a proper environment for the neurons, helping promote neuronal survival in this neurodegenerative disorder.
REST Repression of Neuronal Genes Requires Components of the hSWI·SNF Complex (2002)

A function of the transcription factor REST is to block the expression of neuronal phenotypic traits in non-neuronal cells. Previous studies have shown that REST-mediated repression requires histone deacetylase activity and that recruitment of deacetylases is mediated by two co-repressors, Sin3A and CoREST. In this study, we show that a repressor domain in CoREST interacts with BRG1-associated factor (BAF) 57, a component of the hSWI.SNF complex. In vivo, BAF57 occupies the neuronal sodium channel gene (Nav1.2) promoter, and targeting to this gene requires REST. In addition to BAF57, the ATPase BRG1 and BAF170, other members of the hSWI.SNF complex, are also present in the REST.CoREST repressor complex. Microinjection of specific antibodies against BRG1, BAF57, or BAF170 into Rat1 fibroblasts relieves repression of RE1 reporter genes. Together, our data suggest that ATP-dependent chromatin remodeling, as well as histone deacetylation, is needed for REST-mediated repression.
Effects of etch depth and ion implantation on surface emitting microlasers (1990)

We fabricated low threshold In0.2Ga0.8As surface emitting microlasers having various etch depths and sizes. Comparison of electrical and optical properties was made between deep etched (deeper than the active layer) and shallow etched (shallower than the active layer) microlasers. Shallow etched microlasers were F-ion implanted to limit current spreading. The ion implanted shallow etched samples, when larger than about 5 µm across, show improved room temperature CW characteristics with lower resistances and lower operating voltages than the deep etched microlasers.
Syntheses and Superoxide Dismuting Activities of Partially (1−4) β-Chlorinated Derivatives of Manganese(III) meso-Tetrakis(N-ethylpyridinium-2-yl)porphyrin (1998)

Manganese(III) β-mono-, di-, tri-, and tetrachloro-5,10,15,20-tetrakis(N-ethylpyridinium-2-yl)porphyrin (MnClxTE-2-PyP5+, with x from 1 to 4) were prepared through β-chlorination of 5,10,15,20-tetrakis(2-pyridyl)porphyrin (H2T-2-PyP) followed by N-ethylation and metallation. Metal centered redox potentials and superoxide dismutation activities were measured. Starting from MnTE-2-PyP5+, whose redox potential and the related superoxide dismutation activity were E°1/2 = +228 mV vs NHE and kcat = 5.7 × 107 M-1 s-1, respectively, the average increase of 55 mV in the redox potential per added chlorine was accompanied by a 65% increase in the rate constant. With E°1/2 = +448 mV, the tetrachlorinated derivative MnCl4TE-2-PyP5+ exhibited the highest superoxide dismuting rate kcat = 4.0 × 108 M-1 s-1. The relationship between the redox properties (thermodynamic and kinetic factors) and the superoxide dismuting activity of such compounds is discussed.
Ultraviolet laser desorption/ionization mass spectrometry of proteins above 100,000 daltons by pulsed ion extraction time-of-flight analysis (1990)

UV laser desorption mass spectra of large proteins (up to 116 kDa) have been obtained on a Wiley-McLaren type time-of-flight instrument with pulsed ion extraction. Intense ion signals could be observed following delay times of several microseconds prior to ion acceleration and extraction. Initial kinetic energy distributions of ions could be determined from the drift time between the probe tip and the ion optical axis and were found to be about 1 eV, in contrast to measurements by retarding potential techniques at the detector site.
Insulin-Like Growth Factor-1 Attenuates the Detrimental Impact of Nonocclusive Coronary Artery Constriction on the Heart (1999)

Coronary artery narrowing (CAN) induces tissue injury, which may involve myocyte necrosis and apoptosis. Insulin-like growth factor (IGF)-1 may counteract cell death, modifying the detrimental effects of myocardial ischemia. On this basis, CAN was produced in female FVB.Igf+/- mice and nontransgenic littermates, and the animals were euthanized 7 days later. CAN consisted of an 82% reduction in the vessel luminal cross-sectional area in both groups of mice. Severe left ventricular dysfunction was present in CAN nontransgenic and transgenic mice, but heart and left ventricular weights increased more in littermates than in FVB.Igf+/- mice. Similarly, the changes in chamber volume and diastolic wall stress were greater in nontransgenic mice. Subacute tissue injury, represented by foci of replacement fibrosis, was 2.6-fold higher in CAN littermates than in FVB.Igf+/- mice. Ongoing myocyte necrosis was 5-fold greater in nontransgenic mice, whereas apoptosis was low and did not differ in the 2 groups of mice. In CAN nontransgenic mice, myocyte necrosis was 12-fold more frequent than apoptosis but, in CAN transgenic mice, these 2 types of cell death were comparable. alpha-Myosin and beta-myosin isoform mRNAs were affected by CAN, but alpha-myosin mRNA was reduced more in nontransgenic mice. In conclusion, myocyte necrosis and replacement fibrosis are the prevailing forms of myocardial damage induced by CAN. Constitutive overexpression of IGF-1 attenuates myocyte necrosis and tissue injury, having no effect on cell apoptosis. These factors limit ventricular dilation, myocardial loading, cardiac hypertrophy, and alterations in alpha- and beta-myosin isoform expression.
Capacitorless one-transistor dynamic random-access memory based on asymmetric double-gate Ge/GaAs-heterojunction tunneling field-effect transistor with n-doped boosting layer and drain-underlap structure (2018)

In this work, we present a capacitorless one-transistor dynamic random-access memory (1T-DRAM) based on an asymmetric double-gate Ge/GaAs-heterojunction tunneling field-effect transistor (TFET) for DRAM applications. The n-doped boosting layer and gate2 drain-underlap structure is employed in the device to obtain an excellent 1T-DRAM performance. The n-doped layer inserted between the source and channel regions improves the sensing margin because of a high rate of increase in the band-to-band tunneling (BTBT) probability. Furthermore, because the gate2 drain-underlap structure reduces the recombination rate that occurs between the gate2 and drain regions, a device with a gate2 drain-underlap length (LG2_D-underlap) of 10 nm exhibited a longer retention performance. As a result, by applying the n-doped layer and gate2 drain-underlap structure, the proposed device exhibited not only a high sensing margin of 1.11 µA/µm but also a long retention time of greater than 100 ms at a temperature of 358 K (85 °C).