gebhart/patrepeval huggingface dataset:
Dual function of human IgA antibodies: inhibition of phagocytosis in circulating neutrophils and enhancement of responses in IL-8-stimulated cells (1995)

We have sought to elucidate the responses of human peripheral blood neutrophils to antigenic surfaces complexed with human specific IgA antibodies obtained either as myeloma proteins that recognize staphylococcal alpha-toxin, or from the serum of patients with subacute bacterial endocarditis due to Streptococcus mutans, or from colostrum. In contrast to IgG, IgA antibodies bound to antigen-coated fluorescent microspheres, and subsequently exposed to complement (or not), did not promote phagocytosis, as measured by flow cytometric enumeration of cell-associated microspheres. Instead, IgA antibodies interfered with complement-dependent phagocytosis mediated by IgG antibodies. These properties were shown by different forms of IgA antibodies, including serum and secretory IgA, as well as by monoclonal or polyclonal antibodies. Neutrophils did not respond to the production of superoxide to IgA antibodies complexed with antigen-coated microspheres or with antigen deposited on a solid surface and IgA antibodies suppressed IgG antibody- and complement-mediated superoxide release. However, neutrophils pretreated with interleukin-8 ingested IgA-opsonized microspheres and released superoxide when exposed to IgA antibody-antigen complexes. IgG antibody-antigen complexes did not stimulate increased superoxide release in interleukin-8-treated neutrophils. These findings were consistent with a selective increase in the surface expression of Fc alpha R by interleukin-8-treated neutrophils. We conclude that IgA antibodies interfere with the phagocytic activities of normal circulating human neutrophils and may promote these activities in inflammatory neutrophils activated by interleukin-8 in which Fc alpha R is up-regulated.
Gut Microbiome and Infant Health: Brain-Gut-Microbiota Axis and Host Genetic Factors. (2016)

The development of the neonatal gut microbiome is influenced by multiple factors, such as delivery mode, feeding, medication use, hospital environment, early life stress, and genetics. The dysbiosis of gut microbiota persists during infancy, especially in high-risk preterm infants who experience lengthy stays in the Neonatal intensive care unit (NICU). Infant microbiome evolutionary trajectory is essentially parallel with the host (infant) neurodevelopmental process and growth. The role of the gut microbiome, the brain-gut signaling system, and its interaction with the host genetics have been shown to be related to both short and long term infant health and bio-behavioral development. The investigation of potential dysbiosis patterns in early childhood is still lacking and few studies have addressed this host-microbiome co-developmental process. Further research spanning a variety of fields of study is needed to focus on the mechanisms of brain-gut-microbiota signaling system and the dynamic host-microbial interaction in the regulation of health, stress and development in human newborns.
Catalytic Asymmetric Strecker Synthesis. Preparation of Enantiomerically Pure α-Amino Acid Derivatives from Aldimines and Tributyltin Cyanide or Achiral Aldehydes, Amines, and Hydrogen Cyanide Using a Chiral Zirconium Catalyst (2000)

Catalytic enantioselective Strecker-type reactions of aldimines with tributyltin cyanide (Bu3SnCN) proceeded smoothly in the presence of a novel chiral zirconium catalyst. High levels of enantioselectivities in the synthesis of α-amino nitrile derivatives with wide substrate generality were obtained via these reactions. In addition, hydrogen cyanide (HCN) was successfully used instead of Bu3SnCN as the cyanide source. Catalytic asymmetric Strecker amino acid synthesis starting from achiral aldehydes, amines, and HCN using a chiral zirconium catalyst has also been achieved. The three-component asymmetric process reported here significantly improves upon the original Strecker reaction, and has advantages over previous reactions using unstable imines (Schiff bases) as starting materials. Moreover, high yields and enantioselectivities have been obtained even in the reactions using aliphatic aldehydes, and both enantiomers of various types of α-amino acid derivatives can be prepared. As demonstrations to show the utility of this reaction, efficient syntheses of homophenylalanine, leucine amide, and pipecolic acid derivatives have been performed. Finally, two novel binuclear zirconium complexes (3 and 4) are postulated to be active chiral catalysts in the reactions of aldimines with Bu3SnCN and the three-component reactions, respectively, and low loading levels of the chiral catalysts (1−2.5 mol %) have been accomplished in both cases.
Natural Osmolyte Trimethylamine N-Oxide Corrects Assembly Defects of Mutant Branched-chain α-Ketoacid Decarboxylase in Maple Syrup Urine Disease (2001)

Maple syrup urine disease is caused by deficiency in the mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex. The clinical phenotype includes often fatal ketoacidosis, neurological derangement, and mental retardation. The type IA mutations Y393N-alpha, Y368C-alpha, and F364C-alpha, which occur in the E1alpha subunit of the decarboxylase (E1) component of the BCKD complex, impede the conversion of an alphabeta heterodimeric intermediate to a native alpha(2)beta(2) heterotetramer in the E1 assembly pathway. In the present study, we show that a natural osmolyte trimethylamine N-oxide (TMAO) at the optimal 1 m concentration restores E1 activity, up to 50% of the wild type, in the mutant E1 carrying the above missense mutations. TMAO promotes the conversion of otherwise trapped mutant heterodimers to active heterotetramers. This slow step does not involve dissociation/reassociation of the mutant heterodimers, which are preformed in the presence of chaperonins GroEL/GroES and Mg-ATP. The TMAO-stimulated mutant E1 activity is remarkably stable upon removal of the osmolyte, when cofactor thiamine pyrophosphate and the transacylase component of the BCKD complex are present. The above in vitro results offer the use of chemical chaperones such as TMAO as an approach to mitigate assembly defects caused by maple syrup urine disease mutations.
The Sources of Effective Germ-Plasm in Hybrid Maize (1944)

The last twenty years have seen a complete change in the corn-breeding methods of the U. S. corn
Multilevel coherent optical system based on Stokes parameters modulation (1990)

A multilevel transmission system that allows efficient exploitation of a single-channel bandwidth in coherent optical communication systems is proposed. It is based on Stokes parameter modulation and a decision on the Poincare sphere. The block scheme of the transmitter, which is able to provide a generic output state of polarization (SOP) starting from a linearly polarized optical field, is shown and described. The propagation along the fiber is described in order to derive the expression of the optical field at the receiver input. The spectral characteristics of the transmitted and the received optical signals are analyzed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Intracephalic transplants of freeze‐Stored rat hippocampal tissue (1986)

The survival and cellular and connective organization of intracephalic transplants of developing, freeze-stored rat hippocampal tissue were examined. Blocks of tissue containing the hippocampus and fascia dentata were obtained from late embryonic (E16-E22) and early postnatal rats (P0-P4) and immersed in a tissue culture medium with 10% of the cryoprotective agent DMSO, frozen at a cooling rate of approximately 1 degree C/minute, and stored for 1-226 days in liquid nitrogen. After quick thawing and washing out of the DMSO the tissue blocks were transplanted to the brain of adult rats. From 2 weeks to 3 months later the recipient brains were processed histologically. The cellular and connective organization of the transplants and their interaction with the host brains were analyzed after thionin cell staining, Timm's staining for hippocampal and dentate afferents, immunohistochemical staining for enkephalin-, CCK-, and somatostatin-reactive neurons and afferents, AChE staining for cholinergic afferents, and silver stains for fiber architectonics and tracing of connections by anterograde axonal degeneration. Freeze-storage narrowed the range of donor ages with good transplant survival. The best surviving hippocampal and dentate transplants thus came from 17-21-day-old embryos. There was no correlation between the length of storage and survival. Structurally the transplants of stored tissue were more frequently fragmented than the transplants of fresh tissue when located outside the brain parenchyma in the brain ventricles. This was in accordance with the results of a previous study of grafts of freeze-stored and fresh hippocampal tissue placed in the anterior eye chamber. Despite the decrease in survival and the tendency for fragmentation many well-structured and organotypically organized hippocampal and dentate transplants were recovered corresponding to the donor ages E19-E21. In addition to the main cell types (granule cells and pyramidal cells) the freeze-stored transplants also contained peptidergic nerve cells reacting for CCK, somatostatin, and enkephalin. The organization of the intrinsic nerve connections and the exchange of connections with the host brain were similar for transplants of stored and fresh tissue. Besides the consistent innervation of the hippocampal and dentate transplants by host cholinergic afferents monitored by AChE staining, several appropriately located dentate transplants thus sent mossy fibers to the host CA3. Others received host perforant path projections. A CA3-associated transplant projection to the denervated perforant path zones in the host fascia dentata was also observed.(ABSTRACT TRUNCATED AT 400 WORDS)
Pilot Design for MIMO OFDM Systems With Virtual Carriers (2009)

We consider the problem of pilot design for channel estimation in multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) systems in the presence of virtual carriers. The design criterion is the average mean-square error (MSE) of the least square (LS) estimates of the channel frequency response over the data carriers. To maximize bandwidth efficiency, the number of pilots is set to its minimum which is equal to the number of unknown channel coefficients. Both the phase shift orthogonal and disjoint pilot schemes are investigated. For a given pilot placement, a closed-form expression for the pilot power distribution for the disjoint scheme is provided. It is found that the optimal power distribution allocates less power to the pilots that are close to the virtual carriers. Pilot placement is obtained using an exhaustive search. The latter is too complex in systems with large number of subcarriers. A suboptimum pilot placement design for the disjoint pilot scheme is presented. It is shown that, unlike fully loaded systems where the two pilot design schemes have similar performance, in the presence of virtual carriers the optimal disjoint scheme not only has lower complexity but also yields more accurate channel estimation and bit error rate performance.
Middle tech: blurring the division between high and low tech in education (1998)

In 1997 the most prestigious high school science fair in the United States—the Westinghouse Science Competition [Berger 94] —was won by Adam Cohen, then a senior at Hunter High School in New York City. Cohen&apos;s project, &amp;quot;Near-Field Photolithography&amp;quot;, involved the construction of a home-built scanning tunneling microscope (or STM—a high-resolution
Molecular Determinants of the Myristoyl-electrostatic Switch of MARCKS (1996)

MARCKS is a protein kinase C (PKC) substrate which binds calcium/calmodulin and actin, and which has been implicated in cell motility, phagocytosis, membrane traffic, and mitogenesis. MARCKS cycles on and off the membrane via a myristoyl electrostatic switch (McLaughlin, S., and Aderem, A.(1995) Trends Biochem. Sci. 20, 272-276). Here we define the molecular determinants of the myristoyl-electrostatic switch. Mutation of the N-terminal glycine results in a nonmyristoylated form of MARCKS which does not bind membranes and is poorly phosphorylated. This indicates that myristic acid targets MARCKS to the membrane, where it is efficiently phosphorylated by PKC. A chimeric protein in which the N terminus of MARCKS is replaced by a sequence, which is doubly palmitoylated, is phosphorylated by PKC but not released from the membrane. Thus two palmitic acid moieties confer sufficient membrane binding energy to render the second, electrostatic membrane binding site superfluous. Mutation of the PKC phosphorylation sites results in a mutant which does not translocate from the membrane to the cytosol. A mutant in which the intervening sequence between the myristoyl moiety and the basic effector domain is deleted, is not displaced from the membrane by PKC dependent phosphorylation, fulfilling a theoretical prediction of the model. In addition to the nonspecific membrane binding interactions conferred by the myristoyl-electrostatic switch, indirect immunofluorescence microscopy demonstrates that specific protein-protein interactions also specify the intracellular localization of MARCKS.
Early accumulation of p62 in neurofibrillary tangles in Alzheimer's disease: possible role in tangle formation (2002)

Neurofibrillary tangles (NFTs) and neuritic plaques (NPs) are two major histopathological lesions in Alzheimer's disease (AD). Although their aetiological relationship is unclear, both NFTs and dystrophic neurites of NPs display immunoreactivity for ubiquitin. This suggests that dysfunction in ubiquitin-mediated proteolysis and the resulting accumulation of ubiquitin-conjugated proteins may contribute to the origination of dystrophic neurites and NFTs. We recently discovered a novel constituent of neuropathological protein aggregates, ubiquitin-binding protein p62, with evidence that the accumulation of ubiquitin-conjugated proteins and p62 into cytoplasmic inclusions might be interconnected. In the present work we examined in detail the role of p62 in AD-type pathology, i.e. NFTs, NPs and neuropil threads. Using immunohistochemistry for p62, ubiquitin and hyperphosphorylated tau, we analysed parietal cortical samples of 15 clinicopathologically verified AD cases and nine nondemented aged subjects with abundant NPs. We found that p62 immunoreactivity appears early during neurofibrillary pathogenesis and is invariably and stably present in NFTs. In contrast, p62 was absent or barely detectable in neuropil threads. Furthermore, NP-associated dystrophic neurites were generally devoid of p62, regardless of their content of hyperphosphorylated tau and/or ubiquitin. The results suggest that early involvement of p62 might be critical in the aggregation of hyperphosphorylated tau into perikaryal aggregates, i.e. NFTs.
An ensemble Kalman filtering approach to highway traffic estimation using GPS enabled mobile devices (2008)

Traffic state estimation is a challenging problem for the transportation community due to the limited deployment of sensing infrastructure. However, recent trends in the mobile phone industry suggest that GPS equipped devices will become standard in the next few years. Leveraging these GPS equipped devices as traffic sensors will fundamentally change the type and the quality of traffic data collected on large scales in the near future. New traffic models and data assimilation algorithms must be developed to efficiently transform this data into usable traffic information. In this work, we introduce a new partial differential equation (PDE) based on the Lighthill-Whitham-Richards PDE, which serves as a flow model for velocity. We formulate a Godunov discretization scheme to cast the PDE into a Velocity Cell Transmission Model (CTM-v), which is a nonlinear dynamical system with a time varying observation matrix. The Ensemble Kalman Filtering (EnKF) technique is applied to the CTM- v to estimate the velocity field on the highway using data obtained from GPS devices, and the method is illustrated in microsimulation on a fully calibrated model of I880 in California. Experimental validation is performed through the unprecedented 100-vehicle Mobile Century experiment, which used a novel privacy-preserving traffic monitoring system to collect GPS cell phone data specifically for this research.
Robust affine invariant matching with application to line features (2002)

Line features in geometric hashing are discussed. Lines are used as the primitive features to compute the geometric invariants, combining the Hough transform with a variation of geometric hashing as a technique for model-based object recognition in seriously degraded single intensity images. The effect of uncertainty of line features on the computed invariants for the case where images are formed under affine viewing transformations is analytically determined. The system is implemented with experiments on polygonal objects, which are modeled by lines. It is shown that the technique is noise resistant and suitable in an environment containing many occlusions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Abnormal NF-kappa B activity in T lymphocytes from patients with systemic lupus erythematosus is associated with decreased p65-RelA protein expression. (1999)

Numerous cellular and biochemical abnormalities in immune regulation have been described in patients with systemic lupus erythematosus (SLE), including surface Ag receptor-initiated signaling events and lymphokine production. Because NF-kappa B contributes to the transcription of numerous inflammatory genes and has been shown to be a molecular target of antiinflammatory drugs, we sought to characterize the functional role of the NF-kappa B protein complex in lupus T cells. Freshly isolated T cells from lupus patients, rheumatoid arthritis (RA) patients, and normal individuals were activated physiologically via the TCR with anti-CD3 and anti-CD28 Abs to assess proximal membrane signaling, and with PMA and a calcium ionophore (A23187) to bypass membrane-mediated signaling events. We measured the NF-kappa B binding activity in nuclear extracts by gel shift analysis. When compared with normal cells, the activation of NF-kappa B activity in SLE patients was significantly decreased in SLE, but not in RA, patients. NF-kappa B binding activity was absent in several SLE patients who were not receiving any medication, including corticosteroids. Also, NF-kappa B activity remained absent in follow-up studies. In supershift experiments using specific Abs, we showed that, in the group of SLE patients who displayed undetectable NF-kappa B activity, p65 complexes were not formed. Finally, immunoblot analysis of nuclear extracts showed decreased or absent p65 protein levels. As p65 complexes are transcriptionally active in comparison to the p50 homodimer, this novel finding may provide insight on the origin of abnormal cytokine or other gene transcription in SLE patients.
Molecular Dissection of Formation of Senescence-Associated Heterochromatin Foci (2007)

Senescence is characterized by an irreversible cell proliferation arrest. Specialized domains of facultative heterochromatin, called senescence-associated heterochromatin foci (SAHF), are thought to contribute to the irreversible cell cycle exit in many senescent cells by repressing the expression of proliferation-promoting genes such as cyclin A. SAHF contain known heterochromatin-forming proteins, such as heterochromatin protein 1 (HP1) and the histone H2A variant macroH2A, and other specialized chromatin proteins, such as HMGA proteins. Previously, we showed that a complex of histone chaperones, histone repressor A (HIRA) and antisilencing function 1a (ASF1a), plays a key role in the formation of SAHF. Here we have further dissected the series of events that contribute to SAHF formation. We show that each chromosome condenses into a single SAHF focus. Chromosome condensation depends on the ability of ASF1a to physically interact with its deposition substrate, histone H3, in addition to its cochaperone, HIRA. In cells entering senescence, HP1gamma, but not the related proteins HP1alpha and HP1beta, becomes phosphorylated on serine 93. This phosphorylation is required for efficient incorporation of HP1gamma into SAHF. Remarkably, however, a dramatic reduction in the amount of chromatin-bound HP1 proteins does not detectably affect chromosome condensation into SAHF. Moreover, abundant HP1 proteins are not required for the accumulation in SAHF of histone H3 methylated on lysine 9, the recruitment of macroH2A proteins, nor other hallmarks of senescence, such as the expression of senescence-associated beta-galactosidase activity and senescence-associated cell cycle exit. Based on our results, we propose a stepwise model for the formation of SAHF.
“Hidden” dUTPase Sequence in Human Immunodeficiency Virus Type 1 gp120 (1999)

A coding region homologous to the sequence for essential eukaryotic enzyme dUTPase has been identified in different genomic regions of several viral lineages. Unlike the nonprimate lentiviruses (caprine arthritis- encephalitis virus, equine infectious anemia virus, feline immunodeficiency virus, and visna virus), where dUTPase is integrated into the pol coding region, this enzyme has never been demonstrated to be present in the primate lentivirus genomes (human immunodeficiency virus type 1 [HIV-1], HIV-2, or the related simian immunodeficiency virus). A novel approach allowed us to identify a weak but significant sequence similarity between HIV-1 gp120 and the human dUTPase. This finding was then extended to all of the primate lentivirus lineages. Together with the recently reported fragmentary structural similarity between the V3 loop region and the Escherichia coli dUTPase (P. D. Kwong, R. Wyatt, J. Robinson, R. W. Sweet, J. Sodroski, and W. A. Hendrickson, Nature 393:648-659, 1998), our results strongly suggest that an ancestral dUTPase gene has evolved into the present primate lentivirus CD4 and cytokine receptor interacting region of gp120.
Quantum band engineering of nitride semiconductors for infrared lasers (2014)

The III-nitride semiconductors have been proposed as candidate materials for new quantum cascade lasers in the nearinfrared (1.5-3 μm), and far-infrared (30-60 μm), due to the large conduction-band offset between GaN and Alcontaining alloys (>1 eV), and the large longitudinal optical (LO) phonon energy (90 meV), respectively. The challenges of III-nitride intersubband devices are twofold: material and design related. Due to large electron effective mass, the nitride intersubband materials require the ability to fine-tune the atomic structure at an unprecedented sub-nanometer level. Moreover, the III-N materials exhibit built-in polarization fields that complicate the design of intersubband lasers. This paper presents recent results on c-plane nitride resonant-tunneling diodes that are important for the prospects of farinfrared nitride lasers. We also report near-infrared absorption and photocurrent measurements in nonpolar (m-plane) AlGaN/GaN superlattices.