gebhart/patrepeval huggingface dataset:
Domain-switched mouse IgM/IgG2b hybrids indicate individual roles for C mu 2, C mu 3, and C mu 4 domains in the regulation of the interaction of IgM with complement C1q (1997)

Although polymeric IgM and monomeric IgG are potent activators of the classical complement pathway, previous studies have indicated that monomeric IgM is inactive. To understand this and to examine the roles of the individual mu domains in complement activation, we created a set of IgM/IgG2b mouse chimeric Abs in which homologous domains of both Abs have been interchanged, either singly or together with adjacent domains. The monomer subunits (H2L2) of the resulting chimeras were analyzed for their capacities to bind C1q and to initiate complement-mediated lysis (CML) of haptenated erythrocytes. When C gamma 2 was flanked by C mu 4, the inherent C1q-binding activity of the C gamma 2 domain was lost. This demonstrates that C mu 4 can suppress the C1q-binding activity of the adjacent C gamma 2 domain, and suggests that C mu 4 may exert a similar effect on the C mu 3 domain in the IgM monomer subunit. When C mu 3 was located in an IgG2b background and potentially freed from the constraints imposed by the IgM background, the monomer was not able to bind C1q or initiate CML. This suggests that these activities are not expressed inherently in the C mu 3 domain. The transplantation of C mu 3 together with C mu 4 into the IgG background permitted polymer formation. This polymer was able to bind C1q, although neither the monomer nor the polymer forms were active in CML; conversely, all IgM polymers with a transplanted C gamma 2 domain were active in both C1q binding and CML, and demonstrated apparent Kd values similar to that of wild-type IgM.
T-lymphocyte development in scid mice is arrested shortly after the initiation of T-cell receptor delta gene recombination. (1991)

Scid mice lack functional lymphocytes because they carry a mutation that impairs rearrangement of immunoglobulin and T-cell receptor (TCR) genes. Rearrangement of TCR delta, but not gamma and beta genes, was routinely observed in DNA of scid thymocytes and thymocyte hybridomas. TCR delta gene rearrangements appeared to involve D delta 1, D delta 2, and J delta 1 elements only; rearrangement of elements upstream of D delta 1 (e.g., V delta 1) was not observed, and transcripts corresponding to fully assembled TCR delta genes (VDJ delta or VDDJ delta) were not detected in RNA from scid thymocytes. These findings suggest that D delta 1, D delta 2, and J delta 1 may be among the first TCR gene elements to undergo recombination and that scid T-lineage cells are developmentally arrested during or shortly after this stage of differentiation. One class of TCR delta recombination fragments (D delta 2-J delta 1) was amplified by the polymerase chain reaction (PCR) and cloned, and the recombination junctions were sequenced. Most fragments showed normal coding joints. Interestingly, five of seven coding joints that lacked N insertions showed evidence of recombination between short stretches (2-3 bp) of homologous sequence. As discussed, the general absence of V delta-, J gamma-, and J beta-associated rearrangements, despite the occurrence of normal D delta 2-J delta 1 rearrangements, raises the possibility that the scid mutation may cause premature cessation of TCR gene recombination and thereby arrest early T-cell development.
Alzheimer's Disease: Molecular Understanding Predicts Amyloid-Based Therapeutics (2003)

Degenerative diseases of the brain were long considered among the most obscure and intractable of human maladies. However, recent advances in understanding their mechanisms have brought us to the verge of potential disease-modifying agents. This progress is perhaps best exemplified by the case of Alzheimer's disease. The application of molecular pathology and genetics has led to the recognition that the four genes implicated to date in familial Alzheimer's disease all chronically elevate cerebral levels of the amyloid beta-protein (Abeta). Accordingly, small molecule inhibitors of the beta- and gamma-secretases, the proteases that generate Abeta from its precursor, are under active development, and some have shown in vivo efficacy in mouse models. An alternative approach, active or passive immunization against Abeta, has received extensive pre-clinical validation in mice, but an effective preparation free of significant side effects in humans is still awaited. Several other potential therapies are also reviewed here. If one or more of these varied approaches is ultimately proven to slow or prevent dementia, Alzheimer's disease will become a salient example of the successful application of reductionist biology to the most complex of organs, the human cerebral cortex.
Reticulocyte maturation: mitoptosis and exosome release. (2002)

During the differentiation of erythroid cells, a vast program of maturation takes place, leading to decay or elimination of organelles, including the nucleus, mitochondria, ribosomes, lysosomes, endoplasmic reticulum and Golgi apparatus. During the last step of red cell maturation, remaining organelles, primarily mitochondria and ribosomes but also vestiges of others are finally cleared from the cell. This cleaning session also affects specific proteins that are partially or entirely removed from the cell surface. The interplay of the various events and their causal relationships are approached here.
DNA Methylation Changes in Sera of Women in Early Pregnancy Are Similar to Those in Advanced Breast Cancer Patients (2004)

In normal human pregnancy, the uterus and its arterial system, including the decidua and the adjacent third of the myometrium, are invaded by cytotrophoblasts (1)(2), which initiate conversion of the decidual vascular system from a high-pressure/low-flow system to a low-pressure/high-flow system that meets the needs of the fetus and placenta (3). The trophoblastic invasion in humans occurs between weeks 8 and 18 of pregnancy (4). The invasion process into the uterus shows many similarities to the invasion of malignant cells during metastasis in that both types of cells have to pass through a basal membrane (5). One of the most important diseases of pregnant women, preeclampsia, is known to be associated with a failure of complete trophoblastic invasion in the first third of the myometrium (6).

Epigenetic alterations, including changes in DNA methylation status, are among the most common molecular alterations in human neoplasia (7). DNA methylation changes are also involved in mammalian development, starting with a wave of demethylation during cleavage, followed by genome-wide de novo methylation after implantation (8). Recently, Ohgane et al.(9) reported that the differentiation of a trophoblast lineage is associated with DNA methylation and demethylation. In many cases, aberrant methylation of the CpG island genes has been correlated with a loss of gene expression, and it has been proposed that DNA methylation provides an alternative to gene deletion or mutation for the loss of gene function (7). Moreover, it is now widely known that methylated DNA can be detected in various body fluids, including serum and plasma, and that the methylation status of some genes can be used for early detection of, or even risk assessment for, various types of human neoplasia (10).

Cell-free fetal and maternal DNA can be detected in the maternal bloodstream (11) and is reported to …
Antiviral Activities of 9- R -2-Phosphonomethoxypropyl Adenine (PMPA) and Bis(isopropyloxymethylcarbonyl)PMPA against Various Drug-Resistant Human Immunodeficiency Virus Strains (1998)

9-R-2-Phosphonomethoxypropyl adenine (PMPA) is an acyclic nucleoside phosphonate analog that has demonstrated efficacy against human immunodeficiency virus (HIV). We recently described the synthesis, metabolism, and biological activities of bis(isopropyloxymethylcarbonyl)PMPA [bis(poc)PMPA] as an orally bioavailable prodrug for PMPA. Among a large panel of drug-resistant HIV type 1 variants, only the K65R virus was resistant to PMPA. K65R virus also showed reduced susceptibility to bis(poc)PMPA, although the prodrug could still inhibit these viruses at submicromolar, nontoxic concentrations. Among a panel of seven primary clinical isolates from patients with diverse treatment histories, only one isolate showed reduced susceptibility to PMPA and was found to carry three mutations (M41L, T69N, R73K) in its reverse transcriptase catalytic domain.
Prelithiated Silicon Nanowires as an Anode for Lithium Ion Batteries (2011)

Silicon is one of the most promising anode materials for the next-generation high-energy lithium ion battery (LIB), while sulfur and some other lithium-free materials have recently shown high promise as cathode materials. To make a full battery out of them, either the cathode or the anode needs to be prelithiated. Here, we present a method for prelithiating a silicon nanowire (SiNW) anode by a facile self-discharge mechanism. Through a time dependence study, we found that 20 min of prelithiation loads ∼50% of the full capacity into the SiNWs. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) studies show that the nanostructure of SiNWs is maintained after prelithiation. We constructed a full battery using our prelithiated SiNW anode with a sulfur cathode. Our work provides a protocol for pairing lithium-free electrodes to make the next-generation high-energy LIB.
Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase:  Crystallographic Evidence, (1997)

The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) cycles through five detectable kinetic intermediates: holoenzyme, Michaelis complex, ternary product complex, tetrahydrofolate (THF) binary complex, and THF.NADPH complex. Isomorphous crystal structures analogous to these five intermediates and to the transition state (as represented by the methotrexate-NADPH complex) have been used to assemble a 2.1 A resolution movie depicting loop and subdomain movements during the catalytic cycle (see Supporting Information). The structures suggest that the M20 loop is predominantly closed over the reactants in the holoenzyme, Michaelis, and transition state complexes. But, during the remainder of the cycle, when nicotinamide is not bound, the loop occludes (protrudes into) the nicotinamide-ribose binding pocket. Upon changing from the closed to the occluded conformation, the central portion of the loop rearranges from beta-sheet to 3(10) helix. The change may occur by way of an irregularly structured open loop conformation, which could transiently admit a water molecule into position to protonate N5 of dihydrofolate. From the Michaelis to the transition state analogue complex, rotation between two halves of ecDHFR, the adenosine binding subdomain and loop subdomain, closes the (p-aminobenzoyl)glutamate (pABG) binding crevice by approximately 0.5 A. Resulting enhancement of contacts with the pABG moiety may stabilize puckering at C6 of the pteridine ring in the transition state. The subdomain rotation is further adjusted by cofactor-induced movements (approximately 0.5 A) of helices B and C, producing a larger pABG cleft in the THF.NADPH analogue complex than in the THF analogue complex. Such movements may explain how THF release is assisted by NADPH binding. Subdomain rotation is not observed in vertebrate DHFR structures, but an analogous loop movement (residues 59-70) appears to similarly adjust the pABG cleft width, suggesting that these movements are important for catalysis. Loop movement, also unobserved in vertebrate DHFR structures, may preferentially weaken NADP+ vs NADPH binding in ecDHFR, an evolutionary adaptation to reduce product inhibition in the NADP+ rich environment of prokaryotes.
Selection for intrabody solubility in mammalian cells using GFP fusions (2011)

Single-chain antibody fragments (scFv) expressed in the cytoplasm of mammalian cells, also called intrabodies, have many applications in functional proteomics. These applications are, however, limited by the aggregation-prone behaviour of many intrabodies. We show here that two scFv with highly homologous sequences and comparable soluble expression levels in Escherichia coli cytoplasm have different behaviours in mammalian cells. When over-expressed, one of the scFv aggregates in the cytoplasm whereas the second one is soluble and active. When expressed at low levels, using a retroviral vector, as a fusion with the green fluorescent protein (GFP) the former does not form aggregates and is degraded, resulting in weakly fluorescent cells, whereas the latter is expressed as a soluble protein, resulting in strongly fluorescent cells. These data suggest that the GFP signal can be used to evaluate the soluble expression of intrabodies in mammalian cells. When applied to a subset of an E.coli-optimised intrabody library, we showed that the population of GFP+ cells contains indeed soluble mammalian intrabodies. Altogether, our data demonstrate that the requirements for soluble intrabody expression are different in E.coli and mammalian cells, and that intrabody libraries can be directly optimised in human cells using a simple GFP-based assay.
Crystal Structure of the Herpes Simplex Virus 1 DNA Polymerase (2006)

Herpesviruses are the second leading cause of human viral diseases. Herpes Simplex Virus types 1 and 2 and Varicella-zoster virus produce neurotropic infections such as cutaneous and genital herpes, chickenpox, and shingles. Infections of a lymphotropic nature are caused by cytomegalovirus, HSV-6, HSV-7, and Epstein-Barr virus producing lymphoma, carcinoma, and congenital abnormalities. Yet another series of serious health problems are posed by infections in immunocompromised individuals. Common therapies for herpes viral infections employ nucleoside analogs, such as Acyclovir, and target the viral DNA polymerase, essential for viral DNA replication. Although clinically useful, this class of drugs exhibits a narrow antiviral spectrum, and resistance to these agents is an emerging problem for disease management. A better understanding of herpes virus replication will help the development of new safe and effective broad spectrum anti-herpetic drugs that fill an unmet need. Here, we present the first crystal structure of a herpesvirus polymerase, the Herpes Simplex Virus type 1 DNA polymerase, at 2.7 A resolution. The structural similarity of this polymerase to other alpha polymerases has allowed us to construct high confidence models of a replication complex of the polymerase and of Acyclovir as a DNA chain terminator. We propose a novel inhibition mechanism in which a representative of a series of non-nucleosidic viral polymerase inhibitors, the 4-oxo-dihydroquinolines, binds at the polymerase active site interacting non-covalently with both the polymerase and the DNA duplex.
Microstructure to substrate self-assembly using capillary forces (2001)

We have demonstrated the fluidic self-assembly of micromachined silicon parts onto silicon and quartz substrates in a preconfigured pattern with submicrometer positioning precision. Self-assembly is accomplished using photolithographically defined part and substrate binding sites that are complementary shapes of hydrophobic self-assembled monolayers. The patterned substrate is passed through a film of hydrophobic adhesive on water, causing the adhesive to selectively coat the binding sites. Next, the microscopic parts, fabricated from silicon-on-insulator wafers and ranging in size from 150/spl times/150/spl times/15 /spl mu/m/sup 3/ to 400/spl times/400/spl times/50 /spl mu/m/sup 3/, are directed toward the substrate surface under water using a pipette. Once the hydrophobic pattern on a part comes into contact with an adhesive-coated substrate binding site, shape matching occurs spontaneously due to interfacial free energy minimization. In water, capillary forces of the adhesive hold the parts in place with an alignment precision of less than 0.2 /spl mu/m. Permanent bonding of the parts onto quartz and silicon is accomplished by activating the adhesive with heat or ultraviolet light. The resulting rotational misalignment is within /spl sim/0.3/spl deg/. Using square sites, 98-part arrays have been assembled in less than 1 min with 100% yield. The general microassembly approach described here may be applied to parts ranging in size from the nano- to milliscale, and part and substrate materials including semiconductors, glass, plastics, and metals.
Protection of BALB/c mice against homologous and heterologous species of Brucella by rough strain vaccines derived from Brucella melitensis and Brucella suis biovar 4 (1996)

Results encourage evaluation, in primary host species, of VTRM1 and VTRS1, along with RB51, as alternative vaccines to strain 19, Rev 1, or other smooth phase vaccines.
Comparison of the Closed Conformation of the β1,4-galactosyltransferase-1 (β4Gal-T1) in the Presence and Absence of α-lactalbumin (LA) (2003)

beta 1,4-Galactosyltransferase (beta 4Gal-T1) transfers galactose from UDP-galactose to N-acetylglucosamine (GlcNAc) in the presence of Mn(2+) ion. However, in the presence of alpha-lactalbumin (LA) it transfers Gal to glucose (Glc) instead to GlcNAc. Upon substrate binding, beta 4Gal-T1 undergoes transition, from an open to a closed conformation. Although both the acceptor and donor substrates can induce the necessary conformational changes, the enzyme has been crystallized only in the closed conformation in the presence of its preferred donor, UDP-Gal. The closed conformation induced by the sugar acceptors or the less preferred donor substrates has been observed only when complexed with LA. The crystal structure of beta 4Gal-T1 in the presence of UDP-Gal was previously determined at 2.8 A resolution. We report here the same structure at 2.3 A resolution, which provides a better description of this closed conformation. We have also further refined the structures of beta 4Gal-T1.LA complexes containing the sugar acceptor and the less preferred sugar nucleotide donor substrates and compared the conformational changes in the enzyme induced by substrates with and without LA. Based on the binding of UDP-sugar molecules, a rational hypothesis is proposed for the conformational changes induced by the donor substrate.
Syntheses of two potential food mutagens (2003)

Abstract The syntheses of the potential heterocyclic amine food mutagens l,4,6‐trimethyl‐2‐aminoimidazo[4,5‐ c ]‐pyridine and 1,5,7‐trimethyl‐2‐aminoimidazo[4,5‐ b ]pyridine are described.
Characterization of a Chlamydia psittaci DNA Binding Protein (EUO) Synthesized during the Early and Middle Phases of the Developmental Cycle (1998)

ABSTRACT The EUO gene (for early upstream open reading frame) of Chlamydia psittaci was previously found to be transcribed better at 1 than at 24 h postinfection. We found that the EUO gene encodes a minor protein that is expressed within 1 h of infection of host cells with C. psittaci 6BC but that protein quantity peaks during the logarithmic growth phase of reticulate bodies (RBs), declines late in the infection (after 20 h) when RBs reorganize into elementary bodies (EBs), and is absent in infectious EBs. EUO protein lacks homology to known proteins but does contain a putative helix-turn-helix motif. We found that recombinant EUO binds to DNA in vitro with a relatively broad specificity. Using the bp −200 to +67 promoter region of the cysteine-rich envelope protein ( crp ) operon as a model, we show that EUO protein preferentially binds to AT-rich sequences and protects crp DNA from DNase I from approximately bp −60 to −9. We also found that native EUO protein in extracts of RBs binds to the promoter region of the crp operon, demonstrating that the DNA binding property of EUO protein is not an artifact of recombinant methods. Although EUO protein appears to bind to the crp operon with high affinity in vitro ( K d of about 15 nM), it is not known whether the protein binds the crp DNA in vivo.
Simultaneous observation of the quantization and the interference pattern of a plasmonic near-field (2015)

Surface plasmon polaritons can confine electromagnetic fields in subwavelength spaces and are of interest for photonics, optical data storage devices and biosensing applications. In analogy to photons, they exhibit wave-particle duality, whose different aspects have recently been observed in separate tailored experiments. Here we demonstrate the ability of ultrafast transmission electron microscopy to simultaneously image both the spatial interference and the quantization of such confined plasmonic fields. Our experiments are accomplished by spatiotemporally overlapping electron and light pulses on a single nanowire suspended on a graphene film. The resulting energy exchange between single electrons and the quanta of the photoinduced near-field is imaged synchronously with its spatial interference pattern. This methodology enables the control and visualization of plasmonic fields at the nanoscale, providing a promising tool for understanding the fundamental properties of confined electromagnetic fields and the development of advanced photonic circuits.
Isolation of a T-Cell Clone Showing HLA-DRB1*0405-Restricted Cytotoxicity for Hematopoietic Cells in a Patient With Aplastic Anemia (1997)

The existence of T cells capable of inhibiting in vitro hematopoiesis has been shown in aplastic anemia (AA), although whether such inhibition is mediated by a specific immune reaction involving an HLA allele remained unknown. We isolated a CD4+ Vβ21+ T-cell clone that was most dominant among Vβ21+ T cells in the bone marrow (BM) of an AA patient whose HLA-DRB1 alleles included 1501 and 0405. The T-cell clone named NT4.2 lysed an autologous Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) and phytohemagglutinin-stimulated lymphocytes (PHA-blasts) as well as allogeneic LCLs sharing HLA-DRB1*0405. Cytotoxicity against LCL cells and PHA-blasts by NT4.2 was blocked by anti–HLA-DR monoclonal antibody (MoAb) or anti-CD3 MoAb. NT4.2 also lysed autologous BM mononuclear cells enriched with CD34+ cells that had been cultured for one week in the presence of colony-stimulating factors as well as allogeneic CD34+ cells of a normal individual carrying HLA-DRB1*0405, cultured in the same way. Moreover, NT4.2 strongly inhibited colony formation by hematopoietic progenitor cells derived from cultured CD34+ cells sharing HLA-DRB1*0405. These results indicate that the AA patient has T cells capable of killing hematopoietic cells in an HLA-DRB1*0405-restricted manner and that such cytotoxic T cells may contribute to the pathogenesis of AA.
Comprehensive genomic characterization of head and neck squamous cell carcinomas (2020)

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. We find that human papillomavirus-associated (HPV) tumors are dominated by helicase domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss of TP53 mutations and CDKN2A with frequent copy number alterations including a novel amplification of 11q22. A subgroup of oral cavity tumors with favorable clinical outcomes displayed infrequent CNAs in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and wild-type TP53. Other distinct subgroups harbored novel loss of function alterations of the chromatin modifier NSD1, Wnt pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumors. Therapeutic candidate alterations were identified in the majority of HNSCC's.