gebhart/patrepeval huggingface dataset:
Compartmentalization of λ subtype expression in the B cell repertoire of mice with a disrupted or normal Cχgene segment (1994)

The establishment of the B cell repertoire depends on two major parameters. The first is determined by mechanistic processes that give rise to a great diversity of B cell receptors from a combination of multiple gene segments. The second is dominated by selective processes that recruit B cell clones via their immunoglobulin receptors. To assess the impact of these parameters on the composition of B cell repertoire, we constructed a mouse model displaying a B cell repertoire limited in its diversity. To this end, we disrupted the C kappa segment by gene targeting. B cells from such mutant mice do not express the kappa light chain. Their light chain repertoire is therefore limited by the expression of only four main lambda light chains: lambda 1, lambda 2(V2), lambda 2(Vx) and lambda 3. In this study we described the proportions of each lambda subtype in various lymphoid compartments. Our results show that the lambda 1 subtype is dominant in the spleen and the bone marrow. Moreover, lambda 1 prevalence is independent of the wild or mutant C kappa genotype. These results suggest that the mechanistic processes are mainly responsible for the bias in lambda subtype expression. On the other hand, the lambda 2(V2) and/or lambda 3 subtypes are expressed at higher levels in the peritoneal cavity. Their prevalence is again observed regardless of the C kappa genotype and seems to be due to B1 cells. These results suggest that different mechanistic processes could control lambda subtype expression in B1 and B2 cell lineages.
Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism (1999)

Fluorescence resonance energy transfer and fluorescence polarization anisotropy are used to investigate single molecules of the enzyme staphylococcal nuclease. Intramolecular fluorescence resonance energy transfer and fluorescence polarization anisotropy measurements of fluorescently labeled staphylococcal nuclease molecules reveal distinct patterns of fluctuations that may be attributed to protein conformational dynamics on the millisecond time scale. Intermolecular fluorescence resonance energy transfer measurements provide information about the dynamic interactions of staphylococcal nuclease with single substrate molecules. The experimental methods demonstrated here should prove generally useful in studies of protein folding and enzyme catalysis at single-molecule resolution.
High Sensitivity and Specificity of Chromosomal Pertubations in Human Invasive Breast Cancer (BrCa) Associated with Circulating Nucleic Acids (CNA) Using Concatemers of Short Sequence DNA Tags in Next Generation Sequencing (NGS) (2011)

Study Objective NGS platforms differ by read lengths and read numbers per run. We demonstrated the power of CNA sequencing in predicting invasive ductal and lobular BrCa with the Roche 454 Titanium platform. This study compares our long sequence data with higher numbers of short sequence concatemers compatible with short reader NGS platforms. Methods CNA from 178 invasive BrCa (65 Stage 1/113 Stage 2) patients (155 ductal/23 lobular) and 108 normal females was compared to a random subset of 52 BrCa and 35 controls processed in a Super-SAGE like procedure (SuSa) yielding DNA concatemers. Both were sequenced on a Roche Titanium and aligned to the human genome. Results The SuSa provided a 16-fold increase of informative reads (154,000 vs 9,400 reads/sample). 500 rounds of random splitting of the groups as training and validation data sets (50/50) were performed. The increased data density of SuSa facilitated the selection of genomic regions that separate BrCa patients from controls in the validation sets with higher (84%±6%) accuracy compared to the native (70%±4%) data set. The C-statistic from ROC curves was 0.90±0.05 in the SuSa validation sets vs. 0.77±0.03 native. Conclusion These data show that NGS of serum DNA concatemers can detect genomic instability in BrCa with increased sensitivity and high specificity without prior knowledge of the unique genomic fingerprint of the neoplasm.
Thermosensitive, extracellular neutral proteases in Bacillus subtilis: isolation, characterization, and genetics (1979)

Two mutants (NT02 and NT17), each producing a thermosensitive neutral protease, were isolated from Bacillus subtilis NP58, a transformant which acquired the property of hyperproduction of neutral protease from Bacillus natto IAM 1212. The neutral proteases produced by these two mutants were partially purified and enzymologically characterized. The two mutant neutral proteases displayed increased thermosensitivity as well as altered pH optima compared with those of the NP58 enzyme. In addition, the hydrolytic activity of the thermosensitive neutral proteases on synthetic peptide substrates was found to be extremely different. These results strongly suggest that the site of mutation in each of the temperature-sensitive strains is located within the structural gene for neutral protease (nprE). Previous studies indicated the existence of a specific regulator gene (nprR) in addition to the structural gene for neutral protease. Phage PBS1-mediated transduction and deoxyribonucleic acid-mediated transformation studies with the parental and mutant strains suggest that the chromosomal order of these genes is recA-pyrA-nprR-nprE-fruB-metC. Moreover, the results of these genetic analyses imply that the mutations to thermosensitivity are located proximate to each other within the nprE gene.
The leukemia inhibitory factor (LIF) (1991)

Leukemia inhibitory factor (LIF) is a glycoprotein able to enforce differentiation and/or suppress clonogenic self-renewal in a number of myeloid leukemic cell lines. When acting on normal embryonic stem cells, it has the opposite action of preventing differentiation commitment. LIF is not a proliferative factor when acting alone on normal hemopoietic cells, but can potentiate the action of interleukin 3 on blast cell and megakaryocyte precursors. When injected in vivo, LIF stimulates rises in megakaryocyte numbers and platelet levels. LIF also exhibits striking functional effects on a wide range of other cells including hepatic parenchymal cells, neurones, adipocytes, osteoblasts and gonadal cells. The polyfunctionality of LIF suggests strongly that it is normally intended to be produced locally and act as a local regulator. Despite its wide range of actions, LIF remains a promising candidate for clinical use in thrombocytopenia and myeloid leukemia.
The investment value of mutual fund portfolio disclosure (2007)

This paper shows that publicly disclosed mutual fund portfolio holdings contain valuable information about stock fundamentals and future returns. We develop a model to efficiently aggregate this information across actively-managed funds with differential skills to predict individual stock returns. This stock-level measure, which we call the "generalized-inverse alpha" (GIA), selects portfolios of stocks that exhibit much better performance relative to a "copycat strategy" that simply mimics the stockholdings of funds. We use the GIA model to study the source of fund managers' stock selection ability, and find that some managers have skills in uncovering information from fundamental research about the future earnings of stocks. Notably, the forecasting power of our measures is not subsumed by publicly-available quantitative predictors such as momentum, value, and earnings quality, nor is it subsumed by methods shown in past research to forecast stock returns using fund holdings or trades.
Use of a transposon (Tndif) to obtain suppressing and nonsuppressing insertions of the dif resolvase site of Escherichia coli. (1996)

The dif locus is a RecA-independent recombination site, located in the terminus region of the chromosome of Escherichia coli. This site functions to reduce circular dimer chromosomes to monomers before cell division. Strains lacking this site exhibit the Dif phenotype, in which a fraction of the cells form extended filaments with abnormal nucleoids, and the SOS system is induced. We have used a transposon (Tndif), as well as linear transformation, to position dif in 19 locations around the chromosome. All of the suppressing insertions that we obtained were within 10 kb of the normal site, even in strains in which the normal symmetry, between the origin of replication and dif had been altered by 200 kb. We also observed that the nonsuppressing insertions in the terminus region became suppressing if a deletion occurred that extended from the ectopic site up to or past the normal location of dif. We propose that dif is normally located at the center of converging polarities in the terminus region and that deletions that restore suppression do so by placing ectopic sites once again at the center of this polarity. Similar results and conclusions are described in this issue.
Clinical Relevance of Plasma Prostaglandin F2α Metabolite Concentrations in Patients with Idiopathic Pulmonary Fibrosis (2013)

We demonstrated significant associations of plasma concentrations of PGF2α metabolites with disease severity and prognosis, which support a potential pathogenic role for PGF2α in human IPF.
The HLA‐A,B,C genotype of the class I negative cell line Daudi reveals novel HLA‐A and ‐B alleles (1995)

Daudi, a lymphoblastoid B cell line derived from an African Burkitt lymphoma does not express HLA-A,B,C antigens at the cell surface. Although HLA-A,B,C heavy chains are made normally they do not assemble into functional molecules because beta 2-microglobulin is absent. Previous serological analysis of somatic cell hybrids indicated that the HLA haplotypes of Daudi encoded HLA-A1, A10(A26), B17, and B16(38) antigens. Here we describe the application of molecular methods: ARMS-PCR, cDNA cloning and sequencing, immunoprecipitation and gel electrophoresis, to define the class I genotype of the Daudi cell line which is HLA-A*0102, A*6601, B*5801, B*5802, Cw*0302 and Cw*0602. With the exception of the B38 antigen, which is not a product of the alleles defined, the genotype is consistent with the serological description. Two previously undiscovered alleles emerged from this analysis: A*0102 and B*5802. The A*0102 allele differs from A*0101 by 5 nucleotide substitutions within exon 2 where it has a motif shared with A*30 alleles; the B*5802 allele differs from B*5801 by 3 substitutions in exon 3 where it has a motif shared with B*14 alleles. Subtyping HLA-A1 alleles showed A*0102 was well represented amongst individuals typed serologically as A1 in an African population but was absent from caucasoids. B*5802 has been found in a second individual. Thus the novel A and B alleles are not specific to the Daudi tumor. Overall, this analysis of a single East African cell illustrates the power of molecular methods to define new class I HLA alleles in non-caucasoid populations.
The Human Hair Follicle Engages in Glutaminolysis and Aerobic Glycolysis: Implications for Skin, Splanchnic and Neoplastic Metabolism (1994)

On maintenance in supplemented Williams E medium, human hair follicles grow at the normal rate, and retain their normal anagen morphology, for up to 10 days. This permits us to study their metabolism under near-physiological conditions. The ATP content of freshly isolated follicles was 124.4 +/- 10.6 pmol/follicle (mean +/- SEM; n = 50). The energy charge was 0.81 +/- 0.08 and the glycogen content 2.3 +/- 0.3 nmol/follicle. These did not alter significantly during any metabolic studies, which were performed for up to 6 h in supplemented Williams E medium. We found that the major fuel was glucose, which at physiological concentrations yields 5.47 +/- 0.77 nmol ATP/follicle/h, but 90% of the glucose was metabolised to lactate, and only 10% oxidised. Glutamine was also an important fuel, generating 2.16 +/- 0.33 nmol ATP/follicle/h, but this too was largely metabolised to lactate rather than oxidised. Lipid fuels such as palmitate or beta-hydroxybutyrate only yielded 0.72 +/- 0.15 and 0.72 +/- 0.14 nmol ATP/follicle/h, respectively, and their oxidation did not inhibit glucose utilisation. No glucose-fatty acid cycle operates in the hair follicle, therefore, but a glucose-glutamine cycle does, since the presence of glutamine will inhibit glucose utilisation.
Presence of dendritic cells, MCP‐1, and activated microglia/macrophages in amyotrophic lateral sclerosis spinal cord tissue (2003)

Dendritic cells are potent antigen-presenting cells that initiate and amplify immune responses. To determine whether dendritic cells participate in inflammatory reactions in amyotrophic lateral sclerosis (ALS), we examined mRNA expression of dendritic cell surface markers in individual sporadic ALS (sALS), familial ALS (fALS), and nonneurological disease control (NNDC) spinal cord tissues using semiquantitative and real-time reverse transcription polymerase chain reaction (RT-PCR). Immature (DEC205, CD1a) and activated/mature (CD83, CD40) dendritic cell transcripts were significantly elevated in ALS tissues. The presence of immature and activated/mature dendritic cells (CD1a(+) and CD83(+)) was confirmed immunohistochemically in ALS ventral horn and corticospinal tracts. Monocytic/macrophage/microglial transcripts (CD14, CD18, SR-A, CD68) were increased in ALS spinal cord, and activated CD68(+) cells were demonstrated in close proximity to motor neurons. mRNA expressions of the chemokine MCP-1, which attracts monocytes and myeloid dendritic cells, and of the cytokine macrophage-colony stimulating factor (M-CSF) were increased in ALS tissues. The MCP-1 protein was expressed in glia in ALS but not in control tissues and was increased in the CSF of ALS patients. Those patients who progressed most rapidly expressed significantly more dendritic transcripts than patients who progressed more slowly. These results support the involvement of immune/inflammatory responses in amplifying motor neuron degeneration in ALS.
Evidence for an antigen-specific cellular immune response in skin lesions of patients with psoriasis vulgaris (1995)

Psoriasis vulgaris is an inflammatory skin disease characterized by excessively increased keratinocyte proliferation. Several lines of evidence support the idea that T cells infiltrating psoriatic skin lesions play a vital role in the pathogenesis of the disease. To establish whether lesional accumulation and activation of T lymphocytes reflect a specific local immune response, the TCR beta-chain variable (V beta) region gene usage was studied in chronic psoriatic plaques, normal skin, and paired blood lymphocytes. By semiquantitative PCR, we found that overexpression of either or both V beta 2 and V beta 6 gene families characterized the TCR repertoires of normal skin and psoriatic skin lesions. However, sequence analysis of the complementarity-determining region 3 (CDR3) of these V beta gene families demonstrated a marked TCR oligoclonality only in psoriatic lesions, not in normal skin or in blood lymphocytes. The amino acid sequences of the lesional TCR clones revealed that certain conserved junctional motifs were shared by different patients. A second biopsy taken from one of the psoriasis patients 18 mo later from a different anatomical site disclosed that the same TCR clones were again dominating. These data suggest that lesional psoriatic T lymphocytes expressing the prevailing TCR V beta genes represent an oligoclonal T cell subset that expanded from a few progenitor T cells in response to Ag in the skin of psoriasis patients. They are derived from a polyclonal T cell population that, by the expression of V beta 2 or V beta 6 TCR, appears to be predisposed for homing to the skin.
METASTASIS-INDUCING DNA REGULATES THE EXPRESSION OF THE OSTEOPONTIN GENE BY BINDING THE TRANSCRIPTION FACTOR TCF-4 (2002)

Small 1,000-bp fragments of genomic DNA obtained from human malignant breast cancer cell lines when transfected into a benign rat mammary cell line enhance transcription of the osteopontin gene and thereby cause the cells to metastasize in syngeneic rats. To identify the molecular events underlying this process, transient cotransfections of an osteopontin promoter-reporter construct and fragments of one metastasis-inducing DNA (Met-DNA) have identified the active components in the Met-DNA as the binding sites for the T-cell factor (Tcf) family of transcription factors. Incubation of cell extracts with active DNA fragments containing the sequence CAAAG caused retardation of their mobilities on polyacrylamide gels, and Western blotting identified Tcf-4, beta-catenin, and E-cadherin in the relevant DNA complexes in vitro. Transfection of an expression vector for Tcf-4 inhibited the stimulated activity of the osteopontin promoter-reporter construct caused by transiently transfected active fragments of Met-DNA or permanently transfected Met-DNA. This stimulated activity of the osteopontin promoter-reporter construct is accompanied by an increase in endogenous osteopontin mRNA but not in fos or actin mRNAs in the transfected cells. Permanent transfection of the benign rat mammary cell line with a 20-bp fragment from the Met-DNA containing the Tcf recognition sequence CAAAG caused an enhanced permanent production of endogenous osteopontin protein in vitro and induced the cells to metastasize in syngeneic rats in vivo. The corresponding fragment without the CAAAG sequence was without either effect. Therefore, the regulatory effect of the C9-Met-DNA is exerted, at least in part, by a CAAAG sequence that can sequester the endogenous inhibitory Tcf-4 and thereby promote transcription of osteopontin, the direct effector of metastasis in this system.
Assessment of chemical modifications of sites in the CDRs of recombinant antibodies (2014)

Modifications like asparagine deamidation, aspartate isomerization, methionine oxidation, and lysine glycation are typical degradations for recombinant antibodies. For the identification and functional evaluation of antibody critical quality attributes (CQAs) derived from chemical modifications in the complementary-determining regions (CDRs) and the conserved regions, an approach employing specific stress conditions, elevated temperatures, pH, oxidizing agents, and forced glycation with glucose incubation, was applied. The application of the specific stress conditions combined with ion exchange chromatography, proteolytic peptide mapping, quantitative liquid chromatography mass spectrometry, and functional evaluation by surface plasmon resonance analysis was adequate to identify and functionally assess chemical modification sites in the CDRs of a recombinant IgG1. LC-Met-4, LC-Asn-30/31, LC-Asn-92, HC-Met-100c, and HC Lys-33 were identified as potential CQAs. However, none of the assessed degradation products led to a complete loss of functionality if only one light or heavy chain of the native antibody was affected.
Integration of mini-retroviral DNA: a cell-free reaction for biochemical analysis of retroviral integration. (1989)

After retroviral infection of a permissive cell, the viral RNA is reverse-transcribed to make a DNA copy of the viral genome. Integration of this DNA copy into the host genome is a necessary step for efficient viral replication. We have developed a cell-free system for integration of exogenous mini-retroviral DNA. The termini of this linear mini-Moloney murine leukemia virus (MoMLV) DNA are designed to mimic the ends of authentic unintegrated MoMLV DNA. The viral proteins required for integration can be provided either as a cytoplasmic extract of MoMLV-infected NIH 3T3 cells or as disrupted MoMLV particles. Phage lambda DNA serves as the target for integration. Genetic markers present on the mini-MoMLV DNA enable integration events to be detected, and the recombinants recovered, by selection in Escherichia coli. Integration, which occurs at heterogeneous locations in the target DNA, is absolutely dependent on the presence of a source of viral proteins and a divalent cation in the reaction mixture. The fidelity of the integration reaction was confirmed by sequencing the junctions between the integrated MoMLV DNA and adjacent lambda DNA sequence. In each case, as expected for authentic MoMLV DNA integration, a 4-base-pair duplication of target DNA sequence flanked the integrated MoMLV DNA.
Response letter: “epigenetic modulation of a miR-296-5p:HMGA1 axis regulates Sox2 expression and glioblastoma stem cells” (2016)

In this issue of Translational Cancer Research Ferrucci and Zollo provide a thoughtful commentary discussing our recent Oncogene publication titled “Epigenetic Modulation of a miR-296-5p:HMGA1 Axis Regulates Sox2 expression and Glioblastoma Stem Cells”. The experts examined our results with a critical eye and comment on the strengths and weaknesses of our study while at the same time providing very thoughtful and considerate suggestions for future studies and new directions.
Residual Networks Behave Like Ensembles of Relatively Shallow Networks (2016)

In this work we propose a novel interpretation of residual networks showing that they can be seen as a collection of many paths of differing length. Moreover, residual networks seem to enable very deep networks by leveraging only the short paths during training. To support this observation, we rewrite residual networks as an explicit collection of paths. Unlike traditional models, paths through residual networks vary in length. Further, a lesion study reveals that these paths show ensemble-like behavior in the sense that they do not strongly depend on each other. Finally, and most surprising, most paths are shorter than one might expect, and only the short paths are needed during training, as longer paths do not contribute any gradient. For example, most of the gradient in a residual network with 110 layers comes from paths that are only 10-34 layers deep. Our results reveal one of the key characteristics that seem to enable the training of very deep networks: Residual networks avoid the vanishing gradient problem by introducing short paths which can carry gradient throughout the extent of very deep networks.
Brain Oscillations Control Timing of Single-Neuron Activity in Humans (2007)

A growing body of animal research suggests that neurons represent information not only in terms of their firing rates but also by varying the timing of spikes relative to neuronal oscillations. Although researchers have argued that this temporal coding is critical in human memory and perception, no supporting data from humans have been reported. This study provides the first analysis of the temporal relationship between brain oscillations and single-neuron activity in humans. Recording from 1924 neurons, we find that neuronal activity in various brain regions increases at specific phases of brain oscillations. Neurons in widespread brain regions were phase locked to oscillations in the theta- (4-8 Hz) and gamma- (30-90 Hz) frequency bands. In hippocampus, phase locking was prevalent in the delta- (1-4 Hz) and gamma-frequency bands. Individual neurons were phase locked to various phases of theta and delta oscillations, but they only were active at the trough of gamma oscillations. These findings provide support for the temporal-coding hypothesis in humans. Specifically, they indicate that theta and delta oscillations facilitate phase coding and that gamma oscillations help to decode combinations of simultaneously active neurons.