gebhart/patrepeval huggingface dataset:
Invariant Polymorphism in Virus Capsid Assembly (2009)

Directed self-assembly of designed viral capsids holds significant potential for applications in materials science and medicine. However, the complexity of preparing these systems for assembly and the difficulty of quantitative experimental measurements on the assembly process have limited access to critical mechanistic questions that dictate the final product yields and isomorphic forms. Molecular simulations provide a means of elucidating self-assembly of viral proteins into icosahedral capsids and are the focus of the present study. Using geometrically realistic coarse-grained models with specialized molecular dynamics methods, we delineate conditions of temperature and coat protein concentration that lead to the spontaneous self-assembly of T = 1 and T = 3 icosahedral capsids. In addition to the primary product of icosahedral capsids, we observe a ubiquitous presence of nonicosahedral yet highly symmetric and enclosed aberrant capsules in both T = 1 and T = 3 systems. This polymorphism in assembly products recapitulates the scope and morphology of particle types that have been observed in mis-assembly experiments of virus capsids. Moreover, we find that this structural polymorphism in the end point structures is an inherent property of the coat proteins and arises from condition-dependent kinetic mechanisms that are independent of the elemental mechanisms of capsid growth (as long as the building blocks of the coat proteins are all monomeric, dimeric, or trimeric) and the capsid T number. The kinetic mechanisms responsible for self-assembly of icosahedral capsids and aberrant capsules are deciphered; the self-assembly of icosahedral capsids requires a high level of assembly fidelity, whereas self-assembly of nonicosahedral capsules is a consequence of an off-pathway mechanism that is prevalent under nonoptimal conditions of temperature or protein concentration during assembly. The latter case involves kinetically trapped dislocations of pentamer-templated proteins with hexameric organization. These findings provide insights into the complex processes that govern viral capsid assembly and suggest some features of the assembly process that can be exploited to control the assembly of icosahedral capsids and nonicosahedral capsules.
PSF1, a DNA Replication Factor Expressed Widely in Stem and Progenitor Cells, Drives Tumorigenic and Metastatic Properties (2010)

PSF1 (partner of sld five 1) is an evolutionarily conserved DNA replication factor implicated in DNA replication in lower species that is strongly expressed in a wide range of normal stem cell populations and progenitor cell populations. Because stem and progenitor cells possess high proliferative capacity, we hypothesized that PSF1 may play an important role in tumor growth. To begin to investigate PSF1 function in cancer cells, we cloned the mouse PSF1 promoter and generated lung and colon carcinoma cells that stably express a PSF1 promoter-reporter gene. Reporter expression in cells correlated with endogenous PSF1 mRNA expression. In a tumor cell xenograft model, high levels of reporter expression correlated with high proliferative activity, serial transplantation potential, and metastatic capability. Notably, cancer cells expressing reporter levels localized to perivascular regions in tumors and displayed expression signatures related to embryonic stem cells. RNAi-mediated silencing of endogenous PSF1 inhibited cancer cell growth by disrupting DNA synthesis and chromosomal segregation. These findings implicate PSF1 in tumorigenesis and offer initial evidence of its potential as a theranostic target.
The Link Module from Ovulation- and Inflammation-associated Protein TSG-6 Changes Conformation on Hyaluronan Binding (2003)

The solution structure of the Link module from human TSG-6, a hyaladherin with important roles in inflammation and ovulation, has been determined in both its free and hyaluronan-bound conformations. This reveals a well defined hyaluronan-binding groove on one face of the Link module that is closed in the absence of ligand. The groove is lined with amino acids that have been implicated in mediating the interaction with hyaluronan, including two tyrosine residues that appear to form essential intermolecular hydrogen bonds and two basic residues capable of supporting ionic interactions. This is the first structure of a non-enzymic hyaladherin in its active state, and identifies a ligand-induced conformational change that is likely to be conserved across the Link module superfamily. NMR and isothermal titration calorimetry experiments with defined oligosaccharides have allowed us to infer the minimum length of hyaluronan that can be accommodated within the binding site and its polarity in the groove; these data have been used to generate a model of the complex formed between the Link module and a hyaluronan octasaccharide.
Monolithically integrated InP-based tunable wavelength conversion (2004)

In this work, we describe tunable wavelength converters based on a photodiode receiver integrated with a tunable laser transmitter. Devices are fabricated on a robust InP ridge/InGaAsP waveguide platform. The photodiode receiver consists of an integrated SOA pre-amplifier and a PIN diode to improve sensitivity. The laser transmitter consists of a 1550 nm widely tunable SGDBR laser modulated either directly or via an integrated modulator outside the laser cavity. An SOA post-amplifier provides high output power. The integrated device allows signal monitoring, transmits at 2.5 GB/s, and removes the requirements for filtering the input wavelength at the output. Integrating the SGDBR yields a compact wavelength agile source that requires only two fiber connections, and no off-chip high speed electrical connections. Analog and digital performance of directly and externally modulated wavelength converters is also described.
Phase noise in coupled oscillators: theory and experiment (1997)

Phase noise in mutually synchronized oscillator systems is analyzed for arbitrary coupling and injection-locking topologies, neglecting amplitude noise, and amplitude modulation (AM) to phase modulation (PM) conversion. When the coupling phase is chosen properly (depending on the oscillator model), the near-carrier phase noise is reduced to 1/N that of a single oscillator, provided the coupling network is reciprocal. This is proved In general, and illustrated with specific cases of globally coupled and nearest-neighbor coupled oscillator chains. A slight noise degradation is found for unilaterally coupled (nonreciprocal) chains. The 1/N reduction for reciprocal coupling applies over nearly the entire range of free-running frequency distributions required for beam-scanning, and is verified experimentally using a linear chain of coupled GaAs MESFET voltage-controlled oscillators (VCOs) operating at X-band. The effect of a nonoptimum coupling phase on the phase noise of the system is also studied. As the coupling phase deviates from the optimum value, the phase noise increases significantly near the locking range edge for noise offset frequency near the carrier.
Dataflow machine architecture (1986)

Dataflow machines are programmable computers of which the hardware is optimized for fine-grain data-driven parallel computation. The principles and complications of data-driven execution are explained, as well as the advantages and costs of fine-grain parallelism. A general model for a dataflow machine is presented and the major design options are discussed. Most dataflow machines described in the literature are surveyed on the basis of this model and its associated technology. For general-purpose computing the most promising dataflow machines are those that employ packet-switching communication and support general recursion. Such a recursion mechanism requires an extremely fast mechanism to map a sparsely occupied virtual space to a physical space of realistic size. No solution has yet proved fully satisfactory. A working prototype of one processing element is described in detail. On the basis of experience with this prototype, some of the objections raised against the dataflow approach are discussed. It appears that the overhead due to fine-grain parallelism can be made acceptable by sophisticated compiling and employing special hardware for the storage of data structures. Many computing-intensive programs show sufficient parallelism. In fact, a major problem is to restrain parallelism when machine resources tend to get overloaded. Another issue that requires further investigation is the distribution of computation and data structures over the processing elements.
Controlled Fabrication and Electrical Properties of Long Quasi-One-Dimensional Superconducting Nanowire Arrays (2007)

We report a general method for reliably fabricating quasi-one-dimensional superconducting nanowire arrays, with good control over nanowire cross section and length, and with full compatibility with device processing methods. We investigate Nb nanowires with individual nanowire cross sectional areas that range from bulklike to 10 x 11 nm, and with lengths from 1 to 100 microm. Nanowire size effects are systematically studied. In particular, a comprehensive investigation of influence of nanowire length on superconductivity is reported for the first time. All results are interpreted within the context of phase-slip models.
High speed CMOS chip to chip communication circuit (1991)

Communication circuits between chips through transmission lines are demonstrated. In standard packages, a single-output 75- Omega line driver in a 2- mu m CMOS process reaches a data rate of 700 Mb/s, and a differential-output 50- Omega line driver plus a receiver in a 1.2- mu m CMOS process works up to a data rate of 1 Gb/s. By using leadless chip carriers, the 75- Omega line driver in a 1.2- mu m CMOS process gives a maximum data rate of 1.3 Gb/s. These are measured results. The differential driver and receiver should be able to work at a data rate of 1.25 Gb/s with a leadless chip carrier. The impact of packaging on high speed chip to chip communication is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clinical pharmacokinetics and metabolism of irinotecan (CPT-11). (2001)

CPT-11 belongs to the class of topoisomerase I inhibitors, and it acts as a prodrug of SN-38, which is approximately 100-1000-fold more cytotoxic than the parent drug. CPT-11 has shown a broad spectrum of antitumor activity in preclinical models as well as clinically, with responses observed in various disease types including colorectal, lung, cervical, and ovarian cancer. The pharmacokinetics and metabolism of CPT-11 are extremely complex and have been the subject of intensive investigation in recent years. Both CPT-11 and SN-38 are known in an active lactone form and an inactive carboxylate form, between which an equilibrium exists that depends on the pH and the presence of binding proteins. CPT-11 is subject to extensive metabolic conversion by various enzyme systems, including esterases to form SN-38, UGT1A1 mediating glucuronidation of SN-38, as well as CYP3A4, which forms several pharmacologically inactive oxidation products. Elimination routes of CPT-11 also depend on the presence of drug-transporting proteins, notably P-glycoprotein and canalicular multispecific organic anion transporter, present on the bile canalicular membrane. The various processes mediating drug elimination, either through metabolic breakdown or excretion, likely impact substantially on interindividual variability in drug handling. Strategies to individualize CPT-11 administration schedules based on patient differences in enzyme or protein expression or by coadministration of specific agents modulating side effects are under way and may ultimately lead to more selective chemotherapeutic use of this agent.
Transduction of human melanoma cell lines with the human interleukin-7 gene using retroviral-mediated gene transfer: comparison of immunologic properties with interleukin-2 (1993)

Two human melanoma cell lines were transduced with the human interleukin (IL)-7 and IL-2 genes using retroviral-mediated gene transfer. Stable, high-level cytokine expression was achieved. The in vitro growth of transduced tumors was unaltered. Neither of the IL-2- transduced melanoma cell lines grew in athymic mice, whereas one IL-7- transduced melanoma line showed retarded in vivo growth. This is consistent with animal studies suggesting a predominantly T-cell response to IL-7-transduced tumors and a more nonspecific response to IL-2-transduced tumors. Both IL-7- and IL-2-transduced melanoma cell lines could induce cytotoxic lymphocytes in mixed lymphocyte-tumor cultures. The expression of putative melanoma antigens (MAGE)-1 and MAGE-3 was unaltered by cytokine transduction. In one cell line, IL-7 transduction resulted in a marked inhibition of the immunosuppressive peptide transforming growth factor (TGF)beta 1. The results allow a comparison of immunobiologic properties of IL-7- and IL-2-transduced human melanoma cell lines in consideration of their use in genetically engineered tumor vaccines. IL-7 transduction results in stable cytokine expression and phenotypic alterations that appear to be favorable for enhanced immunogenicity and it deserves clinical testing.
Identification and characterization of the eps (Exopolysaccharide) gene cluster from Streptococcus thermophilus Sfi6 (1996)

We report the identification and characterization of the eps gene cluster of Streptococcus thermophilus Sfi6 required for exopolysaccharide (EPS) synthesis. This report is the first genetic work concerning EPS production in a food microorganism. The EPS secreted by this strain consists of the following tetrasaccharide repeating unit:-->3)-beta-D-Galp-(1-->3)-[alpha-D-Galp-(1-->6)]-beta-D- D-Galp-(1-->3)-alpha-D-Galp-D-GalpNAc-(1-->. The genetic locus The genetic locus was identified by Tn916 mutagenesis in combination with a plate assay to identify Eps mutants. Sequence analysis of the gene region, which was obtained from subclones of a genomic library of Sfi6, revealed a 15.25-kb region encoding 15 open reading frames. EPS expression in the non-EPS-producing heterologous host, Lactococcus lactis MG1363, showed that within the 15.25-kb region, a region with a size of 14.52 kb encoding the 13 genes epsA to epsM was capable of directing EPS synthesis and secretion in this host. Homology searches of the predicted proteins in the Swiss-Prot database revealed high homology (40 to 68% identity) for epsA, B, C, D, and E and the genes involved in capsule synthesis in Streptococcus pneumoniae and Streptococcus agalactiae. Moderate to low homology (37 to 18% identity) was detected for epsB, D, F, and H and the genes involved in capsule synthesis in Staphylococcus aureus for epsC, D, and E and the genes involved in exopolysaccharide I (EPSI) synthesis in Rhizobium meliloti for epsC to epsJ and the genes involved in lipopolysaccharide synthesis in members of the Enterobacteriaceae, and finally for eps K and lipB of Neisseria meningitidis. Genes (epsJ, epsL, and epsM) for which the predicted proteins showed little or no homology with proteins in the Swiss-Prot database were shown to be involved in EPS synthesis by single-crossover gene disruption experiments.
Homing and engraftment potential of Sca-1+lin− cells fractionated on the basis of adhesion molecule expression and position in cell cycle (2000)

Engraftment potential of hematopoietic stem cells (HSCs) is likely to be dependent on several factors including expression of certain adhesion molecules (AMs) and degree of mitotic quiescence. The authors investigated the functional properties and engraftment potential of Sca-1(+)lin(-) cells subfractionated on the basis of expression, or lack thereof, of CD11a, CD43, CD49d, CD49e, or CD62L and correlated that expression with cell cycle status and proliferative potential of engrafting fractions. Donor-derived chimerism in mice receiving CD49e(+) or CD43(+) Sca-1(+)lin(-) cells was greater than that in mice receiving cells lacking these 2 markers, while Sca-1(+)lin(-) cells positive for CD11a and CD62L and bright for CD49d expression mediated minimal engraftment. AM phenotypes enriched for engraftment potential contained the majority of high proliferative potential-colony forming cells, low proliferative potential-colony forming cells, and cells providing rapid in vitro expansion. Cell cycle analysis of AM subpopulations revealed that, regardless of their bone marrow repopulating potential, Sca-1(+)lin(-) AM(-) cells contained a higher percentage of cells in G(0)/G(1) than their AM(+) counterparts. Interestingly, engrafting phenotypes, regardless of the status of their AM expression, were quicker to exit G(0)/G(1) following in vitro cytokine stimulation than their opposing phenotypes. When engrafting phenotypes of Sca-1(+)lin(-) AM(+) or AM(-) cells were further fractionated by Hoechst 33342 into G(0)/G(1) or S/G(2)+M, cells providing long-term engraftment were predominantly contained within the quiescent fraction. These results define a theoretical phenotype of a Sca-1(+)lin(-) engrafting cell as one that is mitotically quiescent, CD43(+), CD49e(+), CD11a(-), CD49d(dim), and CD62L(-). Furthermore, these data suggest that kinetics of in vitro proliferation may be a good predictor of engraftment potential of candidate populations of HSCs. (Blood. 2000;96:1380-1387)
A NOVEL IMMUNOSUPPRESSANT, FTY720, WITH A UNIQUE MECHANISM OF ACTION, INDUCES LONG-TERM GRAFT ACCEPTANCE IN RAT AND DOG ALLOTRANSPLANTATION1 (1996)

A new compound with an immunosuppressive property was purified from culture filtrates of Isaria sinclairii and was chemically modified to FTY720. Rat spleen cells incubated with FTY720 demonstrated features characteristic of apoptosis--such as the absence of surface microvilli, chromatin condensation, and the formation of apoptotic bodies--by electron microscopy, and genemic DNA fragmentation by agarose gel electrophoresis. When FTY720 was administered in liver-allografted rats at a dose of 0.5 mg/kg from day 1 to day 14 after transplantation, the recipients survived significantly longer than the control group. Pretransplant treatment with 5 mg/kg of FTY720 one day before and on the day of grafting induced a remarkable prolongation of recipient survival, and three of 10 recipients survived for longer than 50 days. Furthermore, administration of FTY720 at 5 mg/kg on days 3 and day 4 after grafting also prolonged survival. In canine kidney allografting, a pretransplant 2-day course of FTY720 at 5 mg/kg prolonged graft survival. Daily administration of FTY720 in combination with CsA resulted in a significant prolongation of graft survival in a synergistic manner. In addition, FTY720 appeared to be nontoxic in canine recipients. These results demonstrated that FTY720, having a unique mechanism of action, induces long-term graft acceptance in rat and dog allotransplantation.
neoantigenR: An annotation based pipeline for tumor neoantigen identification from sequencing data (2017)

Abstract Studies indicate that more than 90% of human genes are alternatively spliced, suggesting the complexity of the transcriptome assembly and analysis. The splicing process is often disrupted, resulting in both functional and non-functional end-products (Sveen et al. 2016) in many cancers. Harnessing the immune system to fight against malignant cancers carrying aberrantly mutated or spliced products is becoming a promising approach to cancer therapy. Advances in immune checkpoint blockade have elicited adaptive immune responses with promising clinical responses to treatments against human malignancies (Tumor Neoantigens in Personalized Cancer Immunotherapy 2017). Emerging data suggest that recognition of patient-specific mutation-associated cancer antigens (i.e. from alternative splicing isoforms) may allow scientists to dissect the immune response in the activity of clinical immunotherapies (Schumacher and Schreiber 2015). The advent of high-throughput sequencing technology has provided a comprehensive view of both splicing aberrations and somatic mutations across a range of human malignancies, allowing for a deeper understanding of the interplay of various disease mechanisms. Meanwhile, studies show that the number of transcript isoforms reported to date may be limited by the short-read sequencing due to the inherit limitation of transcriptome reconstruction algorithms, whereas long-read sequencing is able to significantly improve the detection of alternative splicing variants since there is no need to assemble full-length transcripts from short reads. The analysis of these high-throughput long-read sequencing data may permit a systematic view of tumor specific peptide epitopes (also known as neoantigens) that could serve as targets for immunotherapy (Tumor Neoantigens in Personalized Cancer Immunotherapy 2017). Currently, there is no software pipeline available that can efficiently produce mutation-associated cancer antigens from raw high-throughput sequencing data on patient tumor DNA (The Problem with Neoantigen Prediction 2017). In addressing this issue, we introduce a R package that allows the discoveries of peptide epitope candidates, which are the tumor-specific peptide fragments containing potential functional neoantigens. These peptide epitopes consist of structure variants including insertion, deletions, alternative sequences, and peptides from nonsynonymous mutations. Analysis of these precursor candidates with widely used tools such as netMHC allows for the accurate in-silico prediction of neoantigens. The pipeline named neoantigeR is currently hosted in https://github.com/ICBI/neoantigeR .
Cancer progression and tumor cell motility are associated with the FGFR4 Arg(388) allele. (2002)

Expression analysis of genes encoding components of the phosphotyrosine signaling system by cDNA array hybridization revealed elevated levels of FGFR4 transcripts in several mammary carcinoma cell lines. In the FGFR4 gene transcript from MDA-MB-453 mammary carcinoma cells, a G to A conversion was discovered that results in the substitution of glycine by arginine at position 388 in the transmembrane domain of the receptor. The Arg(388) allele was also found in cell lines derived from a variety of other tumor types as well as in the germ-line of cancer patients and healthy individuals. Analysis of three geographically separated groups indicated that it occurs in approximately 50% of the human population. Investigation of the clinical data of 84 breast cancer patients revealed that homo- or heterozygous carriers of the Arg(388) allele had a significantly reduced disease-free survival time (P = 0.01) within a median follow-up of 62 months. Moreover, the FGFR4 Arg(388) allele was associated with early lymph node metastasis and advanced tumor-node-metastasis (TNM) stage in 82 colon cancer patients. Consistent with this finding, MDA-MB-231 mammary tumor cells expressing FGFR4 Arg(388) exhibited increased motility relative to cells expressing the FGFR4 Gly(388) isotype. Our results support the conclusion that the FGFR4 Arg(388) allele represents a determinant that is innocuous in healthy individuals but predisposes cancer patients for significantly accelerated disease progression.