gebhart/patrepeval huggingface dataset:
Toward targeting B cell cancers with CD4+ CTLs: identification of a CD19-encoded minor histocompatibility antigen using a novel genome-wide analysis (2008)

Some minor histocompatibility antigens (mHags) are expressed exclusively on patient hematopoietic and malignant cells, and this unique set of antigens enables specific targeting of hematological malignancies after human histocompatability leucocyte antigen (HLA)-matched allogeneic stem cell transplantation (allo-SCT). We report the first hematopoietic mHag presented by HLA class II (HLA-DQA1*05/B1*02) molecules to CD4(+) T cells. This antigen is encoded by a single-nucleotide polymorphism (SNP) in the B cell lineage-specific CD19 gene, which is an important target antigen for immunotherapy of most B cell malignancies. The CD19(L)-encoded antigen was identified using a novel and powerful genetic strategy in which zygosity-genotype correlation scanning was used as the key step for fine mapping the genetic locus defined by pairwise linkage analysis. This strategy was also applicable for genome-wide identification of a wide range of mHags. CD19(L)-specific CD4(+) T cells provided antigen-specific help for maturation of dendritic cells and for expansion of CD8(+) mHag-specific T cells. They also lysed CD19(L)-positive malignant cells, illustrating the potential therapeutic advantages of targeting this novel CD19(L)-derived HLA class II-restricted mHag. The currently available immunotherapy strategies enable the exploitation of these therapeutic effects within and beyond allo-SCT settings.
A Tripartite Nuclear Localization Signal in the PDZ-domain Protein L-periaxin (2000)

The murine Periaxin gene encodes two PDZ-domain proteins in myelin-forming Schwann cells of the vertebrate peripheral nervous system (Dytrych, L., Sherman, D. L., Gillespie, C. S., and Brophy, P. J. (1998) J. Biol. Chem. 273, 5794-5800). Here we show that L-periaxin is targeted to the nucleus of embryonic Schwann cells. Subsequently, the protein redistributes to the plasma membrane processes of the myelinating Schwann cell where it is believed to function in a signaling complex. In contrast, L-periaxin remains in the nucleus when expressed ectopically in oligodendrocytes, the myelin-forming glia of the central nervous system. The nuclear localization signal (NLS) is basic and tripartite and comprises three signals that act synergistically. Nuclear targeting of L-periaxin is energy-dependent and is inhibited by cell-cell contact. These data show that L-periaxin is a member of a growing family of proteins that can shuttle between the nucleus and cortical signaling/adherence complexes.
Role of spin-dependent interface scattering in generating current-induced torques in magnetic multilayers (2000)

We present a calculation of current-induced torques in metallic magnetic multilayers derived from the spin-dependent transmission and reflection properties of the magnetic layers. A scattering formalism is employed to calculate the torques in a magnetic-nonmagnetic-magnetic trilayer, for currents perpendicular to the layers, in both the ballistic and diffusive regimes.
Treating OSA: Current and emerging therapies beyond CPAP (2017)

Continuous positive airway pressure (CPAP) is the standard treatment for moderate-to-severe obstructive sleep apnoea (OSA). However, adherence to CPAP is limited and non-CPAP therapies are frequently explored. Oral appliance (OA) therapy is currently widely used for the treatment of snoring, mild, moderate and severe OSA. The most commonly used and studied OA consists of a maxillary and mandibular splint which hold the lower jaw forward during sleep. The efficacy of OA is inferior to CPAP; however, the effectiveness as measured by sleepiness, quality of life, endothelial function and blood pressure is similar likely due to higher acceptance and subjective adherence. Upper airway stimulation augments neural drive by unilaterally stimulating the hypoglossal nerve. The Stimulation Therapy for Apnea Reduction (STAR) study enrolled 126 patients and demonstrated a 68% reduction in OSA severity. A high upfront cost and variable response are the main limitations. Oropharyngeal exercises consist of a set of isometric and isotonic exercises involving the tongue, soft palate and lateral pharyngeal wall. The collective reported trials (n = 120) showed that oropharyngeal exercises can ameliorate OSA and snoring (~30-40%). Nasal EPAP devices consist of disposable one-way resister valve. A systematic review (n = 345) showed that nasal EPAP reduced OSA severity by 53%. The Winx device consists of a mouthpiece placed inside the oral cavity that is connected by tubing to a console that generates negative pressure. Winx may provide successful therapy for ~30-40% of OSA patients. In conclusion, several non-CPAP therapies to treat OSA are currently available.
Phylogenetic Relationships of Varieties and Geographical Groups of the Human Pathogenic Fungus Histoplasma capsulatum Darling (1999)

The phylogeny of 46 geographically diverse Histoplasma capsulatum isolates representing the three varieties capsulatum, duboisii, and farciminosum was evaluated using partial DNA sequences of four protein coding genes. Parsimony and distance analysis of the separate genes were generally congruent and analysis of the combined data identified six clades: (i) class 1 North American H. capsulatum var. capsulatum, (ii) class 2 North American H. capsulatum var. capsulatum, (iii) Central American H. capsulatum var. capsulatum, (iv) South American H. capsulatum var. capsulatum group A, (v) South American H. capsulatum var. capsulatum group B, and (vi) H. capsulatum var. duboisii. Although the clades were generally well supported, the relationships among them were not resolved and the nearest outgroups (Blastomyces and Paracoccidioides) were too distant to unequivocally root the H. capsulatum tree. H. capsulatum var. farciminosum was found within the South American H. capsulatum var. capsulatum group A clade. With the exception of the South American H. capsulatum var. capsulatum group A clade, genetic distances within clades were an order of magnitude lower than those between clades, and each clade was supported by a number of shared derived nucleotide substitutions, leading to the conclusion that each clade was genetically isolated from the others. Under a phylogenetic species concept based on possession of multiple shared derived characters, as well as concordance of four gene genealogies, H. capsulatum could be considered to harbor six species instead of three varieties.
Cluster-level Logging of Containers with Containers (2016)

This article shows how cluster-level logging infrastructure can be implemented using open source tools and deployed using the very same abstractions that are used to compose and manage the software systems being logged. Collecting and analyzing log information is an essential aspect of running production systems to ensure their reliability and to provide important auditing information. Many tools have been developed to help with the aggregation and collection of logs for specific software components (e.g., an Apache web server) running on specific servers (e.g., Fluentd and Logstash.) They are accompanied by tools such as Elasticsearch for ingesting log information into persistent storage and tools such as Kibana7 for querying log information.
Insights into Processing and Cyclization Events Associated with Biosynthesis of the Cyclic Peptide Kalata B1 (2012)

Plant cyclotides are the largest family of gene-encoded cyclic proteins. They act as host defense molecules to protect plants and are promising candidates as insecticidal and nematocidal agents in agriculture. For this promise to be realized a greater understanding of the post-translational processing of these proteins is needed. Cyclotides are cleaved from precursor proteins with subsequent ligation of the N and C termini to form a continuous peptide backbone. This cyclization step is inefficient in transgenic plants and our work aims to shed light on the specificity requirements at the excision sites for cyclic peptide production. Using the prototypic cyclotide kalata B1 (kB1) expressed from the Oak1 gene, MALDI-TOF mass spectrometry was used to examine the cyclization efficiency when mutants of the Oak1 gene were expressed in transgenic Nicotiana benthamiana. Cleavage at the N terminus of the cyclotide domain occurs rapidly with no strict specificity requirements for amino acids at the cleavage site. In contrast, the C-terminal region of the cyclotide domain in the P2, P1, P1', and P2' positions is highly conserved and only specific amino acids can occupy these positions. The cyclization reaction requires an Asn at position P1 followed by a small amino acid (Ala, Gly, Ser) at the P1' position. The P2' position must be filled by Leu or Ile; in their absence an unusual post-translational modification occurs. Substitution of the P2' Leu with Ala leads to hydroxylation of the neighboring proline. Through mutational analysis this novel proline hydroxylation motif was determined to be Gly-Ala-Pro-Ser.
The IL-6R chain controls lung CD4+CD25+ Treg development and function during allergic airway inflammation in vivo (2005)

Due to an error in manuscript preparation, an incorrect shRNA sequence for IRS2 was published. The correct hairpin sequence is a 19-nt stretch beginning from nt 703 of the published IRS2 cDNA sequence (XM_357863). The oligonucleotides cloned into the U6 construct for the IRS2U6 adenovirus are as follows: tcgagGTGACGCTGCAGCTTATGAttcaagagaTCATAAGCTGCAGCGTCACttttt (forward) and ctagAAAAAGTGACGCTGCAGCTTATGAtctcttgaaTCATAAGCTGCAGCGTCACc (reverse). In addition, the shRNA cassettes were cloned into the adenoviral cosmid pAxcwit, which lacks a promoter, and not the cosmid pAxCAwtit, as published..
The broad autism phenotype predicts child functioning in autism spectrum disorders (2013)

Our results suggest that broad autism symptomatology in parents is moderately associated with their child's autism symptomatology. This result extended to TDC families, suggesting that the BAPQ and SRS capture subtle, subclinical social variation in both children and adults. These findings could help define multi-generational social impairments in future phenotypic and genetic studies.
Evidence for a Partially Folded Intermediate in α-Synuclein Fibril Formation (2001)

Intracellular proteinaceous aggregates (Lewy bodies and Lewy neurites) of alpha-synuclein are hallmarks of neurodegenerative diseases such as Parkinson's disease, dementia with Lewy bodies, and multiple systemic atrophy. However, the molecular mechanisms underlying alpha-synuclein aggregation into such filamentous inclusions remain unknown. An intriguing aspect of this problem is that alpha-synuclein is a natively unfolded protein, with little or no ordered structure under physiological conditions. This raises the question of how an essentially disordered protein is transformed into highly organized fibrils. In the search for an answer to this question, we have investigated the effects of pH and temperature on the structural properties and fibrillation kinetics of human recombinant alpha-synuclein. Either a decrease in pH or an increase in temperature transformed alpha-synuclein into a partially folded conformation. The presence of this intermediate is strongly correlated with the enhanced formation of alpha-synuclein fibrils. We propose a model for the fibrillation of alpha-synuclein in which the first step is the conformational transformation of the natively unfolded protein into the aggregation-competent partially folded intermediate.
Characterization of the carbon starvation‐inducible and stationary phase‐inducible gene slp encoding an outer membrane lipoprotein in Escherichia coli (1994)

Escherichia coli induces the expression of more than 50 proteins in response to starvation for a carbon source. Strains MC7 (csi7::phoA) and MC19 (csi19::phoA) contain fusions of a signal peptide-deficient phoA reporter sequence to a csi (carbon starvation-inducible) gene. PhoA expression increased when these strains were deprived of a carbon source or entered stationary phase but did not when the cells were deprived of a nitrogen source or subjected to osmotic, oxidative or thermal stress. Mapping and sequence analysis of the cloned phoA fusions in strains MC7 and MC19 indicated that they had occurred in different locations within the same previously unidentified gene. The wild-type allele of this gene was cloned and the encoded protein was found to be a new lipoprotein. Therefore we propose to call this locus slp (starvation lipoprotein). The 22 kDa Slp protein is associated with the outer membrane fraction. The slp gene was located at 78.6 centisomes on the E. coli genetic map. The -10 and -35 regions upstream of the mRNA start site were characteristic of a sigma 70 promoter. The major transcript from this promoter was sufficiently large to contain slp sequences but not the downstream open reading frame. Induction of beta-galactosidase activity from a slp::lacZ translational fusion during carbon starvation or stationary phase was independent of cAMP, RpoS (KatF) and DnaK, all of which are known to affect the expression of certain starvation-inducible or stationary phase-inducible proteins.
Modelling condensation and the initiation of chondrogenesis in chick wing bud mesenchymal cells levitated in an ultrasound trap (2010)

Chick wing bud mesenchymal cell micromass culture allows the study of a variety of developmental mechanisms, ranging from cell adhesion to pattern formation. However, many cells remain in contact with an artificial substratum, which can influence cytoskeletal organisation and differentiation. An ultrasound standing wave trap facilitates the rapid formation of 2-D monolayer cell aggregates with a defined zero time-point, independent from contact with a surface. Aggregates formed rapidly (within 2 min) and intercellular membrane spreading occurred at points of contact. This was associated with an increase in peripheral F-actin within 10 min of cell-cell contact and aggregates had obtained physical integrity by 30 min. The chondrogenic transcription factor Sox9 could be detected in cells in the ultrasound trap within 3 h (ultrasound exposure alone was not responsible for this effect). This approach facilitates the study of the initial cell-cell interactions that occur during condensation formation and demonstrates that a combination of cell shape and cytoskeletal organisation is required for the initiation and maintenance of a differentiated phenotype, which is lost when these phenomena are influenced by contact with an artificial substrate.
TREATMENT OF EXPERIMENTAL ANEURYSMS WITH AN EMBOLIC-CONTAINING DEVICE AND LIQUID EMBOLIC AGENT (2009)

Within the limitations of this experimental study, treatment of large, wide-necked aneurysms with the ECD and LEA may be feasible. Suboptimal technique and ECD geometry can cause leakage of LEA into the parent vessel or incomplete apposition of the ECD/glue to the aneurysm wall. However, the ECD and glue injection technique did achieve complete occlusion in 1 aneurysm that persisted 1 year later. The histopathological findings in this instance are moderately encouraging. Further investigations of an ECD with N-butyl cyanoacrylate or another LEA are warranted.
Frequency Selected Ultrafast Infrared Vibrational Echo Studies of Liquids, Glasses, and Proteins (2002)

Ultrafast infrared frequency selected vibrational echo (FSVE) experiments are used to study temperature-dependent dynamic interactions in liquids, glasses, and proteins. Vibrational echo experiments measure vibrational dephasing. In general, the large bandwidths associated with ultrashort IR pulses will excite multiple vibrational transitions of a molecular system. In addition to the 0−1 transition of a particular mode of interest, the 1−2 transition, other modes, combination bands, and modes of other species can be excited. A one-dimensional vibrational echo experiment involving multiple transitions can be difficult to address theoretically. By selecting the proper detection wavelengths (a frequency slice through a 2D time-frequency vibrational echo), FSVE makes it possible to effectively isolate a two state system (in terms of the dynamical experimental observables) from within a complex multistate system. First, the FSVE method is used to study the dynamics of CO stretching mode of RuTPPCOPy (TPP = 5,10,15,20-tetraphenylporphyrin, Py = pyridine) in two solvents: poly(methyl methacrylate) (PMMA) and 2-methyltetrahydrofuran (2-MTHF). The results demonstrate the fundamental difference in the influence of a glassy and a liquid solvent on vibrational dephasing. In PMMA, a glass at all temperatures studied, the dephasing rate is linear in temperature. In 2-MTHF, the dephasing is linear for temperatures below Tg, but it changes form, becoming very steep slightly above Tg. Calculations using a model frequency−frequency correlation function (FFCF) show that the different temperature dependences in PMMA and 2-MTHF can be modeled in a unified manner, with at least two solvent motions contributing to the dephasing in liquids, that is, inertial and diffusive motions. FSVE is then applied to the study of the dynamics of the protein myoglobin in water by observing the vibrational dephasing of the stretching mode of CO bound to the active site of myoglobin (Mb-CO). The A1 and A3 conformational substates of Mb-CO are found to have different dephasing rates with different temperature dependences. A frequency−frequency correlation function derived from molecular dynamics simulations of Mb-CO at 298 K is used to calculate the vibrational echo decay. The calculated decay shows substantial agreement with the experimentally measured decays. The FSVE experiment probes protein dynamics and provides an observable that can be used to test structural assignments for the Mb-CO conformational substates.
Does p53 status influence tumor response to anticancer therapies? (2000)

Abnormalities in the tumor suppressor gene p53 have been identified in over 60% of human cancers. Since it plays such a pivotal role in cell growth regulation and apoptosis, the status of the p53 gene has been proposed as one of the major determinants of a tumor's response to anticancer therapies. In this review we examine the relationship between functional p53 and sensitivity/resistance to both chemotherapy and radiotherapy, and discuss the potential use of some of the current gene therapy approaches to restore functional p53 to tumors as a means of modulating the effects of radiation and chemotherapy.
Sequence-Independent Helical Wrapping of Single-Walled Carbon Nanotubes by Long Genomic DNA (2006)

Because of their nanometer sizes and molecular recognition capabilities, biological systems have garnered much attention as vehicles for the directed assembly of nanoscale materials.1-6 One of the greatest challenges of this research has been to successfully interface biological systems with electronic materials, such as semiconductors and metals. As a means to address some of these issues, Sarikaya, Belcher, and others have used a combinatorial technique called phage display7-9 to discover new families of peptides that showed binding affinities to various substrates. More recently, Zheng and co-workers used combinatorial DNA libraries to isolate short DNA oligomers (30−90 bases) that could disperse single-walled carbon nanotubes (SWCNT) in water.10 Through a systematic analysis, they found that short oligonucleotides having repeating sequences of gunanines and thymines (dGdT)n could wrap in a helical manner around a CNT with periodic pitch.11 Although helix formation around SWCNTs having regular pitches is an effective method for dispersing and separating CNTs, the need for specific repeating sequences limits use to nonnatural DNA that must be synthesized with optimal lengths of less than 150 bases. In contrast, we demonstrate here that long genomic single-stranded DNA (≫100 bases) of a completely random sequence of bases can be used to disperse CNTs efficiently through the single-stranded DNA's (ssDNA) ability to form tight helices around the CNTs with distinct periodic pitches. Although this process occurs irrespective of the DNA sequence, we show that this process is highly dependent on the removal of complementary strands. We also demonstrate that although the helix pitch-to-pitch distances remain constant down the length of a single CNT, the distances are variable from one DNA-CNT to another. Finally, we report initial work that shows that methods developed to align long dsDNA can be applied in a similar fashion to produce highly dense arrays of aligned ssDNA-CNT hybrids.
Alternating copolymerization of carbon dioxide and epoxide by manganese porphyrin: The first example of polycarbonate synthesis from 1‐atm carbon dioxide (2003)

Abstract The first successful example of the formation of polycarbonate from 1‐atm carbon dioxide and epoxide was demonstrated by the alternating copolymerization of carbon dioxide and epoxide with manganese porphyrin as a catalyst. The copolymerization of carbon dioxide and cyclohexene oxide with (porphinato)manganese acetate proceeded under the 1‐atm pressure of carbon dioxide to give a copolymer with an alternating sequence. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3549–3555, 2003
Cellular Trajectories of Peptide-Modified Gold Particle Complexes:  Comparison of Nuclear Localization Signals and Peptide Transduction Domains (2004)

Gold nanoparticles modified with nuclear localization peptides were synthesized and evaluated for their subcellular distribution in HeLa human cervical epithelium cells, 3T3/NIH murine fibroblastoma cells, and HepG2 human hepatocarcinoma cells. Video-enhanced color differential interference contrast microscopy and transmission electron microscopy indicated that transport of nanoparticles into the cytoplasm and nucleus depends on peptide sequence and cell line. Recently, the ability of certain peptides, called protein transduction domains (PTDs), to transclocate cell and nuclear membranes in a receptor- and temperature-independent manner has been questioned (see for example, Lundberg, M.; Wikstrom, S.; Johansson, M. (2003) Mol. Ther. 8, 143-150). We have evaluated the cellular trajectory of gold nanoparticles carrying the PTD from HIV Tat protein. Our observations were that (1) the conjugates did not enter the nucleus of 3T3/NIH or HepG2 cells, and (2) cellular uptake of Tat PTD peptide-gold nanoparticle conjugates was temperature dependent, suggesting an endosomal pathway of uptake. Gold nanoparticles modified with the adenovirus nuclear localization signal and the integrin binding domain also entered cells via an energy-dependent mechanism, but in contrast to the Tat PTD, these signals triggered nuclear uptake of nanoparticles in HeLa and HepG2 cell lines.
The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes (1997)

The Arabidopsis thaliana MALE STERILITY 2 (MS2) gene product is involved in male gametogenesis. The first abnormalities in pollen development of ms2 mutants are seen at the stage in microsporogenesis when microspores are released from tetrads. Expression of the MS2 gene is observed in tapetum of wild-type flowers at, and shortly after, the release of microspores from tetrads. The MS2 promoter controls GUS expression at a comparable stage in the tapetum of transgenic tobacco containing an MS2 promoter-GUS fusion. The occasional pollen grains produced by mutant ms2 plants have very thin pollen walls. They are also sensitive to acetolysis treatment, which is a test for the presence of an exine layer. The MS2 gene product shows sequence similarity to a jojoba protein that converts wax fatty acids to fatty alcohols. A possible function of the MS2 protein as a fatty acyl reductase in the formation of pollen wall substances is discussed.