gebhart/patrepeval huggingface dataset:
Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers (2009)

Cancers are clonal expansions, but how a single, transformed human cell grows into a billion-cell tumor is uncertain because serial observations are impractical. Potentially, this history is surreptitiously recorded within genomes that become increasingly numerous, polymorphic, and physically separated after transformation. To correlate physical with epigenetic pairwise distances, small 2,000- to 10,000-cell gland fragments were sampled from left and right sides of 12 primary colorectal cancers, and passenger methylation at 2 CpG-rich regions was measured by bisulfite sequencing. Methylation patterns were polymorphic but differences were similar between different parts of the same tumor, consistent with relatively isotropic or "flat" clonal expansions that could be simulated by rapid initial population expansions. Methylation patterns were too diverse to be consistent with very rare cancer stem cells but were more consistent with multiple ( approximately 4 to 1,000) long-lived cancer stem cell lineages per cancer gland. Our study illustrates the potential to reconstruct the unperturbed biology of human cancers from epigenetic passenger variations in their present-day genomes.
BAFF/BLyS Receptor 3 Comprises a Minimal TNF Receptor-like Module That Encodes a Highly Focused Ligand-Binding Site (2003)

BAFF/BLyS, a member of the tumor necrosis family (TNF) superfamily of ligands, is a crucial survival factor for B cells. BAFF binds three receptors, TACI, BCMA, and BR3, with signaling through BR3 being essential for promoting B cell function. Typical TNF receptor (TNFR) family members bind their cognate ligands through interactions with two cysteine-rich domains (CRDs). However, the extracellular domain (ECD) of BR3 consists of only a partial CRD, with cysteine spacing distinct from other modules described previously. Herein, we report the solution structure of the BR3 ECD. A core region of only 19 residues adopts a stable structure in solution. The BR3 fold is analogous to the first half of a canonical TNFR CRD but is stabilized by an additional noncanonical disulfide bond. BAFF-binding determinants were identified by shotgun alanine-scanning mutagenesis of the BR3 ECD expressed on phage. Several of the key BAFF-binding residues are presented from a beta-turn that we have shown previously to be sufficient for ligand binding when transferred to a structured beta-hairpin scaffold [Kayagaki, N., Yan, M., Seshasayee, D., Wang, H., Lee, W., French, D. M., Grewal, I. S., Cochran, A. G., Gordon, N. C., Yin, J., Starovasnik, M. A, and Dixit, V. M. (2002) Immunity 10, 515-524]. Outside of the turn, mutagenesis identifies additional hydrophobic contacts that enhance the BAFF-BR3 interaction. The crystal structure of the minimal hairpin peptide, bhpBR3, in complex with BAFF reveals intimate packing of the six-residue BR3 turn into a cavity on the ligand surface. Thus, BR3 binds BAFF through a highly focused interaction site, unprecedented in the TNFR family.
Atypical Protein Kinase C ι Protects Human Leukemia Cells against Drug-induced Apoptosis (1997)

Protein kinase C (PKC) isozymes play distinct roles in cellular function. In human K562 leukemia cells, PKC alpha is important for cellular differentiation and PKC betaII is required for proliferation. In this report, we assess the role of the atypical PKC isoform PKC iota in K562 leukemia cell physiology. K562 cells were stably transfected with expression plasmids containing the cDNA for human PKC iota in sense or antisense orientation to increase or decrease cellular PKC iota levels, respectively. Overexpression or inhibition of expression of PKC iota had no significant effect on the proliferative capacity of K562 cells nor their sensitivity to phorbol myristate acetate-induced cytostasis and megakaryocytic differentiation, suggesting that PKC iota does not play a critical role in these processes. Rather, PKC iota serves to protect K562 cells against drug-induced apoptosis. K562 cells, which are resistant to most apoptotic agents, undergo apoptosis when treated with the protein phosphatase inhibitor okadaic acid (OA). Overexpression of PKC iota leads to increased resistance to OA-induced apoptosis whereas inhibition of PKC iota expression sensitizes cells to OA-induced apoptosis. Overexpression of the related atypical PKC zeta has no protective effect, demonstrating that the effect is isotype-specific. PKC iota also protects K562 cells against taxol-induced apoptosis, indicating that it plays a general protective role against apoptotic stimuli. These data support a role for PKC iota in leukemia cell survival.
Suppressor System in Bacillus subtilis 168 (1969)

Multiple auxotrophic strains of Bacillus subtilis 168 were tested for joint one-step reversion of two or more auxotrophic markers to the wild-type phenotype. Mu8u5u5, a strain requiring leucine, methionine, and threonine, yielded revertants that grew without added methionine or threonine and proved to have a suppressor gene. When transferred by transformation with deoxyribonucleic acid, this suppressor gene also suppressed the adenine mutation in another strain, Mu8u5u6. The one-step double revertants fell into two distinct classes: strains of class su + I grow well in broth; strains of class su + II grow poorly. Strains su + II tend to revert frequently to the su + I or su − state. Conditional lethal mutants of phage φe were isolated which can grow on the su + and not on the su − strains.
Afamelanotide for Erythropoietic Protoporphyria (2015)

Afamelanotide had an acceptable side-effect and adverse-event profile and was associated with an increased duration of sun exposure without pain and improved quality of life in patients with erythropoietic protoporphyria. (Funded by Clinuvel Pharmaceuticals and others; ClinicalTrials.gov numbers, NCT01605136 and NCT00979745.).
Superresolution video reconstruction with arbitrary sampling lattices and nonzero aperture time (1997)

Printing from an NTSC source and conversion of NTSC source material to high-definition television (HDTV) format are some of the applications that motivate superresolution (SR) image and video reconstruction from low-resolution (LR) and possibly blurred sources. Existing methods for SR image reconstruction are limited by the assumptions that the input LR images are sampled progressively, and that the aperture time of the camera is zero, thus ignoring the motion blur occurring during the aperture time. Because of the observed adverse effects of these assumptions for many common video sources, this paper proposes (i) a complete model of video acquisition with an arbitrary input sampling lattice and a nonzero aperture time, and (ii) an algorithm based on this model using the theory of projections onto convex sets to reconstruct SR still images or video from an LR time sequence of images. Experimental results with real video are provided, which clearly demonstrate that a significant increase in the image resolution can be achieved by taking the motion blurring into account especially when there exists large interframe motion.
Mass spectrometry-based plasma proteomics: state of the art and future outlook (2014)

Mass spectrometry-based plasma proteomics is a field where intense research has been performed during the last decade. Being closely linked to biomarker discovery, the field has received a fair amount of criticism, mostly due to the low number of novel biomarkers reaching the clinic. However, plasma proteomics is under gradual development with improvements on fractionation methods, mass spectrometry instrumentation and analytical approaches. These recent developments have contributed to the revival of plasma proteomics. The goal of this review is to summarize these advances, focusing in particular on fractionation methods, both for targeted and global mass spectrometry-based plasma analysis.
Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral (2000)

DsRed is a recently cloned 28-kDa fluorescent protein responsible for the red coloration around the oral disk of a coral of the Discosoma genus. DsRed has attracted tremendous interest as a potential expression tracer and fusion partner that would be complementary to the homologous green fluorescent protein from Aequorea, but very little is known of the biochemistry of DsRed. We now show that DsRed has a much higher extinction coefficient and quantum yield than previously reported, plus excellent resistance to pH extremes and photobleaching. In addition, its 583-nm emission maximum can be further shifted to 602 nm by mutation of Lys-83 to Met. However, DsRed has major drawbacks, such as strong oligomerization and slow maturation. Analytical ultracentrifugation proves DsRed to be an obligate tetramer in vitro, and fluorescence resonance energy transfer measurements and yeast two-hybrid assays verify oligomerization in live cells. Also, DsRed takes days to ripen fully from green to red in vitro or in vivo, and mutations such as Lys-83 to Arg prevent the color change. Many potential cell biological applications of DsRed will require suppression of the tetramerization and acceleration of the maturation.
Multiple antigenic determinants on type III collagen (1991)

Eight monoclonal antibodies have been produced against human pepsin-soluble type III collagen. All antibodies were shown to be highly specific for type III collagen and did not cross-react with a range of other collagen types or connective-tissue proteins. Examination of type III collagen from other species showed that these antibodies had a wide range of species specificities, indicating that several distinct epitopes were being recognized. The location of the epitopes was investigated by using reactivity of the antibodies to CNBr fragments and to sequential fragments formed by tryptic digestion of renaturing type III collagen. These data also indicated that several distinct epitopes were recognized and that they were located over the length of the type III collagen.
Identification of the Arg‐Gly‐Asp sequence in laminin A chain as a latent cell‐binding site being exposed in fragment P1 (1990)

A single RGD-containing sequence present within an epidermal growth factor-like repeat of the short arms of laminin is shown by peptide inhibition to block integrin receptors recognizing a latent cell-binding site of laminin. Based on proteolysis data it is proposed that masking occurs by folding of the globular domain IVa over the cell-binding site in the adjacent rod-like structures of laminin A chain.
A new monoclonal antibody, mAb 204-11, that influences the binding of platelet GPVI to fibrous collagen (2003)

The newly identified platelet collagen receptor glycoprotein VI binds to fibrous collagen, inducing platelet activation. Several antibodies against GPVI have been reported, including a patient's auto-antibodies, that activates platelets through their ability to crosslink this glycoprotein. We have developed a monoclonal antibody (mAb) against GPVI using the recombinant extracellular domain of GPVI as an antigen. This antibody, mAb 204-11, induced platelet aggregation and tyrosine phosphorylation of proteins similar to those induced by GPVI-reactive proteins, collagen and convulxin. Its interaction with GPVI was analyzed by measuring the effect of the antibody on GPVI binding to collagen using a dimeric form of recombinant GPVI, GPVI-Fc2. MAb 204-11 inhibited the binding of GPVI-Fc2 to fibrous collagen particles, but enhanced the GPVI binding to immobilized collagen, suggesting that the antibody binds to a region near the collagen binding site of GPVI. MAb 204-11 also inhibited the GPVI binding to convulxin at a low concentration, but not completely. Since mAb 204-11 reacts specifically with GPVI and is applicable for immunoblotting and immunoprecipitation, this antibody would be useful for studies on GPVI.
Nuclear medicine dosimetry (2006)

A brief overview is provided of the history of the development of internal dose methods for use in nuclear medicine. Basic methods of internal dosimetry and the systems that have been developed for use in nuclear medicine are described. The development of the MIRD system and the International Radiopharmaceutical Dosimetry Symposium series is outlined. The evolution of models and tools for calculating dose estimates is reviewed. Current efforts in developing more patient-specific methods, particularly for use in therapy calculations, development of small scale and microdosimetry techniques, and of relating internal radiation doses to observed biological effects are described and evaluated.
Selective modification of a private I-A allo-stimulating determinant(s) upon association of antigen with an antigen-presenting cell. (1984)

A large panel of alloreactive, interleukin 2 (IL-2)-producing T cell hybridomas was constructed from B10 alpha BALB/c primary mixed lymphocyte cultures (MLC). Functional hybrids had specificity for either I-Ad or I-Ed. These cells were used to probe determinants on Ia molecules in an attempt to detect molecular association between a nominal antigen and an Ia molecule on an antigen-presenting cell (APC). The response of a small number of these clones was significantly blocked by the addition of the Ir gene-controlled copolymer L-glutamic acid60-L-alanine30-L-tyrosine10 (GAT) to culture. A comparison of the inhibited and uninhibited hybrids revealed an identical dose response curve. Further, both types of hybrids were activated by the same stimulator cell and frequently recognized the identical Ia molecule on that cell. Nevertheless, the inhibitory effect of GAT was localized to the stimulator cell and not to the T cell hybrids. All of the hybrids whose stimulation was blocked had specificity for the I-A molecule, which is the gene product known to control and restrict responsiveness to GAT. Further, only GT, but not a number of other related antigens, was also specifically inhibitory, which correlates with the known associational specificity of these antigens on an APC. Finally, the same stimulator cell could be shown to coordinately lose an allostimulatory determinant(s), while it was gaining an I-Ad plus GAT determinant(s). The implications of these findings on the nature of antigen-Ia association and on the role of polymorphic Ia determinants are discussed.
The Drosophila ecdysone receptor (EcR) Gene Is Required Maternally for Normal Oogenesis (2000)

Abstract Oogenesis in Drosophila is regulated by the steroid hormone ecdysone and the sesquiterpenoid juvenile hormone. Response to ecdysone is mediated by a heteromeric receptor composed of the EcR and USP proteins. We have identified a temperature-sensitive EcR mutation, EcRA483T, from a previously isolated collection of EcR mutations. EcRA483T is predicted to affect all EcR protein products (EcR-A, EcR-B1, and EcR-B2) since it maps to a common exon encoding the ligand-binding domain. In wild-type females, we find that both EcR-A and EcR-B1 are expressed in nurse cells and follicle cells throughout oogenesis. EcR mutant females raised at permissive temperature and then shifted to restrictive temperature exhibit severe reductions in fecundity. Oogenesis in EcR mutant females is defective, and the spectrum of oogenic defects includes the presence of abnormal egg chambers and loss of vitellogenic egg stages. Our results demonstrate a requirement for EcR during female reproduction and suggest that EcR is required for normal oogenesis.
A toll quality 8 kb/s speech codec for the personal communications system (PCS) (1994)

A toll quality speech codec at 8 kb/s suitable for the future personal communications system is presented. The codec is currently under standardization by the ITU-T (successor of CCITT) where the codec terms of reference were mainly determined considering PCS application. The encoding algorithm is based on algebraic code-excited linear prediction (ACELP) and has a speech frame of 10 ms. Efficient pitch and codebook search strategies, along with efficient quantization procedures, have been developed to achieve toll quality encoded speech with a complexity implementable on current fixed-point DSP chips. Formal subjective listening tests, performed by ITU-T SG 12, showed that the codec quality is equivalent to that of G.726 ADPCM at 32 kb/s in error-free conditions and it outperforms G.726 under error conditions. The codec performs adequately under tandeming conditions, and can support a frame erasure rate up to 3% with a degradation in its performance that is still worse than the ITU-T requirements, and this is one subject of study for the next phase. The algorithm has been implemented on a single fixed-point DSP for the ITU-T subjective rest, and required about 29 MIPS. An optimized version, however, requires 24 MIPS without any speech quality degradation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Applying and implementing the MPEG-4 multimedia standard (1999)

MPEG-4's many algorithms and high-performance requirements pose a challenge for designers of a new generation of flexible, low-power coder/decoder VLSI implementations for mobile and portable applications. In addition to introducing MPEG4, this article looks at how the standard will enhance existing applications and enable new ones, and then discusses the ongoing effort to design an optimized MPEG-4 processor platform.
Multi-Camera Surveillance: Object-Based Summarization Approach (2004)

An automatic object tracking and video summarization method for multicamera systems with a large number of non-overlapping field-of-view cameras is explained. In this system, video sequences are stored for each object as opposed to storing a sequence for each camera. Objectbased representation enables annotation of video segments, and extraction of content semantics for further analysis and summarization. Objects are tracked at each camera by background subtraction and mean-shift analysis. Then the correspondence of objects between different cameras is established by using a Bayesian Belief Network. This framework empowers the user to get a concise response to queries such as “which locations did an object visited on Monday and what did he do there?”
Excitatory Amino Acids as a Final Common Pathway for Neurologic Disorders (1994)

In many neurologic disorders, injury to neurons may be caused at least in part by overstimulation of receptors for excitatory amino acids, including glutamate and aspartate. These neurologic conditions range from acute insults such as stroke, hypoglycemia, trauma, and epilepsy (Table 1) to chronic neurodegenerative states such as Huntington's disease, the acquired immunodeficiency syndrome (AIDS) dementia complex, amyotrophic lateral sclerosis, and perhaps Alzheimer's disease (Table 2)13.Glutamate is the principal excitatory neurotransmitter in the brain, and its interactions with specific membrane receptors are responsible for many neurologic functions, including cognition, memory, movement, and sensation4. In addition, excitatory . . .
Future of ToxicologyMechanisms of Toxicity and Drug Safety:  Where Do We Go from Here? (2006)

Recent high-profile drug withdrawals increase the pressure on regulators and the pharmaceutical industry to improve preclinical safety testing. Understanding mechanisms of drug toxicity is an essential step toward improving drug safety testing by providing the basis for mechanism-based risk assessments. Nonetheless, despite several decades of research on mechanisms of drug-induced toxicity and the application of various new technologies to preclinical safety assessment, the overall impact on preclinical safety testing has been modest. Assessing the risk of exposing humans to new drug candidates still depends on preclinical testing in animals, which in many, but not all cases, predicts outcomes in humans accurately. The following offers a perspective on the challenges and opportunities facing efforts to improve preclinical safety testing and outlines gaps and needs that must be addressed. A case is built for focusing solutions on defined problems within the current safety testing paradigm rather than imposing wholesale change. Targets for application of new technologies, including in silico screening, biomarkers, surrogate assays and 'omic technologies, are outlined. Improving drug safety testing will depend on improving the application of mechanism-based risk assessment but will also require improving public and private collaborations in order to focus research regarding the mechanism of drug-induced toxicity on the most important problems.
Crystal Structure of lac Repressor Core Tetramer and Its Implications for DNA Looping (1995)

The crystal structure of the tryptic core fragment of the lac repressor of Escherichia coli (LacR) complexed with the inducer isopropyl-beta-D-thiogalactoside was determined at 2.6 A resolution. The quaternary structure consists of two dyad-symmetric dimers that are nearly parallel to each other. This structure places all four DNA binding domains of intact LacR on the same side of the tetramer, and results in a deep, V-shaped cleft between the two dimers. Each monomer contributes a carboxyl-terminal helix to an antiparallel four-helix bundle that functions as a tetramerization domain. Some of the side chains whose mutation reduce DNA binding form clusters on a surface near the amino terminus. Placing the structure of the DNA binding domain complexed with operator previously determined by nuclear magnetic resonance onto this surface results in two operators being adjacent and nearly parallel to each other. Structural considerations suggest that the two dimers of LacR may flexibly alter their relative orientation in order to bind to the known varied spacings between two operators.
Immunotherapy with immune checkpoint inhibitors in colorectal cancer: what is the future beyond deficient mismatch-repair tumours? (2019)

Following initial success in melanoma and lung tumours, immune checkpoint inhibitors (ICIs) are now well recognized as a major immunotherapy treatment modality for multiple types of solid cancers. In colorectal cancer (CRC), the small subset that is mismatch-repair-deficient and microsatellite-instability-high (dMMR/MSI-H) derive benefit from immunotherapy; however, the vast majority of patients with proficient MMR (pMMR) or with microsatellite stable (MSS) CRC do not. Immunoscore and the consensus molecular subtype classifications are promising biomarkers in predicting therapeutic efficacy in selected CRC. In pMRR/MSS CRC, biomarkers are also needed to understand the molecular mechanisms governing immune reactivity and to predict their relationship to treatment. The continuous development of such biomarkers would offer new perspectives and more personalized treatments by targeting oncological options, including ICIs, which modify the tumour-immune microenvironment. In this review, we focus on CRC and discuss the current status of ICIs, the role of biomarkers to predict response to immunotherapy, and the approaches being explored to render pMMR/MSS CRC more immunogenic through the use of combined therapies.