gebhart/patrepeval huggingface dataset:
Introduction to compressed sensing (2012)

Compressed sensing (CS) is an exciting, rapidly growing, field that has attracted considerable attention in signal processing, statistics, and computer science, as well as the broader scientific community. Since its initial development only a few years ago, thousands of papers have appeared in this area, and hundreds of conferences, workshops, and special sessions have been dedicated to this growing research field. In this chapter, we provide an up-to-date review of the basics of the theory underlying CS. This chapter should serve as a review to practitioners wanting to join this emerging field, and as a reference for researchers. We focus primarily on the theory and algorithms for sparse recovery in finite dimensions. In subsequent chapters of the book, we will see how the fundamentals presented in this chapter are expanded and extended in many exciting directions, including new models for describing structure in both analog and discrete-time signals, new sensing design techniques, more advanced recovery results and powerful new recovery algorithms, and emerging applications of the basic theory and its extensions.
BCR-ABL Gene Expression Is Required for Its Mutations in a Novel KCL-22 Cell Culture Model for Acquired Resistance of Chronic Myelogenous Leukemia (2009)

Acquired resistance through genetic mutations is a common phenomenon in several cancer therapies using molecularly targeted drugs, best exemplified by the BCR-ABL inhibitor imatinib in treating chronic myelogenous leukemia (CML). Overcoming acquired resistance is a daunting therapeutic challenge, and little is known about how these mutations evolve. To facilitate understanding the resistance mechanisms, we developed a novel culture model for CML acquired resistance in which the CML cell line KCL-22, following initial response to imatinib, develops resistant T315I BCR-ABL mutation. We demonstrate that the emergence of BCR-ABL mutations do not require pre-existing BCR-ABL mutations derived from the original patient as the subclones of KCL-22 cells can form various BCR-ABL mutations upon imatinib treatment. BCR-ABL mutation rates vary from cell clone to clone and passages, in contrast to the relatively stable mutation rate of the hypoxanthine-guanine phosphoribosyltransferase gene. Strikingly, development of BCR-ABL mutations depends on its gene expression because BCR-ABL knockdown completely blocks KCL-22 cell relapse on imatinib and acquisition of mutations. We further show that the endogenous BCR-ABL locus has significantly higher mutagenesis potential than the transduced randomly integrated BCR-ABL cDNA. Our study suggests important roles of BCR-ABL gene expression and its native chromosomal locus for acquisition of BCR-ABL mutations and provides a new tool for further studying resistance mechanisms.
Gamma-Secretase and Notch Signaling: Novel Therapeutic Targets In Breast Cancer (2005)

Abstract : We are on track and have made significant progress in our project. We have determined that, as predicted by our hypothesis, LY411,575 is a Notch inhibitor which synergizes with paclitaxel. We have discovered an additional synergism with tamoxifen. We have made several key mechanistic observations on how Notch inhibition causes growth arrest and death in breast cancer cells regardless of ER status. We have determined the optimal conditions for in vivo administration of LY411,575 and we have obtained preliminary xenograft data which confirm significant anti- tumor activity at safe doses of this compound. We expect to complete our study and publish its results within the expected 3-year time frame. We expect our results will not only demonstrate that a GSI/paclitaxel regimen is a promising treatment for ER negative breast cancer, but also that a GSI/tamoxifen combination could be just as promising in ER positive cancers. Based on these data, we will propose 2 phase 1 clinical trials of this compound or its close derivative(s) produced by Eli Lilly in the neo-adjuvant setting at first. In conclusion, we expect that the completion of this project will directly lead to the identification of a new broadly active class of agents for the treatment of breast cancer, the clarification of their primary mode of action and the suggestion of possible combination therapeutic regimens.
Molecular genetics of Streptococcus thermophilus (1990)

The metabolism and genetics of Streptococcus thermophilus (presently Streptococcus salivarius ssp. thermophilus) have only been investigated recently despite its widespread use in milk fermentation processes. The development of recombinant DNA technology has allowed impressive progress to be made in the knowledge of thermophilic dairy streptococci. In particular, it has permitted a careful analysis of phenotypically altered variants which were derived from a mother strain by plasmid or chromosomal DNA reorganization. While natural phage defense mechanisms of S. thermophilus remain poorly documented, information on the bacteriophages responsible for fermentation failures has accumulated. The lysogenic state of two S. thermophilus strains has also been demonstrated for the first time. Gene transfer techniques for this species have been established and improved to the point that targeted manipulation of their chromosomal determinants is now feasible. Cloning and expression vectors have been constructed, and a few heterologous genes were successfully expressed in S. thermophilus. The first homologous genes, involved in carbohydrate utilization, have been cloned and sequenced, shedding some light on the molecular organization of key metabolic steps.
Complex Interplay between Epitope Specificity and Isotype Dictates the Biological Activity of Anti-human CD40 Antibodies (2018)

Anti-CD40 monoclonal antibodies (mAbs) that promote or inhibit receptor function hold promise as therapeutics for cancer and autoimmunity. Rules governing their diverse range of functions, however, are lacking. Here we determined characteristics of nine hCD40 mAbs engaging epitopes throughout the CD40 extracellular region expressed as varying isotypes. All mAb formats were strong agonists when hyper-crosslinked; however, only those binding the membrane-distal cysteine-rich domain 1 (CRD1) retained agonistic activity with physiological Fc gamma receptor crosslinking or as human immunoglobulin G2 isotype; agonistic activity decreased as epitopes drew closer to the membrane. In addition, all CRD2-4 binding mAbs blocked CD40 ligand interaction and were potent antagonists. Thus, the membrane distal CRD1 provides a region of choice for selecting CD40 agonists while CRD2-4 provides antagonistic epitopes.
Psilocybin with psychological support for treatment-resistant depression: six-month follow-up (2017)

Although limited conclusions can be drawn about treatment efficacy from open-label trials, tolerability was good, effect sizes large and symptom improvements appeared rapidly after just two psilocybin treatment sessions and remained significant 6 months post-treatment in a treatment-resistant cohort. Psilocybin represents a promising paradigm for unresponsive depression that warrants further research in double-blind randomised control trials.
Random Boolean network models and the yeast transcriptional network (2003)

The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that, for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state, regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.
Metal Incorporation in Modified PNA Duplexes (2003)

Substitution of bipyridine for a nucleobase leads to modified peptide nucleic acid (PNA) single strands that are bridged in the presence of Ni2+ into a duplex containing a combination of hydrogen and coordinative bonds. CD experiments demonstrate that the duplex adopts a structure similar to that of an unmodified 10-bp PNA duplex, and UV melting experiments show a very sensitive dependence of the duplex stability on the substitution of a nucleobase pair with a pair of ligands or a metal-ligand alternative base pair.
“Fibonacci’s Route” to Regioregular Oligo(3-hexylthiophene)s (2013)

We describe a new synthetic approach to regioregular monodisperse oligo(3-alkylthiophene)s allowing for simple separation of regioregular material in gram quantities. The number of repeat units follows the Fibonacci numbers up to a length of 21. In a small adaption of this approach, introduction of a protecting group was used to synthesize an oligo(3-hexylthiophene) with 36 repeating units, the longest regioregular 3-hexylthiophene oligomer synthesized to date.
TEMPORAL ENVELOPE CORRECTION FOR ATTACK RESTORATION IN LOW BIT-RATE AUDIO CODING (2011)

At reduced bit rates, the audio compression affects transient parts of signals, which results in pre-echo and loss of attack character. We propose in this paper an attacks restoration method based on the correction of the temporal envelope of the decoded signal, using a small set of coefficients transmitted through an auxiliary channel. The proposed approach is evaluated for single and multiple coding-decoding, using objective perceptual measures. The experimental results for MP3 and AAC coding exhibits an efficient restoration of the attacks and a significant improvement of the audio quality. 1.
Translating the epitranscriptome (2016)

RNA modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. Whereas the importance of transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications has been well described and is unquestioned for decades, the significance of internal messenger RNA (mRNA) modifications has only recently been revealed. Novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mRNAs. Thus far, N<sup>6</sup> -methyladenosine (m<sup>6</sup> A), pseudouridine (Ψ), 5-methylcytosine (m<sup>5</sup> C) and N<sup>1</sup> -methyladenosine (m<sup>1</sup> A) were identified in eukaryal, and to some extent in prokaryal mRNAs. Several of the functions of these mRNA modifications have previously been reported, but many aspects remain elusive. Modifications can be important factors for the direct regulation of protein synthesis. The potential diversification of genomic information and regulation of RNA expression through editing and modifying mRNAs is versatile and many questions need to be addressed to completely elucidate the role of mRNA modifications. Herein, we summarize and highlight some recent findings on various co- and post-transcriptional modifications, describing the impact of these processes on gene expression, with emphasis on protein synthesis. WIREs RNA 2017, 8:e1375. doi: 10.1002/wrna.1375 For further resources related to this article, please visit the WIREs website.
Hyperactivity, elevated dopaminergic transmission, and response to amphetamine in M1 muscarinic acetylcholine receptor-deficient mice (2001)

Acetylcholine serves an important modulatory role in the central nervous system. Pharmacological evidence has suggested that cholinergic activity can modulate central dopaminergic transmission; however, the nature of this interaction and the receptors involved remain undefined. In this study we have generated mice lacking the M1 muscarinic acetylcholine receptor and examined the effects of M1 deletion on dopaminergic transmission and locomotor behavior. We report that M1 deficiency leads to elevated dopaminergic transmission in the striatum and significantly increased locomotor activity. M1-deficient mice also have an increased response to the stimulatory effects of amphetamine. Our results provide direct evidence for regulation of dopaminergic transmission by the M1 receptor and are consistent with the idea that M1 dysfunction could be a contributing factor in psychiatric disorders in which altered dopaminergic transmission has been implicated.
Blind separation and restoration of signals mixed in convolutive environment (2002)

This paper proposes new neural network approaches for separating and restoring signals mixed through FIR channels. Firstly, a set of maximal entropy based training rules are developed. Secondly, a new scheme for restoring the original signals is proposed for the 2/spl times/2 case. Computer simulation results for speech signals are presented to verify the proposed approaches.
Monocyte Chemotactic Protein-1 Receptor CCR2B Is a Glycoprotein That Has Tyrosine Sulfation in a Conserved Extracellular N-Terminal Region (2000)

Monocyte chemotactic protein-1 (MCP-1) binding to its receptor, CCR2B, plays an important role in a variety of diseases involving infection, inflammation, and/or injury. In our effort to understand the molecular basis of this interaction and its biological consequences, we recognized a conserved hexad of amino acids at the N-terminal extracellular domain of several chemokine receptors, including CCR2B. Human embryonic kidney 293 cells expressing Flag-tagged CCR2B containing site-directed mutations in this region, 21-26, including a consensus tyrosine sulfation site were used to determine MCP-1 binding and its biological consequences. The results showed that several of these amino acids are important for MCP-1 binding and consequent lamellipodium formation, chemotaxis, and signal transduction involving adenylate cyclase inhibition and Ca(2+) influx into cytoplasm. Mutations that prevented adenylate cyclase inhibition and Ca(2+) influx did not significantly inhibit lamellipodium formation and chemotaxis, suggesting that these signaling events are not involved in chemotaxis. CCR2B was found to be sulfated at Tyr(26); this sulfation was abolished by the substitution of Tyr with Ala and severely reduced by substitution of Asp(25), a part of the consensus sulfation site. The expressed CCR2B was found to be N:-glycosylated, as N:-glycosidase F treatment of the receptor or growth of the cells in tunicamycin reduced the receptor size to the same level, from 50 to 45 kDa. Thus, CCR2B is the first member of the CC chemokine receptor family shown to be a glycoprotein that is sulfated at the N-terminal Tyr. These post-translational modifications probably have significant biological functions.
Overview of Dual rail with Precharge logic styles to thwart implementation-level attacks on hardware cryptoprocessors (2009)

The security of cryptographic implementations relies not only on the algorithm quality but also on the countermeasures to thwart attacks aiming at disclosing the secrecy. These attacks can take advantage of leakages of the secret appearing through the power consumption or the electromagnetic radiations also called ¿Side Channels¿. This is for instance the case of the Differential Power Analysis (DPA) or the Correlation Power Analysis (CPA). Fault injections is another threatening attack type targeting specific nets in a view to change their value. The major principle to fight the side-channel attack consists in making the power consumption constant. The masking method allows the designer to get a power consumption which has a constant mean and a variance given by a random variable. Another manner is the Hiding method which consists in generating a constant power consumption by using a Dual-rail with Precharge phase Logic (DPL). This paper presents an overview of the various logic styles that have been promoted in the last six years, with an emphasis on their relative advantages and drawbacks.
Embryonic expression of an Nkx2‐5/Cre gene using ROSA26 reporter mice (2001)

Nkx2-5, one of the earliest cardiac-specific markers in vertebrate embryos, was used as a genetic locus to knock in the Cre recombinase gene by homologous recombination. Offspring resulting from heterozygous Nkx2-5/Cre mice mated to ROSA26 (R26R) reporter mice provided a model system for following Nkx2-5 gene activity by beta-galactosidase (beta-gal) activity. beta-gal activity was initially observed in the early cardiac crescent, cardiomyocytes of the looping heart tube, and in the epithelium of the first pharyngeal arch. In later stage embryos (10.5-13.5 days postcoitum, dpc), beta-gal activity was observed in the stomach and spleen, the dorsum of the tongue, and in the condensing primordium of the tooth. The Nkx2-5/Cre mouse model should provide a useful genetic resource to elucidate the role of loxP manipulated genetic targets in cardiogenesis and other developmental processes.
Stem cell‐mediated accelerated bone healing observed with in vivo molecular and small animal imaging technologies in a model of skeletal injury (2008)

Adult stem cells are promising therapeutic reagents for skeletal regeneration. We hope to validate by molecular imaging technologies the in vivo life cycle of adipose-derived multipotent cells (ADMCs) in an animal model of skeletal injury. Primary ADMCs were lentivirally transfected with a fusion reporter gene and injected intravenously into mice with bone injury or sham operation. Bioluminescence imaging (BLI), [(18)F]FHBG (9-(fluoro-hydroxy-methyl-butyl-guanine)-micro-PET, [(18)F]Fluoride ion micro-PET and micro-CT were performed to monitor stem cells and their effect. Bioluminescence microscopy and immunohistochemistry were done for histological confirmation. BLI showed ADMC's traffic from the lungs then to the injury site. BLI microscopy and immunohistochemistry confirmed the ADMCs in the bone defect. Micro-CT measurements showed increased bone healing in the cell-injected group compared to the noninjected group at postoperative day 7 (p < 0.05). Systemically administered ADMC's traffic to the site of skeletal injury and facilitate bone healing, as demonstrated by molecular and small animal imaging. Molecular imaging technologies can validate the usage of adult adipose tissue-derived multipotent cells to promote fracture healing. Imaging can in the future help establish therapeutic strategies including dosage and administration route.
Mie resonances: Sensors for physical and chemical cluster interface properties (1997)

Abstract Metal clusters exhibit unique optical properties due to the excitation of Mie plasmon resonances. It is well known since decades that measured resonances of clusters, surrounded by some adsorbate, or some solid or liquid embedding material (as e.g., in colloidal systems), are often not described quantitatively by Mie's theory. Only recently, these discrepancies were traced back to complex physical and chemical influences of the cluster‐matrix interlayer onto the optical response. They prove often to be more important than cluster size effects. These findings opened a new field of surface/interface research where deviations of measured Mie resonances from the predictions of Mie's theory are used as sensitive sensors for physical and chemical interface properties and processes in cluster‐matter. By combining optical spectroscopy experiments on free clusters in UHV and on the same clusters after embedding, this method was calibrated to separate, quantitatively, the cluster‐matrix interface effects from other cluster effects like shape and structure effects, nonlocal dielectric effects and cluster size effects. Among all metals, silver exhibits the most pronounced Mie resonances, so silver clusters were used as model systems and were embedded in a broad variety of solid and liquid embedding media, in course of the investigations reported in the present Progress Report. A theoretical description of the obtained data, based upon static and dynamic charge transfer processes of the cluster electrons into/out of adsorbate states is, however, only at its beginning. It allows to ascribe the extremely short decay times of the resonances of the order of 1 to 10 fs to phase relaxation processes; the decay times are in good correspondence with results of direct femtosecond‐experiments.
Cloning and expression ofSLC10A4, a putative organic anion transport protein (2006)

To date, we have shown that this protein has no capacity to transport taurocholate relative to SLC10A1; however, given its ubiquitous tissue distribution, it may play a more active role in transporting other endogenous organic anions.
Comparison of deuterated leucine, valine, and lysine in the measurement of human apolipoprotein A-I and B-100 kinetics (1990)

The production rates of apolipoprotein (apo)B-100 in very low density lipoprotein and in low density lipoprotein and apolipoprotein A-I in high density lipoprotein were determined using a primed-constant infusion of [5,5,5,-2H3]leucine, [4,4,4,-2H3]valine, and [6,6-2H2,1,2-13C2]lysine. The three stable isotope-labeled amino acids were administered simultaneously to determine whether absolute production rates calculated using a stochastic model were independent of the tracer species utilized. Three normolipidemic adult males were studied in the constantly fed state over a 15-h period. The absolute production rates of very low density lipoprotein apoB-100 were 11.4 +/- 5.8 (leucine), 11.2 +/- 6.8 (valine), and 11.1 +/- 5.4 (lysine) mg per kg per day (mean +/- SDM). The absolute production rates for low density lipoprotein apoB-100 were 8.0 +/- 4.7 (leucine), 7.5 +/- 3.8 (valine), and 7.5 +/- 4.2 (lysine) mg per kg per day. The absolute production rates for high density lipoprotein apoA-I were 9.7 +/- 0.2 (leucine), 9.4 +/- 1.7 (valine, and 9.1 +/- 1.3 (lysine) mg per kg per day. There were no statistically significant differences in absolute synthetic rates of the three apolipoproteins when the plateau isotopic enrichment values of very low density lipoprotein apoB-100 were used to define the isotopic enrichment of the intracellular precursor pool. Our data indicate that deuterated leucine, valine, or lysine provided similar results when used for the determination of apoA-I and apoB-100 absolute production rates within plasma lipoproteins as part of a primed-constant infusion protocol.
Monocyte surface expression of Fcγ receptor RI (CD64), a biomarker reflecting type-I interferon levels in systemic lupus erythematosus (2010)

Expression of CD64 on circulating monocytes is IFN-I inducible and highly correlated with ISG expression. Flow-cytometry analysis of CD64 expression on circulating monocytes is a convenient and rapid approach for estimating IFN-I levels in SLE patients.
Design of an N7-Glycosylated Purine Nucleoside for Recognition of GC Base Pairs by Triple Helix Formation (1995)

Pyrimidine oligodeoxyribonucleotides bind in the major groove of DNA parallel to the purine Watson-Crick strand by formation of specific hydrogen bonds between thymine and adenine (T•AT triplet) and protonated cytosine and guanine (C+GC triplet) on the Hoogsteen face of the purine base. Alternatively, purine oligodeoxyribonucleotides bind in an antiparallel orientation relative to the purine Watson-Crick strand by formation of G•GC and A•AT triplets. The prerequisite protonation of cytosine in C+GC triplets leads to a considerable pH dependence in the binding affinity of C-containing oligodeoxyribonucleotides (Figure 1). Substitution of 5-methylcytosine (^mC) for cytosine results in increased binding affinities near physiological pH. In an attempt to eliminate the necessity for protonation, recent efforts have been directed toward the synthesis of nonnatural nucleosides which display the hydrogen bonding functionality of protonated cytosine.
Dosage effect on uropathogenic Escherichia coli anti-adhesion activity in urine following consumption of cranberry powder standardized for proanthocyanidin content: a multicentric randomized double blind study (2010)

Administration of PAC-standardized cranberry powder at dosages containing 72 mg of PAC per day may offer some protection against bacterial adhesion and virulence in the urinary tract. This effect may offer a nyctohemeral protection.