gebhart/patrepeval huggingface dataset:
Invader Assay for SNP Genotyping (2003)

In the basic Invader assay, two synthetic oligonucleotides, the invasive and signal probes, anneal in tandem to the target strand to form the overlapping complex shown schematically as primary reaction in Fig. 1. The signal probe is designed to have two regions: a target-specific region that is complementary to the target sequence, and a 5′ arm or flap that is noncomplementary to both the target and the invasive probe sequences. Structure-specific 5′ nucleases (), known as Cleavase enzymes, recognize this overlapping complex and cleave the signal probe at the site of its overlap with the 3′ end of the invasive probe, as shown by the arrow in Fig. 1 (, , ). This cleavage releases the noncomplementary 5′ flap of the signal probe plus one nucleotide of its target-specific region. The cleaved 5′ flap serves as a signal for the presence, and enables quantitative analysis, of the specific target in the sample. Open image in new window Fig. 1. Invader assay for analysis of the (A) C677 and (B) T677 polymorphisms in the human methylenetetrahydrofolate reductase (MTHFR) gene. The sense strand of the MTHFR gene was used for the analysis. The invasive and primary (signal) probes overlap by one nucleotide at the polymorphic site (shown in bold case). The primary probes have two regions: the target-specific region and the non-complementary 5′ flap. The overlapping complex is specifically cleaved by a structure-specific 5′ nuclease at the site of the overlap (shown by arrows) releasing the 5′ flap of the primary probe. In the secondary reaction, the cleaved 5′ flap from the primary reaction forms an overlapping complex with the FRET cassette. The FRET cassette for the C677 allele includes the FAM (F) dye and Z21 quencher, while the FRET cassette for the T677 allele includes Redmond Red− (R) and the Z21 quencher. The cleavage sites of the FRET cassettes in the presence of cleaved 5′ flaps are shown by arrows.
Flagellin Treatment Protects against Chemicals, Bacteria, Viruses, and Radiation (2008)

Sudden exposure of human populations to chemicals, pathogens, or radiation has the potential to result in substantial morbidity. A potential means of rapidly protecting such populations might be to activate innate host defense pathways, which can provide broad protection against a variety of insults. However, innate immune activators can, by themselves, result in severe inflammatory pathology, which in large part is driven by hemopoietic-derived cytokines such as TNF-alpha. We reasoned that, because it preferentially activates epithelial cells, the TLR5 agonist flagellin might not induce severe inflammatory pathology and yet be an ideal agent to provide such non-specific protection, particularly at the mucosal surfaces that serve as a front line of host defense. In accordance, we observed that systemic treatment of mice with purified flagellin did not induce the serologic, histopathologic, and clinical hallmarks of inflammation that are induced by LPS but yet protected mice against chemicals, pathogens, and ionizing radiation. Flagellin-elicited radioprotection required TLR5, the TLR signaling adaptor MyD88, and was effective if given between 2 h before to 4 h after exposure to irradiation. Flagellin-elicited radioprotection was, in part, mediated via effects on cells in bone marrow but yet rescued mortality without a pronounced rescue of radiation-induced anemia or leukopenia. Thus, systemic administration of flagellin may be a relatively safe means of providing temporary non-specific protection against a variety of challenges.
In Situ Metabolic Profiling of Single Cells by Laser Ablation Electrospray Ionization Mass Spectrometry (2009)

Depending on age, phase in the cell cycle, nutrition, and environmental factors, individual cells exhibit large metabolic diversity. To explore metabolic variations in cell populations, laser ablation electrospray ionization (LAESI) mass spectrometry (MS) was used for the in situ analysis of individual cells at atmospheric pressure. Single cell ablation was achieved by delivering mid-IR laser pulses through the etched tip of a GeO(2)-based glass fiber. Metabolic analysis was performed from single cells and small cell populations of Allium cepa and Narcissus pseudonarcissus bulb epidermis, as well as single eggs of Lytechinus pictus. Of the 332 peaks detected for A. cepa, 35 were assigned to metabolites with the help of accurate ion masses and tandem MS. The metabolic profiles from single cells of the two plant species included a large variety of oligosaccharides including possibly fructans in A. cepa, and alkaloids, e.g., lycorine in N. pseudonarcissus. Analysis of adjacent individual cells with a difference in pigmentation showed that, in addition to essential metabolites found in both variants, the pigmented cells contained anthocyanidins, other flavonoids, and their glucosides. Analysis of single epidermal cells from different scale leaves in an A. cepa bulb showed metabolic differences corresponding to their age. Our results indicate the feasibility of using LAESI-MS for the in situ analysis of metabolites in single cells with potential applications in studying cell differentiation, changes due to disease states, and response to xenobiotics.
PHYLOGENETIC ORIGINS OF ANTIBODY STRUCTURE (1968)

The sea lamprey, Petromyzon marinus, has been found to produce specific antibodies after immunization with bacteriophage f2. Antibody activity is localized in 6.6S and 14S fractions of lamprey serum. The 6.6S antibodies were purified by a combination of zone electrophoresis, ion exchange chromatography, and gel filtration. Antigenic analysis of the 6.6S antibodies showed them to be free of other serum proteins and antigenically similar or identical to the 14S fraction. Evidence has been obtained which suggests that the 6.6S immunoglobulins consist of light components (molecular weight 25,000) and heavy components (molecular weight 70,000). In the immunoglobulin, these polypeptides appear to be linked via weak interactions but not by interchain disulfide bonds. Molecular weight analyses support the view that the chains can undergo concentration-dependent dissociation in aqueous solutions. Amino acid analyses showed that the compositions of the light and heavy components were similar and that aspartic acid or asparagine was the predominant amino terminal residue. Starch gel electrophoresis indicated that the subunits of lamprey antibodies are diffusely heterogeneous. The heavy chain mobility corresponded to that of micro-chains and resembled that of heavy chains of shark and sting ray immunoglobulins. In the course of the fractionation a 46S natural hemagglutinin composed of lower molecular weight subunits was isolated. This hemagglutinin did not resemble the lamprey immunoglobulin although it had a similar zone electrophoretic mobility in the beta-region. These studies are consistent with the hypothesis that micro-chains were the earliest of the heavy chain classes to emerge and further support the view that the multichain structure of immunoglobulins is a fundamental feature of antibody molecules.
The Physiology of Obese-Hyperglycemic Mice [ob/obMice] (2007)

This review summarizes key aspects of what has been learned about the physiology of leptin deficiency as it can be observed in obese-hyperglycemic ob/ob mice. These mice lack functional leptin. They are grossly overweight and hyperphagic, particularly at young ages, and develop severe insulin resistance. They have been used as a model for obesity and as a rich source of pancreatic islets with high insulin release capacity. The leptin deficiency manifests also with regard to immune function, the cardiovascular system including angiogenesis, supportive tissue function, malignancies, and reproductive function. ob/ob Mice are well suited for studies on the interaction between leptin and insulin, and for studies on initial aspects of metabolic disturbances leading to type-2 diabetes.
MR imaging of the arthritic knee: improved discrimination of cartilage, synovium, and effusion with pulsed saturation transfer and fat-suppressed T1-weighted sequences. (1994)

3D MR imaging with fat-suppressed or STS techniques provides good discrimination among articular structures in arthritic knees. Fat-suppressed imaging is faster than STS imaging and offers better contrast between cartilage and synovium. These techniques may improve monitoring of arthritic disease progression and therapeutic response.
RTP Payload Format for H.264 Video (2005)

This memo describes an RTP Payload format for the ITU-T Recommendation
H.264 video codec and the technically identical ISO/IEC International
Standard 14496-10 video codec. The RTP payload format allows for
packetization of one or more Network Abstraction Layer Units (NALUs),
produced by an H.264 video encoder, in each RTP payload. The payload
format has wide applicability, as it supports applications from simple
low bit-rate conversational usage, to Internet video streaming with
interleaved transmission, to high bit-rate video-on-demand.
[STANDARDS-TRACK]
Automatic Parameter Selection for Denoising Algorithms Using a No-Reference Measure of Image Content (2010)

Across the field of inverse problems in image and video processing, nearly all algorithms have various parameters which need to be set in order to yield good results. In practice, usually the choice of such parameters is made empirically with trial and error if no "ground-truth" reference is available. Some analytical methods such as cross-validation and Stein's unbiased risk estimate (SURE) have been successfully used to set such parameters. However, these methods tend to be strongly reliant on restrictive assumptions on the noise, and also computationally heavy. In this paper, we propose a no-reference metric Q which is based upon singular value decomposition of local image gradient matrix, and provides a quantitative measure of true image content (i.e., sharpness and contrast as manifested in visually salient geometric features such as edges,) in the presence of noise and other disturbances. This measure 1) is easy to compute, 2) reacts reasonably to both blur and random noise, and 3) works well even when the noise is not Gaussian. The proposed measure is used to automatically and effectively set the parameters of two leading image denoising algorithms. Ample simulated and real data experiments support our claims. Furthermore, tests using the TID2008 database show that this measure correlates well with subjective quality evaluations for both blur and noise distortions.
Novel Prognostic Immunohistochemical Biomarker Panel for Estrogen Receptor–Positive Breast Cancer (2006)

A panel of five antibodies can significantly improve on traditional prognosticators in predicting outcome for ER-positive breast cancer patients.
Chronic diarrhea associated with vagal nerve stimulation (2002)

Frequent side effects vagus nerve stimulation (VNS) include hoarseness, cough, and throat pain. Although the vagus nerve physiologically regulates gastrointestinal motility, changes in bowel movement frequency are not included as side effects of VNS. We report a patient who developed chronic diarrhea associated with VNS.

A 35-year-old man had complex partial seizures since age 14, occurring up to six times per month. Multiple medications including phenytoin, carbamazepine, gabapentin, felbamate, and topiramate did not control the seizures. Intracranial EEG monitoring demonstrated both right and left temporal origin seizures, excluding the patient from consideration for resective surgery and leading to referral for VNS.

After an uncomplicated VNS implantation, the stimulator was set at 0.25 mA/30 Hz/500 ms/30-s on/5-min off/magnet 0.50 mA. The patient was discharged the following day with only a sore throat. One week later, he reported two seizures and an increase in bowel movements. At that time, the stimulator intensity …
A Novel Class of Adenosine A3 Receptor Ligands. 2. Structure Affinity Profile of a Series of Isoquinoline and Quinazoline Compounds (1998)

1-Substituted 3-(2-pyridinyl)isoquinolines have been shown to form a novel class of adenosine A3 receptor ligands. In the present study further investigations of this new lead and the structure affinity relationships of this class of compounds are described. First, the influence of an amide group at position 1 of the isoquinoline ring on the adenosine A3 receptor affinity was determined. A carboxamide proved to be a useful spacer between the isoquinoline and a phenyl ring. N-[2-(2-pyridinyl)isoquinolin-4-yl]benzamide (VUF8507, compound 6) had an affinity of 200 nM at the adenosine A3 receptor. Second, we investigated the effects of substitution of the benzamide ring of 6 with a series of mono- and disubstituted N-[3-(2-pyridinyl)isoquinoline]benzamides. The ratio of the tautomers of the benzamides was determined in the solid state and in solution by spectroscopic techniques (IR and NMR). Affinities were determined in radioligand binding assays at rat brain A1 and A2A receptors and at cloned human A3 receptor. The benzamides showed higher adenosine A3 receptor affinity than aliphatic amides. We propose that the adenosine A3 receptor affinity of the different benzamides is related to their presence in either the iminol or amide form. Ligands present in the iminol form showed relatively high adenosine A3 receptor affinity. Finally, we explored the influence of replacement of C4 of the isoquinoline ring by a nitrogen atom. Comparison of isoquinolines with the corresponding quinazolines revealed that both compounds showed similar adenosine A3 receptor affinity. These investigations led to potent and selective human adenosine A3 receptor ligands with affinities in the nanomolar range. The subtype-selective compound 4-methoxy-N-[2-(2-pyridinyl)quinazolin-4-yl]benzamide (VUF8504, 13) with an affinity of 17.0 nM at the human adenosine A3 receptor might become a useful tool in the pharmacological characterization or the investigation of the physiological function of this receptor.
Partially Parallel Encoder Architecture for Long Polar Codes (2014)

Due to the channel achieving property, the polar code has become one of the most favorable error-correcting codes. As the polar code achieves the property asymptotically, however, it should be long enough to have a good error-correcting performance. Although the previous fully parallel encoder is intuitive and easy to implement, it is not suitable for long polar codes because of the huge hardware complexity required. In this brief, we analyze the encoding process in the viewpoint of very-large-scale integration implementation and propose a new efficient encoder architecture that is adequate for long polar codes and effective in alleviating the hardware complexity. As the proposed encoder allows high-throughput encoding with small hardware complexity, it can be systematically applied to the design of any polar code and to any level of parallelism.
Antiulcer activity of 5-benzylthiazolidine-2,4-dione derivatives. (1983)

5-Benzylthiazolidine-2, 4-dione derivatives were prepared and examined for antisecretory and antiulcer activities using pylorus-ligated rats and water-immersion stress rats. Some of these compounds, in particular, 5-(2, 4, 5-tripropoxybenzyl) thiazolidine-2, 4-dione (4) and 5-(2, 4-dimethoxybenzyl) thiazolidine-2, 4-dione (23), exhibited pronounced pharmacological activities. Structure-activity relationships are discussed.
Hierarchical Control of Lymphocyte Survival (1996)

After an immune response, the body must eliminate the excess cells generated to fight the foreign invader. Recent work indicates that this removal occurs as a result of an intricate network of regulatory processes. In their Perspective, Boise and Thompson synthesize this new evidence for the control of lymphocyte number by proteases, Bcl-2-related proteins, cytokines, and adhesion factors.
Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq (2018)

Abstract Pairing CRISPR-based genetic screens with single-cell transcriptional phenotypes (Perturb-seq) has advanced efforts to explore the function of mammalian genes and genetic networks. We present strategies for Perturb-seq that enable direct capture of CRISPR sgRNAs within 3’ or 5’ single-cell RNA-sequencing libraries using the 10x Genomics platform. This technology greatly expands the accessibility, scalability, and flexibility of Perturb-seq, specifically enabling use with programmed combinatorial perturbations and multiplexing with multi-omic measurements.
An Efficient Boosting Algorithm for Combining Preferences (1998)

. The problem of combining preferences arises in several applications, such as combining the results of different search engines. This work describes an efficient algorithm for combining multiple preferences. We first give a formal framework for the problem. We then describe and analyze a new boosting algorithm for combining preferences called RankBoost. We also describe an efficient implementation of the algorithm for a restricted case. We discuss two experiments we carried out to assess the performance of RankBoost. In the first experiment, we used the algorithm to combine different WWW search strategies, each of which is a query expansion for a given domain. For this task, we compare the performance of RankBoost to the individual search strategies. The second experiment is a collaborative-filtering task for making movie recommendations. Here, we present results comparing RankBoost to nearest-neighbor and regression algorithms. 1 Introduction Consider the followingmovie-recommendati...
Induced pluripotent stem cells: opportunities and challenges (2011)

Somatic cells have been reprogrammed into pluripotent stem cells by introducing a combination of several transcription factors, such as Oct3/4, Sox2, Klf4 and c-Myc. Induced pluripotent stem (iPS) cells from a patient's somatic cells could be a useful source for drug discovery and cell transplantation therapies. However, most human iPS cells are made by viral vectors, such as retrovirus and lentivirus, which integrate the reprogramming factors into the host genomes and may increase the risk of tumour formation. Several non-integration methods have been reported to overcome the safety concern associated with the generation of iPS cells, such as transient expression of the reprogramming factors using adenovirus vectors or plasmids, and direct delivery of reprogramming proteins. Although these transient expression methods could avoid genomic alteration of iPS cells, they are inefficient. Several studies of gene expression, epigenetic modification and differentiation revealed the insufficient reprogramming of iPS cells, thus suggesting the need for improvement of the reprogramming procedure not only in quantity but also in quality. This report will summarize the current knowledge of iPS generation and discuss future reprogramming methods for medical application.
Envelope membrane proteins that interact with chloroplastic precursor proteins. (1994)

The post-translational transport of cytoplasmically synthesized precursor proteins into chloroplasts requires proteins in the envelope membranes. To identify some of these proteins, label transfer cross-linking was performed using precursor to the small subunit of ribulose-1,5-bisphosphate carboxylase (prSSU) that was blocked at an early stage of the transport process. Two envelope proteins were identified: an 86-kD protein and a 75-kD protein, both present in the outer membrane. Labeling of both proteins required prSSU and could not be accomplished with SSU lacking a transit peptide. Labeling of the 75-kD protein occurred only when low levels of ATP were present, whereas labeling of the 86-kD protein occurred in the absence of exogenous ATP. Although both labeled proteins were identified as proteins of the outer envelope membrane, the labeled form of the 75-kD protein could only be detected in fractions containing mixed envelope membranes. Based on these observations, we propose that prSSU first binds in an ATP-independent fashion to the 86-kD protein. The energy-requiring step is association with the 75-kD protein and assembly of a translocation contact site between the inner and outer membrane of the chloroplastic envelope.
Traffic descriptor mapping and traffic control for frame relay over ATM network (1998)

Frame relay (FR) service via an FR interface over a common asynchronous transfer mode (ATM) backbone network requires an FR-to-ATM interworking unit (IWU), the functionality of which directly impacts the engineering of the overall network in terms of the capacity required, quality of service (QoS) expected, and the interference among different types of services being offered on the same platform. In the absence of a traffic shaping function in the equipment at the customer's location, the issue of policing and bandwidth allocation becomes much more critical. This paper focuses on the issue of FR traffic descriptor mapping, the issue of traffic policing in the frame mode and the cell mode, and the implication on the QoS when the same bandwidth resources are shared by the ATM [cell relay (CR)] and FR virtual connections. Some major conclusions that we draw from the computer simulations are: (1) the performance is somewhat independent of the mode in which traffic policing is implemented; (2) from a cost standpoint it is more advantageous to use the cell mode for traffic policing; (3) the allocation of bandwidth in the multiplexer and the switching fabric is greatly dependent on the type of service interface used since the FR traffic becomes much burstier after frame-to-cell conversion process; and (4) it becomes necessary to provide a traffic shaping function after the conversion process in order to achieve high bandwidth utilization, fair allocation of bandwidth resources, and guaranteed QoS.
Photoaddressed liquid crystal spatial light modulators (1989)

The general problems and limitations of photoaddressed liquid crystal spatial light modulators (SLMs) are discussed, and experimental results are presented. A GaAs wafer photoaddressed nematic liquid crystal SLM is described in detail with experimental results. The edge enhancing or differentiating SLM is discussed, and the results of GaAs photoaddressing are reported. The preliminary experimental behavior of photoaddressed ferroelectric liquid crystal SLMs is described.
Common Co-activation of AXL and CDCP1 in EGFR-mutation-positive Non-Small Cell Lung Cancer Associated With Poor Prognosis (2018)

Epidermal growth factor receptor (EGFR)-mutation-positive non-smallcell lung cancer (NSCLC) is incurable, despite high rates of response to EGFR tyrosine kinase inhibitors (TKIs). We investigated receptor tyrosine kinases (RTKs), Src family kinases and focal adhesion kinase (FAK) as genetic modifiers of innate resistance in EGFR-mutation-positive NSCLC. We performed gene expression analysis in two cohorts (Cohort 1 and Cohort 2) of EGFR-mutation-positive NSCLC patients treated with EGFR TKI. We evaluated the efficacy of gefitinib or osimertinib with the Src/FAK/Janus kinase 2 (JAK2) inhibitor, TPX0005 in vitro and in vivo. In Cohort 1, CUB domain-containing protein-1 (CDCP1) was an independent negative prognostic factor for progression-free survival (hazard ratio of 1.79, p=0.0407) and overall survival (hazard ratio of 2.23, p=0.0192). A two-gene model based on AXL and CDCP1 expression was strongly associated with the clinical outcome to EGFR TKIs, in both cohorts of patients. Our preclinical experiments revealed that several RTKs and non-RTKs, were up-regulated at baseline or after treatment with gefitinib or osimertinib. TPX-0005 plus EGFR TKI suppressed expression and activation of RTKs and downstream signaling intermediates. Co-expression of CDCP1 and AXL is often observed in EGFR-mutation-positive tumors, limiting the efficacy of EGFR TKIs. Co-treatment with EGFR TKI and TPX-0005 warrants testing.