gebhart/patrepeval huggingface dataset:
Simian virus 40-infected, interferon-treated cells contain 2‘,5‘-oligoadenylates which do not activate cleavage of RNA. (1984)

2',5'-oligoadenylates can be assayed sensitively in cell extracts by use of an antiserum having maximum specificity for any compound containing the moiety -pA2'pA2'pA-. These compounds reached high concentrations (25-2000 nM) in monkey CV-1 cells after infection with simian virus 40 (SV40) and treatment with human leukocyte interferon. The levels were highest late in infection and increased in parallel with the accumulation of SV40 late messenger RNAs. Alone, neither interferon nor SV40 caused the 2',5'-oligoadenylate concentrations to increase above the levels present in untreated CV-1 cells, 3 nM or less. Analyses by high performance liquid chromatography revealed little or no (p)pp(A2'p)2A or (p)pp(A2'p)3A, and the extracts showed only very low activity in functional assays with ppp(A2'p)nA-dependent nucleases, equivalent to 3 nM ppp(A2'p)3A or less. Some of the 2',5'-oligoadenylates eluted in the positions of the nonphosphorylated "cores," (A2'p)nA, and a substantial fraction was found in several peaks intermediate between ppp(A2'p)3A and cores. The positions of most of these peaks did not change when digestion with alkaline phosphatase was performed before chromatography, indicating that most of the 2',5'-oligoadenylates lack exposed phosphate groups. In contrast to the effects of infection with SV40, addition of poly(I) X poly(C) to interferon-treated CV-1 cells led to accumulation of high levels (up to 3000 nM) of 2',5'-oligoadenylate-5'-di- or triphosphates capable of activating the ppp(A2'p)nA-dependent ribonuclease.
Low loss and high extinction ratio strictly nonblocking 16×16 thermooptic matrix switch on 6-in wafer using silica-based planar lightwave circuit technology (2001)

We describe a silica-based 16/spl times/16 strictly nonblocking thermooptic matrix switch with a low loss and a high extinction ratio. This matrix switch, which employs a double Mach-Zehnder interferometer (MZI) switching unit and a matrix arrangement to reduce the total waveguide length, is fabricated with 0.75% refractive index difference waveguides on a 6-in silicon wafer using silica-based planar lightwave circuit (PLC) technology. We obtained an average insertion loss of 6.6 dB and an average extinction ratio of 53 dB in the worst polarization case. The operating wavelength bandwidth completely covers the gain band of practical erbium-doped fiber amplifiers (EDFAs). The total power consumption needed for operation is reduced to 17 W by employing a phase-trimming technique which eliminates the phase-error in the interferometer switching unit.
The making of bispecific antibodies (2017)

During the past two decades we have seen a phenomenal evolution of bispecific antibodies for therapeutic applications. The 'zoo' of bispecific antibodies is populated by many different species, comprising around 100 different formats, including small molecules composed solely of the antigen-binding sites of two antibodies, molecules with an IgG structure, and large complex molecules composed of different antigen-binding moieties often combined with dimerization modules. The application of sophisticated molecular design and genetic engineering has solved many of the technical problems associated with the formation of bispecific antibodies such as stability, solubility and other parameters that confer drug properties. These parameters may be summarized under the term 'developability'. In addition, different 'target product profiles', i.e., desired features of the bispecific antibody to be generated, mandates the need for access to a diverse panel of formats. These may vary in size, arrangement, valencies, flexibility and geometry of their binding modules, as well as in their distribution and pharmacokinetic properties. There is not 'one best format' for generating bispecific antibodies, and no single format is suitable for all, or even most of, the desired applications. Instead, the bispecific formats collectively serve as a valuable source of diversity that can be applied to the development of therapeutics for various indications. Here, a comprehensive overview of the different bispecific antibody formats is provided.
Sequence-Specific Covalent Modification of DNA by Crosslinking Oligonucleotides. Catalysis by RecA and Implication for the Mechanism of Synaptic Joint Formation (1995)

Oligodeoxynucleotides (ODNs) were conjugated to chlorambucil and used as affinity labeling reagents to study joint molecule formation by the Escherichia coli recombinase recA. Chlorambucil is a bifunctional nitrogen mustard which alkylates the N-7 position of guanine in the major groove of double-stranded DNA (dsDNA). Incoming ODNs at least 30 nucleotides long cross-linked to a long homologous duplex DNA in the presence of recA and ATP gamma S. Efficient cross-linkage to the complementary recipient strand of the joint occurred preferentially at guanines positioned 5' relative to the appended chlorambucil group. The pattern of recipient strand alkylation was identical to that observed within a protein-free duplex and indicated that strand exchange had occurred prior to alkylation. Modification of the outgoing homologous strand of the joint was less efficient and spanned a 15-20 nucleotide long region offset to the 3' side of the tethered chlorambucil. Alkylation of both recipient and outgoing strands in the same joint molecule occurred with low frequency. By contrast, no affinity alkylation of the displaced strand was observed within a synthetic D-loop. These reaction patterns suggest that the incoming ODN approaches from the minor groove of the duplex to yield a poststrand exchange joint in which the major groove of the newly formed heteroduplex harbors the outgoing strand in an unpaired state. No evidence was obtained for the involvement of a triple-stranded DNA intermediate in recombination.
Concise Review: The Potential Use of Intestinal Stem Cells to Treat Patients with Intestinal Failure (2016)

Intestinal failure is a rare life-threatening condition that results in the inability to maintain normal growth and hydration status by enteral nutrition alone. Although parenteral nutrition and whole organ allogeneic transplantation have improved the survival of these patients, current therapies are associated with a high risk for morbidity and mortality. Development of methods to propagate adult human intestinal stem cells (ISCs) and pluripotent stem cells raises the possibility of using stem cell-based therapy for patients with monogenic and polygenic forms of intestinal failure. Organoids have demonstrated the capacity to proliferate indefinitely and differentiate into the various cellular lineages of the gut. Genome-editing techniques, including the overexpression of the corrected form of the defective gene, or the use of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 to selectively correct the monogenic disease-causing variant within the stem cell, make autologous ISC transplantation a feasible approach. However, numerous techniques still need to be further optimized, including more robust ex vivo ISC expansion, native ISC ablation, and engraftment protocols. Large-animal models can to be used to develop such techniques and protocols and to establish the safety of autologous ISC transplantation because outcomes in such models can be extrapolated more readily to humans. Stem Cells Translational Medicine 2017;6:666-676.
Production of 2-methyl-1-butanol in engineered Escherichia coli (2008)

Recent progress has been made in the production of higher alcohols by harnessing the power of natural amino acid biosynthetic pathways. Here, we describe the first strain of Escherichia coli developed to produce the higher alcohol and potential new biofuel 2-methyl-1-butanol (2MB). To accomplish this, we explored the biodiversity of enzymes catalyzing key parts of the isoleucine biosynthetic pathway, finding that AHAS II (ilvGM) from Salmonella typhimurium and threonine deaminase (ilvA) from Corynebacterium glutamicum improve 2MB production the most. Overexpression of the native threonine biosynthetic operon (thrABC) on plasmid without the native transcription regulation also improved 2MB production in E. coli. Finally, we knocked out competing pathways upstream of threonine production (DeltametA, Deltatdh) to increase its availability for further improvement of 2MB production. This work led to a strain of E. coli that produces 1.25 g/L 2MB in 24 h, a total alcohol content of 3 g/L, and with yields of up to 0.17 g 2MB/g glucose.
Episialin, a carcinoma-associated mucin, is generated by a polymorphic gene encoding splice variants with alternative amino termini. (1990)

Episialin is a mucin-type glycoprotein present at the luminal side of most glandular epithelial cells. We have isolated cDNA clones encoding episialin and determined the structure of the gene. The gene encodes a transmembrane protein which consists of, for the greater part, tandem repeats of 20 amino acids. The number of these repeats varies between 40 and 90 among different alleles. The repeats and most of the remainder of the protein are very rich in potential O-linked glycosylation sites. Two different splice variants were found. Interestingly, the proteins encoded by these two variants differ in their signal sequences and in the extreme amino-terminal parts of the mature proteins, suggesting alternative processing of these two species.
Microfluidic devices for fluidic circulation and mixing improve hybridization signal intensity on DNA arrays (2003)

Reactions of biomolecules with surface mounted materials on microscope slides are often limited by slow diffusion kinetics, especially in low volumes where diffusion is the only means of mixing. This is a particular problem for reactions where only small amounts of analyte are available and the required reaction volume limits the analyte concentration. A low volume microfluidic device consisting of two interconnected 9 mm x 37.5 mm reaction chambers was developed to allow mixing and closed loop fluidic circulation over most of the surface of a microscope slide. Fluid samples are moved from one reaction chamber to the other by the rotation of a magnetic stirring bar that is driven by a standard magnetic stirrer. We demonstrate that circulation and mixing of different reagents can be efficiently accomplished by this closed loop device with solutions varying in viscosity from 1 to 16.2 centipoise. We also show by example of a microarray hybridization that the reaction efficiency can be enhanced 2-5 fold through fluid mixing under conditions where diffusion is rate limiting. For comparison, similar results were achieved with a disposable commercial device that covers only half of the reaction area of the closed loop device.
Nasal Delivery of Antigen with the B Subunit ofEscherichia coliHeat-Labile Enterotoxin Augments Antigen-Specific T-Cell Clonal Expansion and Differentiation (2004)

Escherichia coli heat-labile enterotoxin has unique immunogenic and adjuvant properties when administered mucosally to mice. These properties have revealed the potential for its use in the development of mucosal vaccines, an area of increasing interest. However, the inherent toxicity mediated by the A subunit precludes its widespread use. This problem has led to attempts to dissociate toxicity from adjuvant function by use of the B subunit. The ability of the B subunit of E. coli heat-labile enterotoxin (EtxB) to enhance responses against antigens coadministered intranasally is demonstrated here with the use of the DO11.10 adoptive-transfer model, in which ovalbumin (OVA)-specific adoptively transferred T cells can be monitored directly by flow cytometry. Intranasal delivery of OVA with EtxB resulted in increased T-cell proliferative and systemic antibody responses against antigens. The increased Th2 cytokine production detected following in vitro restimulation of splenocyte and cervical lymph node (CLN) cells from the immunized mice correlated with increased OVA-specific immunoglobulin G1 antibody production. Flow cytometric analysis of T cells from mice early after immunization directly revealed the ability of EtxB to support antigen-specific clonal expansion and differentiation. Furthermore, while responses were first detected in the CLNs, they rapidly progressed to the spleen, where they were further sustained. Examination of CD69 expression on dividing cells supported the notion that activation induced by the presence of antigens is not sufficient to drive T-cell differentiation. Furthermore, a lack of CD25 expression on dividing cells suggested that EtxB-mediated T-cell clonal expansion may occur without a sustained requirement for interleukin 2.
Afterload induced changes in myocardial relaxation A mechanism for diastolic dysfunction (1999)

Diastolic LV dysfunction was induced by elevated afterload in healthy hearts of rabbits and dogs. If this mechanism could be shown to be operative in the failing heart, reversal of diastolic dysfunction should contribute to the beneficial effects of vasodilating and inotropic therapy on pulmonary congestion.
Primitive Neuroectodermal Tumors of Adrenal Gland (2010)

Adrenal primitive neuroectodermal tumor is a very rare tumor. It originates in primitive neuroectoderma and is found mainly in 20-30-year-old young populations. It has non-specific clinical or imaging manifestation and its diagnosis is mostly based on pathological examinations. The tumor is fast-developing, highly malignant with poor prognosis.
High-Throughput Characterization of 10 New Minor Histocompatibility Antigens by Whole Genome Association Scanning (2010)

Patients with malignant diseases can be effectively treated with allogeneic hematopoietic stem cell transplantation (allo-SCT). Polymorphic peptides presented in HLA molecules, the so-called minor histocompatibility antigens (MiHA), play a crucial role in antitumor immunity as targets for alloreactive donor T cells. Identification of multiple MiHAs is essential to understand and manipulate the development of clinical responses after allo-SCT. In this study, CD8+ T-cell clones were isolated from leukemia patients who entered complete remission after allo-SCT, and MiHA-specific T-cell clones were efficiently selected for analysis of recognition of a panel of EBV-transformed B cells positive for the HLA restriction elements of the selected T-cell clones. One million single nucleotide polymorphisms (SNP) were determined in the panel cell lines and investigated for matching with the T-cell recognition data by whole genome association scanning (WGAs). Significant association with 12 genomic regions was found, and detailed analysis of genes located within these genomic regions revealed SNP disparities encoding polymorphic peptides in 10 cases. Differential recognition of patient-type, but not donor-type, peptides validated the identification of these MiHAs. Using tetramers, distinct populations of MiHA-specific CD8+ T cells were detected, demonstrating that our WGAs strategy allows high-throughput discovery of relevant targets in antitumor immunity after allo-SCT.
Amino Acid Residues Stabilizing a Bacillus α-Amylase against Irreversible Thermoinactivation (1989)

The alpha-amylase of Bacillus licheniformis (BLA) is stable and active at high temperature. More than 80% of its activity is retained after heat treatment at 90 degrees C for 30 min, and the optimum temperature for its activity is 80-85 degrees C. In contrast, the alpha-amylase of Bacillus amyloliquefaciens (BAA), the amino acid sequence of which shows 80% homology with that of BLA, is rapidly inactivated at 90 degrees C. Various chimeric genes were constructed from the structural genes for the two enzymes, and their products were analyzed for stability as to irreversible thermoinactivation. Two regions in the amino acid sequence of BLA comprising Gln178 (region I) and the 255th-270th residues (region II), respectively, were shown to determine the thermostability of BLA. Region I plays a major role in determining the thermostability. By means of site-directed mutagenesis of the BAA gene, deletion of Arg176 and Gly177 in region I and substitutions of alanine for Lys269 and aspartic acid for Asn266 in region II were shown to be responsible for the enhancement of the thermostability. Mutant BAAs containing the above deletion and substitutions showed almost the same thermostability as BLA as to irreversible thermoinactivation. Nevertheless, the mutant BAAs showed a temperature optimum as low as that of BAA (65 degrees C), indicating that they are still susceptible to reversible inactivation at temperatures higher than 65 degrees C.
Spatial Control of Condensation and Freezing on Superhydrophobic Surfaces with Hydrophilic Patches (2013)

Abstract Certain natural organisms use micro‐patterned surface chemistry, or ice‐nucleating species, to control water condensation and ice nucleation for survival under extreme conditions. As an analogy to these biological approaches, it is shown that functionalized, hydrophilic polymers and particles deposited on the tips of superhydrophobic posts induce precise topographical control over water condensation and freezing at the micrometer scale. A bottom‐up deposition process is used to take advantage of the limited contact area of a non‐wetting aqueous solution on a superhydrophobic surface. Hydrophilic polymer deposition on the tips of these geometrical structures allows spatial control over the nucleation, growth, and coalescence of micrometer‐scale water droplets. The hydrophilic tips nucleate water droplets with extremely uniform nucleation and growth rates, uniform sizes, an increased stability against coalescence, and asymmetric droplet morphologies. Control of freezing behavior is also demonstrated via deposition of ice‐nucleating AgI nanoparticles on the tips of these structures. This combination of the hydrophilic polymer and AgI particles on the tips was used to achieve templating of ice nucleation at the micrometer scale. Preliminary results indicate that control over ice crystal size, spatial symmetry, and position might be possible with this method. This type of approach can serve as a platform for systematically analyzing micrometer‐scale condensation and freezing phenomena, and as a model for natural systems.
CMU robust vocabulary-independent speech recognition system (1991)

Efforts to improve the performance of CMU's robust vocabulary-independent (VI) speech recognition systems on the DARPA speaker-independent resource management task are discussed. The improvements are evaluated on 320 sentences randomly selected from the DARPA June 88, February 89, and October 89 test sets. The first improvement involves more detailed acoustic modeling. The authors incorporated more dynamic features computed from the LPC cepstra and reduced error by 15% over the baseline system. The second improvement comes from a larger database. With more training data, the third improvement comes from a more detailed subword modeling. The authors incorporated the word boundary context into their VI subword modeling and it resulted in a 30% error reduction. Decision-tree allophone clustering was used to find more suitable models for the subword units not covered in the training set and further reduced error by 17%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Countering detector manipulation attacks in quantum communication through detector self-testing (2022)

In practical quantum key distribution systems, imperfect physical devices open security loopholes that challenge the core promise of this technology. Apart from various side channels, a vulnerability of single-photon detectors to blinding attacks has been one of the biggest concerns, and has been addressed both by technical means as well as advanced protocols. In this work, we present a countermeasure against such attacks based on self-testing of detectors to confirm their intended operation without relying on specific aspects of their inner working, and to reveal any manipulation attempts. We experimentally demonstrate this countermeasure with a typical InGaAs avalanche photodetector, but the scheme can be easily implemented with any single photon detector.
Positive Allosteric Modulators of the Metabotropic Glutamate Receptor Subtype 2 (mGluR2) (2005)

This article describes recent medicinal chemistry progress toward selective potentiators of the metabotropic glutamate receptor 2 (mGluR2). Groups at Lilly and Merck have identified new classes of potentiators that exhibit selectivity for mGluR2 over the seven other subtypes of mGluRs. Structure-activity relationships as well as pharmacokinetic properties and in vivo activity are reviewed.
Energizing 5G: Near- and Far-Field Wireless Energy and Data Trantransfer as an Enabling Technology for the 5G IoT (2017)

We are surrounded in our daily lives by a multitude of small, relatively inexpensive computing devices, many equipped with communication and sensing features. From these has evolved the concept of "pervasive intelligence" [1], [2], a basis from we can envision our future world as an Internet of Things/Internet of Everything (IoT/IoE), in terms of both a consumer IoT/IoE (interconnected devices within an individual's environment) and the Industrial IoT (interconnectedness to improve business-to-business services, mainly through machineto-machine interactions) [3].
The Effects of Portfolio Assessment on Elementary School Students' Science Knowledge, Inquiry Ability and Science Attitudes (1999)

The major purposes of this study are to examine the effects of portfolio assessment on elementary school student's science knowledge, inquiry ability, science attitudes and to investigate students' perceptions on portfolio assessment. Control group consists of 45 fourth-graders at M-Elementary school located at Miwon, Chongwon-gun, Chung-buk and experimental group 36 fourth-graders of G-Elementary school located in Daejeon-si. The inventories of scientific knowledge I, inquiry ability, and science attitudes were administered to both groups as a pre-test. The experimental group was given portfolio assessment instruction and control group traditional instruction for about six weeks. Inventories about scientific knowledge 2, inquiry ability, and science attitudes were administered to both groups as a post-test. A questionnaire on the perception on portfolio assessment was given to experimental group after the treatment. The results were statistically analyzed with SPSS. Control group showed higher score on scientific knowledge than that of experimental group (p
A phase II trial of continuous infusion of 5‐fluorouracil, mitoxantrone, and cisplatin for metastatic hepatocellular carcinoma (2005)

FMP therapy had significant antitumor activity with acceptable toxicity in patients with metastatic HCC.
Raven's Advanced Progressive Matrices: Norms for First-Year University Students and the Development of a Short Form (1998)

Five hundred and six first-year university students completed Raven's Advanced Progressive Matrices. Scores on Set II ranged from 6 to 35 (M= 22.17, SD = 5.60). The first 12 items of Set II were found to add little to the discriminative power of the test. Exploratory and confirmatory factor analyses failed to confirm Dillon et al.'s two-factor solution and suggested that a single-factor best represented performance on Set II. A short-form of Set II, consisting of 12 items extracted from the original 36, was developed and found to possess acceptable psychometric properties. Although this short form differed considerably in content from the short form previously devised by Arthur and Day, the two short forms did not differ with respect to concurrent validity and predictive power.