gebhart/patrepeval huggingface dataset:
Kinetic analysis of the interactions of recombinant human VpreB and Ig V domains (1995)

The surrogate light chain, composed of VpreB and lambda 5/14.1 proteins, is selectively expressed on B cell precursors, and is important for B cell development. The surrogate light chain associates with cell surface mu-chains on preB cells, but little is known about the ligand specificity and affinity of VpreB binding. To analyze its interactions with Igs, we made recombinant human VpreB protein and measured its affinity for H and L chain V domains using surface plasmon resonance. The recombinant VpreB protein existed as a homodimer in solution. VpreB chains associated with each other with an apparent Kd = 5 x 10(-7) M, and bound to a human VH domain, a mouse VH domain, and a human VL domain with a similar affinity. VpreB protein also bound to human Fab fragments of IgG with an apparent Kd = 6 x 10(-7) M, but showed a very low affinity for human Fc fragments of IgG. VpreB-Fab complex formation was reproduced by the formation of a trimolecular VpreB-VH-VL complex. Thus, VpreB proteins can associate with each other and also form complexes with Ig at sites different from those involved in VH-VL interaction. By flow cytometry, biotinylated VpreB protein bound to surface Ig-positive B cells but not T cells. Receptors that contain VpreB could be cross-linked by either Ig or by self-association.
Beyond the conventional transistor (2002)

This paper focuses on approaches to continuing CMOS scaling by introducing new device structures and new materials. Starting from an analysis of the sources of improvements in device performance, we present technology options for achieving these performance enhancements. These options include high-dielectric-constant (high-k) gate dielectric, metal gate electrode, double-gate FET, and strained-silicon FET. Nanotechnology is examined in the context of continuing the progress in electronic systems enabled by silicon microelectronics technology. The carbon nanotube field-effect transistor is examined as an example of the evaluation process required to identify suitable nanotechnologies for such purposes.
Targeting Pan-Resistant Bacteria With Antibodies to a Broadly Conserved Surface Polysaccharide Expressed During Infection (2012)

Our findings raise potential new therapeutic options against PNAG-producing bacteria, including even pan-resistant pathogens.
Inhibitors of the HIV-1 capsid, a target of opportunity (2018)

Small molecules that bind to the viral capsid protein can be potent inhibitors of HIV infection. Capsid-targeting drugs are predicted to exhibit high barriers to viral resistance, and ongoing work in this area is contributing to an understanding of the molecular biology of HIV uncoating and maturation.
An Antisense Pectin Methylesterase Gene Alters Pectin Chemistry and Soluble Solids in Tomato Fruit. (1992)

Pectin methylesterase (PME, EC 3.1.11) demethoxylates pectins and is believed to be involved in degradation of pectic cell wall components by polygalacturonase in ripening tomato fruit. We have introduced antisense and sense chimeric PME genes into tomato to elucidate the role of PME in fruit development and ripening. Fruits from transgenic plants expressing high levels of antisense PME RNA showed <10% of wild-type PME enzyme activity and undetectable levels of PME protein and mRNA. Lower PME enzyme activity in fruits from transgenic plants was associated with an increased molecular weight and methylesterification of pectins and decreased levels of total and chelator soluble polyuronides in cell walls. The fruits of transgenic plants also contained higher levels of soluble solids than wild-type fruits. This trait was maintained in subsequent generations and segregated in normal Mendelian fashion with the antisense PME gene. These results indicate that reduction in PME enzyme activity in ripening tomato fruits had a marked influence on fruit pectin metabolism and increased the soluble solids content of fruits, but did not interfere with the ripening process.
The use of avidin-biotin interaction in immunoenzymatic techniques. (1979)

Biotin was covalently attached to antibodies, antigens and enzymes, and the effects of this labeling on the antigen and antibody binding capacity and on enzymatic activity were tested. Based on avidin-biotin interaction, the labeled proteins were used in quantitative enzyme-immunoassay and enzyme-immunohistochemical staining procedures. Two procedures were developed. In the first procedure, named the Bridged Avidin-Biotin (BRAB) technique four steps were used sequentially in order to quantify or detect an immobilized antigen: 1) incubation with biotin-labeled antibody; 2) incubation with avidin; 3) incubation with biotin-labeled enzyme; 4) measurement or histochemical staining of the enzyme. The technique is based on the observation that avidin possesses four active sites. In the second procedure, named the Labeled Avidin-Biotin (LAB) technique, biotin-labeled antibody and enzyme-labeled avidin are used sequentially. Enzyme-associated antigen is then quantified or revealed immunohistochemically. The optimal conditions for enzyme-immunoassay and enzyme-immunohistochemical staining using BRAB and LAB procedures were established.
Low-loss photonic device in Ge–Sb–S chalcogenide glass (2016)

Low-loss waveguides constitute an important building block for integrated photonic systems. In this work, we investigated low-loss photonic device fabrication in Ge<sub>23</sub>Sb<sub>7</sub>S<sub>70</sub> chalcogenide glass using electron beam lithography followed by plasma dry etching. High-index-contrast waveguides with a low propagation loss of 0.5 dB/cm and microdisk resonators with an intrinsic quality factor (Q-factor) of 1.2×10<sup>6</sup> were demonstrated. Both figures represent, to the best of our knowledge, the best low-loss results reported thus far in submicrometer single-mode chalcogenide glass devices.
Recognizing stereotypical motor movements in the laboratory and classroom (2009)

Individuals with Autism Spectrum Disorders (ASD) frequently engage in stereotyped and repetitive motor movements. Automatically detecting these movements in real-time using comfortable, miniature wireless sensors could advance autistic research and enable new intervention tools for the classroom that help children and their caregivers monitor and cope with this potentially problematic class of behavior. We present activity recognition results for stereotypical hand flapping and body rocking using data collected from six children with ASD repeatedly observed in both laboratory and classroom settings. In the classroom, an overall recognition accuracy of 88.6% (TP: 0.85; FP: 0.08) was achieved using three sensors. Challenges encountered when applying machine learning to this domain, as well as implications for the development of real-time classroom interventions and research tools, are discussed.
Two-dimensional bend sensing with a cantilever-mounted FBG (2005)

A technique for simultaneous measurement of a 2D bend by using a cantilever-mounted fibre Bragg grating (FBG) is experimentally demonstrated. The value of the two-dimensional deflections is acquired from the central wavelength and chirp bandwidth of the reflection spectrum via the inverse sensitivity matrix. Moreover, an interrogation system with an intensity modulator and a Mach–Zehnder interferometer structure is demonstrated, not only providing wavelength information, but also distinguishing the direction of the horizontal deflection. The measured vertical deflection sensitivity reaches 0.135 nm mm−1, and its horizontal counterparts along the positive and negative axes achieve 0.602 nm mm−1 and −0.572 nm mm−1, respectively.
NCAM140 Interacts with the Focal Adhesion Kinase p125 and the SRC-related Tyrosine Kinase p59 (1997)

Axonal growth cones respond to adhesion molecules and extracellular matrix components by rapid morphological changes and growth rate modification. Neurite outgrowth mediated by the neural cell adhesion molecule (NCAM) requires the src family tyrosine kinase p59(fyn) in nerve growth cones, but the molecular basis for this interaction has not been defined. The NCAM140 isoform, which is found in migrating growth cones, selectively co-immunoprecipitated with p59(fyn) from nonionic detergent (Brij 96) extracts of early postnatal mouse cerebellum and transfected rat B35 neuroblastoma and COS-7 cells. p59(fyn) did not associate significantly with the NCAM180 isoform, which is found at sites of stable neural cell contacts, or with the glycophosphatidylinositol-linked NCAM120 isoform. pp60(c-)src, a tyrosine kinase that promotes neurite growth on the neuronal cell adhesion molecule L1, did not interact with any NCAM isoform. Whereas p59(fyn) was constitutively associated with NCAM140, the focal adhesion kinase p125(fak), a nonreceptor tyrosine kinase known to mediate integrin-dependent signaling, became recruited to the NCAM140-p59(fyn) complex when cells were reacted with antibodies against the extracellular region of NCAM. Treatment of cells with a soluble NCAM fusion protein or with NCAM antibodies caused a rapid and transient increase in tyrosine phosphorylation of p125(fak) and p59(fyn). These results suggest that NCAM140 binding interactions at the cell surface induce the assembly of a molecular complex of NCAM140, p125(fak), and p59(fyn) and activate the catalytic function of these tyrosine kinases, initiating a signaling cascade that may modulate growth cone migration.
A Serious Person (1996)

Review of From Pentagon to Penitentiary, Book Four of The Education of a Reluctant Radical by Carl Marzani.This article can also be found at the Monthly Review website, where most recent articles are published in full.Click here to purchase a PDF version of this article at the Monthly Review website.
Recent developments and future trends in PLC programming languages and programming tools for real-time control (2002)

The programmable logic controller (PLC) is changing to reflect the demands of sequencing and continuous processing applications. The PLC can be thought of as a hardened computer with high speed I/O and communications ports with bus interfacing for multiprocessor or coprocessor enhancements, and a BIOS that supports those features. PLC manufacturers now retain control over both aspects of the PLC which interoperate in a proprietary manner. Via the delineation of the two may come a standard real time operating system or real time kernel which would give rise to true applications portability. Specific topics addressed include relay ladder logic, a structured approach to error dynamic diagnostic information (EDDI), state control language, and process control function blocks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nonalcoholic Fatty Liver Disease: Pathology and Pathogenesis (2010)

Nonalcoholic fatty liver disease (NAFLD) is recognized as the leading cause of chronic liver disease in adults and children. NAFLD encompasses a spectrum of liver injuries ranging from steatosis to steatohepatitis with or without fibrosis. Fibrosis may progress to cirrhosis and complications including hepatocellular carcinoma. Histologic findings represent the complexity of pathophysiology. NAFLD is closely associated with obesity and is most closely linked with insulin resistance; the current Western diet, high in saturated fats and fructose, plays a significant role. There are several mechanisms by which excess triglycerides are acquired and accumulate in hepatocytes. Formation of steatotic droplets may be disordered in NAFLD. Visceral adipose tissue dysfunction in obesity and insulin resistance results in aberrant cytokine expression; many cytokines have a role in liver injury in NAFLD. Cellular stress and immune reactions, as well as the endocannabinoid system, have been implicated in animal models and in some human studies.
Spine Loss and Other Persistent Alterations of Hippocampal Pyramidal Cell Dendrites in a Model of Early-Onset Epilepsy (1998)

To explore the anatomical substrates for network hyperexcitability in adult rats that become chronically epileptic after recurrent seizures in infancy, the dendritic and axonal arbors of biocytin-filled hippocampal pyramidal cells were reconstructed. On postnatal day 10, tetanus toxin was unilaterally injected into the hippocampus and produced brief but recurrent seizures for 1 week. Later, hippocampal slices taken from these rats exhibited synchronized network bursts in area CA3C. Both the apical and basilar dendritic arbors of CA3C pyramidal cells were markedly abnormal in these epileptic rats. There was a considerable reduction in the density of dendrite spines, although the extent of this loss could vary among dendritic segments. Spine density on terminal segments of the basilar and apical dendrites was reduced on average by 35 and 20%, respectively. In addition, the diameters of these same dendritic segments were markedly reduced. Dendritic spine loss has previously been suggested to indicate a partial deafferentation of epileptic neurons, but this interpretation is difficult to reconcile with the critical role recurrent excitatory synaptic transmission plays in the generation of synchronized network burst. In this study, axonal arbors of CA3C pyramidal cells exhibited normal branching patterns, branching complexity, and varicosity density. This suggests that if deafferentation occurs, synapses other than recurrent excitatory ones are lost. The morphological abnormalities reported here would be expected to significantly alter electrical signaling within dendrites that may contribute importantly to seizures and other behavioral sequelae of early-onset epilepsy.
Cell-free Fetal DNA Is Increased in Plasma of Women with Hyperemesis Gravidarum (2001)

Nausea and vomiting of moderate intensity are especially common complaints in early gestation. Hyperemesis gravidarum (HG), which is the most severe form of this disorder, occurs in 0.5–2% of pregnancies and is associated with weight loss, ketonemia, ketonuria, electrolyte imbalance, dehydration, and possible hepatic and renal damage.

Recently, the presence of cell-free fetal DNA in maternal plasma or serum has been demonstrated (1). It has been reported that the concentration of fetal DNA in maternal plasma is increased in pregnancies involving preterm delivery (2), preeclampsia (3)(4), and trisomy 21 (5)(6). In the present study, we evaluated the concentration of fetal DNA in maternal plasma in HG patients.

Pregnant women diagnosed with HG and admitted to Showa University Hospital were recruited. In this study, HG was defined according to the following criteria: ( a ) persistent nausea and vomiting; ( b ) weight loss (>2 kg); and ( c ) ketonuria (>2+, urine dipstick). Maternal blood samples were obtained at the time of admission from 35 patients with HG carrying a single fetus between 7 and 16 weeks of gestation. Sixteen of 35 blood samples collected from the HG patients carrying a male fetus were …
Total syntheses of polyketide‐derived bioactive natural products (2006)

Recent progress of total syntheses in our laboratory has been described along with our background and methodologies. The target bioactive polyketides are classified into three categories according to their structures: (i) lactone-fused polycyclic compounds [(+)-cochleamycin A, (+)-tubelactomicin A, and (-)-tetrodecamycin], (ii) aromatic compounds [(-)-tetracycline, (-)-BE-54238B, lymphostin, and (-)-lagunamycin], and (iii) acyclic polyketides [xanthocillin X dimethylether, (+)-trichostatin D, and (+)-actinopyrone A]. Features of the total syntheses are described. Original methodologies have been developed and applied to construct the inherent structures of the target molecules. Most syntheses cited herein are the first total syntheses, and the absolute structures of the target molecules have been determined.
Allyloxycarbonyl group: a versatile blocking group for nucleotide synthesis (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAllyloxycarbonyl group: a versatile blocking group for nucleotide synthesisYoshihiro Hayakawa, Hisatoyo Kato, Mamoru Uchiyama, Hisaki Kajino, and Ryoji NoyoriCite this: J. Org. Chem. 1986, 51, 12, 2400–2402Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://doi.org/10.1021/jo00362a052RIGHTS & PERMISSIONSArticle Views1311Altmetric-Citations113LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (391 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase. (1986)

The nucleotide sequence of a 1455-base pair TaqI-HinfI fragment of the rbs operon of Escherichia coli K12 has been determined. It includes the 3' terminus of rbsB (the gene for ribose-binding protein) and the entire rbsK gene, encoding ribokinase. Potential consensus promoter sequences and a stable stem-loop structure are present in the rbsB-rbsK intercistronic region. The regulatory significance of these sequence features is discussed with respect to the rbs operon. rbsK has been cloned downstream from the Serratia marcescens trp promoter on a multicopy plasmid. Cells harboring this plasmid, when grown on minimal ribose plus ampicillin, express ribokinase at the level of 2% of the soluble protein, and induction with indoleacrylic acid raises ribokinase levels another 8-fold. Ribokinase has been purified to homogeneity (216 mumol/min/mg) from a strain harboring this plasmid. Protein sequence analyses of peptides generated by cyanogen bromide cleavage and o-iodosobenzoic acid cleavage confirmed the translation initiation site and the reading frame of the DNA sequence. Amino acid compositions of native ribokinase and the C-terminal dodecapeptide agree with the predicted amino acid compositions, confirming the accuracy of the DNA sequence and the translation termination site.
Efficient Non-Viral Ocular Gene Transfer with Compacted DNA Nanoparticles (2006)

As no deleterious effects on retinal function were observed, this treatment strategy appears to be clinically viable and provides a highly efficient non-viral technology to safely deliver and express nucleic acids in the retina and other ocular tissues.
Negative autoregulation of BCL-6 is bypassed by genetic alterations in diffuse large B cell lymphomas (2002)

Thirty to forty percent of diffuse large B cell lymphomas (DLBCL) carry BCL-6 translocations that disrupt its 5' regulatory region. This same region is also subject to somatic hypermutations, although only a small fraction of these mutations have a detectable effect on transcription. Here, we show that transcription of the BCL-6 gene is negatively self-regulated in multiple cell types. This mechanism operates by means of the interaction of two BCL-6-binding sites within exon 1 of the gene and the BCL-6 protein itself, which is a potent transcription repressor. Because the DLBCL-associated "activating mutations" specifically target these exon 1 binding sites, and because the entire exon 1 is usually removed in the BCL-6-translocated tumors, this autoregulation is bypassed in 30-40% of all DLBCL cases. Our results not only demonstrate an important mechanism governing the expression of BCL-6, but also explain how BCL-6 is deregulated in a large number of DLBCL patients, providing a better understanding of BCL-6-related lymphomagenesis.
Zika virus infection in pregnant women and their children: A review (2021)

Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) transmitted primarily by Aedes mosquitoes. ZIKV can be transmitted to humans by non-vector borne mechanisms such as sexual intercourse, maternal-foetal transmission or blood transfusion. In 2015, ZIKV emerged in the Americas, and spread to 87 countries and territories with autochthonous transmission, distributed across four of the six WHO regions. Most ZIKV infections in pregnancy are asymptomatic, but mother to child transmission of the virus can occur in 20 to 30% of cases and cause severe foetal and child defects. Children exposed to ZIKV while in utero might develop a pattern of structural anomalies and functional disabilities secondary to central nervous system damage, known as congenital Zika syndrome, and whose most common clinical feature is microcephaly. Normocephalic children born to mothers with ZIKV infection in pregnancy, and with no observable Zika-associated birth defects, may also present with later neurodevelopmental delay or post-natal microcephaly. Screening and detection of ZIKV infection in pregnancy is essential, because most women with ZIKV infection are asymptomatic and clinical manifestations are non-specific. However, the diagnosis of ZIKV infection poses multiple challenges due to limited resources and scarce laboratory capabilities in most affected areas, the narrow window of time that the virus persists in the bloodstream, the large proportion of asymptomatic infections, and the cross-reactivity with other flaviviruses such as Dengue virus (DENV). Molecular methods (RT-PCR) are the most reliable tool to confirm ZIKV infection, as serodiagnosis requires confirmation with neutralization tests in case of inconclusive or positive serology results. Prenatal ultrasound assessment is essential for monitoring foetal development and early detection of possible severe anomalies. A mid- and long-term follow-up of children exposed to ZIKV while in utero is necessary to promptly detect clinical manifestations of possible neurological impairment. Tweetable abstract: Zika virus infection during pregnancy is a cause of pregnancy loss and disability in children. Protection against mosquito bites, access to sexual and reproductive health services, prompt screening and detection of ZIKV infection in pregnancy, and prenatal ultrasound monitoring are key control strategies whilst a vaccine is not available.