gebhart/patrepeval huggingface dataset:
Bacterial phylogeny based on 16S and 23S rRNA sequence analysis (1994)

Molecular phylogeny increasingly supports the understanding of organismal relationships and provides the basis for the classification of microorganisms according to their natural affiliations. Comparative sequence analysis of ribosomal RNAs or the corresponding genes currently is the most widely used approach for the reconstruction of microbial phylogeny. The highly and less conserved primary and higher order structure elements of rRNAs document the history of microbial evolution and are informative for definite phylogenetic levels. An optimal alignment of the primary structures and a careful data selection are prerequisites for reliable phylogenetic conclusions. rRNA based phylogenetic trees can be reconstructed and the significance of their topologies evaluated by applying distance, maximum parsimony and maximum likelihood methods of phylogeny inference in comparison, and by fortuitous or directed resampling of the data set. Phylogenetic trees based on almost equivalent data sets of bacterial 23S and 16S rRNAs are in good agreement and their overall topologies are supported by alternative phylogenetic markers such as elongation factors and ATPase subunits. Besides their phylogenetic information content, the differently conserved primary structure regions of rRNAs provide target sites for specific hybridization probes which have been proven to be powerful tools for the identification of microbes on the basis of their phylogenetic relationships.
Preprocessing occlusion for real-time selective refinement (1999)

Article Free Access Share on Preprocessing occlusion for real-time selective refinement Authors: Fei-Ah Law School of Computing, National University of Singapore, Lower Kent Ridge Road, Singapore 119260 School of Computing, National University of Singapore, Lower Kent Ridge Road, Singapore 119260View Profile , Tiow-Seng Tan View Profile Authors Info & Claims I3D '99: Proceedings of the 1999 symposium on Interactive 3D graphicsApril 1999 Pages 47–53https://doi.org/10.1145/300523.300528Published:26 April 1999Publication History 12citation477DownloadsMetricsTotal Citations12Total Downloads477Last 12 Months33Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
LEAFY expression and flower initiation in Arabidopsis (1997)

During the initial vegetative phase, the Arabidopsis shoot meristem produces leaves with associated lateral shoots at its flanks, while the later reproductive phase is characterized by the formation of flowers. The LEAFY gene is an important element of the transition from the vegetative to the reproductive phase, as LEAFY is both necessary and sufficient for the initiation of individual flowers. We have analyzed in detail the expression of LEAFY during the plant life cycle, and found that LEAFY is extensively expressed during the vegetative phase. In long days, Arabidopsis plants flower soon after germination, and this is paralleled by rapid upregulation of LEAFY. In short days, Arabidopsis plants flower several weeks later than in long days, but LEAFY expression increases gradually before flowering commences. Application of the plant hormone gibberellin, which hastens flowering in short days, enhances the gradual change in LEAFY expression observed in short days. Changes in LEAFY expression before the transition to flowering suggest that the time point of this transition is at least partly controlled by the levels of LEAFY activity that are prevalent at a given time of the life cycle. This assumption is borne out by the finding that increasing the copy number of endogenous LEAFY reduces the number of leaves produced before the first flower is formed. Thus, LEAFY combines properties of flowering-time and flower-meristem-identity genes, indicating that LEAFY is a direct link between the global process of floral induction and the regional events associated with the initiation of individual flowers.
All-fiber ring soliton laser mode locked with a nonlinear mirror (1991)

An amplifying nonlinear-optical fiber loop mirror is used as the gain element in an all-fiber ring laser. The resulting double-loop structure resembles a figure eight. The output of the amplifying nonlinear-optical fiber loop mirror is fed back to the input through an optical isolator to ensure unidirectional operation. The laser produces 2-ps transform-limited pulses. The pulse energy corresponds to that of the fundamental soliton in the fiber used.
USH2A Gene Editing Using the CRISPR System (2017)

Usher syndrome (USH) is a rare autosomal recessive disease and the most common inherited form of combined visual and hearing impairment. Up to 13 genes are associated with this disorder, with USH2A being the most prevalent, due partially to the recurrence rate of the c.2299delG mutation. Excluding hearing aids or cochlear implants for hearing impairment, there are no medical solutions available to treat USH patients. The repair of specific mutations by gene editing is, therefore, an interesting strategy that can be explored using the CRISPR/Cas9 system. In this study, this method of gene editing is used to target the c.2299delG mutation on fibroblasts from an USH patient carrying the mutation in homozygosis. Successful in vitro mutation repair was demonstrated using locus-specific RNA-Cas9 ribonucleoproteins with subsequent homologous recombination repair induced by an engineered template supply. Effects on predicted off-target sites in the CRISPR-treated cells were discarded after a targeted deep-sequencing screen. The proven effectiveness and specificity of these correction tools, applied to the c.2299delG pathogenic variant of USH2A, indicates that the CRISPR system should be considered to further explore a potential treatment of USH.
450 MHz PowerPC/sup TM/ microprocessor with enhanced instruction set and copper interconnect (2003)

This superscalar microprocessor implements the PowerPC/sup TM/ Architecture specification incorporating AltiVec/sup TM/ technology. Two instructions per cycle can be dispatched to two of seven execution units in this microarchitecture designed for high execution performance, high memory bandwidth, and low power. The processor includes 8-way set-associative 32 KB instruction and data caches, a floating-point unit, two integer units, a branch unit, a load/store unit, a vector arithmetic/logic unit, a vector permute unit, and a system unit. An L2 tag and cache controller with a dedicated L2 bus interface supports L2 cache sizes of 512 KB, 1MB, or 2 MB with 2-way set associativity. At 450 MHz, and with a 2M B L2 cache, this processor is estimated to have a SPECint95 and SPECfp95 performance of 20. The processor shares many microarchitectural features with the PowerPC 750/sup TM/ microprocessor. New to this processor are two vector execution units which are part of the AltiVec/sup TM/ instruction set implementation, memory subsystem bandwidth enhancements, symmetric multiprocessing support and improved floating-point performance. Supporting up to 8 simultaneous data cache misses, the memory subsystem sustains bandwidths of 3.2 GB/s on the L2 data SRAM interface running at 200 MHz or 1.6 GB/s on the system interface running at 100 MHz.
Crushed Cartilage Grafts over Alar Dome Reduction in Open Rhinoplasty (1993)

Primary and secondary nasal tip deformities can be repaired more easily with an open technique rather than with the traditional closed methods that have been used for the over-projecting tip. Division of the alar domes with a side-to-side repair followed by the onlay of a single crushed cartilage graft to prevent postoperative cartilaginous deformities has been shown to be a reliable maneuver in both primary and secondary rhinoplasties.
Relationship of CD146 expression to activation of circulating T cells: exploratory studies in healthy donors and patients with connective tissue diseases (2013)

The endothelial cell adhesion molecule, CD146, is expressed on ≈ 2% of normal circulating T cells, correlating with T cell activation, endothelial interactions and T helper type 17 (Th17) effector functions. In this study, we have characterized CD146 expression in circulating T cells from healthy controls and patients with stable, well-controlled autoimmune connective tissue diseases (CTDs). In vitro, anti-CD3/anti-CD28 stimulation induced CD146 expression in both CD4 and CD8 T cells. In healthy controls and CTD patients, CD146 was associated with expression of recent and chronic activation markers (CD25(+), OX-40(+), CD69(+), CD27(-)) and was confined to CD45RO(+)/RA(-)/CD28(+) populations within the CD4 subset. Except for CD69, these markers were not associated with CD146 in the CD8 subset. Surprisingly, most CTD patients exhibited no T cell hyperactivation ex vivo. In five of five patients with secondary Sjögren's syndrome circulating T cells appeared activated despite therapy, and CD146 up-regulation, associated with activation markers, was observed both on CD4 and CD8 T cells. There was no association between CD146 and putative pro-atherogenic T cell subsets. In conclusion, the relationship of CD146 expression to T cell activation differs between T cell subsets in healthy subjects and correlates with systemic hyperactivity, where present, in patients with CTDs, as exemplified by the patients with secondary Sjögren's syndrome in this study.
How I treat priapism (2015)

Priapism is a disorder of persistent penile erection unrelated to sexual interest or desire. This pathologic condition, specifically the ischemic variant, is often associated with devastating complications, notably erectile dysfunction. Because priapism demonstrates high prevalence in patients with hematologic disorders, most commonly sickle cell disease (SCD), there is significant concern for its sequelae in this affected population. Thus, timely diagnosis and management are critical for the prevention or at least reduction of cavernosal tissue ischemia and potential damage consequent to each episode. Current guidelines and management strategies focus primarily on reactive treatments. However, an increasing understanding of the molecular pathophysiology of SCD-associated priapism has led to the identification of new potential therapeutic targets. Future agents are being developed and explored for use in the prevention of priapism.
Linkage analysis of familial Alzheimer disease, using chromosome 21 markers. (1991)

Chromosome 21 markers were tested for linkage to familial Alzheimer disease (FAD) in 48 kindreds. These families had multiple cases of Alzheimer disease (AD) in 2 or more generations with family age-at-onset means (M) ranging from 41 to 83 years. Included in this group are seven Volga German families which are thought to be genetically homogeneous with respect to FAD. Autopsy documentation of AD was available for 32 families. Linkage to the 21 q11-q21 region was tested using D21S16, D21S13, D21S110, D21S1/S11, and the APP gene as genetic markers. When linkage results for all the families were summed, the LOD scores for these markers were consistently negative and the entire region was formally excluded. Linkage results were also summed for the following family groups; late-onset (M greater than 60), early-onset (M less than or equal to 60), Volga Germans (M = 56), and early-onset non-Volga Germans (M less than or equal to 60). For the first three groups, LOD scores were negative for this region. For the early-onset non-Volga German group (six families), small positive LOD scores of Zmax = 0.78 (recombination fraction theta = .15), Zmax = 0.27 (theta = .15), and Zmax = 0.64 (theta = .0), were observed for D21S13, D21S16, and D21S110, respectively. The remainder of the long arm of chromosome 21 was tested for linkage to FAD using seven markers spanning the q22 region. Results for these markers were also predominantly negative. Thus it is highly unlikely that a chromosome 21 gene is responsible for late-onset FAD and at least some forms of early-onset FAD represented by the Volga German kindreds.
PKBα is required for adipose differentiation of mouse embryonic fibroblasts (2006)

Protein kinase Balpha (PKBalpha) is a key regulator of metabolism, proliferation and differentiation. We have explored the role of PKBalpha in adipogenesis using wild-type and PKBalpha-knockout mouse embryonic fibroblasts (MEFs) and show that lack of PKBalpha prevents MEF differentiation into adipocytes. Expression of ectopic PKBalpha in PKBalpha-deficient cells restores adipogenesis. We identified 80 genes whose expression was upregulated in wild-type MEFs during adipogenesis but whose expression was significantly reduced in PKBalpha-deficient MEFs under the same conditions. Significantly, the regulator of adipogenesis Krüppel-like transcription factor 15 gene expression was downregulated in PKBalpha-deficient MEFs but could be restored by expressing an active PKBalpha in the deficient cells. The level of lipocalin 2, renin 1 and receptor-activity-modifying protein 3 genes expressed by adipose cells was also decreased in PKBalpha-deficient MEFs, and are inhibited by LY294002 treatment during early adipocyte differentiation of 3T3-L1 cells. The results underscore an essential role for PKBalpha in the transcriptional program required for adipogenesis.
Acinetobacter baumannii Strain M2 Produces Type IV Pili Which Play a Role in Natural Transformation and Twitching Motility but Not Surface-Associated Motility (2013)

Several investigators have documented the presence of genes predicted to encode proteins required for the biogenesis of TFP in many A. baumannii genomes. Furthermore, some have speculated that TFP may play a role in the unique surface-associated motility phenotype exhibited by many A. baumannii clinical isolates, yet there has been no experimental evidence to prove this. Unfortunately, progress in understanding the biology and virulence of A. baumannii has been slowed by the difficulty of constructing and complementing mutations in this species. Strain M2, a recently characterized clinical isolate, is amenable to genetic manipulation. We have established a reproducible system for the generation of marked and/or unmarked mutations using a modified recombineering strategy as well as a genetic complementation system utilizing a modified mini-Tn7 element in strain M2. Using this strategy, we demonstrated that strain M2 produces TFP and that TFP are not required for surface-associated motility exhibited by strain M2.
Characterization and applications of Type I CRISPR-Cas systems (2020)

CRISPR-Cas constitutes the adaptive immune system of bacteria and archaea. This RNA-mediated sequence-specific recognition and targeting machinery has been used broadly for diverse applications in a wide range of organisms across the tree of life. The compact class 2 systems, that hinge on a single Cas effector nuclease have been harnessed for genome editing, transcriptional regulation, detection, imaging and other applications, in different research areas. However, most of the CRISPR-Cas systems belong to class 1, and the molecular machinery of the most widespread and diverse Type I systems afford tremendous opportunities for a broad range of applications. These highly abundant systems rely on a multi-protein effector complex, the CRISPR associated complex for antiviral defense (Cascade), which drives DNA targeting and cleavage. The complexity of these systems has somewhat hindered their widespread usage, but the pool of thousands of diverse Type I CRISPR-Cas systems opens new avenues for CRISPR-based applications in bacteria, archaea and eukaryotes. Here, we describe the features and mechanism of action of Type I CRISPR-Cas systems, illustrate how endogenous systems can be reprogrammed to target the host genome and perform genome editing and transcriptional regulation by co-delivering a minimal CRISPR array together with a repair template. Moreover, we discuss how these systems can also be used in eukaryotes. This review provides a framework for expanding the CRISPR toolbox, and repurposing the most abundant CRISPR-Cas systems for a wide range of applications.
The Functional Architecture of an Acetylcholine Receptor-mimicking Antibody (1997)

Malpha2-3 is a monoclonal antibody that partially mimics the nicotinic acetylcholine receptor (AChR). Its three-dimensional structure has been previously predicted by molecular modeling, suggesting that 29 complementarity determining region (CDR) residues and 2 framework residues are exposed to solvent. To identify the antibody residues that bind to the antigen, i.e. snake toxin that binds specifically to AChR, we (i) produced the scFv form of Malpha2-3 fused to alkaline phosphatase, in the periplasmic space of Escherichia coli; (ii) submitted approximately 75% of exposed residues of the fused scFv to individual or combined mutations, and (iii) identified the residues whose mutations affect scFv binding to the toxin, using a sensitive enzyme-linked immunosorbent assay. 11 critical residues were identified, including 8 heavy chain residues, 2 framework residues, and 1 light chain residue. They cover a surface of approximately 800 A2, with a subset of most critical residues (VHD31, VHY32, and VHG101) and several aromatic residues. This functional architecture not only constitutes a plausible complementary binding surface for the snake toxin but also offers a structural basis to ultimately understand the capacity of the antibody to partially mimic AChR.
Characterization of the effector mechanism of help for antigen-presenting and bystander resting B cell growth mediated by Ia-restricted Th2 helper T cell lines. (1988)

The mechanism of help for resting B cell growth in MHC-restricted T-B collaboration was investigated using an in vitro polyclonal model for these T cell-B cell interactions. In the presence of rabbit anti-mouse Ig, small, size-selected B cells elicit help from syngeneic Ia-restricted Th2 cell lines specific for F(ab')2 rabbit globulin. Both Ag-presenting and bystander B cells receive signals from stimulated Th cells that lead to B cell proliferation. The results suggest that the direct activation of resting Ag-presenting and bystander B cells by Th2 cells is mediated by a similar effector mechanism. Although proliferative responses by Ag-presenting B cells are of greater magnitude, help for both Ag-presenting and bystander B cell populations is characterized by the lack of a requirement for membrane Ig cross-linking, by identical kinetics, and by the necessity for direct cell contact or close proximity with Th cells. B cell proliferation is not induced by exposure to the sequence of diffusable mediators released from a synchronized Ag-specific T-B interaction. The T cell-dependent proliferation by both B cell populations can be inhibited by excess mitomycin C-treated syngeneic "cold target" B cells, demonstrating a requirement for a short-range T cell-B cell interaction. mAb inhibition experiments fail to identify a role for class II, LFA-1, or CD4 membrane molecules in the delivery of help to bystander B cells. Antibody against H2d bystander class II molecules has no effect on bystander B cell proliferation at concentrations that completely block Ag presentation by H2d B cells to an H2d-restricted Th cell line. Antibodies against the cell adhesion molecule LFA-1 or the Th cell molecule CD4 do inhibit bystander B cell proliferation, but only to the extent that they block T cell activation and the induction of help. The inductive stimulus leading to resting B cell growth results from an early, short-range interaction with Th cells. B cell proliferation is supported by T cell soluble mediators as a consequence of this interaction, which is required for at least 8 hr after T cell recognition of Ag/Ia on the surface of Ag-presenting B cells.
Properties of fiber Raman amplifiers and their applicability to digital optical communication systems (1988)

Bit error rate performances of fiber Raman amplifiers both as booster amplifiers and as detection preamplifiers are studied in intensity modulation/direct detection optical communication systems. It is theoretically shown that, in the booster amplifier application, receiver sensitivity degradation due to amplification can be made less than 0.2 dB for signal-to-noise power ratio larger than 20 dB, and thus an allowable transmission line loss can be increased approximately by the value of Raman gain. For detection preamplifier use, receiver sensitivities in the Raman preamplifier system are numerically calculated in terms of minimum detectable signal power at 100-Mbit/s and 2-Gbit/s bit rates. In both bit rates, it is shown that, for a Raman gain greater than 20 dB, minimum detectable signal power can be improved by more than 15 dB over the conventional detection level without Raman amplification. Preliminary experiments are carried out using a 1.32- mu m Nd:YAG laser and a 1.4- mu m laser diode as pump and signal light sources, respectively. The experimental results are in good agreement with theoretical estimations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Correlation of O6-Methylguanine Methyltransferase (MGMT) Promoter Methylation With Clinical Outcomes in Glioblastoma and Clinical Strategies to Modulate MGMT Activity (2008)

Resistance to alkylating agents via direct DNA repair by O 6 -methylguanine methyltransferase (MGMT) remains a significant barrier to the successful treatment of patients with malignant glioma. The relative expression of MGMT in the tumor may determine response to alkylating agents, and epigenetic silencing of the MGMT gene by promoter methylation plays an important role in regulating MGMT expression in gliomas. MGMT promoter methylation is correlated with improved progression-free and overall survival in patients treated with alkylating agents. Strategies to overcome MGMT-mediated chemoresistance are being actively investigated. These include treatment with nontoxic pseudosubstrate inhibitors of MGMT, such as O 6 -benzylguanine, or RNA interference-mediated gene silencing of MGMT. However, systemic application of MGMT inhibitors is limited by an increase in hematologic toxicity. Another strategy is to deplete MGMT activity in tumor tissue using a dose-dense temozolomide schedule. These alternative schedules are well tolerated; however, it remains unclear whether they are more effective than the standard dosing regimen or whether they effectively deplete MGMT activity in tumor tissue. Of note, not all patients with glioblastoma having MGMT promoter methylation respond to alkylating agents, and even those who respond will inevitably experience relapse. Herein we review the data supporting MGMT as a major mechanism of chemotherapy resistance in malignant gliomas and describe ongoing studies that are testing resistance-modulating strategies.
A 650-pJ/bit MedRadio Transmitter With an FIR-Embedded Phase Modulator for Medical Micro-Power Networks (MMNs) (2013)

This paper presents a 400-MHz energy-efficient Medical Micro-power Networks transmitter for neural-muscular signal sensing and stimulation applications. The transmitter can fulfill the transmission requirements defined in the MedRadio band, including the recently added 413-MHz to 457-MHz channels. The half-sine shaped offset-QPSK modulation is adopted to meet the transmission mask requirement while supporting a maximum data rate of 4 Mbps within the 6-MHz channel bandwidth. The signal modulation is performed by the proposed FIR-embedded phase modulator which employs a phase-domain FIR filter to suppress the unwanted side-lobe energy. Fabricated in a 0.18-µm CMOS process, the presented transmitter consumes only 2.6 mW from a 1-V supply, resulting in an energy efficiency of 650 pJ/bit. The measured error vector magnitude is 2.5%.