gebhart/patrepeval huggingface dataset:
The Bearded box, a novel 3′ UTR sequence motif, mediates negative post-transcriptional regulation of Bearded and Enhancer of split Complex gene expression (1997)

During the development of the Drosophila adult peripheral nervous system (PNS), inhibitory cell-cell interactions mediated by the Notch receptor are essential for proper specification of sensory organ cell fates. We have reported previously (M. W. Leviten, E. C. Lai and J. W. Posakony (1997) Development 124, 4039-4051) that the 3' untranslated regions (UTRs) of many genes involved in Notch signalling, including Bearded (Brd) and the genes of the Enhancer of split Complex (E(spl)-C), contain (often in multiple copies) two novel heptanucleotide sequence motifs, the Brd box (AGCTTTA) and the GY box (GTCTTCC). Moreover, the molecular lesion associated with a strong gain-of-function mutant of Brd suggested that the loss of these sequence elements from its 3' UTR might be responsible for the hyperactivity of the mutant gene. We show here that the wild-type Brd 3' UTR confers negative regulatory activity on heterologous transcripts in vivo and that this activity requires its three Brd box elements and, to a lesser extent, its GY box. We find that Brd box-mediated regulation decreases both transcript and protein levels, and our results suggest that deadenylation or inhibition of polyadenylation is a component of this regulation. Though Brd and the E(spl)-C genes are expressed in spatially restricted patterns in both embryos and imaginal discs, we find that the regulatory activity that functions through the Brd box is both temporally and spatially general. A Brd genomic DNA transgene with specific mutations in its Brd and GY boxes exhibits hypermorphic activity that results in characteristic defects in PNS development, demonstrating that Brd is normally regulated by these motifs. Finally, we show that Brd boxes and GY boxes in the E(spl)m4 gene are specifically conserved between two distantly related Drosophila species, strongly suggesting that E(spl)-C genes are regulated by these elements as well.
A comparison of load balancing techniques for scalable Web servers (2000)

Scalable Web servers can be built using a network of workstations where server capacity can be extended by adding new workstations as the workload increases. The topic of our article is a comparison of different method to do load-balancing of HTTP traffic for scalable Web servers. We present a classification framework the different load-balancing methods and compare their performance. In addition, we evaluate in detail one class of methods using a prototype implementation with instruction-level analysis of processing overhead. The comparison is based on a trace driven simulation of traces from a large ISP (Internet Service Provider) in Norway. The simulation model is used to analyze different load-balancing schemes based on redirection of request in the network and redirection in the mapping between a canonical name (CNAME) and IP address. The latter is vulnerable to spatial and temporal locality, although for the set of traces used, the impact of locality is limited. The best performance is obtained with redirection in the network.
Broad-Spectrum Anti-biofilm Peptide That Targets a Cellular Stress Response (2014)

Bacteria form multicellular communities known as biofilms that cause two thirds of all infections and demonstrate a 10 to 1000 fold increase in adaptive resistance to conventional antibiotics. Currently, there are no approved drugs that specifically target bacterial biofilms. Here we identified a potent anti-biofilm peptide 1018 that worked by blocking (p)ppGpp, an important signal in biofilm development. At concentrations that did not affect planktonic growth, peptide treatment completely prevented biofilm formation and led to the eradication of mature biofilms in representative strains of both Gram-negative and Gram-positive bacterial pathogens including Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, methicillin resistant Staphylococcus aureus, Salmonella Typhimurium and Burkholderia cenocepacia. Low levels of the peptide led to biofilm dispersal, while higher doses triggered biofilm cell death. We hypothesized that the peptide acted to inhibit a common stress response in target species, and that the stringent response, mediating (p)ppGpp synthesis through the enzymes RelA and SpoT, was targeted. Consistent with this, increasing (p)ppGpp synthesis by addition of serine hydroxamate or over-expression of relA led to reduced susceptibility to the peptide. Furthermore, relA and spoT mutations blocking production of (p)ppGpp replicated the effects of the peptide, leading to a reduction of biofilm formation in the four tested target species. Also, eliminating (p)ppGpp expression after two days of biofilm growth by removal of arabinose from a strain expressing relA behind an arabinose-inducible promoter, reciprocated the effect of peptide added at the same time, leading to loss of biofilm. NMR and chromatography studies showed that the peptide acted on cells to cause degradation of (p)ppGpp within 30 minutes, and in vitro directly interacted with ppGpp. We thus propose that 1018 targets (p)ppGpp and marks it for degradation in cells. Targeting (p)ppGpp represents a new approach against biofilm-related drug resistance.
Markers of Wound Healing in Vocal Fold Secretions from Patients with Laryngeal Pathology (2004)

This study seeks to determine the ability of enzyme-linked immunosorbent assays of vocal fold secretions to detect and describe the inflammatory response in the vocal folds. Vocal fold and palatal secretions were collected during operation from patients with a range of vocal fold disorders and from control patients. The secretions were subjected to assays for interleukin-1beta, prostaglandin E2, and transforming growth factor beta. The results indicate a differential expression of mediators associated with the wound healing cascade in the vocal folds. The prostaglandin E2 levels clearly differentiated vocal fold secretions associated with laryngeal disease versus control sites. Furthermore, the interleukin-1beta concentrations were significantly elevated in subjects with epithelial lesions of the vocal folds as opposed to lesions of the lamina propria. Although still in its infancy, such analysis may ultimately hold scientific and clinical utility in the study and management of patients with vocal fold disease.
Shot-to-shot directional designature using near-field hydrophone data (2013)

A method for shot-to-shot directional designature using near-field hydrophone measurements is presented. The algorithm is compared with traditional designature methods and data examples are given on a variable depth streamer dataset from the Norwegian North Sea.
SH2 and SH3 Domains: Elements that Control Interactions of Cytoplasmic Signaling Proteins (1991)

Src homology (SH) regions 2 and 3 are noncatalytic domains that are conserved among a series of cytoplasmic signaling proteins regulated by receptor protein-tyrosine kinases, including phospholipase C-gamma, Ras GTPase (guanosine triphosphatase)-activating protein, and Src-like tyrosine kinases. The SH2 domains of these signaling proteins bind tyrosine phosphorylated polypeptides, implicated in normal signaling and cellular transformation. Tyrosine phosphorylation acts as a switch to induce the binding of SH2 domains, thereby mediating the formation of heteromeric protein complexes at or near the plasma membrane. The formation of these complexes is likely to control the activation of signal transduction pathways by tyrosine kinases. The SH3 domain is a distinct motif that, together with SH2, may modulate interactions with the cytoskeleton and membrane. Some signaling and transforming proteins contain SH2 and SH3 domains unattached to any known catalytic element. These noncatalytic proteins may serve as adaptors to link tyrosine kinases to specific target proteins. These observations suggest that SH2 and SH3 domains participate in the control of intracellular responses to growth factor stimulation.
Facile and Efficient Asymmetric Synthesis of α‐Aminoalkylphosphonic Acids (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Organic reactions in ionic liquids: ionic liquid-promoted efficient synthesis of disubstituted and trisubstituted thioureas derivatives (2005)

In ionic liquid [Bmim][BF4], a series of disubstituted and trisubstituted thiourea derivatives were synthesized from phenyl and butyl isothiocyanate with a variety of amine in excellent yield.
Cell-lineage antigens of the stem cell-megakaryocyte-platelet lineage are associated with the platelet IIb-IIIa glycoprotein complex (1985)

The stem cell-platelet lineage is uniquely defined by platelet cell- lineage antigens. These antigens are present on all stem cells measured by the spleen colony assay and become restricted to the platelet cell lineage as differentiation proceeds. In this study, anti-platelet serum (APS) has been used to identify cells in the bone marrow that express platelet cell-lineage antigens and to identify platelet cell surface molecules expressing these antigens. Anti-platelet IgG extensively absorbed with brain, thymus, and peritoneal cells bound selectively to stem cells, megakaryocyte progenitor cells (Mk-CFC), and megakaryocytes in CBA mouse bone marrow and to blood platelets. No other hemopoietic cell type, tissue, cell line, or tumor cell bound significant amounts of antibody against platelet cell-lineage antigens as determined by ability to absorb the anti-stem cell activity in APS. Studies with lactoperoxidase-labeled platelets showed that two major iodinated proteins of Mr = 114,000 and 138,000 were immunoprecipitated with APS and with antiserum that had been extensively absorbed. These proteins correspond to the platelet IIb-IIIa glycoprotein complex, which is known to express receptors for collagen and fibrinogen, molecules known to influence hemopoietic cell proliferation and tumor cell growth. A panel of six monoclonal antibodies against human IIb-IIIa inhibited spleen colony formation by 17% to 100%, J15 and A5.15 also being cytotoxic for granulocyte-macrophage progenitor cells and Mk-CFC. Other platelet monoclonal antibodies did not inhibit spleen colony formation. Although APS inhibited fibrinogen binding to platelets and platelet aggregation, these activities were greatly reduced with absorbed antiserum. Furthermore, fibrinogen treatment of bone marrow did not block the anti-stem cell activity in APS. Thus the evidence is consistent with expression of platelet cell-lineage antigens on the platelet IIb-IIIa glycoprotein complex at a site removed from the fibrinogen binding site.
[Clinical fracture of joint prostheses]. (1995)

Ten Ti6Al4V joint prostheses, including 8 hips and 2 knees, were fractured after 1 to 13 years in vivo service following the primary arthroplasty. The metallographs and electronic microscopies, taken from the retrieved components, demonstrated that there are typical characteristics of stress corrosion fatigue. The excessive chemical content of raw material, the presence of interior defects, such as inclosures and porosities, incorrect design features, which violate biomechanic principles, the overheating and improper surface finishing of the parts, and the clinical varus positioning of the hip stem contribute to the device failure. Policies are proposed to overcome this problem. Among them are drawing national mandatory standards on surgical implants, taking strigent administration measures to ensure the quality of joint prostheses and the establishment of training centers for arthroplasty.
Tuberin Regulates p70 S6 Kinase Activation and Ribosomal Protein S6 Phosphorylation (2002)

Although the cellular functions of TSC2 and its protein product, tuberin, are not known, somatic mutations in the TSC2 tumor suppressor gene are associated with tumor development in lymphangioleiomyomatosis (LAM). We found that ribosomal protein S6 (S6), which exerts translational control of protein synthesis and is required for cell growth, is hyperphosphorylated in the smooth muscle-like cell lesions of LAM patients compared with smooth muscle cells from normal human blood vessels and trachea. Smooth muscle (SM) cells derived from these lesions (LAMD-SM) also exhibited S6 hyperphosphorylation, constitutive activation of p70 S6 kinase (p70S6K), and increased basal DNA synthesis. In parallel, TSC2-/- smooth muscle cells (ELT3) and TSC2-/- epithelial cells (ERC15) also exhibited hyperphosphorylation of S6, constitutive activation of p70S6K, and increased basal DNA synthesis. Re-introduction of wild type tuberin into LAMD-SM, ELT3, and ERC15 cells abolished phosphorylation of S6 and significantly inhibited p70S6K activity and DNA synthesis. Rapamycin, an immunosuppressant, inhibited hyperphosphorylation of S6, p70S6K activation, and DNA synthesis in LAMD-SM cells. Interestingly, the basal levels of phosphatidylinositol 3-kinase, Akt/protein kinase B, and p42/p44 MAPK activation were unchanged in LAMD-SM and ELT3 cells relative to levels in normal human tracheal and vascular SM. These data demonstrate that tuberin negatively regulates the activity of S6 and p70S6K specifically, and suggest a potential mechanism for abnormal cell growth in LAM.
Characterization of Primary Isolate-Like Variants of Simian-Human Immunodeficiency Virus (1999)

Several different strains of simian-human immunodeficiency virus (SHIV) that contain the envelope glycoproteins of either T-cell-line-adapted (TCLA) strains or primary isolates of human immunodeficiency virus type 1 (HIV-1) are now available. One of the advantages of these chimeric viruses is their application to studies of HIV-1-specific neutralizing antibodies in preclinical AIDS vaccine studies in nonhuman primates. In this regard, an important consideration is the spectrum of antigenic properties exhibited by the different envelope glycoproteins used for SHIV construction. The antigenic properties of six SHIV variants were characterized here in neutralization assays with recombinant soluble CD4 (rsCD4), monoclonal antibodies, and serum samples from SHIV-infected macaques and HIV-1-infected individuals. Neutralization of SHIV variants HXBc2, KU2, 89.6, and 89.6P by autologous and heterologous sera from SHIV-infected macaques was restricted to an extent that these viruses may be considered heterologous to one another in their major neutralization determinants. Little or no variation was seen in the neutralization determinants on SHIV variants 89.6P, 89.6PD, and SHIV-KB9. Neutralization of SHIV HXBc2 by sera from HXBc2-infected macaques could be blocked with autologous V3-loop peptide; this was less true in the case of SHIV 89.6 and sera from SHIV 89.6-infected macaques. The poorly immunogenic but highly conserved epitope for monoclonal antibody IgG1b12 was a target for neutralization on SHIV variants HXBc2, KU2, and 89.6 but not on 89.6P and KB9. The 2G12 epitope was a target for neutralization on all five SHIV variants. SHIV variants KU2, 89.6, 89.6P, 89.6PD, and KB9 exhibited antigenic properties characteristic of primary isolates by being relatively insensitive to neutralization in peripheral blood mononuclear cells with serum samples from HIV-1-infected individuals and 12-fold to 38-fold less sensitive to inhibition with recombinant soluble CD4 than TCLA strains of HIV-1. The utility of nonhuman primate models in AIDS vaccine development is strengthened by the availability of SHIV variants that are heterologous in their neutralization determinants and exhibit antigenic properties shared with primary isolates.
Functional characterization of HLA-F and binding of HLA-F tetramers to ILT2 and ILT4 receptors (2000)

HLA-F is a human non-classical MHC molecule. Recombinant HLA-F heavy chain was refolded with 2-microglobulin to form a stable complex. This complex was used as an immunogen to produce a highly specific, high-affinity monoclonal antibody (FG1) that was used to study directly the cellular biology and tissue distribution of HLA-F. HLA-F has a restricted pattern of tissue expression in tonsil, spleen, and thymus. HLA-F could be immunoprecipitated from B cell lines and from HUT-78, a T cell line. HLA-F binds TAP, but unlike the classical human class I molecules, was undetected at the cell surface. HLA-F tetramers stain peripheral blood monocytes and B cells. HLA-F tetramer binding could be conferred on non-binding cells by transfection with the inhibitory receptors ILT2 and ILT4. Surface plasmon resonance studies demonstrated a direct molecular interaction of HLA-F with ILT2 and ILT4. These results, together with structural predictions based on the sequence of HLA-F, suggest that HLA-F may be a peptide binding molecule and may reach the cell surface under favorable conditions, which may include the presence of specific peptide or peptides. At the cell surface it would be capable of interacting with LIR1 (ILT2) and LIR2 (ILT4) receptors and so altering the activation threshold of immune effector cells.
Optically Transparent and High Molecular Weight Polyolefin Block Copolymers toward Self-Assembled Photonic Band Gap Materials (2006)

Block copolymers based on readily available olefins have been synthesized to construct self-assembled one-dimensional (1-D) photonic crystals. Using living olefin polymerization via a bis(phenoxyimine)titanium dichloride/MAO catalyst system, optically transparent and high molecular weight polyolefin block copolymers have been prepared with a narrow molecular weight distribution. The resulting copolymers exhibited a partial 1-D photonic band gap with an excellent optical transparency. Random copolymerization of olefin monomers provided a route to tune the refractive index of each block as well as to suppress the crystallinity for optical transparency. Ternary blending of diblock copolymer with homopolymers further afforded a pathway to control the wavelength of the peak reflectivity of the polyolefin-based photonic structures.
Configuring Cisco Denial-of-Service Security Features, Part 1 (2002)

Abstract You are watching the World Series and Matt Williams of the Diamondbacks is at bat. The count is 3 and 2, two out, and the bases are loaded. The phone rings and the ring indicates a long-distance call. Obviously, the caller is not watching the game. You answer the phone, only to find no one there. You curse and slam down the phone. Several seconds later, it hap-pens again. You repeat the process. This series of events occurs several more times until, out of frustration, you turn off the ringer and let all the calls go to voicemail. At work the next morning, your buddy says, “Where were you? I tried to call last night to make sure you were watching the game.” (If you are a Canadian, substitute Stanley Cup finals for World Series, Mats Sundin for Matt Williams, and Toronto Maple Leafs for Diamondbacks, etc. If you live anywhere else, sub-stitute World Cup, Reynaldo, etc.) The point is that the unknown caller was tying up your phone line and denying access to you. It got so bad you had to take your phone off-line. You can see that it is very difficult to protect against this type of attack, save going off-line. Well, you could take this story and create a simple analogy using your router. Someone starts flooding your router or network with dubious packets. The packets cause the system to crash or consume all avail-able resources. Your legitimate clients cannot get through or do anything. When someone hits your router with a denial-of-service attack, he or she holds up critical resources by block-ing the door to lawful business activity. A denial-of-service (DoS) attack is an attack against your network availability.
Mycosis fungoides: radiation therapy (2003)

Radiation therapy is the most effective single agent for the treatment of mycosis fungoides. There are well-defined dose-response relationships for achieving a complete response as well as the durability of this response. Techniques of electron beam therapy have been developed that permit treatment of the entire skin. Total-skin electron beam therapy is an important form of management, especially for patients who have thick generalized plaque or tumorous disease. Radiation therapy may also be used selectively for treatment of extracutaneous disease.
Recombinant adeno-associated virus type 2 replication and packaging is entirely supported by a herpes simplex virus type 1 amplicon expressing Rep and Cap (1997)

Recombinant adeno-associated virus (AAV) type 2 (rAAV) vectors have recently been shown to have great utility as gene transfer agents both in vitro and in vivo. One of the problems associated with the use of rAAV vectors has been the difficulty of large-scale vector production. Low-efficiency plasmid transfection of the rAAV vector and complementing AAV type 2 (AAV-2) functions (rep and cap) followed by superinfection with adenovirus has been the standard approach to rAAV production. The objectives of this study were to demonstrate the ability of a recombinant herpes simplex virus type 1 (HSV-1) amplicon expressing AAV-2 Rep and Cap to support replication and packaging of rAAV vectors. HSV-1 amplicon vectors were constructed which contain the AAV-2 rep and cap genes under control of their native promoters (p5, p19, and p40). An HSV-1 amplicon vector, HSV-RC/KOS or HSV-RC/d27, was generated by supplying helper functions with either wild-type HSV-1 (KOS strain) or the ICP27-deleted mutant of HSV-1, d27-1, respectively. Replication of the amplicon stocks is not inhibited by the presence of AAV-2 Rep proteins, which highlights important differences between HSV-1 and adenovirus replication and the mechanism of providing helper function for productive AAV infection. Coinfection of rAAV and HSV-RC/KOS resulted in the replication and amplification of rAAV genomes. Similarly, rescue and replication of rAAV genomes occurred when rAAV vector plasmids were transfected into cells followed by HSV-RC/KOS infection and when two rAAV proviral cell lines were infected with HSV-RC/KOS or HSV-RC/d27. Production of infectious rAAV by rescue from two rAAV proviral cell lines has also been achieved with HSV-RC/KOS and HSV-RC/d27. The particle titer of rAAV produced with HSV-RC/d27 is equal to that achieved by supplying rep and cap by transfection followed by adenovirus superinfection. Importantly, no detectable wild-type AAV-2 is generated with this approach. These results demonstrate that an HSV-1 amplicon expressing the AAV-2 genes rep and cap along with HSV-1 helper functions supports the replication and packaging of rAAV vectors in a scaleable process.
Micro‐tsunami from a local interplate earthquake detected by cabled offshore tsunami observation in northeastern Japan (2001)

A micro tsunami from an interplate earthquake ( M w 6.1) was observed in 1998 on ocean bottom tsunami meters (OBTMs) deployed east off the northeastern Japan. The offshore tsunami data without complex distortions due to the coastal topography enable us to estimate reliable tsunami source parameters. The observed amplitude was about 1.5 cm at epicentral distance less than 100 km. We numerically computed the tsunami waveform by solving the linear Boussinesq equations. The observed tsunami waveforms are well explained by synthetic waveforms assuming the fault width of 10–15 km. The depth of the fault is estimated as 5–10 km below the seafloor, which is in good agreement with the location of the plate boundary defined by previous seismic studies.