gebhart/patrepeval huggingface dataset:
White space networking with wi-fi like connectivity (2009)

Networking over UHF white spaces is fundamentally different from conventional Wi-Fi along three axes: spatial variation, temporal variation, and fragmentation of the UHF spectrum. Each of these differences gives rise to new challenges for implementing a wireless network in this band. We present the design and implementation of Net7, the first Wi-Fi like system constructed on top of UHF white spaces. Net7 incorporates a new adaptive spectrum assignment algorithm to handle spectrum variation and fragmentation, and proposes a low overhead protocol to handle temporal variation. builds on a simple technique, called SIFT, that reduces the time to detect transmissions in variable channel width systems by analyzing raw signals in the time domain. We provide an extensive evaluation of the system in terms of a prototype implementation and detailed experimental and simulation results.
Chelation in Metal Intoxication (2010)

Chelation therapy is the preferred medical treatment for reducing the toxic effects of metals. Chelating agents are capable of binding to toxic metal ions to form complex structures which are easily excreted from the body removing them from intracellular or extracellular spaces. 2,3-Dimercaprol has long been the mainstay of chelation therapy for lead or arsenic poisoning, however its serious side effects have led researchers to develop less toxic analogues. Hydrophilic chelators like meso-2,3-dimercaptosuccinic acid effectively promote renal metal excretion, but their ability to access intracellular metals is weak. Newer strategies to address these drawbacks like combination therapy (use of structurally different chelating agents) or co-administration of antioxidants have been reported recently. In this review we provide an update of the existing chelating agents and the various strategies available for the treatment of heavy metals and metalloid intoxications.
Expression of human tenascin in synovitis and its regulation by interleukin‐1 (1992)

Tenascin mRNA and protein are increased in inflammatory synovitis, and interleukin-1 is an inducer of tenascin in synovial fibroblasts. This identifies a new pathway by which interleukin-1 alters the extracellular matrix composition in synovitis. Since tenascin has effects on lymphocyte activation and cell adhesion, the induction of tenascin in inflammatory synovitis may play a role in the pathophysiology of arthritis.
The Rise and Fall of Oral Ketoconazole (2015)

Due to its hepatotoxic side effects, oral ketoconazole was withdrawn from the European and Australian markets in 2013. The United States imposed strict relabeling requirements and restrictions for prescription, with Canada issuing a risk communication echoing these concerns. Today, oral ketoconazole is only indicated for endemic mycoses, where alternatives are not available or feasible. Meanwhile, topical ketoconazole is effective, safe, and widely prescribed for superficial mycoses, particularly as the first-line treatment for tinea versicolor.
A poliovirus temperature-sensitive RNA synthesis mutant located in a noncoding region of the genome. (1986)

We have constructed an 8-base-pair insertion mutation in the 3' noncoding region of an infectious poliovirus cDNA clone that gives rise to a temperature-sensitive RNA synthesis mutant upon transfection into mammalian cells. The mutated cDNA was used to establish a cell line that releases the mutant poliovirus in a temperature-dependent fashion, representing a unique persistent viral infection. A poliovirus mutant mapping in the noncapsid region of the viral genome can be complemented in this cell line, implying that the cell line expresses viral proteins at the nonpermissive temperature.
Inhibition of DNA Binding by NF-κB with Pyrrole-Imidazole Polyamides (2002)

Synthetic ligands that bind to predetermined DNA sequences will offer a chemical approach to gene regulation if inhibition of a broad range of transcription factors can be achieved. NF-kappa B is a transcription factor that regulates a multitude of genes, including those involved in immune, inflammatory, and anti-apoptotic responses. NF-kappa B binds as heterodimer predominantly in the major groove. We report the design of polyamides that bind in the minor groove and target overlapping portions of an NF-kappa B binding site (5'-GGGACTTTCC-3'). We find that compounds that target the 5'-GGGACT-3' portion of the site can inhibit DNA binding by NF-kappa B while those that target the 5'-ACTTTCC-3' portion do not. Addition of NF-kappa B to the list of protein-DNA complexes that can be disrupted by minor groove binding ligands potentially increases the utility of polyamides as regulators of gene expression.
3D Nanowire-Based Programmable Logic (2006)

In nanowire-based logic, the semiconducting material (e.g., Si, GaN, SiGe) is grown into individual nanowires rather than being part of the substrate. This offers us the opportunity to stack multiple layers of nanowires to create a three-dimensional logic structure which has high quality semiconductors in all vertical layers. The authors detail a feasible three-dimensional programmable logic architecture which can plausibly be realized from layers of semiconducting nanowires, making only modest assumptions about the control and placement of individual nanowires in the assembly. This shows a natural path for continuing to scale areal logic density once nanowire pitches approach fundamental limits. The authors show that the three dimensional systems are volumetrically efficient, with the surface area reducing roughly in proportion to the number of vertical layers. The authors further show that, on average, delay is reduced 18% from compact layout in three dimensions. For only a 20% area impact, the authors show how to avoid adding any manufacturing steps to physically isolate portions of nanowire layers
Sensing structural intermediates in bacterial flagellar assembly by export of a negative regulator (1993)

The ability of a regulatory protein to sense the integrity of the bacterial flagellar structure was investigated. In response to a defective hook-basal body complex, the anti-sigma 28 FlgM protein inhibits flagellin transcription. In cells with a functional hook-basal body complex, the flagellin genes are transcribed normally and the FlgM protein is expelled into the growth medium. In strains with a defective hook-basal body structure, FlgM is absent from the media. The presence of flagellin protein in the media is substantially reduced in strains carrying a FlgM-LacZ protein fusion, suggesting that the fusion is blocking the flagellar export apparatus. These results suggest that the FlgM protein assesses the integrity of the flagellar hook-basal body complex by itself being a substrate for export by the flagellar-specific export apparatus.
Quantitative Assessment of Peripheral Airway Obstruction on Paired Expiratory/Inspiratory Thin-section Computed Tomography in Chronic Obstructive Pulmonary Disease With Emphysema (2007)

The paired inspiratory/expiratory CT measurements in the limited-lung without emphysema correlated more closely with the PFTs. Our observations suggest that paired inspiratory/expiratory CT scans in the limited-lung excluding emphysema are sensitive for the evaluation of airway obstruction in COPD with emphysema.
A Combinatorial Approach to 2,4,6‐Trisubstituted Triazines with Potent Antimalarial Activity: Combining Conventional Synthesis and Microwave‐Assistance (2008)

Managing malaria. Malaria is responsible for two million deaths per year particularly in developing countries, therefore there is great need for the development of cost effective treatment. The synthesis of a library of trisubstituted triazines with potent antimalarial in vitro activity is reported. Among them, five products may be developed as potential leads in the search for new drugs against plasmodial chloroquine-resistant strains.
Long-Range Nonradiative Transfer of Electronic Excitation Energy in Proteins and Polypeptides (1971)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
[Effects of prenatal exposure to stress and lead on spatial learning and memory development in rats]. (2008)

Prenatal joint exposure to restraint stress and lead might increase the effects of single exposure on the spatial learning and memory ability and serum corticosterone level of offsprings, and the joint influence on corticosterone level might be one of the reasons of further impairment of learning and memory.
The CauliflowerOrGene Encodes a DnaJ Cysteine-Rich Domain-Containing Protein That Mediates High Levels of β-Carotene Accumulation (2006)

Despite recent progress in our understanding of carotenogenesis in plants, the mechanisms that govern overall carotenoid accumulation remain largely unknown. The Orange (Or) gene mutation in cauliflower (Brassica oleracea var botrytis) confers the accumulation of high levels of beta-carotene in various tissues normally devoid of carotenoids. Using positional cloning, we isolated the gene representing Or and verified it by functional complementation in wild-type cauliflower. Or encodes a plastid-associated protein containing a DnaJ Cys-rich domain. The Or gene mutation is due to the insertion of a long terminal repeat retrotransposon in the Or allele. Or appears to be plant specific and is highly conserved among divergent plant species. Analyses of the gene, the gene product, and the cytological effects of the Or transgene suggest that the functional role of Or is associated with a cellular process that triggers the differentiation of proplastids or other noncolored plastids into chromoplasts for carotenoid accumulation. Moreover, we demonstrate that Or can be used as a novel genetic tool to induce carotenoid accumulation in a major staple food crop. We show here that controlling the formation of chromoplasts is an important mechanism by which carotenoid accumulation is regulated in plants.
Limiting factors in acoustic separation of carbon particles in air (2010)

Particles suspended in a fluid that is exposed to an acoustic standing wave experience a time-averaged force that drives them to either the pressure nodes or anti-nodes of the wave. Several filter designs have been successfully implemented using this force to filter small particles in liquids with low flow rates and small cross-sectional areas. It has been suggested that the filtration of small solid particles out of a gas, such as carbon in air (smoke), would be a possible application of acoustic standing wave based particle separation. This study shows the limiting factors, in both power requirements and design factors, of an acoustic filter designed for filtering smoke particles across large cross-sectional areas. It is shown that while filtration is possible, the power needed is impractical. It is also shown that operating the filter within certain settling time parameters optimizes the energy usage of the filter.
Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. (1994)

The reverse transcriptase from human immunodeficiency virus type 1 is a heterodimer consisting of one 66-kDa and one 51-kDa subunit. The p66 subunit contains both a polymerase and an RNase H domain; proteolytic cleavage of p66 removes the RNase H domain to yield the p51 subunit. Although the polymerase domain of p66 folds into an open, extended structure containing a large active-site cleft, that of p51 is closed and compact. The connection subdomain, which lies between the polymerase and RNase H active sites in p66, plays a central role in the formation of the reverse transcriptase heterodimer. Extensive and very different intra- and intersubunit contacts are made by the connection subdomains of each of the subunits. Together, contacts between the two connection domains constitute approximately one-third of the total contacts between subunits of the heterodimer. Conversion of an open p66 polymerase domain structure to a closed p51-like structure results in a reduction in solvent-accessible surface area by 1600 A2 and the burying of an extensive hydrophobic surface. Thus, the monomeric forms of both p66 and p51 are proposed to have the same closed structure as seen in the p51 subunit of the heterodimer. The free energy required to convert p66 from a closed p51-like structure to the observed open p66 polymerase domain structure is generated by the burying of a large, predominantly hydrophobic surface area upon formation of the heterodimer. It is likely that the only kind of dimer that can form is an asymmetric one like that seen in the heterodimer structure, since one dimer interaction surface exists only in p51 and the other only in p66. We suggest that both p51 and p66 form asymmetric homodimers that are assembled from one subunit that has assumed the open conformation and one that has the closed structure.
Mechanisms of Thrombus Formation (2008)

Hemostasis is the process that maintains the integrity of a closed, high-pressure circulatory system after vascular damage. Vessel-wall injury and the extravasation of blood from the circulation rapidly initiate events in the vessel wall and in blood that seal the breach. Circulating platelets are recruited to the site of injury, where they become a major component of the developing thrombus; blood coagulation, initiated by tissue factor, culminates in the generation of thrombin and fibrin. These events occur concomitantly (Figure 1A; also see Video, available with the full text of this article at www.nejm.org), and under normal conditions, regulatory mechanisms contain . . .
Inhibition of Virus DNA Replication by Artificial Zinc Finger Proteins (2005)

Prevention of virus infections is a major objective in agriculture and human health. One attractive approach to the prevention is inhibition of virus replication. To demonstrate this concept in vivo, an artificial zinc finger protein (AZP) targeting the replication origin of the Beet severe curly top virus (BSCTV), a model DNA virus, was created. In vitro DNA binding assays indicated that the AZP efficiently blocked binding of the viral replication protein (Rep), which initiates virus replication, to the replication origin. All of the transgenic Arabidopsis plants expressing the AZP showed phenotypes strongly resistant to virus infection, and 84% of the transgenic plants showed no symptom. Southern blot analysis demonstrated that BSCTV replication was completely suppressed in the transgenic plants. Since the mechanism of viral DNA replication is well conserved among plants and mammals, this approach could be applied not only to agricultural crop protection but also to the prevention of virus infections in humans.
Tumor-Associated Embryonic Antigen-Expressing Vaccines that Target CCR6 Elicit Potent CD8+ T Cell-Mediated Protective and Therapeutic Antitumor Immunity (2007)

Despite its potency, the wider use of immunotherapy for B cell malignancies is hampered by the lack of well-defined tumor-specific Ags. In this study, we demonstrate that an evolutionarily conserved 37-kDa immature laminin receptor protein (OFA-iLRP), a nonimmunogenic embryonic Ag expressed by a variety of tumors, is rendered immunogenic if targeted to the APCs using the CCR6 ligands MIP3alpha/CCL20 and mDF2beta. The CCR6 targeting facilitated efficient Ag cross-presentation and induction of tumor-neutralizing CTLs. Although the Ag targeting alone, without activation of dendritic cells (DCs), is proposed to induce tolerance, and MIP3alpha does not directly activate DCs, the MIP3alpha-based vaccine efficiently induced protective and therapeutic antitumor responses. The responses were as strong as those elicited by the OFA-iLRP fusions with moieties that activated DCs and Th1-type cytokine responses, mDF2beta, or mycobacterial Hsp70 Ag. Although the same cDNA encodes the dimerized high-affinity mature 67-kDa mLRP that is expressed in normal tissues to stabilize the binding of laminin to cell surface integrins, the vaccines expressing OFA-iLRP elicited long-term protective CD8(+) T cell-mediated memory responses against syngeneic B cell lymphoma, indicating the potential application of these simple vaccines as preventive and therapeutic formulations for human use.
Applying TMN to a distributed communications node system with common platform software (2002)

The paper presents techniques for applying the telecommunications management network (TMN) concept to a distributed communications node system with common platform software. Frameworks are presented for ensuring efficiently flexible design of managed objects (MOs) and software components in the distributed communications node system. Based on these frameworks, agent functions are proposed for establishing a telecommunications management network on the distributed communications node system. A method is presented for adding software components with new managed objects for easy development and maintenance of the system.
Metformin inhibits the senescence‐associated secretory phenotype by interfering with IKK/NF‐κB activation (2013)

We show that the antidiabetic drug metformin inhibits the expression of genes coding for multiple inflammatory cytokines seen during cellular senescence. Conditioned medium (CM) from senescent cells stimulates the growth of prostate cancer cells but treatment of senescent cells with metformin inhibited this effect. Bioinformatic analysis of genes downregulated by metformin suggests that the drug blocks the activity of the transcription factor NF-κB. In agreement, metformin prevented the translocation of NF-κB to the nucleus and inhibited the phosphorylation of IκB and IKKα/β, events required for activation of the NF-κB pathway. These effects were not dependent on AMPK activation or on the context of cellular senescence, as metformin inhibited the NF-κB pathway stimulated by lipopolysaccharide (LPS) in ampk null fibroblasts and in macrophages. Taken together, our results provide a novel mechanism for the antiaging and antineoplastic effects of metformin reported in animal models and in diabetic patients taking this drug.
A pattern-oriented intrusion-detection model and its applications (2002)

Operational security problems can lead to intrusion in secure computer systems. The authors justify the need for, and present, a pattern-oriented intrusion-detection model that can be used to analyze object privilege and data flows in secure computer systems to detect operational security problems. This model can address context-dependent intrusion, such as use of covert-storage channels and virus propagation, and has been used to build an intrusion detection system for Trusted XENIX. Pattern-oriented intrusion detection is expected to complement, not replace, current statistical approaches to intrusion detection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structural characterization of recombinant domain II of the basement membrane proteoglycan perlecan (1996)

Mouse perlecan domain II (325 residues), consisting of four cysteine-rich LA modules, one IG module and a link region, was obtained in purified form from a stably transfected mammalian cell clone. Rotary shadowing electron microscopy demonstrated a globular domain connected to a short rod-like segment of variable length. This suggested that tandem arrays of LA modules form rod-like elements. Folding into a native structure was indicated by the sharing of immunological epitopes with tissue perlecan, a CD spectrum demonstrating 37% beta structure and a limited susceptibility to proteolysis. The domain also showed N-glycosylation of a single acceptor site and 7-8 O-linked oligosaccharides. The latter were located mainly in the link region within proline-rich sequences.
microRNA expression in the biology, prognosis, and therapy of Waldenström macroglobulinemia (2008)

Multilevel genetic characterization of Waldenström macroglobulinemia (WM) is required to improve our understanding of the underlying molecular changes that lead to the initiation and progression of this disease. We performed microRNA-expression profiling of bone marrow-derived CD19(+) WM cells, compared with their normal cellular counterparts and validated data by quantitative reverse-transcription-polymerase chain reaction (qRT-PCR). We identified a WM-specific microRNA signature characterized by increased expression of microRNA-363*/-206/-494/-155/-184/-542-3p, and decreased expression of microRNA-9* (ANOVA; P < .01). We found that microRNA-155 regulates proliferation and growth of WM cells in vitro and in vivo, by inhibiting MAPK/ERK, PI3/AKT, and NF-kappaB pathways. Potential microRNA-155 target genes were identified using gene-expression profiling and included genes involved in cell-cycle progression, adhesion, and migration. Importantly, increased expression of the 6 miRNAs significantly correlated with a poorer outcome predicted by the International Prognostic Staging System for WM. We further demonstrated that therapeutic agents commonly used in WM alter the levels of the major miRNAs identified, by inducing downmodulation of 5 increased miRNAs and up-modulation of patient-downexpressed miRNA-9*. These data indicate that microRNAs play a pivotal role in the biology of WM; represent important prognostic marker; and provide the basis for the development of new microRNA-based targeted therapies in WM.
AlternativeO-Glycosylation/O-Phosphorylation of Serine-16 in Murine Estrogen Receptor β (2001)

O-Linked N-acetylglucosamine (O-GlcNAc) is a dynamic post-translational modification abundant on nuclear and cytoplasmic proteins. Recently, we demonstrated that the murine estrogen receptor-beta (mER-beta) is alternatively O-GlcNAcylated or O-phosphorylated at Ser(16). Analyses of mER-betas containing mutations in the three adjacent hydroxyl amino acids at this locus confirmed that Ser(16) is the major site of O-GlcNAc modification on mER-beta and that mutants lacking hydroxyl amino acids at this locus are glycosylation-deficient. Pulse-chase studies in transfected Cos-1 cells demonstrate that the turnover rate of the mutant containing a glutamic acid moiety at Ser(16), which mimics constitutive phosphorylation at this locus, is faster than that of the wild type receptor. Whereas, the mutant without hydroxyl amino acids at this locus is degraded at a slower rate, indicating that O-GlcNAc/O-phosphate at Ser(16) modulates mER-beta protein stability. Luciferase reporter assays also show that the Ser(16) locus mutants have abnormal transactivation activities, suggesting that the two alternative modifications at Ser(16) on mER-beta may also be involved in transcriptional regulation. DNA mobility shift assays show that the mutants do not have altered DNA binding. Green fluorescence protein constructs of both wild type and mutant forms of mER-beta show that the receptor is nearly exclusively localized within the nucleus. It appears that reciprocal occupancy of Ser(16) by either O-phosphate or O-GlcNAc modulates the degradation and activity of mER-beta.