gebhart/patrepeval huggingface dataset:
Optical characteristics and low linewidth enhancement factor in 1.2 μm quantum dot lasers (2003)

The QD density of states, which theoretically is a series of delta function spikes at the quantized energy levels, indicates that threshold current densities are not only low but also temperature independent. Another important property is the degree to which carrier density variations alter the index of refraction of the active layer. Large values of dn/dN can result in antiguiding in narrow stripe lasers, as well as self-focusing and filamentation in broad area emitters. The latter is often described by the linewidth enhancement parameter, /spl alpha/=-4/spl pi///spl lambda/(dn/dN)(dg/dN)/sup -1/. For strained InGaAs single quantum well (QW) lasers, operating near 980nm, the value of /spl alpha/ is typically 2 or higher at carrier densities corresponding to threshold. At the communications wavelengths of 1.3 /spl mu/m and 1.55 /spl mu/m /spl alpha/ is usually much higher unless modulation doping or a large number of quantum wells are employed. However, the elimination or substantial reduction a may be realized by utilizing quantum dot lasers. /spl alpha/ values are predicted to be low and even zero for certain conditions. Since one area of great interest is the production of QD devices at 1.3 /spl mu/m, such structures may have a large applicability to wide bandwidth communications devices and high power amplifiers. We have designed, grown, and characterized quantum dot lasers that feature a layer of InAs quantum dots centered in a single 100 A In/sub 0.2/Ga/sub 0.8/As quantum well structure.
Targeting of Alpha‐Hemolysin by Active or Passive Immunization Decreases Severity of USA300 Skin Infection in a Mouse Model (2010)

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are predominantly those affecting skin and soft tissues. Although progress has been made, our knowledge of the molecules that contribute to the pathogenesis of CA-MRSA skin infections is incomplete. We tested the hypothesis that alpha-hemolysin (Hla) contributes to the severity of USA300 skin infections in mice and determined whether vaccination against Hla reduces disease severity. Isogenic hla-negative (Deltahla) strains caused skin lesions in a mouse infection model that were significantly smaller than those caused by wild-type USA300 and Newman strains. Moreover, infection due to wild-type strains produced dermonecrotic skin lesions, whereas there was little or no dermonecrosis in mice infected with Deltahla strains. Passive immunization with Hla-specific antisera or active immunization with a nontoxigenic form of Hla significantly reduced the size of skin lesions caused by USA300 and prevented dermonecrosis. We conclude that Hla is a potential target for therapeutics or vaccines designed to moderate severe S. aureus skin infections.
Translation of the psbA mRNA of Chlamydomonas reinhardtii requires a structured RNA element contained within the 5' untranslated region. (1994)

Translational regulation is a key modulator of gene expression in chloroplasts of higher plants and algae. Genetic analysis has shown that translation of chloroplast mRNAs requires nuclear-encoded factors that interact with chloroplastic mRNAs in a message-specific manner. Using site-specific mutations of the chloroplastic psbA mRNA, we show that RNA elements contained within the 5' untranslated region of the mRNA are required for translation. One of these elements is a Shine-Dalgarno consensus sequence, which is necessary for ribosome association and psbA translation. A second element required for high levels of psbA translation is located adjacent to and upstream of the Shine-Dalgarno sequence, and maps to the location on the RNA previously identified as the site of message-specific protein binding. This second element appears to act as a translational attenuator that must be overcome to activate translation. Mutations that affect the secondary structure of these RNA elements greatly reduce the level of psbA translation, suggesting that secondary structure of these RNA elements plays a role in psbA translation. These data suggest a mechanism for translational activation of the chloroplast psbA mRNA in which an RNA element containing the ribosome-binding site is bound by message-specific RNA binding proteins allowing for increased ribosome association and translation initiation. These elements may be involved in the light-regulated translation of the psbA mRNA.
XPIR : Private Information Retrieval for Everyone (2015)

Abstract A Private Information Retrieval (PIR) scheme is a protocol in which a user retrieves a record from a database while hiding which from the database administrators. PIR can be achieved using mutuallydistrustful replicated databases, trusted hardware, or cryptography. In this paper we focus on the later setting which is known as single-database computationally- Private Information Retrieval (cPIR). Classic cPIR protocols require that the database server executes an algorithm over all the database content at very low speeds which impairs their usage. In [1], given certain assumptions, realistic at the time, Sion and Carbunar showed that cPIR schemes were not practical and most likely would never be. To this day, this conclusion is widely accepted by researchers and practitioners. Using the paradigm shift introduced by lattice-based cryptography, we show that the conclusion of Sion and Carbunar is not valid anymore: cPIR is of practical value. This is achieved without compromising security, using standard crytosystems, and conservative parameter choices.
Improvements to the Synthesis of Isofagomine, Noeuromycin, Azafagomine, and Isofagomine Lactam, and a Synthesis of Azanoeuromycin and “Guanidine” Isofagomine. (2007)

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.
Preparation and Properties of Antisera against the Lipid‐A component of Bacterial Lipopolysaccharides (1971)

The lipid‐A component of lipopolysaccharides, when presented in a suitable form, acts as an immunogen in rabbits, giving rise to the production of circulating antibodies. Highest anti‐lipid‐A titers were obtained on immunization with acid‐treated bacterial cells coated with lipid A. Anti‐lipid‐A activity of the immune sera could be assayed by passive hemolysis of lipid‐A‐sensitized erythrocytes in the presence of complement. On filtration of the immune globulins on Sephadex G‐200, antibodies against lipid A were detected in the IgM and IgG fractions. Lipid A preparations derived from various Salmonella and one Echerichica coli strain exhibited strong serological cross reactions with anti‐lipid‐A antisera. Furthermore, lipid‐A antiserum also cross‐reacted with all lipopolysaccharides tested, although in some cases to a low degree. On the other hand, only 8 out of 13 antibacterial antisera interacted with lipid‐A‐coated red cells. Finally, it was found that anti‐lipid‐A antibodies are effective in sensitizing E. coli 0111 bacteria for intraperitoneal phagocytosis.
Modulation by tetrahydrouridine (THU) of gemcitabine (2’,2’-difluoro-2’-deoxycytidine, dFdC) pharmacokinetics, metabolism and bioavailability in mice (2007)

1556 Introduction In vivo, dFdC is rapidly inactivated by cytidine deaminase (CD) metabolism to 2’,2’-difluoro-2’-deoxyuridine (dFdU). Therefore, dFdC has poor po bioavailability and needs to be dosed iv. THU is a potent CD inhibitor that we have shown has a po bioavailability of ~20%. We investigated the potential for THU to decrease elimination and first-pass effect by CD, thereby enabling po dosing of dFdC. Methods An LC-MS/MS assay was developed to quantitate dFdC and dFdU in plasma. Male CD2F1 mice were dosed with 100 mg/kg dFdC iv or po with or without 100 mg/kg THU iv or po. At specified times between 5 and 1440 min, mice (N=3) were euthanized. Blood was collected and divided into two fractions. THU was rapidly added to fraction 1, and dFdC and dFdU were quantitated in the plasma. THU was quantitated in plasma from fraction 2. Urine was diluted ≥1:10 in control plasma and assayed for dFdC, dFdU, and THU. Results The lower limit of quantitation was ≤20 ng/ml for all analytes. THU iv and po produced concentrations >400 ng/mL for 3 and 2 h, respectively. dFdC po bioavailability without THU was ~10% (PK# 1&2). iv THU decreased dFdU concentrations (PK# 1&3) but had no effect on iv dFdC PK including clearance (40 and 42 mL/min/kg) and distribution volume (2.14 and 2.44 L/kg). A 60% increased renal dFdC excretion was observed as a compensatory eliminating mechanism when THU blocked CD. Both iv and po THU substantially increased po bioavailability of dFdC (PK# 2&4&5). iv THU revealed absorption of po dFdC to be 59% (PK# 3&4, assuming full CD block with iv THU), but only 10% reached the systemic circulation after first pass (PK# 1&2). po THU increased dFdC po bioavailability to 40% (PK# 3&5). Conclusion Our results suggest that co-administration of THU enables po dosing of dFdC, resulting in easier dosing and potentially prolonged dFdC exposure. This promising approach warrants clinical testing. Support: N01-CM-52202 and P30-CA47904 from the NCI.
Thrombin‐binding affinities of different disulfide‐bonded isomers of the fifth EGF‐like domain of thrombomodulin (1995)

The fifth EGF-like domain of thrombomodulin (TM), both with and without the amino acids that connect the fifth domain to the sixth domain, has been synthesized and refolded to form several different disulfide-bonded isomers. The domain without the connecting region formed three disulfide-bonded isomers upon refolding under redox conditions. Of these three isomers, the (1-2,3-4,5-6) bonded isomer was the best inhibitor of fibrinogen clotting and also of the thrombin-TM interaction that results in protein C activation, but all the isomers were inhibitors in both assays. The isomer containing an EGF-like disulfide-bonding pattern (1-3,2-4,5-6) was not found among the oxidation products. The domain with the connecting region amino acids (DIDE) at the C-terminus formed two isolable products upon refolding in redox buffer. These products had the same two disulfide-bonding patterns as the earliest and latest eluting isomers of the domain without the DIDE. In order to compare the thrombin-binding affinities of these isomers to the isomer with the EGF-like disulfide bonds, acetamidomethyl protection of the second and fourth cysteines was used to force the disulfide bonds into the EGF-like pattern. Thrombin-binding affinity, measured as inhibition of fibrinogen clotting and as inhibition of protein C activation correlated inversely with the number of crossed disulfide bonds. As was found for the domain without the connecting region, the isomer that was the best inhibitor of fibrinogen clotting and of protein C activation was the isomer with no crossing disulfide bonds (1-2,3-4,5-6).(ABSTRACT TRUNCATED AT 250 WORDS)
Interpretation of cytokine signaling through the transcription factors STAT5A and STAT5B (2008)

Transcription factors from the family of Signal Transducers and Activators of Transcription (STAT) are activated by numerous cytokines. Two members of this family, STAT5A and STAT5B (collectively called STAT5), have gained prominence in that they are activated by a wide variety of cytokines such as interleukins, erythropoietin, growth hormone, and prolactin. Furthermore, constitutive STAT5 activation is observed in the majority of leukemias and many solid tumors. Inactivation studies in mice as well as human mutations have provided insight into many of STAT5's functions. Disruption of cytokine signaling through STAT5 results in a variety of cell-specific effects, ranging from a defective immune system and impaired erythropoiesis, the complete absence of mammary development during pregnancy, to aberrant liver function. On a molecular level, STAT5 has been linked to cell specification, proliferation, differentiation, and survival. Evidence is growing that the diverse outcomes of STAT5 signaling are not only determined by the expression of specific receptors but also by the interaction of STAT5 with cofactors and the cell-specific activity of members of the SOCS family, which negatively regulate STAT function. In this review, we focus on emerging concepts and challenges in the field of Janus kinase (JAK)-STAT5 signaling. First, we discuss unique functions of STAT5 in three distinct systems: mammary epithelial cells, hepatocytes, and regulatory T cells. Second, we present an example of how STAT5 can achieve cell specificity in hepatocytes through a physical and functional interaction with the glucocorticoid receptor. Third, we focus on the relevance of STAT5 in the development and progression of leukemia. Next, we discuss lessons derived from human mutations and disease. Finally, we address an emerging issue that the interpretation of experiments from STAT5-deficient mice and cells might be compromised as these cells might reroute and reprogram cytokine signals to the "wrong" STATs and thus acquire inappropriate cues. We propose that mice with mutations in various components of the JAK-STAT signaling pathway are living laboratories, which will provide insight into the versatility of signaling hardware and the adaptability of the software.
The Poxvirus Vectors MVA and NYVAC as Gene Delivery Systems for Vaccination Against Infectious Diseases and Cancer (2008)

Recombinants based on poxviruses have been used extensively as gene delivery systems to study many biological functions of foreign genes and as vaccines against many pathogens, particularly in the veterinary field. Based on safety record, efficient expression and ability to trigger specific immune responses, two of the most promising poxvirus vectors for human use are the attenuated modified vaccinia virus Ankara (MVA) and the Copenhagen derived NYVAC strains. Because of the scientific and clinical interest in these two vectors, here we review their biological characteristics, with emphasis on virus-host cell interactions, viral immunomodulators, gene expression profiling, virus distribution in animals, and application as vaccines against different pathogens and tumors.
High expression of lysine-specific demethylase 1 correlates with poor prognosis of patients with esophageal squamous cell carcinoma (2013)

Recent studies have elucidated the role of lysine-specific demethylase 1 (LSD1), a member of the histone demethylases, in epigenetic regulation of tumor suppressing/promoting genes and neoplastic growth. However, the expression of LSD1 in patients with esophageal squamous cell carcinoma (ESCC) is still unknown. Here, we reported that LSD1 expression was elevated in cancerous tissue and correlated with lymph node metastasis and poorer overall survival in patients with ESCC. Compared to EC109 cells, LSD1 expression was unregulated in aggressive cancer cell lines KYSE450 and KYSE150. Knockdown of LSD1 using lentivirus delivery of LSD1-specific shRNA abrogated the migration and invasion of ESCC cells in vitro. Further, a LSD1 inhibitor, tranylcypromine, suppressed H3K4me2 demethylation and attenuated cellular motility and invasiveness in a dose-dependent manner. Taken together, these data suggested that LSD1 was a potential prognostic maker and may be a molecular target for inhibiting invasion and metastasis in ESCC.
Dynamical decoupling and noise spectroscopy with a superconducting flux qubit (2011)

The characterization and mitigation of decoherence in natural and artificial two-level systems (qubits) is fundamental to quantum information science and its applications. Decoherence of a quantum superposition state arises from the interaction between the constituent system and the uncontrolled degrees of freedom in its environment. Within the standard Bloch-Redfield picture of two-level system dynamics, qubit decoherence is characterized by two rates: a longitudinal relaxation rate Gamma1 due to the exchange of energy with the environment, and a transverse relaxation rate Gamma2 = Gamma1/2 + Gamma_phi which contains the pure dephasing rate Gamma_phi. Irreversible energy relaxation can only be mitigated by reducing the amount of environmental noise, reducing the qubit's internal sensitivity to that noise, or through multi-qubit encoding and error correction protocols (which already presume ultra-low error rates). In contrast, dephasing is in principle reversible and can be refocused dynamically through the application of coherent control pulse methods. In this work we demonstrate how dynamical-decoupling techniques can moderate the dephasing effects of low-frequency noise on a superconducting qubit with energy-relaxation time T1 = 1/Gamma1 = 12 us. Using the CPMG sequence with up to 200 pi-pulses, we demonstrate a 50-fold improvement in the transverse relaxation time T2 over its baseline value. We observe relaxation-limited times T2(CPMG) = 23 us = 2 T1 resulting from CPMG-mediated Gaussian pure-dephasing times in apparent excess of 100 us. We leverage the filtering property of this sequence in conjunction with Rabi and energy relaxation measurements to facilitate the spectroscopy and reconstruction of the environmental noise power spectral density.
Prioritizing candidate disease genes by network-based boosting of genome-wide association data (2011)

Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinations of mutations often linked to complex diseases. Here, we analyze a large-scale, human gene functional interaction network (dubbed HumanNet). We show that candidate disease genes can be effectively identified by GBA in cross-validated tests using label propagation algorithms related to Google's PageRank. However, GBA has been shown to work poorly in genome-wide association studies (GWAS), where many genes are somewhat implicated, but few are known with very high certainty. Here, we resolve this by explicitly modeling the uncertainty of the associations and incorporating the uncertainty for the seed set into the GBA framework. We observe a significant boost in the power to detect validated candidate genes for Crohn's disease and type 2 diabetes by comparing our predictions to results from follow-up meta-analyses, with incorporation of the network serving to highlight the JAK-STAT pathway and associated adaptors GRB2/SHC1 in Crohn's disease and BACH2 in type 2 diabetes. Consideration of the network during GWAS thus conveys some of the benefits of enrolling more participants in the GWAS study. More generally, we demonstrate that a functional network of human genes provides a valuable statistical framework for prioritizing candidate disease genes, both for candidate gene-based and GWAS-based studies.
1-Acyldihydroxyacetone-phosphate Reductase (Ayr1p) of the YeastSaccharomyces cerevisiae Encoded by the Open Reading Frame YIL124w Is a Major Component of Lipid Particles (2000)

Biosynthesis of phosphatidic acid through the dihydroxyacetone phosphate pathway requires NADPH-dependent reduction of the intermediate 1-acyldihydroxyacetone phosphate before the second step of acylation. Studies with isolated subcellular fractions of the yeast Saccharomyces cerevisiae revealed that lipid particles and the endoplasmic reticulum harbor 1-acyldihydroxyacetone-phosphate reductase (ADR) activity. Deletion of the open reading frame YIL124w (in the following named AYR1) abolished reduction of 1-acyldihydroxyacetone phosphate in lipid particles, whereas ADR activity in microsomes of the deletion strain was decreased approximately 3-fold as compared with the wild-type level. This result indicates that (i) both lipid particles and microsomes harbor Ayr1p, which was confirmed by immunological detection of the protein in these two cellular compartments, and (ii) microsomes contain at least one additional ADR activity. As a consequence of this redundancy, deletion of AYR1 neither results in an obvious growth phenotype nor affects the lipid composition of a haploid deletion strain. When a heterozygous AYR1(+)/ayr1(-) diploid strain was subjected to sporulation; however, spores bearing the ayr1 defect failed to germinate, suggesting that Ayr1p plays an essential role at this stage. Overexpression of Ayr1p at a 5- to 10-fold level of wild type caused growth arrest. Heterologous expression of Ayr1p in Escherichia coli resulted in gain of ADR activity in the prokaryote, confirming that YIL124w is the structural gene of the enzyme and does not encode a regulatory or auxiliary component required for reduction of 1-acyldihydroxyacetone phosphate. Taken together, these results identified Ayr1p of the yeast as the first ADR from any organism at the molecular level.
LH (1993)

LH* generalizes Linear Hashing to parallel or distributed RAM and disk files. An LH* file can be created from objects provided by any number of distributed and autonomous clients. It can grow gracefully, one bucket at a time, to virtually any number of servers. The number of messages per insertion is one in general, and three in the worst case. The number of messages per retrieval is two in general, and four in the worst case. The load factor can be about constant, 65-95%, depending on the file parameters. The file can also support parallel operations. An LH* file can be much faster than a single site disk file, and/or can hold a much larger number of objects. It can be more efficient than any file with a centralized directory, or a static parallel or distributed hash file.
Iron-alumina nanocomposites prepared by ball milling (1992)

Small magnetic particles of iron embedded in an insulating alumina matrix have been prepared by ball milling, either by direct milling of a mixture of iron and alumina powders or indirectly by ball-milling enhanced displacement reaction between magnetite and aluminum metal. The average particle size could be reduced to the 10-nm range as indicated by X-ray diffraction linewidths and SEM (scanning electron microscopy). The change in the saturation magnetization and the coercivity relates to the change of the phase composition, decrease of the particle size, and accumulation of internal stresses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>