gebhart/patrepeval huggingface dataset:
Stochastic variational inference (2013)

We develop stochastic variational inference, a scalable algorithm for approximating posterior distributions. We develop this technique for a large class of probabilistic models and we demonstrate it with two probabilistic topic models, latent Dirichlet allocation and the hierarchical Dirichlet process topic model. Using stochastic variational inference, we analyze several large collections of documents: 300K articles from Nature, 1.8M articles from The New York Times, and 3.8M articles from Wikipedia. Stochastic inference can easily handle data sets of this size and outperforms traditional variational inference, which can only handle a smaller subset. (We also show that the Bayesian nonparametric topic model outperforms its parametric counterpart.) Stochastic variational inference lets us apply complex Bayesian models to massive data sets.
Automated DNA profiling employing multiplex amplification of short tandem repeat loci. (1993)

We have employed automated fluorescence-based technology to detect amplified tri-, tetra-, and pentanucleotide short tandem repeat (STR) loci electrophoresed on denaturing polyacrylamide sequencing gels. The system described incorporates an internal size standard in each sample, allowing the STR-PCR products to be sized automatically with a high degree of precision. By utilizing different fluorescent dye markers for loci that have overlapping allele size ranges, we have developed three multiplex STR systems containing a total of 14 different loci. These multiplex systems were then used to evaluate the usefulness of the 14 loci for the identification of individuals. Allele frequency data were collected from a minimum of 50 individuals from each of three different racial groups: Caucasians, Afro-Caribbeans, and Asians. Of the resulting 42 locus population sets, deviation from Hardy-Weinberg equilibria was detected in only the STR HUMCYARO3-Caucasian data. The probabilities of two unrelated individuals matching by chance (pM) at all 14 loci in the three multiplex reactions was < 1 x 10(14). The combination of multiplex STR-PCR and automatic fluorescence-based detection is thus a rapid and powerful technique for individual identification.
ChemInform Abstract: STUDIES ON THE SYNTHESIS OF BISINDOLE ALKALOIDS. VI. NOVEL LACTAM DERIVATIVES S IN THE VINBLASTINE SERIES (1977)

Abstract Die Umsetzung von (I) mit 1 Äquival.
Subclinical hypothyroidism is associated with a low‐grade inflammation, increased triglyceride levels and predicts cardiovascular disease in males below 50 years (2004)

Our study demonstrates that patients with subclinical hypothyroidism have increased levels of triglycerides and signs of low-grade inflammation (raised C-reactive protein levels) and that subclinical hypothyroidism might be a risk factor for development of cardiovascular disease in younger males.
Efficient and tunable diode-pumped femtosecond Yb:glass lasers (1998)

Diode-pumped Yb:phosphate and Yb:silicate glass lasers have been passively mode locked for the first time to the authors' knowledge. Reliable self-starting mode locking without critical cavity alignment has been achieved with intracavity semiconductor saturable-absorber mirrors and soliton mode locking. We generated pulses as short as 58 fs with the Yb:phosphate laser and 61 fs with the Yb:silicate laser at average output powers of 65 and 53 mW, respectively. The pulse repetition rate was 112 MHz. Additionally, we demonstrated tunability of femtosecond pulses from 1025 to 1065 nm for the Yb:phosphate and from 1030 to 1082 nm for the Yb:silicate glasses. The highest mode-locked output power was 405 mW, with 183-fs pulses from the phosphate glass. The diode pump power was 1.68 W, corresponding to 24% optical-to-optical efficiency. The highest cw output power was 510 mW at the same incident pump power.
A 200 mV self-testing encoder/decoder using Stanford ultra-low-power CMOS (2002)

A CMOS test chip that includes a 1k-transistor self-testing encoder/decoder is verifiably error-free at supply voltages down to 20O mV, achieving 1/625 the power-delay product of standard 5 V CMOS. The maximum error-free operating frequency of this circuit as a function of supply and threshold voltage is reported here and voltage scaling of performance is compared with ring-oscillator data reported earlier. The circuit works even when bodies of transistors are forward-biased relative to sources to induce /spl sim/100mV depletion-mode thresholds.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Significance of Id-1 up-regulation and its association with EGFR in bladder cancer cell invasion (2006)

Epidermal growth factor receptor (EGFR) is suggested to be one of the positive factors in the invasive progression of bladder cancer. Id-1 (inhibitor of differentiation or DNA binding), a helix-loop-helix (HLH) transcription factor, was recently identified as a key factor in the EGFR signalling pathway. The aim of this study was to investigate the role of Id-1 in bladder cancer progression and its relation-ship with EGFR. Using clinical specimens from different stages of bladder cancer, immunohistochemical staining was performed to determine if Id-1 expression was positively associated with tumour staging and EGFR expression. The direct role of Id-1 in cancer cell invasion was also investigated through ectopically expressing the Id-1 gene in a RT112 bladder cancer cell line by wound closure and collagen invasion assays. To explore the therapeutic potential of targeting the Id-1 gene in the treatment of invasive bladder cancer, we studied if inactivation of the Id-1 gene through small RNA interference could lead to the suppression of invasion in a MGHU1 bladder cancer cell line. Our results showed that the up-regulation of Id-1 was associated with increased EGFR expression, clinical staging and the invasion ability of bladder cancer cells. Inactivation of Id-1 may be a potential therapeutic target to inhibit the invasion by bladder cancer cells.
Josephson amplifier for qubit readout (2011)

We report on measurements of a Josephson amplifier (J-amp) suitable for quantum-state qubit readout in the microwave domain. It consists of two microstrip resonators which intersect at a Josephson ring modulator. A maximum gain of about 20 dB, a bandwidth of 9 MHz, and a center-frequency tunability of about 60 MHz with gain in excess of 10 dB have been attained for idler and signal of frequencies 6.4 GHz and 8.1 GHz, in accordance with theory. Maximum input power measurements of the J-amp show a relatively good agreement with theoretical prediction. We discuss how the amplifier characteristics can be improved.
Mesenchymal Stem Cells Enhance Wound Healing Through Differentiation and Angiogenesis (2007)

Although chronic wounds are common, treatment for these disabling conditions remains limited and largely ineffective. In this study, we examined the benefit of bone marrow-derived mesenchymal stem cells (BM-MSCs) in wound healing. Using an excisional wound splinting model, we showed that injection around the wound and application to the wound bed of green fluorescence protein (GFP)(+) allogeneic BM-MSCs significantly enhanced wound healing in normal and diabetic mice compared with that of allogeneic neonatal dermal fibroblasts or vehicle control medium. Fluorescence-activated cell sorting analysis of cells derived from the wound for GFP-expressing BM-MSCs indicated engraftments of 27% at 7 days, 7.6% at 14 days, and 2.5% at 28 days of total BM-MSCs administered. BM-MSC-treated wounds exhibited significantly accelerated wound closure, with increased re-epithelialization, cellularity, and angiogenesis. Notably, BM-MSCs, but not CD34(+) bone marrow cells in the wound, expressed the keratinocyte-specific protein keratin and formed glandular structures, suggesting a direct contribution of BM-MSCs to cutaneous regeneration. Moreover, BM-MSC-conditioned medium promoted endothelial cell tube formation. Real-time polymerase chain reaction and Western blot analysis revealed high levels of vascular endothelial growth factor and angiopoietin-1 in BM-MSCs and significantly greater amounts of the proteins in BM-MSC-treated wounds. Thus, our data suggest that BM-MSCs promote wound healing through differentiation and release of proangiogenic factors. Disclosure of potential conflicts of interest is found at the end of this article.
Evaluation of Clumping Factor A Binding Region A in a Subunit Vaccine against Staphylococcus aureus -Induced Mastitis in Mice (2010)

ABSTRACT The present study evaluated the potential of recombinant binding region A of clumping factor A (rClfA-A) to be an effective component of a vaccine against mastitis induced by Staphylococcus aureus in the mouse. rClfA-A and inactivated S. aureus were each emulsified in Freund's adjuvant, mineral oil adjuvant, and Seppic adjuvant; phosphate-buffered saline was used as a control. Seven groups of 12 mice each were immunized intraperitoneally three times at 2-week intervals. The titers of IgG and subtypes thereof (IgG1 and IgG2a) in the rClfA-A-immunized group were more than 1,000-fold higher than those in the killed-bacteria-immunized group ( P &lt; 0.01). Of the three adjuvants used, mineral oil adjuvant induced the highest antibody levels for both antigens ( P &lt; 0.001). Furthermore, the anti-rClfA-A antibody capacities for bacterial adhesion and opsonizing phagocytosis were significantly greater in the rClfA-A-immunized group than in the killed-bacteria-immunized group ( P &lt; 0.05). Lactating mice immunized with either rClfA-A or inactivated vaccine were challenged with S. aureus via the intramammary route. The numbers of bacteria recovered from the murine mammary glands 24 h after inoculation were significantly lower in the rClfA-A group than in the killed-bacteria-immunized group ( P &lt; 0.001). Histologic examination of the mammary glands showed that rClfA-A immunization effectively preserved tissue integrity. Thus, rClfA-A emulsified in an oil adjuvant provides strong immune protection against S. aureus -induced mastitis in the mouse.
The 128-Channel Fully Differential Digital Integrated Neural Recording and Stimulation Interface (2010)

We present a fully differential 128-channel integrated neural interface. It consists of an array of 8 X 16 low-power low-noise signal-recording and generation circuits for electrical neural activity monitoring and stimulation, respectively. The recording channel has two stages of signal amplification and conditioning with and a fully differential 8-b column-parallel successive approximation (SAR) analog-to-digital converter (ADC). The total measured power consumption of each recording channel, including the SAR ADC, is 15.5 ¿W. The measured input-referred noise is 6.08 ¿ Vrms over a 5-kHz bandwidth, resulting in a noise efficiency factor of 5.6. The stimulation channel performs monophasic or biphasic voltage-mode stimulation, with a maximum stimulation current of 5 mA and a quiescent power dissipation of 51.5 ¿W. The design is implemented in 0.35-¿m complementary metal-oxide semiconductor technology with the channel pitch of 200 ¿m for a total die size of 3.4 mm × 2.5 mm and a total power consumption of 9.33 mW. The neural interface was validated in in vitro recording of a low-Mg <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> /high-K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> epileptic seizure model in an intact hippocampus of a mouse.
Stationary points and dynamics in high-dimensional systems (2003)

We present some new theoretical and computational results for the stationary points of bulk systems. First we demonstrate how the potential energy surface can be partitioned into catchment basins associated with every stationary point using a combination of Newton–Raphson and eigenvector-following techniques. Numerical results are presented for a 256-atom supercell representation of a binary Lennard-Jones system. We then derive analytical formulae for the number of stationary points as a function of both system size and the Hessian index, using a framework based upon weakly interacting subsystems. This analysis reveals a simple relation between the total number of stationary points, the number of local minima, and the number of transition states connected on average to each minimum. Finally we calculate two measures of localization for the displacements corresponding to Hessian eigenvectors in samples of stationary points obtained from the Newton–Raphson-based geometry optimization scheme. Systematic differences are found between the properties of eigenvectors corresponding to positive and negative Hessian eigenvalues, and localized character is most pronounced for stationary points with low values of the Hessian index.
Onconase and Amphinase, the Antitumor Ribonucleases from Rana pipiens Oocytes (2008)

Rana pipiens oocytes contain two homologues of pancreatic ribonuclease A that are cytostatic and cytotoxic to human cancer cells. Extensively studied Onconase is in advanced Phase IIIb clinical trials against malignant mesothelioma, while Amphinase is a novel enzyme in pre-clinical development. Onconase is the smallest (104 amino acid residues) member of the ribonuclease A superfamily while Amphinase (114 residues) is the largest among amphibian ribonucleases. Both enzymes share the characteristic frog ribonucleases C-terminal disulfide bond but another signature of this group, the N-terminal pyroglutamate, an integral part of Onconase active site is not conserved in Amphinase. Although Onconase and Amphinase are weak catalysts their enzymatic activities are required for cytostatic and cytotoxic activity. While it was postulated that tRNA is the primary substrate of Onconase in vivo there is also extensive indirect evidence that suggests other RNA species, in particular micro RNAs, may actually be the critical target of these ribonucleases. The cytostatic effects of Onconase and Amphinase are manifested as cell arrest in the G(1) cell cycle phase. Apoptosis then follows involving activation of endonucleases(s), caspases, serine proteases and transglutaminase. Onconase was shown to be strongly synergistic when combined with numerous other antitumor modalities. Onconase and Amphinase are highly cationic molecules and their preferential toxicity towards cancer cells (having distinctly higher negative charge compared to normal cells) may depend on increased binding efficiency to the cell surface by electrostatic interactions.
The Differentiation of Hepatocyte-Like Cells from Monkey Embryonic Stem Cells (2008)

Embryonic stem cells (ESC) hold great potential for the treatment of liver diseases. Here, we report the differentiation of rhesus macaque ESC along a hepatocyte lineage. The undifferentiated monkey ESC line, ORMES-6, was cultured in an optimal culture condition in an effort to differentiate them into hepatocyte-like cells in vitro. The functional efficacy of the differentiated hepatic cells was evaluated using RT-PCR for the expression of hepatocyte specific genes, and Western blot analysis and immunocytochemistry for hepatic proteins such as alpha-fetoprotein (AFP), albumin and alpha1-antitrypsin (alpha1-AT). Functional assays were performed using the periodic acid schiff (PAS) reaction and ELISA. The final yield of ESC-derived hepatocyte-like cells was measured by flow cytometry for cells that were transduced with a liver-specific lentivirus vector containing the alpha1-AT promoter driving the expression of green fluorescence protein (GFP). The treatment of monkey ESC with an optimal culture condition yielded hepatocyte-like cells that expressed albumin, alpha1-AT, AFP, hepatocyte nuclear factor 3beta, glucose-6-phophatase, and cytochrome P450 genes and proteins as determined by RT-PCR and Western blot analysis. Immunofluorescent staining showed the cells positive for albumin, AFP, and alpha1-AT. PAS staining demonstrated that the differentiated cells showed hepatocyte functional activity. Albumin could be detected in the medium after 20 days of differentiation. Flow cytometry data showed that 6.5 +/- 1.0% of the total differentiated cells were positive for GFP. These results suggest that by using a specific, empirically determined, culture condition, we were able to direct monkey ESC toward a hepatocyte lineage.
Cold Hemolytic Syndrome (2006)

Abstract In most cases, immune-mediated hemolysis occurs extravascularly and is associated with IgG antibodies on the surface of red cells. Rare syndromes include IgG antibodies that cause direct intravascular hemolysis, such as paroxysmal cold hemoglobinuria. Also rare are extravascular hemolytic syndromes caused by IgM polyclonal or monoclonal antibodies that demonstrate red cell agglutination at 3°C, so-called cold antibodies. Because cold agglutinin disease has a high association with several lymphoproliferative disorders and IgM monoclonal gammopathies, its management differs significantly from that associated with warm autoimmune hemolytic anemia. This case-based presentation is designed to guide the reader to the diagnosis and to the initiation of prompt, effective therapy.
Effect of III/V-Compound Epitaxy on Si Metal-Oxide-Semiconductor Circuits (1994)

Several approaches to the heteroepitaxial growth of InP on (100)Si employing an electrochemically etched Si mesa, SiO 2 masks, and a maskless procedure were investigated with the objective of achieving area-selective InP integration into Si metal-oxide-semiconductor (Si-MOS) technology. Maskless InP/Si device layer growth by metal-organic vapour-phase epitaxy with good selectivity on a structured InP buffer layer, surrounded by oxide, was achieved. Undesired InP depositions were removed with an SiO 2 emulsion, spun on prior to InP growth. To study the effects on the Si-based electronics, p-metal-oxide-semiconductor field-effect tansistors (MOSFETs) were exposed to the various stages of the heteroepitaxial InP growth process. We have studied the influence of hydride atmospheres and thermal anneals on their electrical performance. A standard InP-on-(100)Si growth procedure was found to be acceptable for the MOS components, as demonstrated by a Schmitt-trigger laser-diode driver circuit.
Procyanidin and Catechin Contents and Antioxidant Capacity of Cocoa and Chocolate Products (2006)

Cocoa and chocolate products from major brands were analyzed blind for total antioxidant capacity (AOC) (lipophilic and hydrophilic ORAC(FL)), catechins, and procyanidins (monomer through polymers). Accuracy of analyses was ascertained by comparing analyses on a NIST standard reference chocolate with NIST certified values. Procyanidin (PC) content was related to the nonfat cocoa solid (NFCS) content. The natural cocoa powders (average 87% of NFCS) contained the highest levels of AOC (826 +/- 103 micromol of TE/g) and PCs (40.8 +/- 8.3 mg/g). Alkalized cocoa (Dutched powders, average 80% NFCS) contained lower AOC (402 +/- 6 micromol of TE /g) and PCs (8.9 +/- 2.7 mg/g). Unsweetened chocolates or chocolate liquor (50% NFCS) contained 496 +/- 40 micromol of TE /g of AOC and 22.3 +/- 2.9 mg/g of PCs. Milk chocolates, which contain the least amount of NFCS (7.1%), had the lowest concentrations of AOC (80 +/- 10 micromol of TE /g) and PCs (2.7 +/- 0.5 mg/g). One serving of cocoa (5 g) or chocolate (15 or 40 g, depending upon the type of chocolate) provides 2000-9100 micromol of TE of AOC and 45-517 mg of PCs, amounts that exceed the amount in a serving of the majority of foods consumed in America. The monomers through trimers, which are thought to be directly bioavailable, contributed 30% of the total PCs in chocolates. Hydrophilic antioxidant capacity contributed >90% of AOC in all products. The correlation coefficient between AOC and PCs in chocolates was 0.92, suggesting that PCs are the dominant antioxidants in cocoa and chocolates. These results indicate that NFCS is correlated with AOC and PC in cocoa and chocolate products. Alkalizing dramatically decreased both the procyanidin content and antioxidant capacity, although not to the same extent.
IL-2 knockout recipient mice reject islet cell allografts (1995)

The IL-2 pathway is portrayed often as central to allograft rejection. To test this hypothesis, we studied IL-2-deficient mice as allograft recipients. IL-2 gene knockout (KO) mice reject islet allografts and demonstrate a classical mononuclear leukocytic infiltrate, containing CD4+ and CD8+ T cells, surrounding and invading the islet allografts. Moreover, allograft rejection in the IL-2 KO mouse is associated with intragraft expression of certain cytokine and CTL attack molecule genes (e.g. IFN-gamma, IL-4, IL-7, IL-10, and granzyme B). In separate experiments, IL-2 KO mice generated CTLs in response to in vivo challenge with allogeneic tumor cells. Although IL-2 KO mice reject allografts in vivo, spleen cells from immunologically naive IL-2 KO mice exhibit a diminished proliferative response to mitogens in vitro that could be restored largely by exogenous IL-2, IL-4, or IL-7. The paradoxical ability to execute graft rejection in vivo despite near absent T cell proliferative responses in vitro may result from the expression of IL-7 in vivo, but not in vitro. Con A-stimulated bulk spleen cell cultures derived from IL-2 KO mice were essentially devoid not only of IL-2 but also IL-7 gene transcripts. These data indicate that 1) IL-2 is not the sole T cell growth factor capable of supporting allograft rejection and 2) expression of IL-4, but not IL-2, during the allograft response does not lead inevitably to tolerance.
Genome analysis : a laboratory manual (1997)

Genome analysis: a laboratory manual , Genome analysis: a laboratory manual , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Src homology 2 domains of Syk and Lyn bind to tyrosine-phosphorylated subunits of the high affinity IgE receptor. (1994)

Aggregation of the high affinity IgE receptor (Fc epsilon RI) on rat basophilic leukemia RBL-2H3 cells results in activation of the protein tyrosine kinases Syk and Lyn. Here, we report that fusion proteins containing the Src homology 2 (SH2) domains of Syk and Lyn precipitated tyrosine-phosphorylated proteins from RBL-2H3 cell lysates. There was no detectable precipitation with the N-terminal Syk SH2 domain, minimal with the C-terminal Syk SH2, and strong when the two SH2 domains were expressed in tandem. The Syk SH2 domains showed pronounced selectivity in the binding of tyrosine-phosphorylated proteins. Thus, Syk SH2 precipitated only three phosphoproteins, two of which were the beta and gamma subunits of Fc epsilon RI. In contrast, the fusion protein with Lyn SH2, in addition to precipitating the same Fc epsilon RI components, bound to many other phosphoproteins. Tyrosine phosphorylation of the beta and gamma subunits of Fc epsilon RI was essential for their precipitation with the SH2 fusion proteins. By direct binding studies, there was more binding of Syk SH2 to Fc epsilon RI gamma than to Fc epsilon RI beta, whereas Lyn SH2 bound only to Fc epsilon RI beta. The Syk SH2 fusion protein competitively inhibited the association of gamma and beta with Syk in lysates of activated cells. The SH2-mediated association of these two protein tyrosine kinases with Fc epsilon RI could play an important role in receptor signaling.
Acting on Their Own Behalf: Affiliation and Political Mobilization among Homeless People (1992)

Homeless people have been portrayed in the literature as passive, isolated, and unable to act on their own behalf. The authors discuss the findings of an ethnographic study of homeless activists which challenge the stereotypical view of homeless people as disaffiliated and disempowered. Collective social action was found to have a long term impact on access to material resources, development of social networks, and construction of positive homeless identity.