gebhart/patrepeval huggingface dataset:
A robust SVD-free approach to matrix completion, with applications to interpolation of large scale data (2013)

Recent SVD-free matrix factorization formulations have enabled rank minimization for systems with millions of rows and columns, paving the way for matrix completion in extremely large-scale applications, such as seismic data interpolation. In this paper, we consider matrix completion formulations designed to hit a target data-fitting error level provided by the user, and propose an algorithm called LR-BPDN that is able to exploit factorized formulations to solve the corresponding optimization problem. Since practitioners typically have strong prior knowledge about target error level, this innovation makes it easy to apply the algorithm in practice, leaving only the factor rank to be determined. Within the established framework, we propose two extensions that are highly relevant to solving practical challenges of data interpolation. First, we propose a weighted extension that allows known subspace information to improve the results of matrix completion formulations. We show how this weighting can be used in the context of frequency continuation, an essential aspect to seismic data interpolation. Second, we propose matrix completion formulations that are robust to large measurement errors in the available data. We illustrate the advantages of LR-BPDN on the collaborative filtering problem using the MovieLens 1M, 10M, and Netflix 100M datasets. Then, we use the new method, along with its robust and subspace re-weighted extensions, to obtain high-quality reconstructions for large scale seismic interpolation problems with real data, even in the presence of data contamination.
Statistical shape modelling: automatic shape model building (2011)

Advanced maternal age is associated with a range of adverse pregnancy outcomes. These risks are independent of parity and remain after adjusting for the ameliorating effects of higher socioeconomic status. The data from this large contemporary cohort will be of interest to healthcare providers and women and will facilitate evidence based counselling of older expectant mothers.
Joining of Self‐Bonded Silicon Carbide by Germanium Metal (1981)

Two self‐bonded SiC bodies containing free Si were joined with liquid Ge at 1180°C in vacuum. Bond strength was measured by four‐point bending test in vacuum at high temperature. The join had a significant strength even above the melting point of Ge metal. Electron probe microanalysis of joint showed a liquid formation temperature of thinner interlayer was ∼1200°C.
Central role of JC virus-specific CD4+ lymphocytes in progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome (2011)

Progressive multi-focal leucoencephalopathy and progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome are caused by infection of the central nervous system with the JC polyoma virus. Both are complications of monoclonal antibody therapy in multiple sclerosis and other autoimmune diseases. Progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome can obscure the diagnosis of progressive multi-focal leucoencephalopathy and lead to severe clinical disability and possibly death. Different from progressive multi-focal leucoencephalopathy, in which demyelination results from oligodendrocyte lysis by JC virus in the absence of an immune response, tissue destruction in progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome is caused by a vigorous immune response within the brain. The cells and mediators that are involved in progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome are as yet poorly understood. We examined two patients with multiple sclerosis, who developed progressive multi-focal leucoencephalopathy and later progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome under natalizumab therapy. Due to initially negative JC viral deoxyribonucleic acid testing in the cerebrospinal fluid, a diagnostic brain biopsy was performed in one patient. Histopathology revealed brain inflammation characterized by a prominent T cell infiltrate (CD4(+)> CD8(+) T cells), but also B/plasma cells and monocytes. Despite very low JC viral load, both patients showed high intrathecal anti-JC virus antibodies. Brain-infiltrating CD4(+) T cells were studied regarding antigen specificity and function. CD4(+) T cells were highly specific for peptides from several JC virus proteins, particularly the major capsid protein VP1. T cell phenotyping revealed CD4(+) Th1 and bifunctional Th1-2 cells. The latter secrete large amounts of interferon-γ and interleukin-4 explaining the strong brain inflammation, presence of plasma cells and secretion of intrathecal anti-VP1 antibodies. The functional phenotype of brain-infiltrating JC virus-specific CD4(+) T cells was confirmed and extended by examining brain-derived JC virus-specific CD4(+) T cell clones. Our data provide novel insight into the pathogenesis of progressive multi-focal leucoencephalopathy-immune reconstitution inflammatory syndrome and indicate that JC virus-specific CD4(+) T cells play an important role in both eliminating JC virus from the brain, but also in causing the massive inflammation with often fatal outcome.
Variations on the GFP Chromophore (2004)

We have determined to 2.1 A resolution the crystal structure of a dark state, kindling fluorescent protein isolated from the sea anemone, Anemonia sulcata. The chromophore sequence Met(63)-Tyr(64)-Gly(65) of the A. sulcata chromoprotein was previously proposed to comprise a 6-membered pyrazine-type heterocycle (Martynov, V. I., Savitsky, A. P., Martynova, N. Y., Savitsky, P. A., Lukyanov, K. A., and Lukyanov, S. A. (2001) J. Biol. Chem. 276, 21012-21016). However, our crystallographic data revealed the chromophore to comprise a 5-membered p-hydroxybenzylideneimidazolinone moiety that adopts a non-coplanar trans conformation within the interior of the GFP beta-can fold. Unexpectedly, fragmentation of the polypeptide was found to occur within the chromophore moiety, at the bond between Cys(62C) and Met(63N1.) Our structural data reveal that fragmentation of the chromophore represents an intrinsic, autocatalytic step toward the formation of the mature chromophore within the specific GFP-like proteins.
Gene drive through a landscape: Reaction–diffusion models of population suppression and elimination by a sex ratio distorter (2015)

Some genes or gene complexes are transmitted from parents to offspring at a greater-than-Mendelian rate, and can spread and persist in populations even if they cause some harm to the individuals carrying them. Such genes may be useful for controlling populations or species that are harmful. Driving-Y chromosomes may be particularly potent in this regard, as they produce a male-biased sex ratio that, if sufficiently extreme, can lead to population elimination. To better understand the potential of such genes to spread over a landscape, we have developed a series of reaction-diffusion models of a driving-Y chromosome in 1-D and radially-symmetric 2-D unbounded domains. The wild-type system at carrying capacity is found to be unstable to the introduction of driving-Y males for all models investigated. Numerical solutions exhibit travelling wave pulses and fronts, and analytical and semi-analytical solutions for the asymptotic wave speed under bounded initial conditions are derived. The driving-Y male invades the wild-type equilibrium state at the front of the wave and completely replaces the wild-type males, leaving behind, at the tail of the wave, a reduced- or zero-population state of females and driving-Y males only. In our simplest model of a population with one life stage and density-dependent mortality, wave speed depends on the strength of drive and the diffusion rate of Y-drive males, and is independent of the population dynamic consequences (suppression or elimination). Incorporating an immobile juvenile stage of fixed duration into the model reduces wave speed approximately in proportion to the relative time spent as a juvenile. If females mate just once in their life, storing sperm for subsequent reproduction, then wave speed depends on the movement of mated females as well as Y-drive males, and may be faster or slower than in the multiple-mating model, depending on the relative duration of juvenile and adult life stages. Numerical solutions are shown for parameter values that may in part be representative for Anopheles gambiae, the primary vector of malaria in sub-Saharan Africa.
Biogenic Nanopalladium Based Remediation of Chlorinated Hydrocarbons in Marine Environments (2013)

Biogenic catalysts have been studied over the last 10 years in freshwater and soil environments, but neither their formation nor their application has been explored in marine ecosystems. The objective of this study was to develop a biogenic nanopalladium-based remediation method for reducing chlorinated hydrocarbons from marine environments by employing indigenous marine bacteria. Thirty facultative aerobic marine strains were isolated from two contaminated sites, the Lagoon of Mar Chica, Morocco, and Priolo Gargallo Syracuse, Italy. Eight strains showed concurrent palladium precipitation and biohydrogen production. X-ray diffraction and thin section transmission electron microscopy analysis indicated the presence of metallic Pd nanoparticles of various sizes (5-20 nm) formed either in the cytoplasm, in the periplasmic space, or extracellularly. These biogenic catalysts were used to dechlorinate trichloroethylene in simulated marine environments. Complete dehalogenation of 20 mg L(-1) trichloroethylene was achieved within 1 h using 50 mg L(-1) biogenic nanopalladium. These biogenic nanoparticles are promising developments for future marine bioremediation applications.
Intrinsic Obstacles to Human Immunodeficiency Virus Type 1 Coreceptor Switching (2004)

The natural evolution of human immunodeficiency virus type 1 infection often includes a switch in coreceptor preference late in infection from CCR5 to CXCR4, a change associated with expanded target cell range and worsened clinical prognosis. Why coreceptor switching takes so long is puzzling, since it requires as few as one to two mutations. Here we report three obstacles that impede the CCR5-to-CXCR4 switch. Coreceptor switch variants were selected by target cell replacement in vitro. Most switch variants showed diminished replication compared to their parental R5 isolate. Transitional intermediates were more sensitive to both CCR5 and CXCR4 inhibitors than either the parental R5 virus or the final R5X4 (or rare X4) variant. The small number of mutations in viruses selected for CXCR4 use were distinctly nonrandom, with a dominance of charged amino acid substitutions encoded by G-to-A transitions, changes in N-linked glycosylation sites, and isolate-specific mutation patterns. Diminished replication fitness, less-efficient coreceptor use, and unique mutational pathways may explain the long delay from primary infection until the emergence of CXCR4-using viruses.
Combined treatment with cyclophosphamide and prednisolone can induce remission of nephrotic syndrome in a patient with renal amyloidosis, associated with rheumatoid arthritis. (1994)

A 67-year-old woman, who had been diagnosed with classical rheumatoid arthritis (RA), was admitted to our hospital because of massive proteinuria. Biopsy of the kidney revealed deposition of amyloid fibrils in the subepithelial and subendothelial spaces of the glomerular capillary walls. Though the treatment with prednisolone and dipyridamole against nephrotic syndrome and amyloidosis due to RA was not effective, cyclophosphamide, which was added after tapering of prednisolone, was able to induce remission of nephrotic syndrome after two years. The levels of CRP and serum amyloid A protein (SAA) returned to within the normal limits. As the impairment of renal function is thought to be due to deposition of amyloid supplied from the precursors of amyloid fibrils filtered from the general circulation in RA patients, remission of nephrotic syndrome might result from the suppression of production of SAA or removal of amyloid fibrils. Cyclophosphamide, which has the potential both to suppress disease activity in RA and to produce degradation of amyloid fibrils in glomeruli, may be useful against renal or systemic amyloidosis complicated by RA.
Multiple-depth shadow maps (2004)

Traditional shadow maps store a single depth value per cell, leading to a binary outcome by the shadow test (either lit or in shadow), and are prone to produce aliased shadow borders. We present a new approach that produces better estimates of shadow percentages and, in combination with percentage closer filtering (PCF), reduces aliasing artifacts using smaller kernel sizes. The new algorithm extends the notions of shadow maps and shadow tests to support the representation of multiple depth values per shadow map cell, as well as multi-valued shadow tests. This new approach has the potential for hardware implementation, but can also be implemented exploiting the programmable capabilities of recent graphics cards.
THE CONDENSATION OF METHYL KETONES WITH FURAN (1955)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTTHE CONDENSATION OF METHYL KETONES WITH FURANR. G. ACKMAN, WILLIAM H. BROWN, and GEORGE F WRIGHTCite this: J. Org. Chem. 1955, 20, 9, 1147–1158Publication Date (Print):September 1, 1955Publication History Published online1 May 2002Published inissue 1 September 1955https://pubs.acs.org/doi/10.1021/jo01126a001https://doi.org/10.1021/jo01126a001research-articleACS PublicationsRequest reuse permissionsArticle Views995Altmetric-Citations70LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Discriminative Metric Learning with Deep Forest (2019)

A Discriminative Deep Forest (DisDF) as a metric learning algorithm is proposed in the paper. It is based on the Deep Forest or gcForest proposed by Zhou and Feng and can be viewed as a gcForest modification. The case of the fully supervised learning is studied when the class labels of individual training examples are known. The main idea underlying the algorithm is to assign weights to decision trees in random forest in order to reduce distances between objects from the same class and to increase them between objects from different classes. The weights are training parameters. A specific objective function which combines Euclidean and Manhattan distances and simplifies the optimization problem for training the DisDF is proposed. The numerical experiments illustrate the proposed distance metric algorithm.
The neural substrates of religious experience (1997)

Religious experience is brain-based, like all human experience. Clues to the neural substrates of religious-numinous experience may be gleaned from temporolimbic epilepsy, near-death experiences, and hallucinogen ingestion. These brain disorders and conditions may produce depersonalization, derealization, ecstasy, a sense of timelessness and spacelessness, and other experiences that foster religious-numinous interpretation. Religious delusions are an important subtype of delusional experience in schizophrenia, and mood-congruent religious delusions are a feature of mania and depression. The authors suggest a limbic marker hypothesis for religious-mystical experience. The temporolimbic system tags certain encounters with external or internal stimuli as depersonalized, derealized, crucially important, harmonious, and/or joyous, prompting comprehension of these experiences within a religious framework.
Application of integrated circuit technology to the fabrication of large numbers of niobium based Josephson junctions (1975)

A batch fabrication technology is described for the production of small niobium based Josephson junctions. This technology uses thermally oxidized silicon wafers as substrates, allowing maximum usage of silicon integrated circuit techniques and equipment. Patterns are produced in rf sputtered niobium films by sputter etching through masks generated by "step and repeat" photolithographic techniques. Typically over 600 junctions are fabricated at one time. Measurements of voltampere curves, Josephson current versus magnetic field, and self resonant step structure were made.
One-Step Preparation of Blue-Emitting (La,Ca)Si<sub>3</sub>(O,N)<sub>5</sub>:Ce<sup>3+</sup>Phosphors for High-Color Rendering White Light-Emitting Diodes (2011)

Highly phase-pure (La,Ca)Si3(O,N)5:Ce3+ blue-emitting phosphors were successfully synthesized via the one-step solid-state reaction from the system La2O3–CaO–CeO2–Si3N4. The synthesized (La,Ca)Si3(O,N)5:Ce3+ exhibits tunable blue broadband emission with the dominant wavelength of 466–479 nm and the external quantum efficiency up to ∼45% under 380 nm near-UV (NUV) excitation. Spectral simulations of the trichromatic white light-emitting diodes (LEDs) using (La,Ca)Si3(O,N)5:Ce3+ demonstrated markedly higher color rendering index Ra values of 93–95, compared to 76–90 attained by the systems using a conventional BAM:Eu2+ phosphor or InGaN blue LED. The present achievement indicates the promising applicability of (La,Ca)Si3(O,N)5:Ce3+ as a blue luminescent source for NUV-converting high-color rendering white LEDs.
In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. (1989)

The allosteric control of aspartate transcarbamoylase (ATCase, EC 2.1.3.2) of Escherichia coli involves feedback inhibition by both CTP and UTP rather than just CTP alone. It has been known that CTP functions as a heterotropic inhibitor of catalysis; however, the inhibition by CTP alone is incomplete (50-70% at various aspartate concentrations) and there is only a partial occupancy of the allosteric binding sites by CTP at saturating concentrations. The logic of these allosteric characteristics can now be understood in that UTP is a synergistic inhibitor of ATCase in the presence of CTP even though UTP has no independent effect at pH 7.0. When saturating concentrations of CTP are present, the concentration of substrate required for half-maximal activity (S0.5) of the native holoenzyme for aspartate increases from 5 to 11 mM. When CTP and UTP are both present, the aspartate requirement increases further (S0.5 = 17 mM). At aspartate concentrations less than 5 mM, the heterotropic inhibition of ATCase is 90-95% in the presence of both pyrimidine nucleotides. UTP does enhance the binding of CTP to the holoenzyme but the number of tight binding sites does not change (n = 3). The binding of UTP is stabilized in the presence of CTP although its binding characteristics are not as strong as those of CTP. The recent crystallographic studies of Kim et al. [Kim, H.K., Pan, Z., Honzatko, R.B., Ke, H.M. & Lipscomb, W.N. (1987) J. Mol. Biol. 196, 853-875] have described a structural asymmetry across the molecular two-fold axis that is consistent with these CTP/UTP interactions. The synergistic inhibition of ATCase by both CTP and UTP provides a satisfying logic for ensuring a balance of endogenous pyrimidine nucleotide pools.
Susceptibility Genes for Rapid Decline of Lung Function in the Lung Health Study (2001)

Abstract The genes that contribute to the genetic susceptibility to chronic obstructive pulmonary disease (COPD) remain largely unknown. We hypothesized that widely divergent rates of decline in lung function in smokers would be a robust phenotype for detection of genes that contribute to COPD severity. We selected 283 rapid decliners (Δ FEV1 = − 154 ± 3 ml/yr) and 308 nondecliners (Δ FEV1 = + 15 ± 2 ml/yr) from among smokers followed for 5 yr in the NHLBI Lung Health Study. Rapid decline of FEV1 was associated with the MZ genotype of the α1-antitrypsin gene (odds ratio [OR] = 2.8, p = 0.03). This association was stronger for a combination of a family history of COPD with MZ (OR = 9.7, p = 0.03). These data suggest that the MZ genotype results in an increased rate of decline in lung function and interacts with other familial factors. Haplotype frequencies of the microsomal epoxide hydrolase (mEH) gene were significantly different between rapid decliners and nondecliners (p = 0.03). A combination of a family history of COPD with homozygosity for the His113/His139 mEH haplotype was also associated with rapid decline of lung function (OR = 4.9, p = 0.04). The α1-antitrypsin S and 3′ polymorphisms, vitamin D-binding protein isoforms, and tumor necrosis factor (TNF- α G-308A and TNF- β A252G) polymorphisms were not associated with rate of decline of lung function.
Primary analysis of the prospective, randomized, phase II trial of GP2+GM-CSF vaccine versus GM-CSF alone administered in the adjuvant setting to high-risk breast cancer patients. (2014)

134 Background: GP2 is a HER2 derived, HLA-A2 + -restricted immunogenic peptide designed to stimulate CD8 + T cells to recognize tumor cells with any level of HER2 expression (IHC 1-3+). Accrual to a prospective, randomized, multi-center, phase II trial of the GP2 vaccine for prevention of breast cancer recurrence has completed. Here, the planned primary analysis of disease-free survival (DFS) is presented. Methods: HLA-A2 + node positive or high-risk node negative breast cancer patients (pts) with any level of HER2 expression rendered disease-free by standard of care therapy (to include trastuzumab where appropriate) were randomized to receive GP2+GM-CSF (VG) or GM-CSF (CG) alone. Pts received 6 monthly inoculations (primary vaccine series = PVS) followed by 4 boosters administered every 6 months. The Kaplan Meier method was used for statistical analysis. The intention-to-treat (ITT) population is defined as the entire randomly assigned population. The per-treatment (PT) group excluded pts who recurred during the PVS or developed a second malignancy. A pre-specified subgroup analysis was performed based on HER2 expression level. HER2 overexpression (OE) is defined as IHC 3 + or FISH >2.2. Results: With 89 VG and 91 CG pts enrolled and vaccinated, there are no differences between groups with respect to age, node positivity, tumor size, grade, ER/PR status, and HER2 expression (p>0.05). The vaccine has been well tolerated with toxicities comparable between the VG and CG. Only one grade 3 local and systemic toxicity reaction has been reported in the VG. At 34 (1-60) month median follow-up, DFS was compared in the ITT (85% VG v 81% CG, p = 0.57) and PT (94% VG v 85% CG, p = 0.17) populations. In OE patients (51 VG and 50 CG) DFS was 94% VG v 89% CG, p = 0.86 (ITT) and 100% VG v 89% CG, p = 0.08 (PT). Conclusions: GP2+GM-CSF is a novel vaccine that is safe and well tolerated. This phase II trial demonstrates potentially greater benefit in pts with HER2 OE tumors, in whom there have been no recurrences in the PT group. This may be due to synergism with trastuzumab therapy, thus justifying a phase III trial evaluating GP2 administered in the adjuvant setting to a HER2 OE population. Clinical trial information: NCT00524277.