gebhart/patrepeval huggingface dataset:
Parsimonious Covariance Matrix Estimation for Longitudinal Data (2002)

This article proposes a data-driven method to identify parsimony in the covariance matrix of longitudinal data and to exploit any such parsimony to produce a statistically efficient estimator of the covariance matrix. The approach parameterizes the covariance matrix through the Cholesky decomposition of its inverse. For longitudinal data, this is a one-step-ahead predictive representation, and the Cholesky factor is likely to have off-diagonal elements that are zero or close to zero. A hierarchical Bayesian model is used to identify any such zeros in the Cholesky factor, similar to approaches that have been successful in Bayesian variable selection. The model is estimated using a Markov chain Monte Carlo sampling scheme that is computationally efficient and can be applied to covariance matrices of high dimension. It is demonstrated through simulations that the proposed method compares favorably in terms of statistical efficiency with a highly regarded competing approach. The estimator is applied to three real examples in which the dimension of the covariance matrix is large relative to the sample size. The first two examples are from biometry and electricity demand modeling and are longitudinal. The third example is from finance and highlights the potential of our method for estimating cross-sectional covariance matrices.
First deep-space flight demonstration of Regenerative pseudo-noise ranging (2012)

Deep-space missions traditionally use sequential, turnaround ranging to measure the distance to the spacecraft. The spacecraft demodulates the uplinked ranging signal (composed of sequential frequency tones) and retransmits it (“turnaround”) onto the downlink. Since this operation is bent-pipe, noise on the uplink within the ranging channel bandwidth is also retransmitted. When the received uplink signal-to-noise ratio (SNR) is low, regenerating the ranging signal can increase the retransmitted ranging SNR by 30 dB or more, compared to the bent-pipe method. The Regenerative pseudo-noise (PN) ranging creates this gain by using a PN digital ranging signal on the uplink and detecting that signal in the spacecraft receiver. The PN signal is regenerated digitally, with no uplink noise, and retransmitted to the ground. We report the first deep-space flight demonstration of regenerative ranging on the New Horizons Mission to Pluto. We provide an overview of the technique, including the operational PN ranging capability deployed at NASA's Deep Space Network (DSN). We describe the regenerative ranging implementation on the New Horizons spacecraft. Finally, we report on the operational flight tests, compare their results to the current trajectory (and sequential ranging), and detail how this technique will aid this mission in the future.
Linear Chromosome-generating System of Agrobacterium tumefaciens C58 (2012)

Agrobacterium tumefaciens C58, the pathogenic bacteria that causes crown gall disease in plants, harbors one circular and one linear chromosome and two circular plasmids. The telomeres of its unusual linear chromosome are covalently closed hairpins. The circular and linear chromosomes co-segregate and are stably maintained in the organism. We have determined the sequence of the two ends of the linear chromosome thus completing the previously published genome sequence of A. tumefaciens C58. We found that the telomeres carry nearly identical 25-bp sequences at the hairpin ends that are related by dyad symmetry. We further showed that its Atu2523 gene encodes a protelomerase (resolvase) and that the purified enzyme can generate the linear chromosomal closed hairpin ends in a sequence-specific manner. Agrobacterium protelomerase, whose presence is apparently limited to biovar 1 strains, acts via a cleavage-and-religation mechanism by making a pair of transient staggered nicks invariably at 6-bp spacing as the reaction intermediate. The enzyme can be significantly shortened at both the N and C termini and still maintain its enzymatic activity. Although the full-length enzyme can uniquely bind to its product telomeres, the N-terminal truncations cannot. The target site can also be shortened from the native 50-bp inverted repeat to 26 bp; thus, the Agrobacterium hairpin-generating system represents the most compact activity of all hairpin linear chromosome- and plasmid-generating systems to date. The biochemical analyses of the protelomerase reactions further revealed that the tip of the hairpin telomere may be unusually polymorphically capable of accommodating any nucleotide.
Time-Resolved in-Situ Experiments on the Crystallization of Natural Gas Hydrates (1996)

Time-resolved X-ray synchrotron techniques have been used, for the first time, to capture the crystalline structural dynamics of common hydrate structures during formation. Measurements were performed on carbon dioxide and propane hydrates at 273.8 K and 3.29−0.42 MPa. Our results indicate that the in-situ crystal lattice structure is in agreement with previous low-temperature single-crystal data, although the in-situ unit cell parameter is lower than those based on low-temperature, single-crystal measurements. We show the effects of two kinetic inhibitors, polyvinylpyrrolidone and tyrosine, on the energy dispersive spectra obtained for the inhibited crystal hydrate.
Studies on the Hydrodynamics of Fluidized Layers II. Streaming of Fluid, Particle Motion and Layer Expansion in Systems Fluidized With a Liquid (1973)

Starting from the physical model, basic equations are derived for the flow of the fluid, particle motion and changes in particle density along the radius. These equations enable the fluid-mechanical properties of fluidized systems to be described. 
The basic equations derived are applied to systems fluidized with a liquid, and equations are presented for the calculation of the inter-granular liquid flow rate, of the change in grain flow rate along the radius and the void fraction.
Zero-Offset Modelling and Simulated Migration by One-Way Wavefront Construction (2005)

P263 Zero-offset modelling and simulated migration by one-way wavefront construction Abstract 1 Assuming a zero-offset configuration of sources/receivers we present an approach to forward modelling based on a one-way wavefront construction process progressing upward from a selected target reflector. Subsequent simulation of migration amplitudes along this target reflector yields reliable estimates of amplitudes from a zero-offset depth migration and a quick (but less accurate) indication of small-offset depth migration amplitudes. The one-way wavefront construction process is based on theory permitting quantities related to the two-way wave propagation (accumulated reflection/transmission coefficients geometric spreading and phase shift due to caustics) to be
THE EVOLUTION OF ISOLATED BILATERAL LUNG CONTUSION FROM BLUNT CHEST TRAUMA IN RATS: CELLULAR AND CYTOKINE RESPONSES (2005)

Lung contusion is the leading cause of death from blunt thoracic trauma in adults, but its mechanistic pathophysiology remains unclear. This study uses a recently developed rat model to investigate the evolution of inflammation and injury in isolated lung contusion. Bilateral lung contusion with minimal cardiac trauma was induced in 54 anesthetized rats by dropping a 0.3-kg hollow cylindrical weight onto a precordial shield (impact energy, 2.45 Joules). Arterial oxygenation, pressure-volume (P-V) mechanics, histology, and levels of erythrocytes, leukocytes, albumin, and inflammatory mediators in bronchoalveolar lavage (BAL) were assessed at 8 min, at 4, 12, 24, and 48 h, and at 7 days after injury. The role of neutrophils in the evolution of inflammatory injury was also specifically studied by depleting these cells with intravenous vinblastine before lung contusion. Arterial oxygenation was severely reduced at 8 min to 24 h postcontusion, but became almost normal by 48 h. Levels of erythrocytes, leukocytes, and albumin in BAL were increased at <or=24 h, and returned toward normal by 48 h. Deficits in P-V mechanics were most apparent at 24 h postcontusion. Levels of macrophage inflammatory polypeptide-2, cytokine-induced neutrophil chemoattractant-1, and interleukin 6 in BAL peaked at 24 h, whereas monocyte chemoattractant protein-1 and interleukin 1beta peaked at 24 to 48 h postcontusion. Histology showed early hemorrhagic injury (8 min-12 h), with neutrophilic infiltration at 24 h and areas of bronchiolitis obliterans organizing pneumonia-associated fibrosis at 7 days. Vinblastine-treated neutropenic rats had significantly reduced lung injury based on total lung volume at 4 h and on BAL albumin levels at 24 h postcontusion. Inflammatory injury from isolated bilateral lung contusion in rats is most severe in the acute period (8 min-24 h) after initial blunt trauma, and includes a component of neutrophil-dependent pathology.
Characterization of vaginal & rectal colonization with multiple serotypes of group B streptococci using multiple colony picks. (2004)

In conclusion, there was a relatively high prevalence of serotype nonconcordance in this population, and 21.6 per cent of patients had multiple GBS serotypes.
3D host cell and pathogen-based bioassay development for testing anti-tuberculosis (TB) drug response and modeling immunodeficiency (2021)

Tuberculosis (TB) is a global health threat that affects 10 million people worldwide. Human Immunodeficiency Virus (HIV) remains one of the major contributors to the reactivation of asymptomatic latent tuberculosis (LTBI). Over the recent years, there has been a significant focus in developing in-vitro 3D models mimicking early events of <i>Mycobacterium tuberculosis</i> (Mtb) pathogenesis, especially formation of the granuloma. However, these models are low throughput and require extracellular matrix. In this article, we report the generation of a matrix-free 3D model, using THP-1 human monocyte/macrophage cells and mCherry-expressing <i>Mycobacterium bovis</i> BCG (Bacilli Camille Guérin), henceforth referred as 3D spheroids, to study the host cell-bacterial interactions. Using mCherry-intensity-based tracking, we monitored the kinetics of BCG growth in the 3D spheroids. We also demonstrate the application of the 3D spheroids for testing anti-TB compounds such as isoniazid (INH), rifampicin (RIF), as well as a host-directed drug, everolimus (EVR) as single and combinational treatments. We further established a dual infection 3D spheroid model by coinfecting THP-1 macrophages with BCG mCherry and pseudotype HIV. In this HIV-TB co-infection model, we found an increase in BCG mCherry growth within the 3D spheroids infected with HIV pseudotype. The degree of disruption of the granuloma was proportional to the virus titers used for co-infection. In summary, this 3D spheroid assay is an useful tool to screen anti-TB response of potential candidate drugs and can be adopted to model HIV-TB interactions.
Supplement from PD-L2 Expression in Human Tumors: Relevance to Anti-PD-1 Therapy in Cancer (2023)

&lt;p&gt;Supplementary Figures S1-S5&lt;/p&gt;
Cloning and sequencing of the cDNA for S-acyl fatty acid synthase thioesterase from the uropygial gland of mallard duck. (1985)

In vitro translation of poly(A)+ RNA from the uropygial glands of mallard ducks (Anas platyrhynchos) generated a 29-kDa protein which cross-reacted with rabbit antibodies prepared against S-acyl fatty acid synthase thioesterase (Kolattukudy, P. E., Rogers, L., and Flurkey, W. (1985) J. Biol. Chem., 260, 10789-10793). A poly(A)+ RNA fraction enriched in this thioesterase mRNA, isolated by sucrose density gradient centrifugation, was used to prepare cDNA which was cloned in Escherichia coli using the plasmid pUC9. Using hybrid-selected translation and colony hybridization, 17 clones were selected which contained the cDNA for S-acyl fatty acid synthase thioesterase. Northern blot analysis showed that the mature mRNA for this thioesterase contained 1350 nucleotides whereas the cloned cDNA inserts contained 1150-1200 base pairs. Five of the 6 clones tested for 5'-sequence had identical sequences, and the three tested for 3'-end showed the same sequence with poly(A) tails. Two clones, pTE1 and pTE3, representing nearly the full length of mRNA, were selected for sequencing. Maxam-Gilbert and Sanger dideoxy chain termination methods were used on the cloned cDNA and on restriction fragments subcloned in M13 in order to determine the complete nucleotide sequence of the cloned cDNA. The nucleotide sequence showed an open reading frame coding for a peptide of 28.8 kDa. Two peptides isolated from the tryptic digest of the thioesterase purified from the gland showed amino acid sequences which matched with two segments of the sequence deduced from the nucleotide sequence. Another segment containing a serine residue showed an amino acid sequence homologous to the active serine-containing segment of the thioesterase domain of fatty acid synthase. Thus, the clones represent cDNA for S-acyl fatty acid synthase thioesterase. The present results constitute the first case of a complete sequence of a thioesterase.
Detecting object usage anomalies (2007)

Interacting with objects often requires following a protocol---for instance, a specific sequence of method calls. These protocols are not always documented, and violations can lead to subtle problems. Our approach takes code examples to automatically infer legal sequences of method calls. The resulting patterns can then be used to detect anomalies such as Before calling next, one normally calls hasNext. To our knowledge, this is the first fully automatic defect detection approach that learns and checks methodcall sequences. Our JADET prototype has detected yet undiscovered defects and code smells in five popular open-source programs, including two new defects in AspectJ.
B Virus -- 1955-58 -- Correspondence, General -- letter, 1958 (1958)

Letter from Ralph, Nelly to Sabin, Albert B. dated 1958-11-15.
Combination Effect of Cetuximab with Radiation in Colorectal Cancer Cells (2010)

Cetuximab enhanced the radiosensitivity of CRC cells in vitro and efficiently inhibited xenograft tumor growth. This study provided a rationale for the clinical application of the selective EGFR inhibitor cetuximab in combination with radiation in CRC.
Homozygous Familial Hypercholesterolemia (2022)

This case report describes a 67-year-old African-American woman with homozygous familial hypercholesterolemia caused by 2 pathogenic variants in the <i>LDLR</i> gene. Initial surgical, pharmacological, and low-density lipoprotein apheresis interventions were insufficient; the addition of proprotein convertase subtilisin-kexin type 9 and angiopoietin-like 3 inhibitors lowered her low-density lipoprotein cholesterol to <70 mg/dL. (<b>Level of Difficulty: Advanced.</b>).
Supplementary Figure 1 from Inositol Hexaphosphate Inhibits Tumor Growth, Vascularity, and Metabolism in TRAMP Mice: A Multiparametric Magnetic Resonance Study (2023)

&lt;p&gt;PDF file - 52K, Dose dependent effect of IP6 feeding on, (A) proliferation (PCNA staining); (B) apoptosis (TUNEL assay); (C) intraductal microvessel density (PECAM-1/CD-31 staining) in dorsolateral prostate of TRAMP mice. Quantification of positive cells is shown as mean and � SEM (error bars) in each group.&lt;/p&gt;
Preparation of low-toxic Zn-Ag-In-Te quantum dots with tunable near-IR emission toward optical applications (2018)

Semiconductor quantum dots (QDs) composed of ZnTe-AgInTe2 solid solution ((AgIn)<sub>x</sub>Zn<sub>2(1-x)</sub>Te<sub>2</sub>, ZAITe) were synthesized by a thermal reaction of corresponding metal acetates and a Te precursor in 1-dodecanethiol. TEM observations revealed that rod-shaped QDs with width of ca. 4 nm and length of ca. 16 nm were formed regardless of chemical composition of particles, x value. The absorption onset and the band-edge PL peak energy were enlarged from 1.13 to 1.53 eV and from 1.23 eV to 1.53 eV, respectively, with a decrease in x from 1.0 to 0.25. The observed optical properties of ZAITe QDs were largely tunable in the near-IR region , being suitable for optical applications.
Epidural opioid analgesia in infant rats I: mechanical and heat responses (1999)

The aim of this study was to investigate the analgesic effects of epidural opioids in neonatal rat pups. The contribution of individual opioid receptor subtypes in the spinal cord to analgesia at different developmental stages was investigated using epidural mu (morphine sulphate), delta (DPDPE) and kappa (U69593) opioid receptor agonists in neonatal rats aged postnatal day (P) 3, 10 and 21. Thresholds for flexion withdrawal reflexes to mechanical stimuli (von Frey hairs) and to noxious heating of the hind paw were low in neonates and increased with postnatal age. The analgesic action of each opioid receptor agonist followed an individual developmental pattern. In mechanical tests, all three opioid agonists were considerably more efficacious analgesics in younger animals and ED50s at P3 were always lower than at P21. In heat tests, the pattern differed. The efficacy of the kappa opioid agonist decreased with postnatal age, morphine efficacy increased over the same period and the effects of the delta agonist remained relatively unchanged. The distribution and concentration of tritiated morphine in the spinal cord following epidural administration did not alter significantly with postnatal age, suggesting that opioid access is not a major determinant of the effects reported here. It is concluded that whereas heat pain is particularly sensitive to spinal kappa opioids in neonates, mechanical sensory thresholds are generally sensitive to all spinal opioids in the newborn. The differing epidural opioid requirements compared to older subjects is likely to be due to developmental changes in spinal cord opioid receptor distribution or pharmacology.
Joint Population Pharmacokinetic Analysis of Zidovudine, Lamivudine, and Their Active Intracellular Metabolites in HIV Patients (2011)

The population pharmacokinetic parameters of zidovudine (AZT), lamivudine (3TC), and their active intracellular metabolites in 75 naïve HIV-infected patients receiving an oral combination of AZT and 3TC twice daily as part of their multitherapy treatment in the COPHAR2-ANRS 111 trial are described. Four blood samples per patient were taken after 2 weeks of treatment to measure drug concentrations at steady state. Plasma AZT and 3TC concentrations were measured in 73 patients, and among those, 62 patients had measurable intracellular AZT-TP and 3TC-TP concentrations. For each drug, a joint population pharmacokinetic model was developed and we investigated the influence of different covariates. We then studied correlations between the mean plasma and intracellular concentrations of each drug. A one-compartment model with first-order absorption and elimination best described the plasma AZT concentration, with an additional compartment for intracellular AZT-TP. A similar model but with zero-order absorption was found to adequately described concentrations of 3TC and its metabolite 3TC-TP. The half-lives of AZT and 3TC were 0.81 h (94.8%) and 2.97 h (39.2%), respectively, whereas the intracellular half-lives of AZT-TP and 3TC-TP were 10.73 h (69%) and 21.16 h (44%), respectively. We found particularly a gender effect on the apparent bioavailability of AZT, as well as on the mean plasma and intracellular concentrations of AZT, which were significantly higher in females than in males. Relationships between mean plasma drug and intracellular metabolite concentrations were also highlighted both for AZT and for 3TC. Simulation with the model of plasma and intracellular concentrations for once- versus twice-daily regimens suggested that a daily dosing regimen with double doses could be appropriate.
Distinct genotypic distribution of cytomegalovirus (CMV) envelope glycoprotein B (gB) in a Cuban cohort of patients with different CMV diseases (2007)

To investigate the association between human CMV glycoprotein B (gB) genotypes and CMV disease, we retrospectively analysed 73 biological samples from 56 Cuban patients with different CMV-related diseases using a multiplex nested PCR for detection of the reported 5 CMV gB genotypes. All 4 main genotypes 1 to 4 were found in the clinical samples while no genotype 5 was detected. Among the individuals analysed, genotype gB-2 was the most prevalent (38%) followed by gB-1 (30%) and mixed infections (16%) being mainly detected among immunosuppressed patients (7 out of 9), although there was no association between mixed infections and CMV rejection in transplant recipients. Genotype gB-4 was the least frequent (5 patients), which was almost exclusively detected in mixed infections (4 out of 5, p<0.0001). Genotype gB-1 was more frequently detected in AIDS patients (47%) although it was not statistically significant, while 68% of transplant patients showed mixed infections (p<0.05). This study represents the first report of human CMV gB genotypes in Cuban patients; however, the study is limited by the small number patients, thus making it difficult to draw firm conclusions about the distribution of CMV genotypes in Cuba. Nevertheless, this preliminary report has allowed us to identify that the main 4 CMV genotypes are present in the Cuban population, with genotypes 2 and 1 being the most frequent strains.
Direct observation of worst-bit leakage currents of DRAM (2006)

We build a method for measuring leakage current of anomalously leaky cells (tail cells) in dynamic random access memories. We find that the traps in tail cells are at a region of stronger electric field in the p-n junction and their energy levels are nearer the midgap than the respective values for average cells.
Simple View on Fingering Instability of Debonding Soft Elastic Adhesives (2009)

We study the crack-front fingering instability of an elastic adhesive tape that is peeled off a solid substrate. Our analysis is based on an energy approach using fracture mechanics and scaling laws and provides simple physical explanations for (i) the fact that the wavelength depends only on the thickness of the adhesive film and (ii) the threshold of the instability, and (iii) additionally estimates the characteristic size of the fingers. The scaling laws for these three observables are in agreement with existing experimental data.
Electrochemically Active Thin Carbon Films with Enhanced Adhesion to Silicon Substrates (2016)

Thin carbon films deposited on technologically relevant substrates, such as silicon wafers, can be easily implemented in miniaturized electrochemical devices and used for sensing applications. However, a major issue in most carbon films is the weak film/substrate adhesion that shortens the working device lifetime. This paper describes the facile preparation of robust thin carbon films on silicon substrates by one-pot sol-gel synthesis. The improved adherence of these carbon films is based on the incorporation of silica through the controlled synthesis of a resorcinol/formaldehyde gel modified with aminopropyltriethoxysilane. The films demonstrate excellent adhesion to the silicon substrate, good homogeneity, excellent electrical conductivity and superior electrochemical performance. Moreover, this approach opens the door to the fabrication of carbon thin-film electrodes by photolithographic techniques.