gebhart/patrepeval huggingface dataset:
Clustering, Classification, and Categorization (2022)

Text analytics consist of the statistics about a text element, which includes the word count, the word histogram, and the word frequency histogram. Most text documents of value are related to other—sometimes many other—documents, and so analytics describing the relative frequency of terms in a document compared to its peers are important for defining key words (tagging, labeling, indexing), search-responsive terms (query terms), and compressed versions of the documents (key words, summary, etc.).This clearly written text explains the functional applications of search, translation, optimization, and learning with regard to text analytics. Generation of analytics is aided by a hybrid, ensemble, or other combinatorial approach in which two or more effective analytic processes are used simultaneously, and their outputs combined to form a better “consensus”. Additional value to the preservation of the information is provided through these methods. Also, since they encompass capabilities of two or more knowledge-generating systems, they can create a “superset” of access points to the data generated. The book also describes the role of functional approaches in the testing and configuration of these systems.
Durvalumab as monotherapy and in combination therapy in patients with lymphoma or chronic lymphocytic leukemia: The FUSION NHL 001 trial (2022)

Durvalumab as monotherapy or in combination is tolerable but requires close monitoring. The high rate of TEAEs during this study may reflect on the difficulty in combining durvalumab with full doses of other agents. Durvalumab alone or in combination appeared to add limited benefit to therapy.
Temperature Dependence of the III—II Transition Rate of KNO3 at Atmospheric Pressure (1965)

The existence of ferroelectric behavior in the Phase III polymorph of potassium nitrate has permitted the direct recording of the rate of transition of the Phase III to the Phase II at temperatures far removed from the normal transformation temperature at atmospheric pressure. The data presented indicates that the III—II transition may be described by two first-order processes which may each be described by a single rate constant. These rate constants as a function of temperature are given.
Modeling of a two-bed silica gel-water adsorption chiller (2013)

This article presents a lumped-parameter model which was recently developed by our group to investigate the performance of multi-bed adsorption chillers. We demonstrate that this model has the same efficacy as distributed model by comparing the predictions from both lumped-parameter and distributed models at various operating conditions. The model is then used to analyze the effect of heat recovery schemes and the effect of other parameters on system performance. Through the experimental validation, it is found that the differences between predictions and experimental data in both cooling capacity and Coefficient of Performance are typically less than 10% in our studied working conditions. This provides useful information for adsorption chiller manufacturers.
Recent Advances in DHODH Inhibition for Acute Myeloid Leukemia (2019)

Medicinal Chemistry Reviews is an outstanding 680 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
Inferences about the Global Population Structures of Cryptosporidium parvum and Cryptosporidium hominis (2008)

Cryptosporidium parvum and Cryptosporidium hominis are two related species of apicomplexan protozoa responsible for the majority of human cases of cryptosporidiosis. In spite of their considerable public health impact, little is known about the population structures of these species. In this study, a battery of C. parvum and C. hominis isolates from seven countries was genotyped using a nine-locus DNA subtyping scheme. To assess the existence of geographical partitions, the multilocus genotype data were mined using a cluster analysis based on the nearest-neighbor principle. Within each country, the population genetic structures were explored by combining diversity statistical tests, linkage disequilibrium, and eBURST analysis. For both parasite species, a quasi-complete phylogenetic segregation was observed among the countries. Cluster analysis accurately identified recently introduced isolates. Rather than conforming to a strict paradigm of either a clonal or a panmictic population structure, data are consistent with a flexible reproductive strategy characterized by the cooccurrence of both propagation patterns. The relative contribution of each pattern appears to vary between the regions, perhaps dependent on the prevailing ecological determinants of transmission.
Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during algal blooms (2021)

Abstract Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global nutrient cycling. When blooms collapse, organic carbon is transferred to higher trophic levels, microbial respiration or sinking in proportions that depend on the dominant mortality agent. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains an open question. Here, we characterized the consequences of viral infection on the microbiome composition and biogeochemical landscape of marine ecosystems by conducting a large-scale mesocosm experiment. Moniroting of seven induced coccolithophore blooms, which showed different degrees of viral infection, revealed that only high levels of viral infection caused significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, viral infection favored the growth of eukaryotic heterotrophs (thraustochytrids) over bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection can increase per-cell rates of extracellular carbon release by 2-4.5 fold. This happened via production of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
Likelihood functions and confidence bounds for total-least-squares problems (2002)

This paper addresses the derivation of likelihood functions and confidence bounds for problems involving over-determined linear systems with noise in all measurements, often referred to as total-least-squares (TLS). It has been shown previously that TLS provides maximum likelihood estimates. But rather than being a function solely of the variables of interest, the associated likelihood functions increase in dimensionality with the number of equations. This has made it difficult to derive suitable confidence bounds, and impractical to use these probability functions with Bayesian belief propagation or Bayesian tracking. This paper derives likelihood functions that are defined only on the parameters of interest. This has two main advantages. First, the likelihood functions are much easier to use within a Bayesian framework; and second it is straightforward to obtain a reliable confidence bound on the estimates. We demonstrate the accuracy of our confidence bound in relation to others that have been proposed. Also, we use our theoretical results to obtain likelihood functions for estimating the direction of 3D camera translation.
Repolarization of polarization-scrambled optical signals due to polarization dependent loss (1997)

We calculate the distribution function of the degree of polarization of an initially polarization scrambled signal propagating long distances in an optical fiber. We show that a significant repolarization can occur for modern-day parameters. We estimate how far the polarization dependent loss must be reduced before repolarization becomes negligible.
LOW GLUCOSE ENHANCES THE CYTOPROTECTIVE EFFECT OF METFORMIN AGAINST DOXORUBICIN-INDUCED CYTOTOXICITY (2019)

Abstract Metformin, an oral anti-diabetic drug, is currently being investigated for its anti-aging properties and has also been used as adjunct therapy in cancer. Cancer is a disease of aging. Type 2 diabetes is also prevalent in older adults. We wanted to test the hypothesis that metformin could protect normal cells during chemotherapy treatment under different glucose conditions. We used C2C12 myoblast cells to study cellular bioenergetics, variations in gene expressions, and biochemical alterations induced by metformin and pegylated liposomal doxorubicin (L-Doxo) under low glucose (2.7 mM or 50 mg/dL) and normal physiologic glucose (5.5 mM, or 100 mg/dL) conditions. Using confocal microscopy, we noted that treatment of C2C12 cells with 30 µg/mL L-Doxo under low glucose and normal physiologic glucose conditions induced cellular defects. Furthermore, L-Doxo treatment dysregulated the expression of mitochondrial fission and fusion genes, which may influence transformation of the network’s connectivity. L-Doxo treatment significantly reduced mitochondrial oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). However, pre-treatment with 100 nM metformin provided protection against L-Doxo-induced damage and increased cell viability and ATP levels in cells even under low glucose conditions. Our data provide further evidence by which low dose metformin exerts protective effects against L-Doxo, a chemotherapeutic drug, under low glucose conditions. Metformin appears to act via AMPKα, Raptor, and SRF, and has significant cellular protective effects that may be useful in cancer and/or aging.
Increased Expression of Adenylyl Cyclase Isoforms in the Adrenal Gland of Diabetic Goto-Kakizaki Rat (2002)

The spontaneously diabetic Goto-Kakizaki rat harbors the same defects expressed in human type 2 diabetes. It is not clear, however, whether stress factors emanating from the adrenal glands are involved in causing the diabetic state. For that reason, the authors studied gland size and expression of adenylyl cyclase isoforms in adrenal glands from Goto-Kakizaki and normal rats. Goto-Kakizaki rat adrenals were found to weigh only about half as much as those of control rats. This decrease was the result of a reduction of the cortex, especially of the zona fasciculata, whereas the medulla was unaffected. Cell density measurements showed that the total number of medullary cells in Goto-Kakizaki rats was lower than that in controls. In the cortex, the cell density did not differ between the two groups; thus, our results point to a marked hypotrophy. In the medulla of Goto-Kakizaki rats, the nuclear size was significantly increased, and there was also an overexpression of adenylyl cyclase 1, 2, 4, 6, and 8 isoforms in the adrenalin-producing cells, indicating an increased functional capacity. In the cortex, despite the cortical hypotrophy, adenylyl cyclase 5 immunoreactivity was markedly increased in Goto-Kakizaki rats, especially in the zona reticularis. It is unclear whether this morphologic change in the diabetic adrenal glands together with the overexpression of different adenylyl cyclase isoforms plays a role in the pathogenesis of this diabetic state or is a genetic defect or compensatory mechanism of diabetes in this spontaneous rodent model of type 2 diabetes.
WDM Weighted Sum in an 8x8 SOA-Based InP Cross-Connect for Photonic Deep Neural Networks (2018)

We demonstrate high fidelity weighted addition of four 10 Gb/s on-off keyed data channels on a SOA-based monolithically integrated cross-connect, with a reading error dispersion below 0.2 with respect to the target. These results open the route to feasible 8x8 one-layer neuron interconnectivity for photonic integrated deep neural networks.
Novel Power Si/4H-SiC Heterojunction Tunneling Transistor (HETT) (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Enzymatic Investigation for Delayed‐type Hypersensitivity Reaction (1991)

Induration is a prominent feature of delayed hypersensitivity reaction (DHR) and is associated with fibrin deposition. To determine whether thrombin and plasmin mediate the development of induration, we examined guinea pig skin extracts of tuberculin reaction sites for the protease activities. To measure their low activities without inactivation by the inhibitors in the extracts, fluorogenic peptide substrates specific to each of the proteases were used. Because thiol proteases in the extracts hydrolyzed the substrates, the two serine protease activities were selected using a serine protease inhibitor. The extracts contained alpha 2-macroglobulin (alpha 2-MG)-trapped thrombin that hydrolyzes the substrate, but no alpha 2-MG-trapped plasmin. To exclude alpha 2-MG-trapped thrombin activity, the extract treated with 0.2 M methylamine was incubated for two hours and the residual activity was excluded from the initial thrombin activity. Thrombin activity paralleled increasing intensity of induration, and plasmin activity was associated with the reduction of induration. Neither induration nor an increase of protease activity was observed at control sites. The results show that thrombin and plasmin mediate the development of induration probably by regulating fibrin deposition in DHR sites and that the present method can measure the protease activities in biological fluids and tissue extracts.
Correlation of glypican-1 expression with TGF-β, BMP, and activin receptors in pancreatic ductal adenocarcinoma (2006)

Glypican1 (GPC1) is a cell surface heparan sulfate proteoglycan that acts as a co-receptor for heparin-binding growth factors as well as for members of the TGF-β family. GPC1 plays a role in pancreatic cancer by regulating growth factor responsiveness. In view of the importance of members of the TGF-β family in pancreatic cancer, in the present study, the role of GPC1 in TGF-β, BMP and activin signaling was analyzed. Quantitative RT-PCR and immunohistochemistry were utilized to analyze GPC1 and TGF-β, BMP and activin receptor expression levels. Panc-1 and T3M4 pancreatic cancer cells were transfected in a stable manner with a GPC1 antisense expression construct. Anchorage-dependent and -independent growth was determined by MTT and soft agar assays. TGF-β1, activin-A and BMP-2 responsiveness was determined by MTT assays and immunoblotting with p21, p-Smad1, and p-Smad2 antibodies. QRT-PCR demonstrated increased GPC1 mRNA levels in pancreatic ductal adenocarcinoma (PDAC) compared to normal pancreatic tissues (NPT), as described previously. There was a significant correlation between GPC1 mRNA levels and TβRII, act-R1a, act-R1b, act-R2a, BMP-R1a, and BMP-R2 mRNA expression in NPT. In contrast, GPC1 mRNA expression correlated directly with act-R1a and BMP-R1a in N0 PDAC cases and with act-R2a and BMP-R1a in lymph node positive cases. Down-regulation of GPC1 resulted in increased doubling time in Panc-1 but not in T3M4 cells, and decreased anchorage-independent growth in both cell lines. GPC1 down-regulation resulted in a slightly altered response towards TGF-β1, activin-A and BMP-2 in terms of growth, p21 induction and Smad2 phosphorylation. In conclusion, enhanced GPC1 expression correlates with BMP and activin receptors in pancreatic cancer. GPC1 down-regulation suppresses pancreatic cancer cell growth and slightly modifies signaling of members of the TGF-β family of growth factors.
Nanostructure fabrication in silicon using cesium to pattern a self-assembled monolayer (1997)

This letter describes the formation of nanometer-scale features in a silicon substrate using a self-assembled monolayer (SAM) of octylsiloxane on silicon dioxide as a resist sensitive to a patterned beam of neutral cesium atoms. The mask that patterned the atomic beam was a silicon nitride membrane perforated with nm and μm scale holes, in contact with the substrate surface. In a two-step wet-chemical etching process, the pattern formed in the SAM was transferred first into the SiO2 layer and then into an underlying silicon substrate. This process demonstrated the formation of silicon features with diameter ∼60 nm.
Sample and hold strategy for quantum measurements of Josephson charge qubits (2001)

We present a design for a charge qubit, and an associated ``quantum sample and hold'' measurement scheme. Using arrays of superconducting islands, connected by tunable tunnel junctions, we can ``sample'' the charge states by turning off the Josephson coupling, and then ``hold'' a Cooper pair on an island for a very long time. This allows for a slow readout using a conventional weakly coupled low-frequency single-electron transistor.
Distributed training of large scale exponential language models (2011)

Shrinkage-based exponential language models, such as the recently introduced Model M, have provided significant gains over a range of tasks [1]. Training such models requires a large amount of computational resources in terms of both time and memory. In this paper, we present a distributed training algorithm for such models based on the idea of cluster expansion [2]. Cluster expansion allows us to efficiently calculate the normalization and expectations terms required for Model M training by minimizing the computation needed between consecutive n-grams. We also show how the algorithm can be implemented in a distributed environment, greatly reducing the memory required per process and training time.
Entangling X-rays through high harmonic down conversion (2023)

We present a method to produce entangled photon pairs in the extreme ultraviolet (EUV) and X-ray regime, using a new highly nonperturbative nonlinear optical process which we term “high harmonic down conversion” (HHDC).
Exploiting femtocellular networks for emergency telemedicine applications in indoor environments (2010)

This paper presents a proposal for a solution for rapid provisioning of mobile broadband data connectivity for emergency telemedicine applications in indoor environments. The proposed solution relies on the exploitation of existing femtocellular network resources available at emergency sites in indoor environments. Extensive simulations are carried out to compare the performance of our new proposed complementary femtocellular approach to the conventional macrocellular mobile networking approach in a UMTS/WCDMA network operating environment. The simulation results indicate at least an order of magnitude reduction in service outage rates when femtocells are utilized, in the comparison to the macrocellular case for multiple dwelling unit buildings located on the cell edge.
Synthesis of Some Substituted 1,3,2-Oxazaphosphorinanes (1987)

Abstract To study the effect of statistically controlled associate dia-stereoisomerism (SCADA), the optical isomers of some derivatives of 2-amino-2-oxo-1,3,2-oxazaphosphorinane, containing the residues of L-α-aminoacids, were synthesized. The magnitude of chemical shift nonequivalence (Δδ) in 31P NMR-spectra of diastereomeric mixtures was maximum for isomeric derivatives of valine; the dependence of Δδ31P on their concentration was investigated.
Predicting the pathogenicity ofRPE65mutations (2009)

To assist in distinguishing disease-causing mutations from nonpathogenic polymorphisms, we developed an objective algorithm to calculate an "estimate of pathogenic probability" (EPP) based on the prevalence of a specific variation, its segregation within families, and its predicted effects on protein structure. Eleven missense variations in the RPE65 gene were evaluated in patients with Leber congenital amaurosis (LCA) using the EPP algorithm. The accuracy of the EPP algorithm was evaluated using a cell-culture assay of RPE65-isomerase activity The variations were engineered into plasmids containing a human RPE65 cDNA and the retinoid isomerase activity of each variant was determined in cultured cells. The EPP algorithm predicted eight substitution mutations to be disease-causing variants. The isomerase catalytic activities of these RPE65 variants were all less than 6% of wild-type. In contrast, the EPP algorithm predicted the other three substitutions to be non-disease-causing, with isomerase activities of 68%, 127%, and 110% of wild-type, respectively. We observed complete concordance between the predicted pathogenicities of missense variations in the RPE65 gene and retinoid isomerase activities measured in a functional assay. These results suggest that the EPP algorithm may be useful to evaluate the pathogenicity of missense variations in other disease genes where functional assays are not available.
Isotropic submillimeter fMRI in the human brain at 7 T: Combining reduced field‐of‐view imaging and partially parallel acquisitions (2012)

Echo-planar imaging is the most widely used imaging sequence for functional magnetic resonance imaging (fMRI) due to its fast acquisition. However, it is prone to local distortions, image blurring, and signal voids. As these effects scale with echo train length and field strength, it is essential for high-resolution echo-planar imaging at ultrahigh field to address these problems. Partially parallel acquisition methods can be used to improve the image quality of echo-planar imaging. However, partially parallel acquisition can be affected by aliasing artifacts and noise enhancement. Another way to shorten the echo train length is to reduce the field-of-view (FOV) while maintaining the same spatial resolution. However, to achieve significant acceleration, the resulting FOV becomes very small. Another problem occurs when FOV selection is incomplete such that there is remaining signal aliased from the region outside the reduced FOV. In this article, a novel approach, a combination of reduced FOV imaging with partially parallel acquisition, is presented. This approach can address the problems described above of each individual method, enabling high-quality single-shot echo-planar imaging acquisition, with submillimeter isotropic resolution and good signal-to-noise ratio, for fMRI at ultrahigh field strength. This is demonstrated in fMRI of human brain at 7T with an isotropic resolution of 650 μm.
Stability of Algorithms for Electro-Magnetic-Transient Simulation of Networks With Switches and Non-Linear Inductors (2019)

This paper extends the analysis of the stability of electromagnetic transient simulation algorithms to non-linear systems with switching elements and non-linear inductor branches. A theoretical analysis based on common quadratic Lyapunov function theory is used to investigate the stability of numerical algorithms for the simulation of lumped strictly passive switched circuits (LSPSC). It is proved that only when certain fundamental physical properties, i.e., passivity and invariance of Lyapunov energy function, are satisfied, the widely used trapezoidal method results in stable simulations of such networks for any time-step size. This is different from the simulation of linear time invariant systems where any real-world stable system has a stable simulation if an A-stable integration method (e.g., trapezoidal rule) is used. Subsequently, it is shown that the problem of simulating a piecewise linear inductor can be equivalent to simulating a LSPSC; and ergo its simulation with the trapezoidal rule is also stable.