gebhart/patrepeval huggingface dataset:
Mirostat: A Perplexity-Controlled Neural Text Decoding Algorithm (2020)

Neural text decoding is important for generating high-quality texts using language models. To generate high-quality text, popular decoding algorithms like top-k, top-p (nucleus), and temperature-based sampling truncate or distort the unreliable low probability tail of the language model. Though these methods generate high-quality text after parameter tuning, they are ad hoc. Not much is known about the control they provide over the statistics of the output, which is important since recent reports show text quality is highest for a specific range of likelihoods. Here, first we provide a theoretical analysis of perplexity in top-k, top-p, and temperature sampling, finding that cross-entropy behaves approximately linearly as a function of p in top-p sampling whereas it is a nonlinear function of k in top-k sampling, under Zipfian statistics. We use this analysis to design a feedback-based adaptive top-k text decoding algorithm called mirostat that generates text (of any length) with a predetermined value of perplexity, and thereby high-quality text without any tuning. Experiments show that for low values of k and p in top-k and top-p sampling, perplexity drops significantly with generated text length, which is also correlated with excessive repetitions in the text (the boredom trap). On the other hand, for large values of k and p, we find that perplexity increases with generated text length, which is correlated with incoherence in the text (confusion trap). Mirostat avoids both traps: experiments show that cross-entropy has a near-linear relation with repetition in generated text. This relation is almost independent of the sampling method but slightly dependent on the model used. Hence, for a given language model, control over perplexity also gives control over repetitions.
Visuohaptic Simulation of Bone Surgery (Technical Report) (2006)

Surgical training has traditionally revolved around an apprenticeship model: residents observe experienced surgeons in the operating room, and eventually are deemed ready to perform their first procedure. In recent years, simulation-based training has emerged as a potential adjunct to this method, and the value of simulation-based learning has been more widely accepted. Simulation can be a safe, cost-effective, customizable, and easilyaccessible tool for gaining experience in surgery. This paper will present methods for simulating surgeries involving bone manipulation, with a specific focus on two categories of procedures: temporal bone surgery and mandibular surgery. Section 1 will provide relevant clinical background on the target procedures. Section 2 will describe the algorithms and data structures used for interactive haptic and graphic rendering, specifically targeted toward providing key sources of intraoperative feedback for surgical interaction with bones. Section 3 will present the results of a study which evaluates the construct validity of our system (its ability to discriminate expert surgeons from novices). Section 4 will describe features of our simulation environment that do not exist in traditional, cadaver-based training labs. Section 5 will discuss our approach to automatically evaluating a trainee’s performance in our environment. We begin with a brief description of the relevant surgical procedures. We begin with a brief description of the relevant surgical procedures.
Lymphadenopathy-Associated Virus: From Molecular Biology to Pathogenicity (1986)

No AccessJournal of Urology1 Aug 1986Lymphadenopathy-Associated Virus: From Molecular Biology to Pathogenicity L. Montagnier L. MontagnierL. Montagnier More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)44959-7AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Lymphadenopathy-Associated Virus: From Molecular Biology to Pathogenicity." The Journal of Urology, 136(2), p. 547 © 1986 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 136Issue 2August 1986Page: 547 Advertisement Copyright & Permissions© 1986 by The American Urological Association Education and Research, Inc.MetricsAuthor Information L. Montagnier More articles by this author Expand All Advertisement PDF downloadLoading ...
Simultaneous Detection of Near-field Topographic and Fluorescence Images of Human Chromosomes Via Scanning Near-field Optical/Atomic-force Microscopy (SNOAM) (1997)

Scanning near-field optical/atomic-force microscopy (SNOAM) provided us with simultaneous topographical and optical images of human chromosomes using a sharp and bent optical fiber as a near-field optical probe. Native chromosomes were spread out onto a coverslip using the surface-spreading whole-mount method. The SNOAM system does not need pretreatment of samples such as metal coating or chemical immobilization. Near-field topographic and fluorescence images provided useful information on native chromosome structure.
Studies on ergothioneine. VIII. Preventive effects of ergothioneine on cadmium-induced teratogenesis. (1982)

The possible preventive effects of ergothioneine on cadmium-induced teratogenesis were examined. Cd (2 mg/kg) was administered i. p. to mice on day 7 of pregnancy. The treatment group of mice was given i. p. ergothioneine daily at a dose of 80 mg/kg during days 5 to 9, whereas the control group was given saline solution. These mice were subjected to Cesarean section on day 17 of gestation, and the number of dead fetuses, the body weight of living fetuses, and external, skeletal and visceral abnormalities were recorded. On the other hand, 109Cd (50μCi/2 mg Cd/kg) was administered i. p. to other pregnant mice on day 7, and the tissue distribution of the Cd was examined on days 8 and 17 of gestation. The results of the series of experiments were as follows. (1) Administration of ergothioneine alone had no effect on external, skeletal and visceral abnormalities. (2) Of 257 cases, fetuses in 79 cases died or were resorbed after Cd administration. The body weight of living fetuses was significantly reduced, and exencephalia (64%), open eye (31.5%) and marked skeletal malformations of cervical, thoracic and lumbar vertebrae were observed. (3) Ergothioneine very significantly reduced the incidences of exencephalia, open eye and skeletal abnormalities caused by Cd. (4) There were no differences between both groups in the in vivo distribution of 109Cd, or in the form of 109Cd present in the liver, kidney and placenta. These results suggest that ergothioneine inhibits Cd-induced teratogenesis through a mechanism other than causing changes in the maternal distribution of Cd and in Cd transfer to fetuses.
Supplementary Materials & Methods and Figure Legend from <i>PTEN</i> Loss Contributes to Erlotinib Resistance in EGFR-Mutant Lung Cancer by Activation of Akt and EGFR (2023)

Supplementary Materials &amp; Methods and Figure Legend from &lt;i&gt;PTEN&lt;/i&gt; Loss Contributes to Erlotinib Resistance in EGFR-Mutant Lung Cancer by Activation of Akt and EGFR
Energy-efficient reconfigurable computing using Spintronic memory (2015)

Reconfigurable computing platforms enable rapid prototyping of arbitrary logic, but purely spatial fabrics suffer from issues with scalability and power consumption. Novel reconfigurable frameworks are being developed which similarly allow arbitrary function mapping, but do so with a mixture of spatial and temporal computing, improving scalability and energy efficiency over purely spatial fabrics. Embedded memories within these frameworks enable rapid function evaluation through lookup table operations, making the memory read/write behavior and power consumption critical design considerations. Emerging nonvolatile nanoscale memories demonstrate enhanced cell density, reliability, and read access performance over modern memory devices, promising vast improvements in energy efficiency for memory-based reconfigurable hardware platforms. Using Spintronic memory, an average 5% improvement in EDP over FPGA can be achieved in a memory-based framework, and tailoring the mapping to exploit features of spintronic memory can further improve EDP an average 1.6%.
Fluorescent Excitation Transfer Immunoassay for the Determination of Spinosyn A in Water (1999)

A fluorescent excitation transfer immunoassay for spinosyn A, a fermentation derived insect control agent, has been developed and applied to the analysis of tap water and wastewater effluent from manufacturing plants. Fluorescein (F) and tetramethylrhodamine (TMR) were chosen as donor and quencher, respectively, for the excitation transfer. Fluorescence quenching was observed from the binding of F-labeled antigen to TMR-labeled antibody. By employing nonlabeled antigen in a competitive immunoassay format, we reversed fluorescence quenching. The assay provides a limit of detection of 0. 01 ppb and a working range of 0.05-1 ppb and allows for the rapid determination of spinosyn A in water with recovery values ranging from 96% to 120%. With the exploitation of the small size of optical fibers, fluorescence from an assay volume of 24 microL could be measured without special vessels.
Discourse generation using utility-trained coherence models (2006)

We describe a generic framework for integrating various stochastic models of discourse coherence in a manner that takes advantage of their individual strengths. An integral part of this framework are algorithms for searching and training these stochastic coherence models. We evaluate the performance of our models and algorithms and show empirically that utility-trained log-linear coherence models outperform each of the individual coherence models considered.
UE Set Selection for RR Scheduling in Distributed Antenna Transmission with Reinforcement Learning (2023)

In this paper, user set selection in the allocation sequences of round-robin (RR) scheduling for distributed antenna transmission with block diagonalization (BD) pre-coding is proposed. In prior research, the initial phase selection of user equipment allocation sequences in RR scheduling has been investigated. The performance of the proposed RR scheduling is inferior to that of proportional fair (PF) scheduling under severe intra-cell interference. In this paper, the multi-input multi-output technology with BD pre-coding is applied. Furthermore, the user equipment (UE) sets in the allocation sequences are eliminated with reinforcement learning. After the modification of a RR allocation sequence, no estimated throughput calculation for UE set selection is required. Numerical results obtained through computer simulation show that the maximum selection, one of the criteria for initial phase selection, outperforms the weighted PF scheduling in a restricted realm in terms of the computational complexity, fairness, and throughput.
Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide (2010)

Biochemical network reconstructions have become popular tools in systems biology. Metabolicnetwork reconstructions are biochemically, genetically, and genomically (BiGG) structured databases of biochemical reactions and metabolites. They contain information such as exact reaction stoichiometry, reaction reversibility, and the relationships between genes, proteins, and reactions. Network reconstructions have been used extensively to study the phenotypic behavior of wild-type and mutant stains under a variety of conditions, linking genotypes with phenotypes. Such phenotypic simulations have allowed for the prediction of growth after genetic manipulations, prediction of growth phenotypes after adaptive evolution, and prediction of essential genes. Additionally, because network reconstructions are organism specific, they can be used to understand differences between organisms of species in a functional context.There are different types of reconstructions representing various types of biological networks (metabolic, regulatory, transcription/translation). This chapter serves as an introduction to metabolic and regulatory network reconstructions and models and gives a complete description of the core Escherichia coli metabolic model. This model can be analyzed in any computational format (such as MATLAB or Mathematica) based on the information given in this chapter. The core E. coli model is a small-scale model that can be used for educational purposes. It is meant to be used by senior undergraduate and first-year graduate students learning about constraint-based modeling and systems biology. This model has enough reactions and pathways to enable interesting and insightful calculations, but it is also simple enough that the results of such calculations can be understoodeasily.
Phase transitions in dipolar spin-1Bose gases (2011)

We study phase transitions in homogeneous spin-$1$ Bose gases in the presence of long-range magnetic dipole--dipole interactions (DDI). We concentrate on three-dimensional (3D) geometries and employ momentum shell renormalization group to study the possible instabilities caused by the DDI. At the zero-temperature limit where quantum fluctuations prevail, we find the phase diagram to be unaffected by the DDI. When the thermal fluctuations dominate, polar and ferromagnetic condensates with DDI become unstable and we discuss this crossover in detail. On the other hand, the spin-singlet condensate remains stable in the presence of DDI.
Genipin-Crosslinked, Proteosaccharide Scaffolds for Potential Neural Tissue Engineering Applications (2022)

Traumatic brain injuries (TBIs) are still a challenge for the field of modern medicine. Many treatment options such as autologous grafts and stem cells show limited promise for the treatment and the reversibility of damage caused by TBIs. Injury beyond the critical size necessitates the implementation of scaffolds that function as surrogate extracellular matrices. Two scaffolds were synthesised utilising polysaccharides, chitosan and hyaluronic acid in conjunction with gelatin. Both scaffolds were chemically crosslinked using a naturally derived crosslinker, Genipin. The polysaccharides increased the mechanical strength of each scaffold, while gelatin provided the bioactive sequence, which promoted cellular interactions. The effect of crosslinking was investigated, and the crosslinked hydrogels showed higher thermal decomposition temperatures, increased resistance to degradation, and pore sizes ranging from 72.789 ± 16.85 µm for the full interpenetrating polymer networks (IPNs) and 84.289 ± 7.658 μm for the semi-IPN. The scaffolds were loaded with Dexamethasone-21-phosphate to investigate their efficacy as a drug delivery vehicle, and the full IPN showed a 100% release in 10 days, while the semi-IPN showed a burst release in 6 h. Both scaffolds stimulated the proliferation of rat pheochromocytoma (PC12) and human glioblastoma multiforme (A172) cell cultures and also provided signals for A172 cell migration. Both scaffolds can be used as potential drug delivery vehicles and as artificial extracellular matrices for potential neural regeneration.
A Postitive Regulatoty Sequence of the Saccharomyuces crevisiae ENO1 Gene1 (1987)

ENO1-'lacZ fusions with various lengths of the ENO1 5'-flanking region were constructed on various types of yeast plasmid vectors. The fully expressed level of beta Gal directed by ENO1-'lacZ fusions differed depending on the type of vector, but on any type of vector, beta Gal activity was not greatly influenced by the carbon source in the medium. The 86-bp DNA region of ENO1 at position -487 to -402 upstream of the initiation codon, in which we had previously delimited the positive regulatory region of ENO1 (Uemura, H., Shiba, T., Paterson, M., Jigami, Y., & Tanaka, H. (1986) Gene 45, 67-75), exerted its function without requiring precise location with respect to the TATA box. The action of the positive regulatory region was not affected by its orientation. In addition, the substitution of the UASs of PHO5, encoding repressible acid phosphatase, with the regulatory region of ENO1 changed the expression of PHO5-'lacZ gene to constitutive, irrespective of the concentration of inorganic phosphate in the medium. Furthermore, the GCR1 gene cloned in a multicopy plasmid increased the expression of the ENO1-'lacZ fused genes.
0139 Centrifugal Instability on a Liquid Lithium Film Flowing down a Concave Plate for the Target and Coolant of BNCT using Accelerators (2009)

We discuss the film flow of liquid lithium planned for the target and coolant of BNCT (Boron Neutron Capture Therapy) using accelerators which makes tumors curable with cell-level selections. We treat of the centrifugal instability to be generated in the boundary layer of the film flowing down on a concave guide plate. The object of our research is the thin film flow in a vacuum because of the ambiance using accelerators, and they serve both as a target of accelerators and as a coolant for the target itself. The latter role requires high-speed film flow for sufficient removals of proton beam heating. In this paper, we predict that the above centrifugal instability will give rise to the transition to turbulent flow in the boundary layer of the film flow.
Investigations in the Biosynthesis of the Pigments of Life: Calculations on the Formation of Uroporphyrinogen III from Hydroxymethylbilan and Description of a New Mechanism for the D‐Ring Inversion (1993)

The direct formation of a spiro tetrapyrrole intermediate from hydroxymethylbilan (1) is energetically less favorable than the formation of a cationic σ complex in the first step of the cyclization to form uroporphyrinogen III (2) [Eq.(a)]. This was shown by calculations on model compounds (A, P = H or Me). The preferred mode of cyclization in the biosynthesis of 2, which proceeds by inversion of the D ring, can be formulated as an alternative mechanism and has stereoselective H abstraction and [1,5] sigmatropic shifts as key steps. P = (CH2)2CO2H, A = CH2CO2H.
A combined variable step size strategy for two microphones acoustic feedback cancellation using proportionate algorithms (2017)

This paper proposes to use a combination of the improved proportionate normalized least mean square (IPNLMS) algorithm and a new algorithm called combined-step- size IPNLMS (CSS-IPNLMS) algorithm in the two microphone closed-loop feedback cancellation technique. The simulation results indicate an improvement in convergence speed of the proposed algorithms as compared to previously suggested methods, especially for the case of the normal feedback path.
DARLS (2011)

We present a new system for visualizing and merging differences in diagrams. It uses animation, dual views, a storyboard, relative re-layout, and layering to visualize differences. The system is also capable of differencing UML class diagrams. An evaluation produced positive results for animation and dual views with difference layer.
Lifetime prediction of glass fiber/derakane 411-350 composites (2004)

The goal of the present effort is to develop and verify a lifetime prediction approach for glass fiber reinforced DERAKANE 411-350 composites subjected to fatigue loading, as well as moisture aging. The approach taken is to use fatigue lifetime data taken from samples that were not aged and use it in conjunction with long-term immersed aging data (for a different laminate), as inputs to a residual strength based lifetime prediction scheme entitled MRLife. We will compare our predicted results to those measured experimentally, and comment on discrepancies observed.
Inhibition of Human Immunodeficiency Virus Replication by a Dual CCR5/CXCR4 Antagonist (2004)

Here we report that the N-pyridinylmethyl cyclam analog AMD3451 has antiviral activity against a wide variety of R5, R5/X4, and X4 strains of human immunodeficiency virus type 1 (HIV-1) and HIV-2 (50% inhibitory concentration [IC(50)] ranging from 1.2 to 26.5 microM) in various T-cell lines, CCR5- or CXCR4-transfected cells, peripheral blood mononuclear cells (PBMCs), and monocytes/macrophages. AMD3451 also inhibited R5, R5/X4, and X4 HIV-1 primary clinical isolates in PBMCs (IC(50), 1.8 to 7.3 microM). A PCR-based viral entry assay revealed that AMD3451 blocks R5 and X4 HIV-1 infection at the virus entry stage. AMD3451 dose-dependently inhibited the intracellular Ca(2+) signaling induced by the CXCR4 ligand CXCL12 in T-lymphocytic cells and in CXCR4-transfected cells, as well as the Ca(2+) flux induced by the CCR5 ligands CCL5, CCL3, and CCL4 in CCR5-transfected cells. The compound did not interfere with chemokine-induced Ca(2+) signaling through CCR1, CCR2, CCR3, CCR4, CCR6, CCR9, or CXCR3 and did not induce intracellular Ca(2+) signaling by itself at concentrations up to 400 microM. In freshly isolated monocytes, AMD3451 inhibited the Ca(2+) flux induced by CXCL12 and CCL4 but not that induced by CCL2, CCL3, CCL5, and CCL7. The CXCL12- and CCL3-induced chemotaxis was also dose-dependently inhibited by AMD3451. Furthermore, AMD3451 inhibited CXCL12- and CCL3L1-induced endocytosis in CXCR4- and CCR5-transfected cells. AMD3451, in contrast to the specific CXCR4 antagonist AMD3100, did not inhibit but enhanced the binding of several anti-CXCR4 monoclonal antibodies (such as clone 12G5) at the cell surface, pointing to a different interaction with CXCR4. AMD3451 is the first low-molecular-weight anti-HIV agent with selective HIV coreceptor, CCR5 and CXCR4, interaction.
Integration of genetic and metabolic features related to sialic acid metabolism distinguishes human breast cell subtypes (2018)

In this report we use 'high-flux' tributanoyl-modified N-acetylmannosamine (ManNAc) analogs with natural N-acetyl as well as non-natural azido- and alkyne N-acyl groups (specifically, 1,3,4-O-Bu3ManNAc, 1,3,4-O-Bu3ManNAz, and 1,3,4-O-Bu3ManNAl respectively) to probe intracellular sialic acid metabolism in the near-normal MCF10A human breast cell line in comparison with earlier stage T-47D and more advanced stage MDA-MB-231 breast cancer lines. An integrated view of sialic acid metabolism was gained by measuring intracellular sialic acid production in tandem with transcriptional profiling of genes linked to sialic acid metabolism. The transcriptional profiling showed several differences between the three lines in the absence of ManNAc analog supplementation that helps explain the different sialoglycan profiles naturally associated with cancer. Only minor changes in mRNA transcript levels occurred upon exposure to the compounds confirming that metabolic flux alone can be a key determinant of sialoglycoconjugate display in breast cancer cells; this result complements the well-established role of genetic control (e.g., the transcription of STs) of sialylation abnormalities ubiquitously associated with cancer. A notable result was that the different cell lines produced significantly different levels of sialic acid upon exogenous ManNAc supplementation, indicating that feedback inhibition of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE)-generally regarded as the 'gatekeeper' enzyme for titering flux into sialic acid biosynthesis-is not the only regulatory mechanism that limits production of this sugar. A notable aspect of our metabolic glycoengineering approach is its ability to discriminate cell subtype based on intracellular metabolism by illuminating otherwise hidden cell type-specific features. We believe that this strategy combined with multi-dimensional analysis of sialic acid metabolism will ultimately provide novel insights into breast cancer subtypes and provide a foundation for new methods of diagnosis.