gebhart/patrepeval huggingface dataset:
Parameter Estimation for Gibbs Distributions (2024)

A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We consider sampling problems coming from Gibbs distributions , which are families of probability distributions over a discrete space \(\Omega\) with probability mass function of the form \(\mu^{\Omega}_{\beta}(\omega)\propto e^{\beta H(\omega)}\) for \(\beta\) in an interval \([\beta_{\min},\beta_{\max}]\) and \(H(\omega)\in\{0\}\cup[1,n]\) . Two important parameters are the partition function , which is the normalization factor \(Z(\beta)=\sum_{\omega\in\Omega}e^{\beta H(\omega)}\) and the vector of pre-image counts \(c_{x}=|H^{-1}(x)|\) . We develop black-box sampling algorithms to estimate the counts using roughly \(\tilde{O}(\frac{n^{2}}{\varepsilon^{2}})\) samples for integer-valued distributions and \(\tilde{O}(\frac{q}{\varepsilon^{2}})\) samples for general distributions, where \(q=\log\frac{Z(\beta_{\max})}{Z(\beta_{\min})}\) (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using \(\tilde{O}(\frac{n^{2}}{\varepsilon^{2}})\) samples for integer-valued distributions and \(\tilde{O}(\frac{q}{\varepsilon^{2}})\) samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate \(Z(\beta_{\max})\) and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of \(n\) and \(q\) up to logarithmic terms.
Gold Nanoparticles as Boron Carriers for Boron Neutron Capture Therapy: Synthesis, Radiolabelling and In Vivo Evaluation (2019)

<i>Background</i>: Boron Neutron Capture Therapy (BNCT) is a binary approach to cancer therapy that requires accumulation of boron atoms preferentially in tumour cells. This can be achieved by using nanoparticles as boron carriers and taking advantage of the enhanced permeability and retention (EPR) effect. Here, we present the preparation and characterization of size and shape-tuned gold NPs (AuNPs) stabilised with polyethylene glycol (PEG) and functionalized with the boron-rich anion cobalt <i>bis</i>(dicarbollide), commonly known as COSAN. The resulting NPs were radiolabelled with <sup>124</sup>I both at the core and the shell, and were evaluated in vivo in a mouse model of human fibrosarcoma (HT1080 cells) using positron emission tomography (PET). <i>Methods</i>: The thiolated COSAN derivatives for subsequent attachment to the gold surface were synthesized by reaction of COSAN with tetrahydropyran (THP) followed by ring opening using potassium thioacetate (KSAc). Iodination on one of the boron atoms of the cluster was also carried out to enable subsequent radiolabelling of the boron cage. AuNPs grafted with mPEG-SH (5 Kda) and thiolated COSAN were prepared by ligand displacement. Radiolabelling was carried out both at the shell (isotopic exchange) and at the core (anionic absorption) of the NPs using <sup>124</sup>I to enable PET imaging. <i>Results</i>: Stable gold nanoparticles simultaneously functionalised with PEG and COSAN (PEG-AuNPs@[<b>4</b>]<sup>-</sup>) with hydrodynamic diameter of 37.8 ± 0.5 nm, core diameter of 19.2 ± 1.4 nm and ξ-potential of -18.0 ± 0.7 mV were obtained. The presence of the COSAN on the surface of the NPs was confirmed by Raman Spectroscopy and UV-Vis spectrophotometry. PEG-AuNPs@[<b>4</b>]<sup>-</sup> could be efficiently labelled with <sup>124</sup>I both at the core and the shell. Biodistribution studies in a xenograft mouse model of human fibrosarcoma showed major accumulation in liver, lungs and spleen, and poor accumulation in the tumour. The dual labelling approach confirmed the in vivo stability of the PEG-AuNPs@[<b>4</b>]<sup>-</sup>. <i>Conclusions</i>: PEG stabilized, COSAN-functionalised AuNPs could be synthesized, radiolabelled and evaluated in vivo using PET. The low tumour accumulation in the animal model assayed points to the need of tuning the size and geometry of the gold core for future studies.
Relationship of Genetic Variability and Depressive Symptoms to Adverse Events After Coronary Artery Bypass Graft Surgery (2008)

A serotonin-related gene polymorphism--5HTTLPR--was associated with adverse cardiac events post CABG, in combination with depressive symptoms. Because depressed patients with the L allele of the 5HTTLPR polymorphism were more likely to have an event compared with the S/S carriers, combining genetic and psychiatric profiling may prove useful in identifying patients at the highest risk for adverse outcomes post CABG.
Power line channel modelling for industrial application (2008)

Motor feeder cable has been shown to be a promising communication medium between the motor and the drive in motor diagnostics and controlling. The communication channel can be used for data transmission from the sensors installed at the motor to the drive or to the control PC. This article deals with both frequency (100 kHz - 30 MHz) and time- domain channel modelling in inverter driven electrical drives.
FLUORESCENCE SPECTRAL CHANGES OF HEMATOPORPHYRIN DERIVATIVE UPON BINDING TO LIPID VESICLES, Staphylococcus aureus AND Escherichia coli CELLS (1985)

Abstract— The binding of hematoporphyrin derivated (Hpd) to lipid vesicles and bacterial membranes was determined by fluorescence spectroscopy. The fluorescence measurements of Hpd in aqueous solutions showed two bands at 613 and 677 nm. In lipid environments of lecithin vesicles the fluorescence spectrum was shifted to 631 and 692 nm, respectively. Hpd was rapidly bound to the cell membrane of Staphylococcus aureus while much less binding occurred in the presence of Escherichia coli. At the same time, spheroplasts of both bacteria were shown to bind Hpd to a similar extent. These results are well correlated with the photoinactivation of the gram positive bacteria with Hpd while the gram negative cells were shown to be resistant. The pH dependence of both Hpd binding to S. aureus as well as the photodynamic inhibitory effect of the same bacteria are similar. It is concluded that the segregation of Hpd to the cell membrane is a prerequisite for its photodynamic effect.
Deposition of osmium thin films using pyrazolate complexes as CVD source reagents (2002)

The reaction of Os3(CO)12 with 1.2 eq. of pyrazole (3,5-(CF3)2-pz)H at 190 °C affords triosmium complex Os3(CO)10(3,5-(CF3)2-pz)(μ-H) (1) as the isolable product. Upon further treatment with excess pyrazole (3,5-(CF3)2-pz)H under more forcing conditions, complex 1 converts to a diosmium pyrazolate complex [Os(CO)3(3,5-(CF3)2-pz)]2 (2) in high yield. These osmium complexes are characterized by spectroscopic methods and single crystal X-ray diffraction study, showing the expected triangular and linear Os–Os backbone and with one and two bridging pyrazolate ligands for complexes 1 and 2, respectively. The thermal properties are studied by TG analysis and the deposition experiments are carried out using a cold-wall CVD apparatus. The as-deposited thin films are characterized using XPS, XRD and SEM and electrical resistivity measurement. It seems that the Os metal thin films are best deposited at an optimal temperature of 450–500 °C and using complex 2 as the source reagent.
Drastic Modification of the Dispersion State of Submicron Silica during Biaxial Deformation of Poly(ethylene terephthalate) (2007)

Deformation-induced modification of the dispersion state of silica nanoparticles in poly(ethylene terephthalate) (PET) has been characterized by means of transmission electron microscopy (TEM) and wide-angle X-ray diffraction (WAXD). We focused on the biaxial deformation applied at a temperature just above the glass transition temperature (110 °C), during the free stretch-blowing process of amorphous PET modified with submicron silica. The first nanocomposite studied contains 2.5 wt % of fractal aggregated pyrogenic silica. The particles are well dispersed after the polymerization of PET, but they agglomerate and orient strongly parallel to the elongation direction after biaxial deformation. They form long streams of particles (>2 μm long) regularly spaced by a distance of 50−100 nm. Interestingly, the silica organization is consistent with the hierarchical structure commonly proposed for the strain-induced crystallization of PET. The particles are rejected from the highly oriented domains induced by the strain, and their spatial organization reveals the superstructure. The second nanocomposite contains 5% of spherical silica with a diameter of 20 nm. Its behavior is drastically different. The silica also forms streams of particles (1−2 μm long); however, the streams are oriented perpendicular to the elongation direction, and that is hardly compatible with the presence of a microfibrillar structure. We assume that this unexpected orientation is produced by the extended growth of mesophases and crystallites perpendicular to the orientation and that stacked lamellae are formed rather than microfibrils.
Mesoporous titania-coated Love wave sensors and FEM model applied to viscosity micro-measurements (2017)

This paper presents the interest of a Love wave sensor coated with a TiO2 mesoporous film as sensitive layer. The main novelty is related to the modelling of the device and simulation by using Finite Element Method with COMSOL Multiphysics software, which is a good way to take into account the physical properties of porous 3D-layers. Experimental devices have shown a good agreement with simulated results. Furthermore, experimental results with several Newtonian liquids, viscosities from 1 to 7 cP, are investigated. The sensitivity with a 300 nm thick porous sensing layer was 30 times that of the bare device, with interesting dynamical issues to be further studied, giving rise to the great potentialities of such architectures for microrheological measurements.
Rational application of macrophage-specific LXR agonists avoids the pitfalls of SREBP-induced lipogenesis (2018)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Can the Direct Cardiac Effects of the Electric Pulses Generated by the TASER X26 Cause Immediate or Delayed Sudden Cardiac Arrest in Normal Adults? (2007)

There is only a small amount of experimental data about whether the TASER X26, a nonlethal weapon that delivers a series of brief electrical pulses to cause involuntary muscular contraction to temporarily incapacitate an individual, can initiate ventricular fibrillation to cause sudden cardiac arrest either immediately or sometime after its use. Therefore, this paper uses the fundamental law of electrostimulation and experimental data from the literature to estimate the likelihood of such events. Because of the short duration of the TASER pulses, the large duration of the cardiac cell membrane time constant, the small fraction of current from electrodes on the body surface that passes through the heart, and the resultant high pacing threshold from the body surface, the fundamental law of electrostimulation predicts that the TASER pulses will not stimulate an ectopic beat in the large majority of normal adults. Since the immediate initiation of ventricular fibrillation in a normal heart requires a very premature stimulated ectopic beat and the threshold for such premature beats is higher than less premature beats, it is unlikely that TASER pulses can immediately initiate ventricular fibrillation in such individuals through the direct effect of the electric field generated through the heart by the TASER. In the absence of preexisting heart disease, the delayed development of ventricular fibrillation requires the electrical stimuli to cause electroporation or myocardial necrosis. However, the electrical thresholds for electroporation and necrosis are many times higher than that required to stimulate an ectopic beat. Therefore, it is highly unlikely that the TASER X26 can cause ventricular fibrillation minutes to hours after its use through direct cardiac effects of the electric field generated by the TASER.
Ganglioside and Non-ganglioside Mediated Host Responses to the Mouse Polyomavirus (2015)

Gangliosides serve as receptors for internalization and infection by members of the polyomavirus family. Specificity is determined by recognition of carbohydrate moieties on the ganglioside by the major viral capsid protein VP1. For the mouse polyomavirus (MuPyV), gangliosides with terminal sialic acids in specific linkages are essential. Although many biochemical and cell culture experiments have implicated gangliosides as MuPyV receptions, the role of gangliosides in the MuPyV-infected mouse has not been investigated. Here we report results of studies using ganglioside-deficient mice and derived cell lines. Knockout mice lacking complex gangliosides were completely resistant to the cytolytic and pathogenic effects of the virus. Embryo fibroblasts from these mice were likewise resistant to infection, and supplementation with specific gangliosides restored infectibility. Although lacking receptors for viral infection, cells from ganglioside-deficient mice retained the ability to respond to the virus. Ganglioside-deficient fibroblasts responded rapidly to virus exposure with a transient induction of c-fos as an early manifestation of a mitogenic response. Additionally, splenocytes from ganglioside-deficient mice responded to MuPyV by secretion of IL-12, previously recognized as a key mediator of the innate immune response. Thus, while gangliosides are essential for infection in the animal, gangliosides are not required for mitogenic responses and innate immune responses to the virus.
Microfluidic genetic and amino acid analysis using an integrated a-Si:H detector (2004)

Hydrogenated amorphous silicon (a-Si:H) PIN photodiodes are used as fluorescence detectors for microfluidic biochemical and chemical analysis devices. A hybrid- integrated detector consisting of a half-ball lens, a ZnS/YF/sub 3/ multilayer optical interference filter with a pinhole, and an annular a-Si:H photodiode is developed that allows the laser excitation to pass up through the central aperture in the photodiode. Using this integrated device, the limit of detection for fluorescein flowing in a 50-/spl mu/m deep channel is 17 nM (S/N = 3). Furthermore, analysis of PCR amplicons generated from Staphylococcus aureus and chiral analysis of glutamic acid are successfully demonstrated. The a-Si:H detector exhibits high sensitivity at the emission wavelengths of commonly used fluorescent dyes and is readily microfabricated and integrated at low cost making it ideal for portable microfluidic bioanalyzers.
Preparation of Urogenital Sinus Mesenchymal Cells for Prostate Tissue Recombination Models (2015)

An appropriate microenvironment provided by the mesenchyme is important for establishing tissue recombination models for epithelial cancer. Urogenital sinus mesenchymal (UGSM) cells derived from embryonic rodent show potent inductive effects for prostate regeneration. Genetic manipulation of these mesenchymal cells allows us to define the contribution of the tumor microenvironment to prostate cancer development. This protocol describes preparation and propagation of murine UGSM cells in culture.
NKG2A expression identifies a subset of human Vδ2 T cells exerting the highest antitumor effector functions (2021)

Human Vδ2 cells are innate-like γδ T effectors performing potent immune surveillance against tumors. The constitutive expression of NKG2A identifies a subset of Vδ2 T cells licensed with an intrinsic hyper-responsiveness against cancer. Indeed, the transcriptomic profiles of NKG2A<sup>+</sup> and NKG2A<sup>-</sup> cells characterize two distinct "intralineages" of Vδ2 T lymphocytes that appear early during development, keep their phenotypes, and show self-renewal capabilities in adult life. The hyper-responsiveness of NKG2A<sup>+</sup> Vδ2 T cells is counterbalanced by the inhibitory signaling delivered by human leukocyte antigen E (HLA-E) expressed on malignant cells as a tumor-escape mechanism. However, either masking or knocking out NKG2A restores the capacity of Vδ2 T cells to exert the highest effector functions even against HLA-E<sup>+</sup> tumors. This is highly relevant in the clinic, as the different degrees of engagement of the NKG2A-HLA-E checkpoint in hepatocellular carcinoma, glioblastoma, and non-small cell lung cancer directly impact patients' overall survival. These findings open avenues for developing combined cellular and immunologic anticancer therapies.
Room Temperature Copper(II)-Catalyzed Oxidative Cyclization of Enamides to 2,5-Disubstituted Oxazoles via Vinylic C–H Functionalization (2012)

A copper(II)-catalyzed oxidative cyclization of enamides to oxazoles via vinylic C-H bond functionalization at room temperature is described. Various 2,5-disubstituted oxazoles bearing aryl, vinyl, alkyl, and heteroaryl substituents could be synthesized in moderate to high yields. This reaction protocol is complementary to our previously reported iodine-mediated cyclization of enamides to afford 2,4,5-trisubstituted oxazoles.
Structure-Based Study to Overcome Cross-Reactivity of Novel Androgen Receptor Inhibitors (2022)

The mutation-driven transformation of clinical anti-androgen drugs into agonists of the human androgen receptor (AR) represents a major challenge for the treatment of prostate cancer patients. To address this challenge, we have developed a novel class of inhibitors targeting the DNA-binding domain (DBD) of the receptor, which is distanced from the androgen binding site (ABS) targeted by all conventional anti-AR drugs and prone to resistant mutations. While many members of the developed 4-(4-phenylthiazol-2-yl)morpholine series of AR-DBD inhibitors demonstrated the effective suppression of wild-type AR, a few represented by 4-(4-(3-fluoro-2-methoxyphenyl)thiazol-2-yl)morpholine (VPC14368) exhibited a partial agonistic effect toward the mutated T878A form of the receptor, implying their cross-interaction with the AR ABS. To study the molecular basis of the observed cross-reactivity, we co-crystallized the T878A mutated form of the AR ligand binding domain (LBD) with a bound VPC14368 molecule. Computational modelling revealed that helix 12 of AR undergoes a characteristic shift upon VPC14368 binding causing the agonistic behaviour. Based on the obtained structural data we then designed derivatives of VPC14368 to successfully eliminate the cross-reactivity towards the AR ABS, while maintaining significant anti-AR DBD potency.
Foaming dynamics in Hele-Shaw cells (2006)

We have studied foaming dynamics in Hele-Shaw cells partially filled with a soap and water mixture. A series of upside-down flips produces an intermittent wetting of the cell and leads to foam formation. As a function of the number of flips, an increasing number of bubbles composes the foam, until saturation is observed. Statistical analysis shows that the bubble size follows a Gamma distribution. Contrary to common belief, this foaming dynamics by "shaking" creates homogeneous foam, even though the system may pass through transient heterogeneous configurations. A mechanistic interpretation is proposed and included into a theoretical model.
Colonic mucosa-associated lymphoid tissue lymphoma: a case series (2019)

Primary colonic mucosa-associated lymphoid tissue (MALT) lymphoma accounts for less than 0.5% of all colon cancers. We report 9 cases of colonic MALT lymphomas (median follow up: 9 [IQR 1-26] years). The disease was multi-focal in 4 patients: the most frequent sites were the cecum in 4 and the rectum in 3 patients. The main endoscopic finding was a polypoid lesion. The treatment modalities were rituximab +/- an alkylating agent (<i>n</i> = 5), an alkylating agent alone (<i>n</i> = 2), surgical resection (<i>n</i> = 1), and endoscopic resection (<i>n</i> = 1). Remission was achieved in 8 cases. Three patients relapsed, and 2 were re-treated. At the end of the study period, 67% of the patients were in remission. All patients were symptom-free. This current series of colonic MALT lymphomas shows the indolent nature of the disease, which may be treated with various modalities.
Microscale Enhancement of Heat and Mass Transfer for Hydrogen Energy Storage (2015)

The document summarized the technical progress associated with OSU’s involvement in the Hydrogen Storage Engineering Center of Excellence. OSU focused on the development of microscale enhancement technologies for improving heat and mass transfer in automotive hydrogen storage systems. OSU’s key contributions included the development of an extremely compact microchannel combustion system for discharging hydrogen storage systems and a thermal management system for adsorption based hydrogen storage using microchannel cooling (the Modular Adsorption Tank Insert or MATI).
Synthesis and electrochromic properties of mesoporous tungsten oxide (2001)

The electrochromic properties of mesoporous tungsten oxide are described and compared to standard sol–gel films of WO3. The block copolymer template used in the synthesis was removed by solvent extraction and calcination methods, leading to mesoporous tungsten oxides which range from amorphous to crystalline depending on the removal treatment. The pores are not ordered but do exhibit a fairly regular diameter with an average size of 4 to 5 nm. The mesoporous tungsten oxides exhibit a well behaved electrochromic response and their electrochemical and optical reversibilities are better than those of the analogous sol–gel film. In addition, the mesoporous films exhibit higher rates for coloration and bleaching. The high surface area of these materials is responsible for this behavior and also leads to multiple peaks in the voltammetric scans.
Revascularization improves vascular hemodynamics − a study assessing cerebrovascular reserve and transit time in Moyamoya patients using MRI (2022)

Cerebrovascular reserve (CVR) reflects the capacity of cerebral blood flow (CBF) to change. Decreased CVR implies poor hemodynamics and is linked to a higher risk for stroke. Revascularization has been shown to improve CBF in patients with vasculopathy such as Moyamoya disease. Dynamic susceptibility contrast (DSC) can measure transit time to evaluate patients suspected of stroke. Arterial spin labeling (ASL) is a non-invasive technique for CBF, CVR, and arterial transit time (ATT) measurements. Here, we investigate the change in hemodynamics 4-12 months after extracranial-to-intracranial direct bypass in 52 Moyamoya patients using ASL with single and multiple post-labeling delays (PLD). Images were collected using ASL and DSC with acetazolamide. CVR, CBF, ATT, and time-to-maximum (Tmax) were measured in different flow territories. Results showed that hemodynamics improved significantly in regions affected by arterial occlusions after revascularization. CVR increased by 16 ± 11% (p < 0.01) and 25 ± 13% (p < 0.01) for single- and multi-PLD ASL, respectively. Transit time measured by multi-PLD ASL and post-vasodilation DSC reduced by 13 ± 7% (p < 0.01) and 9 ± 5% (p < 0.01), respectively. For all regions, ATT correlated significantly with Tmax (R<sup>2 </sup> = <sup> </sup>0.59, p < 0.01). Thus, revascularization improved CVR and decreased transit times. Multi-PLD ASL can serve as an effective and non-invasive modality to examine vascular hemodynamics in Moyamoya patients.