gebhart/patrepeval huggingface dataset:
Dicarboxylic Acid Separation by Dynamic and Size‐Matched Recognition in Solution and in the Solid State (2017)

Bis(trimethylammonium) alkane diiodides dynamically encapsulate dicarboxylic acids through intermolecular hydrogen bonds between the I<sup>-</sup> anions of the hosts and the carboxylic OH groups of the guests. A selective recognition is realized when the size of the I<sup>-</sup> ⋅⋅⋅HOOC(CH<sub>2</sub> /CF<sub>2</sub> )<sub>n</sub> COOH⋅⋅⋅I<sup>-</sup> superanion matches the dication alkyl chain length. Dynamic recognition is also demonstrated in solution, where the presence of the size-matching organic salt boosts the acid solubility profile, thus allowing efficient mixture separation.
Human teneurin-1 is a direct target of the homeobox transcription factor EMX2 at a novel alternate promoter (2011)

We found that human teneurin-1 is directly regulated by EMX2 at a newly identified and conserved promoter region upstream of the published transcription start site, establishing teneurin-1 as the first human EMX2 target gene. We identify and characterize the EMX2 dependent promoter element of human teneurin-1.
Synthesis and Optical Properties of Linker-Free TiO2/CdSe Nanorods (2014)

Linker-free TiO2/CdSe hybrid nanorods (NRs) were prepared by growing CdSe QDs in the presence of TiO2 NR seeds using seeded–growth type colloidal injection approach. TEM studies revealed the abundant formation of anatase TiO2 NRs with different lengths. We found that the as-prepared TiO2 seeds determined the morphology of TiO2/CdSe NRs. The photophysics of these materials were studied by photoluminescence (PL) and femtosecond transient absorption spectroscopy. While we observed the efficient PL quenching in TiO2/CdSe NRs, the bleach dynamics of TiO2/CdSe NRs is similar to that of CdSe NRs. It suggests that while surface traps that arise from the lattice mismatch between CdSe and TiO2 are mainly observed in transient absorption measurements the ultrafast exciton dissociation over the experimental time resolution occurs in TiO2/CdSe NRs.
Developing Ovarian Cancer Sensors Using Molecular Perceptron (2020)

Ovarian cancer patient prognosis and quality of life are significantly affected by the failure to accurately diagnose disease at early stage. Currently, less than 15% of ovarian cancer patients are diagnosed at stage 1, when 5-year survival rates are near 93%. Early detection may save more than 80% of women diagnosed with ovarian cancer. Our goal is to develop long-term implantable carbon nanotube-based sensors for ovarian cancer biomarkers to transiently detect and monitor their levels in patients. The proposed sensors will harness the unique optical properties and sensitivity of single-walled carbon nanotubes. To improve sensitivity and specificity of such sensors, previously developed to detect ovarian cancer biomarkers in vivo, we used molecular perceptron—data analytics-based methods to detect specific spectroscopic fingerprints from the binding of protein biomarkers to the nanotube surface.
P2.040 Multiplexed Fluorescence Immunoassay System For Rapid Serologic Testing at the Point-Of-Care (2013)

<h3>Background</h3> MBio Diagnostics is developing a multiplexed immunoassay platform capable of simultaneous detection of serologic disease markers from a single drop of blood. Here we demonstrate the system in the context of HIV and AIDS-related co-infection testing. Multianalyte testing at the time of HIV diagnosis is essential for individualised management of HIV infection. The MBio System is designed to address the unmet need for timely and cost-effective co-infection testing. <h3>Methods</h3> The MBio multiplexed immunoassay system is based on single-use disposable cartridges and an inexpensive reader. A simple, 10 minute assay protocol was developed for delivering HIV-1 antibody (Ab) reactivity results on whole blood, plasma, or serum samples. A total of 87 whole blood samples were run with the 10 minute assay. 50 HIV-1 Ab negative samples were used to establish cutoffs. 37 HIV-1 Ab positive samples were used to assess system sensitivity. A set of 5 commercially available HIV-1 seroconversion panels were also used to assess the system. System demonstration in the context of syphilis and hepatitis C virus (HCV) testing was also performed on a subset of clinical specimens. <h3>Results</h3> Ab reactivity results using the 10 minute assay protocol showed 100% concordance with known HIV serostatus for the 87 whole blood samples tested. Data for the seroconversion panels showed that MBio System performance meets or exceeds package insert data for FDA-approved HIV Ab rapid diagnostic tests. Simultaneous detection of syphilis (<i>T. pallidum</i>) and HCV Ab reactivity has been demonstrated. <h3>Conclusion</h3> s The dataset presented here demonstrates a simple, 10 minute assay protocol on the MBio multiplexed immunoassay system. Multianalyte testing from unprocessed whole blood at the POC should enable improved therapeutic decision making, particularly in limited resource settings.
Structure-Based Evaluation of Non-nucleoside Inhibitors with Improved Potency and Solubility That Target HIV Reverse Transcriptase Variants (2015)

The development of novel non-nucleoside inhibitors (NNRTIs) with activity against variants of HIV reverse transcriptase (RT) is crucial for overcoming treatment failure. The NNRTIs bind in an allosteric pocket in RT ∼10 Å away from the active site. Earlier analogues of the catechol diether compound series have picomolar activity against HIV strains with wild-type RT but lose potency against variants with single Y181C and double K103N/Y181C mutations. As guided by structure-based and computational studies, removal of the 5-Cl substitution of compound 1 on the catechol aryl ring system led to a new analogue compound 2 that maintains greater potency against Y181C and K103N/Y181C variants and better solubility (510 μg/mL). Crystal structures were determined for wild-type, Y181C, and K103N/Y181C RT in complex with both compounds 1 and 2 to understand the structural basis for these findings. Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket. Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket. Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.
An inv(16)(p13q22) positive acute myeloid leukaemia relapsing as acute precursor B-cell lymphoblastic leukaemia. (2004)

We describe a case of a 38-year old male with inv(16)(p13q22) positive acute myeloid leukaemia (AML) with eosinophilia, relapsing after a molecular remission of almost three years. Remarkably, the leukaemia at relapse was identified as a precursor-B-cell acute lymphoblastic leukaemia (B-ALL) by cytology and immunophenotyping, but was inv(16)(p13q22) positive as revealed by interphase FISH, FICTION analysis, and real-time quantitative PCR. Analysis of immunoglobulin and T-cell receptor genes showed a bi-allelic DH2-JH rearrangement at relapse, but not at diagnosis. These findings indicate a myeloid to lymphoid lineage switch from an inv(16)(p13q22) positive leukaemia and show that IGH gene rearrangements can occur in the presence of CBFB-MYH11 fusion transcripts.
Hydrolysis of di- and trisialo gangliosides in micellar and liposomal dispersion by bacterial neuraminidases (1980)

The hydrolysis of di- and trisialo gangliosides by bacterial neuraminidases was investigated. Slow rates of hydrolysis were obtained with micellar dispersions of the pure gangliosides; the rates increased considerably with mixtures of ganglioside and phospholipids, such as phosphatidylcholine or sphingomyelin. The greatest rates of hydrolysis were obtained with mixtures containing 5-10 mol% ganglioside and 90-95% phospholipid. With the aid of the nonpenetrating reagent trinitrobenzenesulfonic acid, it was ascertained that this mixture consisted of sealed, unilamellar vesicles in which the ganglioside was distributed symmetrically between the two layers of the liposome. When the relative proportion of the ganglioside was increased, the dispersions contained liposomes admixed with micelles of ganglioside and phospholipid. The rates of hydrolysis of the ganglioside could be correlated with the percentage of sealed vesicles in each mixture. Experiments in which another ganglioside (GM1) or cholesterol was incorporated into the mixed dispersions further supported this conclusion. It is suggested that the rate of hydrolysis is affected predominantly by interactions between the carbohydrate chains of ganglioside molecules. The data emphasize that ganglioside metabolism can be best studied when the latter are part of biological or model membranes.
OCCURRENCE OF SOLUBLE ANTIGEN IN THE PLASMA OF MICE WITH VIRUS-INDUCED LEUKEMIA (1964)

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.
A Search for CMB Anisotropies on Arcminute Scales with Bolocam (2008)

This talk describes the results of two sets of observations made in 2003 and 2004 with Bolocam from the Caltech Sub-millimeter Observatory (CSO). Bolocam is a large format camera consisting of 144 bolometers with an eight arcminute field of view at the CSO, and can be operated non-simultaneously at 1.1, 1.4, or 2.1 mm. All of the data described in this talk was collected at 2.1 mm, where the individual beams are approximately one arcminute in size. The observations were made over a total of seventy-nine nights, and consisted of surveys of two science fields, Lynx and the Subaru/XMM Deep Field (SDS1), covering a total area of approximately 1 square degree. The noise properties of the maps are extremely uniform, with RMS variations in coverage of approximately 1.5% for twenty arcsecond map pixels. The point source sensitivity of the maps is approximately 100 μKCMB per beam. Fluctuations in emission from the atmosphere limited the sensitivity of our measurements, and several algorithms designed to remove these fluctuations are described. These algorithms also removed astronomical flux, and simulations were used to determine the effect of this attenuation on a CMB power spectrum. Assuming a flat CMB band power, our data corresponds to an effective angular multipole of l = 5700, with a FWHMl = 2800. At these scales the CMB power spectrum is expected to be dominated by anisotropies induced by the Sunyaev-Zel'dovich effect (SZE), and have a reasonably flat spectrum. Our data is consistent with a CMB band power of 0 μK2CMB, and we set an upper limit for the CMB anisotropies.
Discovery of a Series of Phosphonic Acid-Containing Thiazoles and Orally Bioavailable Diamide Prodrugs That Lower Glucose in Diabetic Animals Through Inhibition of Fructose-1,6-Bisphosphatase (2010)

Oral delivery of previously disclosed purine and benzimidazole fructose-1,6-bisphosphatase (FBPase) inhibitors via prodrugs failed, which was likely due to their high molecular weight (>600). Therefore, a smaller scaffold was desired, and a series of phosphonic acid-containing thiazoles, which exhibited high potency against human liver FBPase (IC(50) of 10-30 nM) and high selectivity relative to other 5'-adenosinemonophosphate (AMP)-binding enzymes, were discovered using a structure-guided drug design approach. The initial lead compound (30j) produced profound glucose lowering in rodent models of type 2 diabetes mellitus (T2DM) after parenteral administration. Various phosphonate prodrugs were explored without success, until a novel phosphonic diamide prodrug approach was implemented, which delivered compound 30j with good oral bioavailability (OBAV) (22-47%). Extensive lead optimization of both the thiazole FBPase inhibitors and their prodrugs culminated in the discovery of compound 35n (MB06322) as the first oral FBPase inhibitor advancing to human clinical trials as a potential treatment for T2DM.
Role of serum periostin in severe obstructive sleep apnea with albuminuria: an observational study (2020)

Elevated serum periostin in patients with OSA despite being overweight/obese may be an indicator of severe OSA with comorbidities, particularly albuminuria.
Privacy is What We Care About (2019)

Federated Learning enables training of a general model through edge devices without sending raw data to the cloud. Hence, this approach is attractive for digital health applications, where data is sourced through edge devices and users care about privacy. Here, we report on the feasibility to train deep neural networks on the Raspberry Pi4s as edge devices. A CNN, a LSTM and a MLP was successfully trained on the MNIST data-set. Further, federated learning was demonstrated experimentally on IID and non-IID samples in a parametric study, to benchmark the model convergence. The weight updates from the workers are shared with the cloud to train the general model through federated learning. With the CNN and the non-IID samples a test-accuracy of up to 85% could be achieved within a training time of 2 minutes, while exchanging less than 10 MB data per device. In addition, we discuss federated learning from an use-case standpoint, elaborating on privacy risks and labeling requirements for the application of emotion detection from sound. Based on the experimental findings, we discuss possible research directions to improve model and system performance. Finally, we provide best practices for a practitioner, considering the implementation of federated learning.
In vivo effects of deoxyspergualin (NKT-01) on lymphocyte activation in response to alloantigens. (1988)

We studied the effects of deoxyspergualin (NKT-01) on the events of lymphocyte activation in vivo by inoculating mice in the footpad with allogeneic spleen cells, and compared the effects with those of cyclosporin A (CyA). The administration of NKT-01 increased the numbers of cells recovered from the popliteal lymph node (PLN) 7 days after inoculation, but inhibited the proliferation of these cells in the presence of exogenous interleukin 2 (IL-2). NKT-01 enhanced IL-2 production, but suppressed the production of macrophage activating factor (MAF) in the mixed lymphocyte reaction between the PLN cells and allogeneic spleen cells treated with mitomycin C. CyA decreased the numbers of PLN cells little, and suppressed the response to exogenous IL-2 and the production of both IL-2 and MAF. Results with tumor cells used as allogeneic cells suggested that there was a close relationship between the suppression of MAF production by NKT-01 and its inhibition of allograft rejection. The findings showed that NKT-01 inhibited both the MAF production by and the response to IL-2 of PLN cells, and that these effects were involved in the suppression of allograft rejection by NKT-01.
Characterizing the mechanism of improved adhesion of modified wood plastic composite (WPC) surfaces (2007)

To have a better knowledge of the phenomena that affect the adhesion characteristics of wood plastic composites (WPCs) a series of surface treatments was performed. The treatments consisted of chemical, mechanical, energetic, physical, and a combination of energetic and physical WPC surface modifications. After each treatment, the composite boards were bonded using a commercial epoxy adhesive, and bond shear strength was determined according to ASTM D 905. All the surface treatments, except the mechanical one, were performed and presented in a previous paper (W. Gramlich et al., J. Adhesion Sci. Technol. 20, 1873–1887 (2006)). Mechanical treatment and surface characterization for all the treatments were performed in the present study. The surface characterization included application of thermodynamic and spectroscopic techniques. Most of the surface treatments improved the adhesive bondability of wood plastic composites and, particularly, the smoothest WPC surfaces increased the shear strength by 100% with respect to the control. Thermodynamic measurements indicate that the WPCs low surface energy of about 25 mJ/m2, is likely due principally to the surface migration of a lubricant component used in the extrusion formulation. The surface energy increased over 45% with respect to the control samples after the chemical treatments. X-ray photoelectron spectroscopy analysis indicated that high oxidation levels of the WPC surfaces resulted in high surface energy and high bond shear strength.
Abstract 2219: High Dose Modified-release Nicotinic Acid Reduces Carotid Atherosclerosis: a Randomized, Placebo-controlled Magnetic Resonance Study (2008)

Background: Large clinical outcome studies (AIM-HIGH and HPS-2THRIVE) are underway testing the strategy of adding high dose nicotinic acid (NA) to statin treatment. However, the effect of this on atherosclerosis progression is unknown. Hypothesis: Nicotinic acid 2g daily would reduce change in carotid wall area, assessed by MRI, compared to placebo. Methods: We performed a double-blind randomized placebo-controlled study of 2g once daily modified release NA added to background statin therapy in 71 patients with low HDL-C &lt;40 mg/dL and either known coronary heart disease with type 2 diabetes mellitus or carotid / peripheral atherosclerosis The pre-specified primary end point was the change in carotid artery wall area, assessed by MRI, after 1 year. We compared the treatment effect using a mixed effect model adjusting for baseline covariates. Results: 22/35 NA and 29/36 placebo patients completed MRI at all time points. Baseline characteristics were similar. In the NA treated group, HDL-C increased 23% (39±6 to 48±7 mg/dL), and LDL-C decreased 19% (85±23 to 69±21 mg/dL). At 12 months, the NA group had a significantly higher reduction in carotid wall area compared to placebo (adjusted treatment difference [95% CI] = −1.64 mm 2 [−3.12, −0.16]; P=0.03). Median (IQR) change in carotid wall area was −1.42 mm 2 (−2.65, 0.79) for NA and 0.47 mm 2 (−0.97, 2.59) for placebo. At 12 months the change in carotid plaque index (calculated by the recognised method of normalising wall area to total vessel area) was also reduced compared to placebo (treatment difference −0.016 [−0.03, −0.0022]; P = 0.02). Even as early as six months, although there was no treatment difference for change in absolute carotid wall area (−0.98 mm 2 [−2.45, 0.49]; P = 0.2), change in carotid plaque index was already significantly lower in the NA treated group (−0.016 [−0.03, 0.0019]; P = 0.03). Conclusions: This is the first demonstration that addition of high dose modified-release nicotinic acid, to statin-treated patients with low HDL-C, reduces carotid atherosclerosis at 12 months compared to placebo.
CD4+ T cell depletion during immunization phase followed by challenge infection. (2016)

&lt;p&gt;Female BALB/c mice were vaccinated with RABV-G mRNA, Rabipur (LIC) or injection buffer alone on days 0 and 21. The CD4+ T cell population was specifically depleted in one mRNA-receiving group by injection of anti-CD4 antibody on days -1, 1, 20 and 22. &lt;b&gt;&lt;i&gt;(A)&lt;/i&gt;&lt;/b&gt; Evaluation of rabies virus neutralizing antibodies in sera of control, vaccinated or vaccinated and CD4-depleted mice 4 weeks after the second immunization using the FAVN test (n = 8/group). Mean and SD is presented. Significance between the buffer control group and immunized groups was calculated using the one-way ANOVA Tukey’s multiple comparison test (* p&lt;0.05). &lt;b&gt;&lt;i&gt;(B&lt;/i&gt;, &lt;i&gt;C)&lt;/i&gt;&lt;/b&gt; Mice were challenged with a lethal dose of rabies virus and &lt;b&gt;&lt;i&gt;(B)&lt;/i&gt;&lt;/b&gt; body weight was monitored daily. A loss of 25% of initial body weight was defined as humane endpoint. Mean and SD is presented. &lt;b&gt;&lt;i&gt;(C)&lt;/i&gt;&lt;/b&gt; Survival of challenged mice. &lt;sup&gt;&lt;b&gt;#&lt;/b&gt;&lt;/sup&gt; note: the sacrificed mouse in the RABV-G mRNA (black diamond) group was excluded from the body weight analysis to demonstrate the healthy state of the remaining animals. This mouse was also negative for rabies specific antibodies (see Fig 5A).&lt;/p&gt;
Metal–Organic Framework Nanoparticles (2018)

Abstract Due to their well‐defined 3D architectures, permanent porosity, and diverse chemical functionalities, metal–organic framework nanoparticles (MOF NPs) are an emerging class of modular nanomaterials. Herein, recent developments in the synthesis and postsynthetic surface functionalization of MOF NPs that strengthen the fundamental understanding of how such structures form and grow are highlighted; the internal structure and external surface properties of these novel nanomaterials are highlighted as well. These fundamental advances have resulted in MOF NPs being used as components in chemical sensors, biological probes, and membrane separation materials, as well as building blocks for colloidal crystal engineering.
Data from Repurposing the FDA-Approved Antiviral Drug Ribavirin as Targeted Therapy for Nasopharyngeal Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Nasopharyngeal carcinoma (NPC) is a squamous cell carcinoma with a proclivity for systemic dissemination, leading many patients to present with advanced stage disease and fail available treatments. There is a notable lack of targeted therapies for NPC, despite working knowledge of multiple proteins with integral roles in NPC cancer biology. These proteins include EZH2, Snail, eIF4E, and IMPDH, which are all overexpressed in NPC and correlated with poor prognosis. These proteins are known to be modulated by ribavirin, an FDA-approved hepatitis C antiviral that has recently been repurposed as a promising therapeutic in several solid and hematologic malignancies. Here, we investigated the potential of ribavirin as a targeted anticancer agent in five human NPC cell lines. Using cellular growth assays, flow cytometry, BrdU cell proliferation assays, scratch wound assays, and invasion assays, we show &lt;i&gt;in vitro&lt;/i&gt; that ribavirin decreases NPC cellular proliferation, migration, and invasion and promotes cell-cycle arrest and cell death. Modulation of EZH2, Snail, eIF4E, IMPDH, mTOR, and cyclin D1 were observed in Western blots and enzymatic activity assays in response to ribavirin treatment. As monotherapy, ribavirin reduced flank tumor growth in multiple NPC xenograft models &lt;i&gt;in vivo&lt;/i&gt;. Most importantly, we demonstrate that ribavirin enhanced the effects of radiotherapy, a central component of NPC treatment, both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. Our work suggests that NPC responds to ribavirin-mediated EZH2, Snail, eIF4E, IMPDH, and mTOR changes and positions ribavirin for clinical evaluation as a potential addition to our NPC treatment armamentarium.&lt;/p&gt;&lt;/div&gt;
Analysis and design of narrowband active noise control systems (2002)

This paper presents an analysis and optimization of narrowband active noise control (ANC) systems using the filtered-X least mean-square (LMS) algorithm. First, we derive an upper bound for the eigenvalue spread of the filtered reference signal's covariance matrix, which provides insights into the algorithm convergence speed. The amplitude of an internally generated sinusoidal reference signal is optimized as the inverse of the secondary path's magnitude response at the corresponding frequency to improve the convergence speed. Second, we analyze the characteristic of asymmetric out-of-band overshoot. Based on the analysis result, the phase of the sinusoidal reference signal is optimized to compensate for the phase shift of the secondary path. This phase optimization leads to the minimization of the out-of-band overshoot.