gebhart/patrepeval huggingface dataset:
AIDS‐Related Dementia and Calcium Homeostasisa (1994)

Approximately a third of adults and half of children with acquired immunodeficiency syndrome (AIDS) eventually suffer from neurological manifestations, including dysfunction of cognition, movement, and sensation. Among the various pathologies reported in the brain of patients with AIDS is neuronal injury and loss. A paradox arises, however, because neurons themselves are for all intents and purposes not infected by human immunodeficiency virus type 1 (HIV-1). This paper reviews evidence suggesting that at least part of the neuronal injury observed in the brain of AIDS patients is related to excessive influx of Ca2+. There is growing support for the existence of HIV- or immune-related toxins that lead indirectly to the injury or death of neurons via a potentially complex web of interactions between macrophages (or microglia), astrocytes, and neurons. Human immunodeficiency virus-infected monocytoid cells (macrophages, microglia, or monocytes), especially after interacting with astrocytes, secrete substances that potentially contribute to neurotoxicity. Not all of these substances are yet known, but they may include eicosanoids, that is, arachidonic acid and its metabolites, as well as platelet-activating factor. Macrophages activated by HIV-1 envelope protein gp120 also appear to release arachidonic acid and its metabolites. These factors can lead to increased glutamate release or decreased glutamate reuptake. In addition, gamma interferon (IFN-gamma) stimulation of macrophages induce release of the glutamate-like agonist quinolinate. Human immunodeficiency virus-infected or gp120-stimulated macrophages also produce cytokines, including tumor necrosis factor-alpha and interleukin-1 beta, which contribute to astrogliosis. A final common pathway for neuronal susceptibility appears to be operative, similar to that observed in stroke, trauma, epilepsy, neuropathic pain, and several neurodegenerative diseases, possibly including Huntington's disease, Parkinson's disease, and amyotrophic lateral sclerosis. This mechanism involves the activation of voltage-dependent Ca2+ channels and N-methyl-D-aspartate (NMDA) receptor-operated channels, and therefore offers hope for future pharmacological intervention. This review focuses on clinically tolerated calcium channel antagonists and NMDA antagonists with the potential for trials in humans with AIDS dementia in the near future.
S-nitrosoglutathione reductase–dependent PPARγ denitrosylation participates in MSC-derived adipogenesis and osteogenesis (2015)

Bone marrow-derived mesenchymal stem cells (MSCs) are a common precursor of both adipocytes and osteoblasts. While it is appreciated that PPARγ regulates the balance between adipogenesis and osteogenesis, the roles of additional regulators of this process remain controversial. Here, we show that MSCs isolated from mice lacking S-nitrosoglutathione reductase, a denitrosylase that regulates protein S-nitrosylation, exhibited decreased adipogenesis and increased osteoblastogenesis compared with WT MSCs. Consistent with this cellular phenotype, S-nitrosoglutathione reductase-deficient mice were smaller, with reduced fat mass and increased bone formation that was accompanied by elevated bone resorption. WT and S-nitrosoglutathione reductase-deficient MSCs exhibited equivalent PPARγ expression; however, S-nitrosylation of PPARγ was elevated in S-nitrosoglutathione reductase-deficient MSCs, diminishing binding to its downstream target fatty acid-binding protein 4 (FABP4). We further identified Cys 139 of PPARγ as an S-nitrosylation site and demonstrated that S-nitrosylation of PPARγ inhibits its transcriptional activity, suggesting a feedback regulation of PPARγ transcriptional activity by NO-mediated S-nitrosylation. Together, these results reveal that S-nitrosoglutathione reductase-dependent modification of PPARγ alters the balance between adipocyte and osteoblast differentiation and provides checkpoint regulation of the lineage bifurcation of these 2 lineages. Moreover, these findings provide pathophysiological and therapeutic insights regarding MSC participation in adipogenesis and osteogenesis.
Covariation of Major and Minor Viral Capsid Proteins in Norovirus Genogroup II Genotype 4 Strains (2011)

We report sequence hypervariability in the viral protein 1 (VP1) interaction domain of VP2 in the norovirus (NoV) genogroup II genotype 4 (GII.4) lineage on 3 levels: (i) the global evolution of pandemic/epidemic strains from the mid-1970s through post-2006, (ii) the local emergence of an epidemic strain, and (iii) an immunocompromised patient chronically shedding NoV. When a quantitative yeast two-hybrid assay was used, VP2 was found to interact with VP1 in a time-ordered, strain-dependent manner among 3 NoV GII.4 strains. Our findings suggest that VP1 and VP2 may covary in virus evolution and that sequence hypervariability of VP2 may be functionally driven. Further investigations are warranted.
Erratum: “Tunneling-electron-induced molecular luminescence from a nanoscale layer of organic molecules on metal substrates” [Appl. Phys. Lett. 84, 969 (2004)] (2004)

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Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects (2020)

Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5-3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.
Comparative assessment of guar gum for enhancing qualitative properties of dehydrated white skinned bitter gourd (Momordica charantia L.) (2022)

The enhancement of physical qualitative properties of a dehydrated product is a highly desirable aspect in processing fresh vegetables. This study compared the use of guar gum (GG) as pre-treatment for enhancing physical qualitative properties of dehydrated white skinned bitter gourd (WSBG). The experiment primarily focused on comparing GG as solo pre-treatment or in combination with other pre-treatment viz. salt solution (SS) or potassium meta bisulphite (KMS) or sodium carbonate (SC) along with water blanching (Wat Blanch) or salt blanching (Sal Blanch). The results are indicative of a significant (P values of &lt; 0.05) impact of using guar gum along with blanching before dehydration of WSBG at 60±5ºC in a mechanical dehydrator, in comparison to untreated control. The findings clearly exhibit solo GG sample T5 (Wat Blanch+1%GG) and combination GG sample T16 (2%Sal Blanch+0.2%KMS+1%SC+1%GG) as most superior with highest RR [9.23 (T5) &amp; 11.30 (T16)] and BD [0.50 g/cm3 (T5) &amp; 1.08 g/cm3 (T16)] in final dried product. The higher retention of RR and BD indicates that GG pretreated samples have better reconstitution than the control (T1). Hence, application of GG as a pre-treatment with blanching is beneficial for developing a quality product with good storage dynamics.
24‐hour intraocular pressure of healthy humans in supine position: rhythm and reproducibility (2012)

Abstract Purpose To evaluate the reproducibility over time of 24H intraocular pressure (IOP) rhythm in healthy humans in supine position. Methods In a sleep laboratory, six healthy young Caucasian male subjects were included in each six weekly 24H sessions of hourly IOP measurements in a control supine position using the pneumatonometer Digilab Modular One. IOP 24H rhythm was modelled using a nonlinear least squares dual harmonic regression analysis. The intra‐ and inter‐subject variability of acrophase, bathyphase, amplitude and IOP values were evaluated. Results A significant nyctohemeral IOP rhythm was noted in 30/36 (83%) sessions. Nocturnal IOP was significantly higher than diurnal IOP (20.1 ± 0.2 vs. 18.8 ± 0.1 mmHg). Reproducible distribution over 24H of intra‐subject acrophase and bathyphase was found respectively in 3/6 (50%) and 4/6 (67%) subjects. Intra‐subject means of amplitude were not statistically different between subjects. IOP values at 2:00, 3:00, 4:00, 10:00, 11:00 AM and 2:00 PM and IOP mesor had fair to good agreement between sessions. Conclusion Most healthy subjects exhibited a nyctohemeral rhythm of IOP with fair reproducible characteristics in supine position. Amplitude is the best reproducible parameter. This result strongly suggests that chronobiological lower IOP therapies could be powerfully studied using paired intra‐subject 24H nyctohemeral rhythm data comparison, during repeated sessions overtime before and after treatment.
Total Synthesis of Calicheamicin–Dynemicin Hybrid Molecules (1992)

Synthetic enediyne cytostatics/antibiotics are the goal of the preparative work described here. Of the four isomeric calicheamicin-dynemicin hybrid compounds obtained, only those with the same configuration as calicheamin at all stereocenters are cytostatically active. One of the active isomers is 1.
Dramatically enhanced molecular ordering and charge transport of a DPP-based polymer assisted by oligomers through antiplasticization (2013)

The existence of a suitable amount of oligomers in a diketopyrrolopyrrole (DPP)-based polymer shows an antiplasticization phenomenon, which leads to dramatically improved molecular ordering and enhanced charge transport performance in organic thin film transistors.
PNPLA3 in end‐stage liver disease: Alcohol consumption, hepatocellular carcinoma development, and transplantation‐free survival (2014)

In end-stage liver disease patients, we identified ALD to be predominantly affected by the PNPLA3 I148M variant resulting in an increased risk of HCC and reduced transplantation free survival. Genetic testing of the I148M genotype in ALD patients awaiting liver transplantation might be beneficial for these patients.
NordicDB: a Nordic pool and portal for genome-wide control data (2010)

A cost-efficient way to increase power in a genetic association study is to pool controls from different sources. The genotyping effort can then be directed to large case series. The Nordic Control database, NordicDB, has been set up as a unique resource in the Nordic area and the data are available for authorized users through the web portal (http://www.nordicdb.org). The current version of NordicDB pools together high-density genome-wide SNP information from similar to 5000 controls originating from Finnish, Swedish and Danish studies and shows country-specific allele frequencies for SNP markers. The genetic homogeneity of the samples was investigated using multidimensional scaling (MDS) analysis and pairwise allele frequency differences between the studies. The plot of the first two MDS components showed excellent resemblance to the geographical placement of the samples, with a clear NW-SE gradient. We advise researchers to assess the impact of population structure when incorporating NordicDB controls in association studies. This harmonized Nordic database presents a unique genome-wide resource for future genetic association studies in the Nordic countries. European Journal of Human Genetics (2010) 18, 1322-1326; doi: 10.1038/ejhg.2010.112; published online 28 July 2010
Resonant Fluorescence Quenching of Aromatic Hydrocarbons by Carbon Disulfide (1999)

The reduction of fluorescence intensities and of fluorescence lifetimes is determined as a function of carbon disulfide (CS2) concentration for four fluorophores. The quenching efficiency of CS2 depends strongly on the energy of the electronic absorption edge of the dye; quenching increases as the dye electronic edge approaches that of CS2. These results are described by the quantum two-level system. Comparison of Stern−Volmer plots of intensity and lifetime data shows that quenching is predominantly diffusion-mediated and furthermore demonstrates that the interaction range is about 6 Å. The impact of CS2 on the fluorescence spectra of important natural materials is discussed.
Characterization of the Loss in Plasmonic Modes of Metal- Insulator-Metal Waveguides by a Prism-Coupling Approach (2009)

A prism-coupler-based method is presented for characterizing plasmonic modes in metal-insulator-metal waveguides from the reflected power in a transverse configuration. The loss is obtained without physically changing the waveguide length as in conventional methods [1].
Simple Technique for a Quick Evaluation of HBT Temperature-Dependent DC Model Parameters in Forward Active Regime (2007)

This paper presents a simple parameter- extraction technique for an HBT temperature- dependant equivalent-circuit DC model, in the forward active regime. The proposed approach is characterized by its ease of implementation. It was applied to predict the DC characteristics of a 1x10 μm 2 emitter-area InGaP/GaAs HBT device.
Abstract 4988: Genome-wide CRISPR screen and metabolite profiling reveal a new mechanism of methotrexate sensitivity (2017)

Abstract The chemotherapeutic drug methotrexate (MTX) inhibits nucleotide biosynthesis and causes cell death by blocking DNA and RNA production. While MTX has had tremendous success as an anti-cancer treatment and is the subject of nearly a thousand ongoing clinical trials, we do not fully understand why certain cancers are more sensitive to it and why resistance emerges. To study these questions, we used a CRISPR-based genetic screen to identify genes that confer sensitivity to MTX. We identified an enzyme that plays a key role in a metabolic pathway that was not known to be associated with MTX sensitivity. Inhibition of the pathway, either by genetic loss of several genes in the pathway or through nutritional modulations, causes dramatic resistance to MTX in cultured cancer cells. Our results improved our understanding of the cellular response to MTX, and suggest that expression levels of enzymes in the pathway may serve as clinical predictor for MTX response in patients. Citation Format: Naama Kanarek, Elizaveta Freinkman, Jason Cantor, Monther Abu-Remaileh, Tim Wang, David M. Sabatini. Genome-wide CRISPR screen and metabolite profiling reveal a new mechanism of methotrexate sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4988. doi:10.1158/1538-7445.AM2017-4988
Improved MMSE algorithm for DFE optimization (2017)

The signal in channels with high-speed designs is attenuated by channel loss, inter-symbol interference, jitter, noise and crosstalk. The main way to recover the signal is by using equalizations, such as Feed-Forward Equalizer, Continuous Time-Linear Equalizer and Decision Feedback Equalizer (DFE). One of the important problems with high-speed design and channel simulations is developing fast optimization algorithms for each equalizer, as each additional tap increases the cost of the chip. The paper proposes a new efficient optimization of DFE for high-speed links. Mathematical formulation of the optimization is discussed. Different test results are given for comparison purposes.
Low noise balanced-CMOS on Si(110) surface for analog/digital mixed signal circuits (2004)

This paper demonstrated CMOS characteristics on a Si(110) surface by using a surface flattening process and radical oxidation. By forming a MOS device on a Si(110) surface, a high-speed and low 1/f noise p-MOSFET can be realized. Furthermore, balanced current drivability of p-MOS and n-MOS in the CMOS (balanced CMOS) on Si(110) surface can be also realized. This is very useful for analog/digital mixed signal circuits.
Analysis of temperature responses to diffused ultrasound focal fields produced by a sector-vortex phased array (1990)

The sector-vortex applicator, a disc-shaped ultrasound phased array with a geometric focus having multiple sectors and tracks, can directly synthesize, without scanning, diffuse focal patterns useful for hyperthermia. Temperature distribution patterns resulting from these acoustic fields have been simulated by solving a steady-state bioheat equation numerically for a wide range of blood perfusion rates. These results suggest that the sector-vortex array will be particularly suitable for heating non-superficial small tumours. The temperature distribution pattern changes due to variations in blood perfusion are interpreted based on spatial frequency domain Fourier analysis of temperature responses to different power deposition patterns. The system behaves like a low-pass spatial frequency filter.
A Near to Far Transformation using Spherical Expansions Phase 1: Verification on Simulated Antennas (2014)

Abstract : Tapan Sarkar wrote a substantial technical paper on a transformation mapping an antennas near-field into its far field. A numerical implementation of Sarkars near-to-far transformation is assessed in this report. This report assesses this near-to-far implementation on the following antenna models using only a finite number of near-field samples: Analytic antenna models where the near field, far field, and the spherical expansions are computable in closed form, Mini-NEC antenna simulations where the near field, far fields and spherical expansions are numerically computed. The implementation described in this report demonstrates that an antennas far field can be extracted from sampled near field measurements provided the spherical expansion includes a sufficient number of terms and that the near-field samples are sufficiently dense. Phase II of this effort extends the implementation to estimate the number of spherical coefficients necessary to deliver user-specified accuracy in the far field and how noisy the near-field measurements affect the far field approximation.
Liposomes composed of unsaturated lipids for membrane modification of human erythrocytes (2011)

Previous studies have shown that certain saturated lipids protect red blood cells (RBCs) during hypothermic storage but provide little protection during freezing or freeze-drying, whereas various unsaturated lipids destabilize RBCs during hypothermic storage but protect during freezing and freeze-drying. The protective effect of liposomes has been attributed to membrane modifications. We have previously shown that cholesterol exchange and lipid transfer between liposomes composed of saturated lipids and RBCs critically depends on the length of the lipid acyl chains. In this study the effect of unsaturated lipids with differences in their number of unsaturated bonds (18:0/18:1, 18:1/18:1, 18:2/18:2) on RBC membrane properties has been studied. RBCs were incubated in the presence of liposomes and both the liposomal and RBC fraction were analyzed by Fourier transform infrared spectroscopy (FTIR) after incubation. The liposomes caused an increase in RBC membrane conformational disorder at suprazero temperatures. The fluidizing effect of the liposomes on the RBC membranes, however, was found to be similar for the different lipids irrespective of their unsaturation level. The gel to liquid crystalline phase transition temperature of the liposomes increased after incubation with RBCs. RBC membrane fluidity increased linearly during the first 8 hours of incubation in the presence of liposomes. The increase in RBC membrane fluidity was found to be temperature dependent and displayed Arrhenius behaviour between 20 and 40°C, with an activation energy of 88 kJ mol⁻¹. Taken together, liposomes composed of unsaturated lipids increase RBC membrane conformational disorder, which could explain their cryoprotective action.
Use of high-resolution fluorescence laparoscopy with fluorophore-conjugated tumor-specific antibodies for the detection of pancreatic cancer metastasis invisible with standard laparoscopy. (2012)

212 Background: Standard laparoscopy for pancreatic cancer often leads to false negative results, causing understaging of the disease. Improved sensitivity and resolution are necessary. Methods: Orthotopic and carcinomatosis mouse models of human pancreatic cancer were established with red fluorescent protein (RFP)-expressing or non-fluorescent BxPC-3 human pancreatic cancer cells. The mice with orthotopic unlabeled pancreatic cancer were administered Alexa 488- or 555-conjugated anti-CEA by tail-vein injection 2-4 weeks after tumor implantation. Diagnostic laparoscopy was performed with a Stryker L9000 LED light source or X8000 xenon light source 24 hours later. Pancreatic tumors were detected and localized under each light mode. After laparoscopy, intravital images were obtained with the OV-100 and Maestro CRI Small Animal Imaging Systems as positive controls. Tumors were collected for histologic analysis. Results: Fluorescence laparoscopy (FL) with the use of 495-nm excitation filter and an LED light source enabled more rapid and accurate identification and localization of primary tumors and metastases than bright light laparoscopy (BL). The use of fluorescent conjugates antibody-labeled tumors improved the accuracy of staging laparoscopy, increasing the sensitivity from 40% in BL to 96% in FL (p&lt;0.001). FL was sufficiently sensitive to detect sub-millimeter tumor deposits that went undetected under BL. With adjustments to the LED light source, we could simultaneously detect tumor lesions of different fluorescent colors and surrounding structures with minimal autofluorescence. Conclusions: The use of FL and fluorophore-labeled anti-CEA antibodies permits rapid detection and accurate localization of primary and metastatic CEA-expressing human pancreatic cancer, including tumors that were undetectable with BL. The introduction of an LED light source allows simultaneous identification of fluorescent tumor of different wavelengths without compromising background illumination. Further development of this technology for clinical use can improve the staging and treatment of pancreatic cancer.