gebhart/patrepeval huggingface dataset:
The Buoyancy of Cryptococcus neoformans Is Affected by Capsule Size (2018)

<i>Cryptococcus neoformans</i> is an environmental pathogenic fungus with a worldwide geographical distribution that is responsible for hundreds of thousands of human cryptococcosis cases each year. During infection, the yeast undergoes a morphological transformation involving capsular enlargement that increases microbial volume. To understand the factors that play a role in environmental dispersal of <i>C. neoformans</i> and <i>C. gattii</i>, we evaluated the cell density of <i>Cryptococcus</i> using Percoll isopycnic gradients. We found differences in the cell densities of strains belonging to <i>C. neoformans</i> and <i>C. gattii</i> species complexes. The buoyancy of <i>C. neoformans</i> strains varied depending on growth medium. In minimal medium, the cryptococcal capsule made a major contribution to the cell density such that cells with larger capsules had lower density than those with smaller capsules. Removing the capsule, by chemical or mechanical methods, increased the <i>C. neoformans</i> cell density and reduced buoyancy. Melanization of the <i>C. neoformans</i> cell wall, which also contributes to virulence, produced a small but consistent increase in cell density. Encapsulated <i>C. neoformans</i> sedimented much more slowly in seawater as its density approached the density of water. Our results suggest a new function for the capsule whereby it can function as a flotation device to facilitate transport and dispersion in aqueous fluids.<b>IMPORTANCE</b> The buoyancy of a microbial cell is an important physical characteristic that may affect its transportability in fluids and interactions with tissues during infection. The polysaccharide capsule surrounding <i>C. neoformans</i> is required for infection and dissemination in the host. Our results indicate that the capsule has a significant effect on reducing cryptococcal cell density, altering its sedimentation in seawater. Modulation of microbial cell density via encapsulation may facilitate dispersal for other important encapsulated pathogens.
Recent Advances with TLR2-Targeting Lipopeptide-Based Vaccines (2007)

The next generation of vaccines are being rationally designed according to rules that govern the way in which antigen is recognised by and stimulates the immune system. Amongst the first cells that encounter potentially dangerous agents such as viruses and bacteria are cells of the innate immune system, such as dendritic cells, that are widely distributed throughout the body including the skin. These cells patrol most tissues and have on their surface an array of receptors that have evolved to recognise many of the surface features of pathogens including the lipids and carbohydrates of structural lipoproteins, glycolipids and glycoproteins. Once encountered, recognised and engaged by a particular receptor on the dendritic cell, pathogenic material may then be transported inside the cell and processed for presentation to cells of the adaptive immune system. The result of this concert of events is a specific cellular or antibody response to particular epitopes of the invading pathogen. If then ways can be found to specifically target dendritic cells, through their specific receptors, then the efficacy and potency of vaccines could well be greatly improved. This review covers some of the approaches that we and others are pursuing in order to achieve this result.
Figure S6 from Modulation of Endoplasmic Reticulum Stress Controls CD4<sup>+</sup> T-cell Activation and Antitumor Function (2023)

&lt;p&gt;Cytosolic Ca2+ levels discriminate among human CD4+ T cell populations&lt;/p&gt;
Fetal Zika virus infection diagnosed by metagenomic next‐generation sequencing of amniotic fluid (2022)

Data sharing not applicable to this article as no datasets were generated or analysed during the current study Appendix S1 Methodology for metagenomic next-generation sequencing and Zika virus reverse-transcription polymerase chain reaction and serology Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Low-cost WDM-PON with colorless bidirectional transceivers (2006)

This paper presents a low-cost bidirectional (BiDi) wavelength-division-multiplexed passive optical network (WDM-PON) employing colorless uncooled BiDi transceivers (TRxs) and superluminescent diode (SLD)-based broadband light sources (BLSs). The C band is allocated for upstream and the E+ band for downstream in consideration of BiDi packaging, SLD development, and wavelength alignment of dual-window arrayed waveguide gratings (AWGs). The BiDi TRx integrates an uncooled Fabry-Perot laser diode (FP-LD), a p-i-n photodiode (PD), and a 45/spl deg/-angled thin-film filter in a small-form-factor (SFF) package. The SLD-based BLSs provide 13-dBm amplified spontaneous emissions (ASEs) with spectral ripples of < 3 dB and polarization dependencies of <1 dB. Colorless operations over 32 100-GHz-spaced channels are demonstrated from -20 to 80/spl deg/C in 155-Mb/s BiDi transmissions over 25 km.
Plug-and-Play priors for model based reconstruction (2013)

Model-based reconstruction is a powerful framework for solving a variety of inverse problems in imaging. In recent years, enormous progress has been made in the problem of denoising, a special case of an inverse problem where the forward model is an identity operator. Similarly, great progress has been made in improving model-based inversion when the forward model corresponds to complex physical measurements in applications such as X-ray CT, electron-microscopy, MRI, and ultrasound, to name just a few. However, combining state-of-the-art denoising algorithms (i.e., prior models) with state-of-the-art inversion methods (i.e., forward models) has been a challenge for many reasons. In this paper, we propose a flexible framework that allows state-of-the-art forward models of imaging systems to be matched with state-of-the-art priors or denoising models. This framework, which we term as Plug-and-Play priors, has the advantage that it dramatically simplifies software integration, and moreover, it allows state-of-the-art denoising methods that have no known formulation as an optimization problem to be used. We demonstrate with some simple examples how Plug-and-Play priors can be used to mix and match a wide variety of existing denoising models with a tomographic forward model, thus greatly expanding the range of possible problem solutions.
Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution (2019)

Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire <i>Drosophila</i> brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.
Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation (2009)

Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance.
Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128 (2017)

While a part of the native gut microflora, the Gram-positive bacterium <i>Enterococcus faecalis</i> can lead to serious infections elsewhere in the body. The draft genome of <i>E. faecalis</i> strain ATCC BAA-2128, isolated from piglet feces, was examined. This draft genome consists of 42 contigs, 12 of which exhibit homology to annotated plasmids.
Optimal conditions for high-speed all-optical SOA-based wavelength shifting (1995)

We analyze the system performance of gain-saturated semiconductor optical amplifier (SOA)-based all-optical wavelength shifting with respect to its dynamic characteristics. When considering the risetime, contrast ratio and intersymbol interference, we find that there exists an optimal probe power and wavelength for high-speed wavelength shifting which reduces the power penalty by 3 dB. The minimum power penalties for the data rates of 10 and 20 Gb/s are 25 and 5 dB, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In vitro and in vivo studies of human lymphocytes genetically engineered to express T cell receptors that recognize a p53 antigenic epitope (2008)

3032 Background: T cell adoptive immunotherapy can mediate objective cancer regression in patients with invasive melanoma. To extend T cell based therapies to patients with common epithelial cancers, the tumor associated antigen (TAA) p53 has been extensively studied in animal models and humans. We investigated tumor recognition in vitro and in vivo by normal lymphocytes gene modified to express an anti-p53 T cell receptor (TCR). Methods: A MSGV1 retroviral construct encoding an HLA-A2.1 restricted p53:264–272 specific α/β TCR (p53:264 TCR), derived from HLA-A2.1 transgenic mice, was used to optimize transduction (Td) of activated peripheral blood lymphocytes (PBL). A panel of well-characterized tumor cell lines with known HLA-A type and p53 gene sequences including the NCI-60 lines were used to test the recognition by p53:264 TCR Td PBL. Results: After Td optimization, expression of the p53:264 TCR was routinely achieved in > 80% of T cells. A panel of tumor cell lines including breast, colon, lung, renal, liver, ovarian, melanoma, central nervous system, and hematopoietic cancers were recognized by p53:264 TCR Td T cells irrespective of the level of p53 expression determined by FACS or western blot. Although this casts doubt on p53 as an ideal TAA based on the concept that p53 overexpression creates a therapeutic window for immune discrimination of tumor from normal cells, with few exceptions a panel of normal cells was ignored by p53:264 TCR Td PBL. We developed a method to expand p53:264 TCR Td PBL up to 1000 fold in vitro and a pilot clinical trial was conducted in metastatic cancer patients with breast, melanoma, esophageal, bile duct, small bowel, and parotid gland tumors. Eleven patients received lymphodepleting conditioning chemotherapy, p53:264 TCR Td PBL, and high dose interleukin-2, and no toxicity attributable to the Td PBL was observed. One patient achieved a partial response in all sites of disease including lung nodules and a hilar lymph node. Conclusions: Lymphocytes transduced with genes encoding anti-p53 TCR can recognize a wide array of cancer cell lines but recognition does not correlate with p53 gene expression. Adoptive immunotherapy clinical studies are underway using these gene-modified cells. No significant financial relationships to disclose.
THE CORRELATION BETWEEN VENOUS AND ARTERIAL EPINEPHRINE LEVELS DURING CPR IN HUMANS (1990)

Paradis, Norman A.; Rivers, Emanuel P.; Martin, Gerard B.; Smithline, Howard A.; Goetting, Mark G.; Appleton, Timothy J.; Cryer, Philip E.; Nowak, Richard M. Author Information
Time optimal entrainment control for circadian rhythm (2019)

The circadian rhythm functions as a master clock that regulates many physiological processes in humans including sleep, metabolism, hormone secretion, and neurobehavioral processes. Disruption of the circadian rhythm is known to have negative impacts on health. Light is the strongest circadian stimulus that can be used to regulate the circadian phase. In this paper, we consider the mathematical problem of time-optimal circadian (re)entrainment, i.e., computing the lighting schedule to drive a misaligned circadian phase to a reference circadian phase as quickly as possible. We represent the dynamics of the circadian rhythm using the Jewett-Forger-Kronauer (JFK) model, which is a third-order nonlinear differential equation. The time-optimal circadian entrainment problem has been previously solved in settings that involve either a reduced-order JFK model or open-loop optimal solutions. In this paper, we present (1) a general solution for the time-optimal control problem of fastest entrainment that can be applied to the full order JFK model (2) an evaluation of the impacts of model reduction on the solutions of the time-optimal control problem, and (3) optimal feedback control laws for fastest entrainment for the full order Kronauer model and evaluate their robustness under some modeling errors.
Metabolic Responses When Different Forms of Carbohydrate Energy Are Consumed during Cycling (1993)

This study examined the effects of consuming the same amount of carbohydrate in solid form, liquid form, or both on metabolic responses during 2 hrs of cycling at 70% peak VO2 and on cycling time-trial performance. Subjects consumed 0.4 g carbohydrate/kg body mass before and every 30 min during exercise. The liquid was a 7% carbohydrate-electrolyte beverage and the solid was a sports bar (1171 kJ) in which 76%, 18%, and 6% of total energy was derived from carbohydrate, fat, and protein, respectively. Blood obtained at baseline, before exercise, and every 30 min was analyzed for glucose, insulin, lactate, hemoglobin, hematocrit, and plasma volume. There were no differences among the treatments for the blood parameters. Total carbohydrate oxidation and time-trial performance were also similar among treatments. Under thermoneutral conditions with equal liquid ingestion, the metabolic and performance responses are similar when consuming carbohydrate as a liquid, solid, or in combination during prolonged, moderate intensity cycling.
A New Vaccine to Battle Covid-19 (2020)

The United States and many parts of the world have now lost control of the Covid-19 pandemic owing to the respiratory spread of SARS-CoV-2 and to inconsistent adherence to effective public health m...
Reversing the Reactivity of Carbonyl Functions with Phosphonium Salts: Enantioselective Total Synthesis of (+)‐Centrolobine (2011)

Schrittsparend: Weniger reaktive Carbonylgruppen können in Gegenwart reaktiverer Carbonylgruppen umgesetzt werden, wenn sie vor der Reaktion mit PPh3 (oder PEt3) und TMSOTf behandelt werden (siehe Schema; TMS=Trimethylsilyl, Tf=Trifluormethansulfonyl). Die Methode kann für Reduktionen und Alkylierungen genutzt werden und ermöglichte die kurze asymmetrische Totalsynthese von (+)-Centrolobin in der höchsten bisher berichteten Gesamtausbeute.
Enhanced bacterial immunity and mammalian genome editing via RNA polymerase-mediated dislodging of Cas9 from double strand DNA breaks (2018)

SUMMARY The ability to target the Cas9 nuclease to DNA sequences via Watson-Crick base pairing with a single guide RNA (sgRNA) has provided a dynamic tool for genome editing and an essential component of adaptive immune systems in bacteria. After generating a double strand break (DSB), Cas9 remains stably bound to it. Here we show persistent Cas9 binding blocks access to DSB by repair enzymes, reducing genome editing efficiency. Cas9 can be dislodged by translocating RNA polymerases, but only if the polymerase approaches one direction towards the Cas9-DSB complex. By exploiting these RNA polymerase-Cas9 interactions, Cas9 can be conditionally converted into a multi-turnover nuclease, mediating increased mutagenesis frequencies in mammalian cells and enhancing bacterial immunity to bacteriophages. These consequences of a stable Cas9-DSB complex provide insights into the evolution of PAM sequences and a simple method of improving selection of highly active sgRNA for genome editing.
Safety and efficacy of delivering high-power short-duration radiofrequency ablation lesions utilizing a novel temperature sensing technology (2018)

Delivery of high-power short-duration RF energy applications, facilitated by a novel ablation catheter system equipped with advanced TC technology, is feasible, safe, and results in the formation of effective ablation lesions.
Roles of Toll-like Receptor Signaling in Inflammatory Bone Resorption (2024)

Toll-like receptors (TLRs) are pattern recognition receptors expressed in immune cells, including neutrophils, macrophages, and dendritic cells. Microbe-associated molecular patterns, including bacterial components, membranes, nucleic acids, and flagella are recognized by TLRs in inflammatory immune responses. Periodontal disease is an inflammatory disease known to cause local infections associated with gingival inflammation, subsequently leading to alveolar bone resorption. Prostaglandin E2 (PGE2) is a key mediator of TLR-induced inflammatory bone resorption. We previously reported that membrane-bound PGE synthase (mPGES-1)-deficient mice failed to induce bone resorption by lipopolysaccharide (LPS), a major pathogenic factor involved in periodontal bone resorption. Further experiments exploring specific pathogen-promoting osteoclast differentiation revealed that various TLR ligands induced osteoclast differentiation in a co-culture model. The ligands for TLR2/1, TLR2/6, TLR3, and TLR5, as well as TLR4, induce osteoclast differentiation associated with the production of PGE2 and the receptor activator of nuclear factor-kappa B ligand (RANKL), an inevitable inducer of osteoclast differentiation in osteoblasts. In vivo, local injection of TLR ligands, including TLR2/1, TLR2/6, and TLR3, resulted in severe alveolar bone resorption. This review summarizes the latest findings on TLR-mediated osteoclast differentiation and bone resorption in inflammatory diseases, such as periodontal diseases.
Cavitation Inception by Dual-Frequency Excitation in High-Intensity Focused Ultrasound Treatment (2011)

In our previous study, we proposed a “triggered high-intensity focused ultrasound (HIFU)” exposure sequence, in which a high-intensity triggering pulse was irradiated just before CW heating waves, to accelerate HIFU treatment. In this study, the second-harmonic was superimposed to the triggering pulse, and the cavitation threshold was investigated by comparing different schemes of second-harmonic superimposition including the case of single-frequency exposure through detecting the subharmonic emission and high-speed camera observation. The experimental results show that cavitation bubbles can be generated most efficiently by using negative-peak-pressure emphasized waves followed by positive-peak-pressure emphasized waves.
Intramedullary Spinal Cord Tumors: Part I—Epidemiology, Pathophysiology, and Diagnosis (2015)

Study Design Broad narrative review. Objectives Intramedullary spinal cord tumors (IMSCT) are rare neoplasms that can potentially lead to severe neurologic deterioration, decreased function, poor quality of life, or death. As such, a better understanding of these lesions is needed. The following article, part one of a two-part series, addresses IMSCT with regards to their epidemiology, histology, pathophysiology, imaging characteristics, and clinical manifestations. Methods The authors performed an extensive review of the peer-reviewed literature addressing the aforementioned objectives. Results Numerous IMSCT exist with varying epidemiology. Each IMSCT has its own hallmark characteristics and may vary with regards to how aggressively they invade the spinal cord. These lesions are often difficult to detect and are often misdiagnosed. Furthermore, radiographically and clinically, these lesions may be difficult to distinguish from one another. Conclusions Awareness and understanding of IMSCT is imperative to facilitate an early diagnosis and plan management.
Léčebná studie Relapsed AML 2001/01, 02 pro děti s relapsemakutní myeloidní leukemie nebo primárně rezistentní nemocízlepšila jejich nadeji na vyléčení. (2011)

Relaps akutni myeloidni leukemie (AML) nebo AML primarně
rezistentni na lecbu je prognosticky velmi nepřiznivým
onemocněnim. V obdobi VIII/2001-III/2009 bylo v CR s touto
diagnozou leceno 20 pacientů ve věku 0-18 let v mezinarodni
studii Relapsed AML 2001/01.
Response to Comment on “Gene Disruption Study Reveals a Nonredundant Role for TRIM21/Ro52 in NF-κB-Dependent Cytokine Expression in Fibroblasts” (2009)

We thank Ozato and colleagues for initiating the discussion on similarities and differences between the two recently reported Ro52/Trim21 deficient mice ([1][1], [2][2]). When generating knockout mice the resulting phenotype may differ depending on several factors, including the gene targeting
Eimeria species which infect the chicken contain virus-like RNA molecules (1990)

There is increasing support for the presence of viruses and virus-like particles inside protozoan cells. This study describes viral-like RNA molecules that have been detected in two species of Eimeria that infect the chicken. The RNA molecule identified in E. maxima has been characterized: subcellular fractionation studies have shown that the RNA is present in the cytoplasm, probably as an abundant ribonucleoprotein that is insensitive to RNAse A treatment. Electron microscopy has demonstrated that this RNA molecule is double stranded. In addition, all E. maxima strains examined so far contain this RNA molecule.
Optimal Color Multiplexing for Low-Cost Structured Light 3D Capture System with Two Projectors (2018)

3D shape reconstruction is one of the most important topics in computer vision and the foundation for a wide field of application. Among various technologies, structured light is one of the most reliable techniques. However, given the field of view of projectors and cameras available in the market, the working distance needed for projectors is typically larger than that for cameras. To reduce the working distance of the projectors while covering the whole working platform, two projectors with their field of view overlapping are used to cover the working area which holds objects to be scanned. We present a spectral analysis based model for the projector-camera system, in order to find the most distinguishable colors for two projectors, and best separate the projected patterns from two projectors. The optimal values of the two colors are determined by the pattern search method in the presence of noise, which is modeled as multivariate Gaussian noise, and characterized for different input colors. The camera sensors' responses to the projector are measured after linearization with gray balance curves. After being properly calibrated, based on one image shot of the object with binary M-array patterns projected on it, the system can reconstruct a 3D shape of the object surface.