gebhart/patrepeval huggingface dataset:
Broad-spectrum adaptive antibiotic resistance associated with Pseudomonas aeruginosa mucin-dependent surfing motility (2018)

Abstract Surfing motility is a novel form of surface adaptation exhibited by the nosocomial pathogen, Pseudomonas aeruginosa , in the presence of the glycoprotein mucin that is found in high abundance at mucosal surfaces especially the lungs of cystic fibrosis and bronchiectasis patients. Here we investigated the adaptive antibiotic resistance of P. aeruginosa under conditions in which surfing occurs compared to cells undergoing swimming. P. aeruginosa surfing cells were significantly more resistant to several classes of antibiotics including aminoglycosides, carbapenems, polymyxins, and fluroquinolones. This was confirmed by incorporation of antibiotics into growth medium, which revealed a concentration-dependent inhibition of surfing motility that occurred at concentrations much higher than those needed to inhibit swimming. To investigate the basis of resistance, RNA-Seq was performed and revealed that surfing influenced the expression of numerous genes. Included amongst genes dysregulated under surfing conditions were multiple genes from the Pseudomonas resistome, which are known to affect antibiotic resistance when mutated. Screening transposon mutants in these surfing-dysregulated resistome genes revealed that several of these mutants exhibited changes in susceptibility to one or more antibiotics under surfing conditions, consistent with a contribution to the observed adaptive resistance. In particular, several mutants in resistome genes, including armR, recG, atpB, clpS, nuoB , and certain hypothetical genes such as PA5130, PA3576 and PA4292, showed contributions to broad-spectrum resistance under surfing conditions and could be complemented by their respective cloned genes. Therefore, we propose that surfing adaption led to extensive multidrug adaptive resistance as a result of the collective dysregulation of diverse genes.
Real-time emotion detection by quantitative facial motion analysis (2023)

We demonstrate that DISC-based facial analysis can be used to reliably identify an individual's emotion and may provide a robust and economic modality for real-time, noninvasive clinical monitoring in the future.
Tumor-resident regulatory T cells in pancreatic cancer express the αvβ5 integrin as a targetable activation marker (2023)

Pancreatic ductal adenocarcinoma (PDAC) has abundant immunosuppressive regulatory T cells (Tregs), which contribute to a microenvironment resistant to immunotherapy. Here, we report that Tregs in the PDAC tissue, but not those in the spleen, express the αvβ5 integrin in addition to neuropilin-1 (NRP-1), which makes them susceptible to the iRGD tumor-penetrating peptide, which targets cells positive for αv integrin- and NRP-1. As a result, long-term treatment of PDAC mice with iRGD leads to tumor-specific depletion of Tregs and improved efficacy of immune checkpoint blockade. αvβ5 integrin <sup>+</sup> Tregs are induced from both naïve CD4 <sup>+</sup> T cells and natural Tregs upon T cell receptor stimulation, and represent a highly immunosuppressive subpopulation of CCR8 <sup>+</sup> Tregs. This study identifies the αvβ5 integrin as a marker for activated tumor-resident Tregs, which can be targeted to achieve tumor-specific Treg depletion and thereby augment anti-tumor immunity for PDAC therapy.
Comparison between coupled KZK-BHTE numerical simulations and scanned HIFU exposures in excised bovine liver (2004)

The use of moving high intensity focused ultrasound (HIFU) treatment protocols is of interest in achieving efficient formation of large-volume lesions in tissue. However, potentially unwanted thermal effects, such as prefocal heating, should be considered. A KZK acoustic model coupled with the BioHeat Transfer Equation has been extended to simulate multiple, moving scans in tissue. Simulation results are compared with experimental data collected over a range of exposure regimes for linear and concentric circular scans with a 3.5-MHz single-element transducer in ex vivo bovine liver. Of particular interest are investigating prefocal thermal buildup and ablating the central core of a circular pattern through conductive heating, that is without direct HIFU exposure. Qualitative agreement is observed between experimental and simulated data; limits of the predictive capability of the model in cavitation regimes will be discussed. [Support provided by the U.S. Army Medical Research Acquisition Activity through The University of Mississippi under terms of Agreement No. DAMD17-02-2-0014. The opinions expressed herein are those of the author(s) and do not necessarily reflect the views of U.S. Army Medical Research Acquisition Activity or The University of Mississippi.]
A low-profile dual-band SIW slot-array antenna based on LH material waveguides for a satellite communication receiver (2014)

Summary form given only. In this paper, a flat and small-footprint slot array antenna is proposed to build a light-weight X- and Ku-band satellite communication receiver. The overall geometry does not necessitate classic metallic waveguides to avoid being bulky and heavy, but has a very compact and low-loss duplexer flanked by the X- and Ku-band slot-array antennas all of which are in the form of SIW(substrate integrated waveguide). Taking it for granted that the SIW technique along with the slot-array design for high directivity in aerospace and defense industries has been around quite some time, there will be a question on the contributing factor of the proposed method. The conventional technology has not shown the case that SIWs and slot-arrays have been incorporated to a low-profile and new concept duplexer. Usually, a metal waveguide duplexer with a considerably large physical volume is located right in front of antennas and they are connected through an external cable or waveguide transition. This prohibits the printing-style system integration of the individual components. Manual cabling can cause degradation in the overall performance due to loss and mechanical error. In order to conduct easy manufacturing in one frame and achieve effective volume-reduction, all the components for the dual-band slot-array system are designed as the metamaterial SIW duplexer cascaded by the SIW X-band slot array and the Ku-band antenna. The proposed geometry is presented as follows with X-band and Ku-band far-field directive radiation patterns.
Diagnosis and prediction of pediatric HIV‐1 infection and AIDS: Current status (1994)

The increase in the incidence of HIV-1 infection in women of child bearing age has resulted in a surge in the number of cases of pediatric AIDS. The World Health Organization (WHO) has estimated that the number of cases of pediatric AIDS worldwide will be at least 10 million by the year 2000. This alarming statistic underscores the need for accurate prediction and diagnosis of pediatric HIV-1 infection which is of paramount importance for the initiation of effective therapeutic interventions. Since circulating maternal anti-HIV-1 antibody persists in the baby for up to 21 months, early conventional serological diagnosis of infection is not possible. Other methods for diagnosis of HIV-1 infection in a child less than 2 years of age have been utilized including the polymerase chain reaction (PCR), measurements of the HIV-1 p24 core protein and anti-HIV-1 IgA, as well in vitro measurements of antibody producing cells. In addition, the ability to predict HIV-1 infection in the child based upon maternal humoral immune responses to the envelope glycoprotein has also been suggested. This review summarizes the recent serological, biological and molecular methodologies used to predict and diagnose pediatric HIV-1 infection and AIDS.
A generalized method for distinguishing between radiation and surface-wave losses in microstrip discontinuities (1990)

A generalized method for calculating both radiation and surface-wave losses is developed for microstrip discontinuities. The losses are determined by a rigorous Poynting vector analysis where the current distribution over the microstrip discontinuities is a result of a full-wave moment method solution. The power loss mechanism of such microstrip discontinuities as open-end, right-angle-bend, gap and stub lines, EMC lines, and rectangular patches are investigated. A self-consistency check of the result based on power conservation is performed to confirm the numerical results. It is found that, above a certain frequency, the surface-wave loss becomes more important than the radiation loss.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phase 1 Safety and Pharmacokinetic Study of Chimeric Murine-Human Monoclonal Antibody cαStx2 Administered Intravenously to Healthy Adult Volunteers (2005)

Hemolytic-uremic syndrome (HUS) is a serious complication of infection by Shiga toxin-producing Escherichia coli. Shiga toxin type 2 (Stx2) is responsible for the renal toxicity that can follow intestinal infection and hemorrhagic colitis due to E. coli. A chimeric mouse-human antibody, designated c alpha Stx2, that has neutralizing activity in a mouse model was produced and tested in healthy adult volunteers. In this phase I dose escalation study, c alpha Stx2 was generally well tolerated. Pharmacokinetic studies indicated that clearance was stable over the dose range of 1.0 to 10 mg/kg of body weight (0.249 +/- 0.023 ml/kg/h) but was higher for the 0.1-mg/kg dose (0.540 +/- 0.078 ml/kg/h), suggesting saturable elimination. A similar nonlinear trend was observed for the volume of distribution, where average values ranged from 0.064 +/- 0.015 liter/kg for the 1.0- to 10-mg/kg doses and 0.043 +/- 0.005 for the 0.01-mg/kg dose. The relatively small volume of distribution suggests that the antibody is limited to the vascular (plasma) compartment. The mean half-life was 165 +/- 66 h, with lowest values observed for the 0.1-mg/kg dose (56.2 +/- 9.7 h) and the highest values reported for the 10.0-mg/kg dose (206.4 +/- 12.4 h). Future studies are needed to confirm the safety of this c alpha Stx2, and innovative clinical trials will be required to measure its efficacy in preventing or treating HUS.
Scalable opto-electronic network (SOENet) (2003)

In applications such as processor-memory interconnect, I/O networks, and router switch fabrics, an interconnection network must be scalable to thousands of high-bandwidth terminals while at the same time being economical in small configurations and robust in the presence of single-point faults. Emerging optical technology enables new topologies by allowing links to cover large distances but at a significant premium in cost compared to high-speed electrical links. Existing topologies do not cost-effectively exploit these optical links. In this paper we introduce SOENet, a family of topologies that exploits emerging high-speed optical and electrical links to provide cost effective scalability, and graceful degradation in the presence of faults. We show that SOENet scales more economically than alternative topologies. For networks scalable to 32,000 nodes, a 32-node SOENet costs 4x less than a 3-D torus. Finally we investigate the fault tolerance properties of these networks and show that they degrade more gracefully in the presence of faults than alternative topologies.
3-D Perspective Displays for Guidance and Traffic Awareness (1999)

In August 1999 the Stanford University GPS Lab performed a series of flight tests designed to explore the possibilities of dynamically updating tunnels, enhanced height-above-terrain awareness, and traffic awareness in a 3D perspective tunnel-in-the-sky display. Based on current accident reports from the NTSB specific experiments regarding CFIT (Controlled Flight Into Terrain) accidents and runway incursions were performed. The results are subjective in nature and point out that a properly researched display holds excellent potential for aviation. Future work in several disciplines is necessary before such a display could be utilized in common practice. All the same, a system that mixes precise positioning information from a sensor such as WAAS, attitude information, and eventually the position and intent of other aircraft from a sensor such as ADS-B into an intuitive image has exciting possibilities.
Optimizing multifunctional fluorescent ligands for intracellular labeling (2022)

Abstract Enzyme-based self-labeling tags enable covalent attachment of synthetic molecules to proteins inside living cells. A frontier of this field is designing multifunctional ligands that contain both fluorophores and affinity tags or pharmacological agents and can still efficiently enter cells. Self-labeling tag ligands with short linkers can enter cells readily but often show less activity due to steric issues; ligands with long linkers can be more potent but show lower cell permeability. Here, we overcome this tug-of-war between efficacy and cell-permeability by devising a rational strategy for making cell permeable multifunctional ligands for labeling HaloTag fusions. We found that the lactone–zwitterion equilibrium sconstant ( K L–Z ) of rhodamines inversely correlates with their distribution coefficients (log D 7.4 ), suggesting that ligands based on dyes exhibiting low K L–Z and high log D 7.4 values, such as Si-rhodamines, would efficiently enter cells. We designed cell-permeable multifunctional HaloTag ligands with a biotin moiety to purify mitochondria or a JQ1 appendage to translocate BRD4 from euchromatin to the nucleolus or heterochromatin. We discovered that translocation of BRD4 to constitutive heterochromatin in cells expressing HaloTag–HP1a fusion proteins can lead to apparent increases in transcriptional activity. These new reagents enable affinity capture and translocation of intracellular proteins in living cells and the use of Si-rhodamines and other low K L– Z /high log D 7.4 dye scaffolds will facilitate the design of new multifunctional chemical tools for biology. SIGNIFICANCE STATEMENT Understanding cellular processes requires tools to measure and manipulate proteins in living cells. Self- labeling tags, such as the HaloTag and SNAP-tag, enable modification of cellular proteins with synthetic molecules. Creating ligands for these systems that have more than one chemical motif remains challenging, however, due to competing demands between cell permeability and functionality. We discovered that multifunctional ligands based on Si-rhodamines efficiently entered cells and enabled affinity purification of mitochondria or translocation of nuclear proteins; the performance of these molecules could be verified by fluorescence microscopy. These compounds should be useful for a variety of biological experiments and our general framework will allow the design of other multifunctional ligands to study living systems.
Supplementary Figure 1, Table 1 from Detection of Promoter Hypermethylation in Salivary Rinses as a Biomarker for Head and Neck Squamous Cell Carcinoma Surveillance (2023)

Supplementary Figure 1, Table 1 from Detection of Promoter Hypermethylation in Salivary Rinses as a Biomarker for Head and Neck Squamous Cell Carcinoma Surveillance
Primary neoplasms of the thoracic and lumbar spine. An analysis of 29 consecutive cases. (1990)

Primary osseous neoplasms of the thoracic and lumbar spine are uncommon lesions. Between 1965 and 1982, of 1971 patients with musculoskeletal neoplasms, only 29 (1.5%) had primary osseous tumors in these locations. There were eight children and 21 adults. Back pain was the most common complaint in 25 patients (86%), and neurologic symptoms or deficits were present in 16 patients (55%). All lesions were visible on routine spine roentgenograms, while computed tomography and myelography demonstrated spinal canal encroachment and extradural spinal cord compression in 19 patients (66%). The histologic diagnoses included 11 benign and 18 malignant lesions. Benign lesions occurred predominantly in children and malignant tumors in adults. Treatment was individualized, based on the histologic diagnoses. Twenty-two patients had surgical resection of their lesions. Laminectomy without stabilization and arthrodesis resulted in late instability and neurologic deterioration in three of seven patients (43%) with malignant lesions. Resection and decompression combined with arthrodesis did not predispose to late instability. Twenty-one patients were followed for a mean of 4.1 years (range, two to 14 years). Eight patients died from malignant disease between one month and seven years after diagnosis.
Provider perspectives on demand creation for maternal vaccines in Kenya (2018)

<b>Background</b> <i>.</i> Expansion of maternal immunization, which offers some of the most effective protection against morbidity and mortality in pregnant women and neonates, requires broad acceptance by healthcare providers and their patients. We aimed to describe issues surrounding acceptance and demand creation for maternal vaccines in Kenya from a provider perspective. <b>Methods</b> <i>.</i> Nurses and clinical officers were recruited for semi-structured interviews covering resources for vaccine delivery, patient education, knowledge and attitudes surrounding maternal vaccines, and opportunities for demand creation for new vaccines. Interviews were conducted in English and Swahili, transcribed verbatim from audio recordings, and analyzed using codes developed from interview guide questions and emergent themes. <b>Results</b> <i>.</i> Providers expressed favorable attitudes about currently available maternal immunizations and introduction of additional vaccines, viewing themselves as primarily responsible for vaccine promotion and patient education. The importance of educational resources for both patients and providers to maintain high levels of maternal immunization coverage was a common theme. Most identified barriers to vaccine acceptance and delivery were cultural and systematic in nature. Suggestions for improvement included improved patient and provider education, including material resources, and community engagement through religious and cultural leaders. <b>Conclusions</b> <i>.</i> The distribution of standardized, evidence-based print materials for patient education may reduce provider overwork and facilitate in-clinic efforts to inform women about maternal vaccines. Continuing education for providers should address communication surrounding current vaccines and those under consideration for introduction into routine schedules. Engagement of religious and community leaders, as well as male decision-makers in the household, will enhance future acceptance of maternal vaccines.
Probabilistic programming for planning problems (2010)

Probabilistic programing is an emerging field at the intersection of statistical learning and programming languages. An appealing property of probabilistic programming languages (PPL) is their support for constructing arbitrary probability distributions. This allows one to model many different domains and solve a variety of problems. We show the link between probabilistic planning and PPLs by introducing a translation that allows one to map probabilistic planning problems onto parameter learning in PPLs. The advantage of our approach is twofold. Firstly, having the expressivity of a programming language simplifies modeling compared to using existing planning languages such as PPDDL. Secondly, there exist effective general-purpose learning algorithms that - having the correct encoding - can readily be used to learn optimal policies. In this paper we use ProbLog - a probabilistic version of Prolog - as programming language, but our approach can be applied on any other PPL as well.
Ebola Virus Glycoprotein Toxicity Is Mediated by a Dynamin-Dependent Protein-Trafficking Pathway (2004)

Ebola virus infection causes a highly lethal hemorrhagic fever syndrome associated with profound immunosuppression through its ability to induce widespread inflammation and cellular damage. Though GP, the viral envelope glycoprotein, mediates many of these effects, the molecular events that underlie Ebola virus cytopathicity are poorly understood. Here, we define a cellular mechanism responsible for Ebola virus GP cytotoxicity. GP selectively decreased the expression of cell surface molecules that are essential for cell adhesion and immune function. GP dramatically reduced levels of alphaVbeta3 without affecting the levels of alpha2beta1 or cadherin, leading to cell detachment and death. This effect was inhibited in vitro and in vivo by brefeldin A and was dependent on dynamin, the GTPase. GP also decreased cell surface expression of major histocompatibility complex class I molecules, which alters recognition by immune cells, and this effect was also dependent on the mucin domain previously implicated in GP cytotoxicity. By altering the trafficking of select cellular proteins, Ebola virus GP inflicts cell damage and may facilitate immune escape by the virus.
The Protective Effect of Oral Application of Corni Fructus on the Disorders of the Cornea, Conjunctiva, Lacrimal Gland and Retina by Topical Particulate Matter 2.5 (2021)

Particulate matter 2.5 (PM<sub>2.5</sub>) may aggravate dry eye disease (DED). Corni Fructus (CF), which is fruit of <i>Cornus officinalis</i> Sieb. et Zucc., has been reported to have various beneficial pharmacological effects, whereas the effect of CF on the eye is still unknown. Therefore, in this study, we investigated the effect of oral administration of water extract of CF (CFW) on the eye, hematology, and biochemistry in a DED model induced by topical exposure to PM<sub>2.5</sub>. Furthermore, the efficacy of CFW compared with cyclosporine (CsA), an anti-inflammatory agent, and lutein, the posterior eye-protective agent. Sprague-Dawley rats were topically administered 5 mg/mL PM<sub>2.5</sub> in both eyes four times daily for 14 days. During the same period, CFW (200 mg/kg and 400 mg/kg) and lutein (4.1 mg/kg) were orally administered once a day. All eyes of rats in the 0.05% cyclosporine A (CsA)-treated group were topically exposed to 20 μL of CsA, twice daily for 14 days. Oral administration of CFW attenuated the PM<sub>2.5</sub>-induced reduction of tear secretion and corneal epithelial damage. In addition, CFW protected against goblet cell loss in conjunctiva and overexpression of inflammatory factors in the lacrimal gland following topical exposure to PM<sub>2.5</sub>. Furthermore, CFW markedly prevented PM<sub>2.5</sub>-induced ganglion cell loss and recovered the thickness of inner plexiform layer. Meanwhile, CFW treatment decreased the levels of total cholesterol and low-density lipoprotein cholesterol in serum induced by PM<sub>2.5</sub>. Importantly, the efficacy of CFW was superior or similar to that of CsA and lutein. Taken together, oral administration of CFW may have protective effects against PM<sub>2.5</sub>-induced DED symptoms via stabilization of the tear film and suppression of inflammation. Furthermore, CFW may in part contribute to improving retinal function and lipid metabolism disorder.
Challenges for the translation of T cell costimulatory blockade therapies to the clinic (2002)

Click to increase image sizeClick to decrease image sizeautoimmunitycostimulatory pathwaysT cellstolerancetransplantation