gebhart/patrepeval huggingface dataset:
Strong Human Endogenous Retrovirus-Specific T Cell Responses Are Associated with Control of HIV-1 in Chronic Infection (2011)

Eight percent of the human genome is composed of human endogenous retroviruses (HERVs), which are thought to be inactive remnants of ancient infections. Previously, we showed that individuals with early HIV-1 infection have stronger anti-HERV T cell responses than uninfected controls. In this study, we investigated whether these responses persist in chronic HIV-1 infection and whether they have a role in the control of HIV-1. Peripheral blood mononuclear cells (PBMCs) from 88 subjects diagnosed with HIV-1 infection for at least 1 year (median duration of diagnosis, 13 years) were tested for responses against HERV peptides in gamma interferon (IFN-γ) enzyme immunospot (ELISPOT) assays. Individuals who control HIV-1 viremia without highly active antiretroviral therapy (HAART) had stronger and broader HERV-specific T cell responses than HAART-suppressed patients, virologic noncontrollers, immunologic progressors, and uninfected controls (P < 0.05 for each pairwise comparison). In addition, the magnitude of the anti-HERV T cell response was inversely correlated with HIV-1 viral load (r(2) = 0.197, P = 0.0002) and associated with higher CD4(+) T cell counts (r(2) = 0.072, P = 0.027) in untreated patients. Flow cytometric analyses of an HLA-B51-restricted CD8(+) HERV response in one HIV-1-infected individual revealed a less activated and more differentiated phenotype than that stimulated by a homologous HIV-1 peptide. HLA-B51 tetramer dual staining within this individual confirmed two different T cell populations corresponding to these HERV and HIV-1 epitopes, ruling out cross-reactivity. These findings suggest a possible role for anti-HERV immunity in the control of chronic HIV-1 infection and provide support for a larger effort to design an HIV-1 vaccine that targets conserved antigens such as HERV.
Optical coherence tomography for increasing the diagnostic yield of TBNA (2012)

Introduction: Bronchial biopsy techniques of peripheral nodules are associated with poor diagnostic yields. Optical coherence tomography (OCT) can be used to assess tissue microstructure in vivo, however is typically restricted to airway or pleural-based approaches. The aim of this study was to develop a transbronchial OCT catheter, and to investigate the potential of OCT to differentiate nodules from parenchyma with the goal of increasing the TBNA diagnostic yield of peripheral nodules. Methods: We developed a narrow diameter OCT catheter compatible with standard 21-guage TBNA needles. Safety and feasibility was demonstrated in 3 swine, in vivo. To determine the accuracy of OCT for differentiating nodules from surrounding parenchyma, OCT was conducted in 55 surgically resected tissue specimens. 2 OCT experts, 2 pathologists, and 2 pulmonologists interpreted the OCT data offline. Results: Successful imaging was conducted in all swine. Image criteria for differentiating parenchyma from nodule included signal void spaces corresponding to alveoli, and linear regularly spaced specular reflections representing collapsed alveoli. Nodules were found to have a generalized homogeneous appearance. Blinded readers diagnosed the OCT images as nodule or parenchyma with an average accuracy of 95.6%. Conclusions: We have developed the first transbronchial OCT catheter that is compatible with standard 21-gauge TBNA needles, and have demonstrated that OCT can accurately differentiate nodules from surrounding parenchyma. We anticipate that transbronchial OCT may be useful in increasing the diagnostic yield of TBNA by confirming the needle placement within the target nodule prior to biopsy.
Enhanced Durability Transparent Superhydrophobic Anti-Soiling Coatings for CSP Applications (2014)

Optically transparent superhydrophobic (SH) coatings based on multifunctional silica nanoparticles and polymeric binders were developed and their optical and abrasion resistance properties were studied. Three key factors are emphasized: i) The optical clarity of the coatings. Particle deagglomeration and surface functionalization techniques were developed to obtain particle size distributions with an average size smaller than 200 nm. The particles were uniformly dispersed in organic binders and resulted in coatings with an average roughness value smaller than 30 nm. The nano-sized particles do not scatter light at wavelengths &gt; 250 nm because of their small dimensions. ii) Enhanced particle-binder interfaces. We have introduced a double functionality on the particle’s surface in order to partially crosslink them with the polymeric binder. This multifunctional configuration significantly improves the abrasion resistance of the coatings without degrading their SH properties. iii) Accelerated weathering durability. Coatings were subjected to simulated solar UV exposure. Our ongoing studies indicate that the coatings are environmentally durable over several years of simulated UVA exposure. The nanostructure-property interdependencies underlined in the above three key factors are utilized in the development of transparent SH coatings with enhanced durability.
Scanning probe microscopy of polymeric methyltrioxorhenium (1996)

The surface of polymeric methyltrioxorhenium (poly‐MTO), which is an intercalation compound with water layers as the guest in a lamellar host lattice, is shown by scanning probe techniques to consist of randomly intersecting crystalline regions with small crystallite facets. The edges of these facets exhibit steps (see Figure), the size of which can be explained in terms of the layered structure. magnified image
Memoirs of an ehealth device development (2011)

Despite the rapidly growing industry interest in wireless remote home health care solutions a number of technical, regulatory and business challenges bridle more rapid telehealth device growth. The current paper highlights several challenges encountered in a Qualcomm internal development of a telehealth-targeting wireless hub. These include: 1) supporting non-standard protocol implementations across a number of wireless medical devices 2) determining optimum carrier and the appropriate wireless modem provider 3) navigating through a myriad of certifications and 4) managing development amidst undefined volume expectations.
Universal Deep Image Compression via Content-Adaptive Optimization with Adapters (2022)

Deep image compression performs better than conventional codecs, such as JPEG, on natural images. However, deep image compression is learning-based and encounters a problem: the compression performance deteriorates significantly for out-of-domain images. In this study, we highlight this problem and address a novel task: universal deep image compression. This task aims to compress images belonging to arbitrary domains, such as natural images, line drawings, and comics. To address this problem, we propose a content-adaptive optimization framework; this framework uses a pre-trained compression model and adapts the model to a target image during compression. Adapters are inserted into the decoder of the model. For each input image, our framework optimizes the latent representation extracted by the encoder and the adapter parameters in terms of rate-distortion. The adapter parameters are additionally transmitted per image. For the experiments, a benchmark dataset containing uncompressed images of four domains (natural images, line drawings, comics, and vector arts) is constructed and the proposed universal deep compression is evaluated. Finally, the proposed model is compared with non-adaptive and existing adaptive compression models. The comparison reveals that the proposed model outperforms these. The code and dataset are publicly available at https://github.com/kktsubota/universal-dic.
Enantioselective Epoxidation of ω-Bromo-2-methyl-1-alkenes Catalyzed by Chloroperoxidase. Effect of Chain Length on Selectivity and Efficiency (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEnantioselective Epoxidation of ω-Bromo-2-methyl-1-alkenes Catalyzed by Chloroperoxidase. Effect of Chain Length on Selectivity and EfficiencyFrederick J. Lakner, Kevin P. Cain, and Lowell P. HagerView Author Information Department of Biochemistry University of Illinois Urbana, Illinois 61801 Cite this: J. Am. Chem. Soc. 1997, 119, 2, 443–444Publication Date (Web):January 15, 1997Publication History Received26 August 1996Published online15 January 1997Published inissue 1 January 1997https://pubs.acs.org/doi/10.1021/ja962998xhttps://doi.org/10.1021/ja962998xrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views571Altmetric-Citations78LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Catalysts,Ethers,Hydrocarbons,Organic reactions,Oxides Get e-Alerts
Author Correction: Nanofocusing of hard X-ray free electron laser pulses using diamond based Fresnel zone plates (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Single-exposure dual-energy computed radiography: improved detection and processing. (1990)

Recent reports have emphasized the potential for dual-energy computed radiographic applications. An improved method for single-exposure material-selective imaging with a photostimulable phosphor computed radiography system was investigated. The essential elements of the technique are (a) prefiltration with gadolinium, which divides the incident broad-beam x-ray spectrum into low-energy and high-energy peaks; (b) a cassette consisting of four photostimulable phosphor plates that record images of increasing mean energies, with a computed energy separation of 23 keV from the front to the rear plate; (c) spatially dependent scatter and beam-hardening corrections; and (d) a noise-reduction algorithm based on noise correlations between bone-selective and soft-tissue-selective dual-energy images. These elements result in improved material cancellation and signal-to-noise ratio throughout the image.
Effect of waveguiding properties on the axial mode competition in stripe-geometry semiconductor lasers (1981)

Based on the multimode rate equations taking account of transverse mode and carrier density distributions, the axial mode behavior in semiconductor lasers is investigated. The axial mode stability is significantly affected by these distributions. Above threshold, because of hole burning in the carrier density distribution, the gain at any wavelength except the lasing wavelength does not maintain the value at threshold. If the nonlasing mode wavelength is located in the gain decreasing spectral region, its light output decreases with the increase of current. These characteristics are observed in the experiment for a CSP laser. For axial mode stabilization, a large built-in refractive index step is effective so long as single transverse mode operation is maintained. If the injection current region is defined separately from the guiding region, the wider width of the injection current region leads to a more stabilized axial mode.
Is cytomegalovirus infection dangerous in cytomegalovirus-seropositive recipients after liver transplantation? (2011)

Cytomegalovirus (CMV) infections contracted after liver transplantation put patients at an increased risk of morbidity and mortality. We analyzed the effects of CMV infection by time of onset, mortality, and graft failure risk factors in liver recipients who were CMV donor-positive/recipient-positive (D+/R+). We reviewed 618 medical records for consecutive adult liver transplant cases. CMV pp65 antigenemia assays to determine patient CMV status were administered monthly. The incidences of CMV infection and disease were 55.7% (344 of 618 records) and 5.5% (34 of 618 records), respectively. The differences in patient survival and graft failure rates for CMV-infected and CMV-uninfected patients were not significant (P = 0.707 and P = 0.973), but the rates were lower in patients with CMV disease than in CMV-uninfected patients (P = 0.005 and P = 0.030, respectively). The recurrence of hepatitis B virus and hepatocellular carcinoma, hepatic dysfunction, infection, numerous pp65-staining cells, and CMV disease were found to be the risk factors for mortality and graft failure in CMV D+/R+ adult liver transplant patients. In conclusion, the occurrence of CMV disease, and not asymptomatic CMV infection, was a risk factor for mortality and graft failure in adult liver transplant recipients with CMV D+/R+.
Prefrontal cortical regulation of brainwide circuit dynamics and reward-related behavior (2015)

Motivation for reward drives adaptive behaviors, whereas impairment of reward perception and experience (anhedonia) can contribute to psychiatric diseases, including depression and schizophrenia. We sought to test the hypothesis that the medial prefrontal cortex (mPFC) controls interactions among specific subcortical regions that govern hedonic responses. By using optogenetic functional magnetic resonance imaging to locally manipulate but globally visualize neural activity in rats, we found that dopamine neuron stimulation drives striatal activity, whereas locally increased mPFC excitability reduces this striatal response and inhibits the behavioral drive for dopaminergic stimulation. This chronic mPFC overactivity also stably suppresses natural reward-motivated behaviors and induces specific new brainwide functional interactions, which predict the degree of anhedonia in individuals. These findings describe a mechanism by which mPFC modulates expression of reward-seeking behavior, by regulating the dynamical interactions between specific distant subcortical regions.
Design of a Pressure-Sensing Laparoscopic Grasper (2011)

This paper describes a magnetic, nonoperative device and control system designed to treat long-gap esophageal atresia LEA. This congenital disorder occurs in approximately 100 newborn infants every year and is characterized by a discontinuity in the esophagus between the mouth and stomach. Our device builds upon previous work investigating the use of internal permanent magnets to stretch the proximal and distal esophageal pouches together until anastomosis occurs. We implement a hydraulic standoff device for the proximal magnet assembly to control the distance between the two magnets independent of the esophageal gap size. The standoff allows for controllable, intermittent force between the two pouches and provides a layer of safety from runaway magnetic forces that could potentially damage delicate esophageal tissue. The proximal device comes in two variations: a convex tip for stretching the esophagus and a concave mating tip for meeting the distal end during anastomosis. A light emitting diode LED and phototransistor pair estimates the esophageal gap size for the duration of the procedure, and a fluid pressure sensor enables the force on the esophageal tissue to be calculated. The external control circuitry, physician interface, and pump are described that demonstrate the core functionality of the system.
Development and Multi-Scale Validation of a Finite Element Football Helmet Model (2019)

Head injury is a growing concern within contact sports, including American football. Computational tools such as finite element (FE) models provide an avenue for researchers to study, and potentially optimize safety tools, such as helmets. The goal of this study was to develop an accurate representative helmet model that could be used in further study of head injury to mitigate the toll of concussions in contact sports. An FE model of a Schutt Air XP Pro football helmet was developed through three major steps: geometry development, material characterization, and model validation. The fully assembled helmet model was fit onto a Hybrid III dummy head-neck model and National Operating Committee on Standards for Athletic Equipment (NOCSAE) head model and validated through a series of 67 representative impacts similar to those experienced by a football player. The kinematic and kinetic response of the model was compared to the response of the physical experiments, which included force, head linear acceleration, head angular velocity, and carriage acceleration. The outputs between the model and the physical tests were quantitatively evaluated using CORelation and Analysis (CORA), amounting to an overall averaged score of 0.76. The model described in this study has been extensively validated and can function as a building block for innovation in player safety.
Relapsing Campylobacter Coli Bacteremia with Reactive Arthritis in a Patient with X-linked Agammaglobulinemia (2007)

A patient genetically diagnosed with X-linked agammaglobulinemia repeatedly developed bacteremia due to Campylobacter coli (C. coli) for one year and seven months in spite of immunoglobulin replacement therapy. Throughout the clinical course, C. coli with identical genetic patterns was repeatedly isolated from both blood and stool cultures, thus indicating that the patient had latent intestinal infection. The bacteremia was always accompanied by reactive arthritis. Since the immunoglobulin level was extremely low with severe B cell deficiency, the reactive arthritis must have been induced in a humoral immunity-independent manner. Adding oral minocycline following intravenous meropenem was very effective; the stool cultures became negative and the patient has been well for more than one year without relapse of bacteremia.
The Packed Bed Reactor Experiment: An Overview of Hardware and Science (2016)

In this poster we summarize the science and hardware of the Packed Bed Reactor Experiment, which starts operating in the ISS on June 1, 2016.
Synthesized Pectin from Food Waste and Its Application in Electrolyte Gelation for CO2 Reduction (2022)

The utilization of in-situ resources such as food waste or plants grown on Mars combined with the available Martian regolith and atmosphere presents a path towards battery separators with increased sustainability, energy density, and durability. Separators that focus on CO 2 reduction take advantage of both a highly relevant source of materials on Mars and a solution to an increasingly relevant problem of the increase of atmospheric CO 2 on Earth. In this paper we evaluate the electrochemical and thermal properties of gel electrolytes synthesized from food waste and their performance in CO 2 reduction. Our work focuses on the extraction of pectins from soybean hull and tomato pomace as sources of inedible biomass. Cross-linking and ionic activity of the pectin-based gel electrolytes are determined by the integration of monovalent and divalent cations. A biomass-based polymer electrolyte provides a novel method of using in-situ resources for chemical conversion and energy storage that is critical for long-term space travel.
Rhythm and timing as vulnerabilities in neurodevelopmental disorders (2021)

Millions of children are impacted by neurodevelopmental disorders (NDDs), which unfold early in life, have varying genetic etiologies and can involve a variety of specific or generalized impairments in social, cognitive and motor functioning requiring potentially lifelong specialized supports. While specific disorders vary in their domain of primary deficit (e.g. autism spectrum disorder (social), attention-deficit/hyperactivity disorder (attention), developmental coordination disorder (motor) and developmental language disorder (language)), comorbidities between NDDs are common. Intriguingly, many NDDs are associated with difficulties in skills related to rhythm, timing and synchrony though specific profiles of rhythm/timing impairments vary across disorders. Impairments in rhythm/timing may instantiate vulnerabilities for a variety of NDDs and may contribute to both the primary symptoms of each disorder as well as the high levels of comorbidities across disorders. Drawing upon genetic, neural, behavioural and interpersonal constructs across disorders, we consider how disrupted rhythm and timing skills early in life may contribute to atypical developmental cascades that involve overlapping symptoms within the context of a disorder's primary deficits. Consideration of the developmental context, as well as common and unique aspects of the phenotypes of different NDDs, will inform experimental designs to test this hypothesis including via potential mechanistic intervention approaches. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.
Taking 2D materials from lab to tab, and to technology (2015)

status: Published
Picomolar Inhibitors of HIV-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl Ethers (2014)

Catechol diethers that incorporate a 6-cyano-1-naphthyl substituent have been explored as non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). Promising compounds are reported that show midpicomolar activity against the wild-type virus and sub-20 nM activity against viral variants bearing Tyr181Cys and Lys103Asn mutations in HIV-RT. An X-ray crystal structure at 2.49 Å resolution is also reported for the key compound 6e with HIV-RT.
Observational Multicenter Study on the Prognostic Relevance of Coagulation Activation in Risk Assessment and Stratification in Locally Advanced Breast Cancer. Outline of the ARIAS Trial (2020)

A hypercoagulable state may either underlie or frankly accompany cancer disease at its onset or emerge in course of cancer development. Whichever the case, hypercoagulation may severely limit administration of cancer therapies, impose integrative supporting treatments and finally have an impact on prognosis. Within a flourishing research pipeline, a recent study of stage I-IIA breast cancer patients has allowed the development of a prognostic model including biomarkers of coagulation activation, which efficiently stratified prognosis of patients in the study cohort. We are now validating our risk assessment tool in an independent cohort of 108 patients with locally advanced breast cancer with indication to neo-adjuvant therapy followed by breast surgery. Within this study population, we will use our tool for risk assessment and stratification in reference to 1. pathologic complete response rate at definitive surgery, intended as our primary endpoint, and 2. rate of thromboembolic events, intended as our secondary endpoint. Patients' screening and enrollment procedures are currently in place. The trial will be shortly enriched by experimental tasks centered on next-generation sequencing techniques for identifying additional molecular targets of treatments which may integrate current standards of therapy in high-risk patients.