gebhart/patrepeval huggingface dataset:
GMMA-Based Vaccines: The Known and The Unknown (2021)

Generalized Modules for Membrane Antigens (GMMA) are outer membrane vesicles derived from Gram-negative bacteria engineered to provide an over-vesiculating phenotype, which represent an attractive platform for the design of affordable vaccines. GMMA can be further genetically manipulated to modulate the risk of systemic reactogenicity and to act as delivery system for heterologous polysaccharide or protein antigens. GMMA are able to induce strong immunogenicity and protection in animal challenge models, and to be well-tolerated and immunogenic in clinical studies. The high immunogenicity could be ascribed to their particulate size, to their ability to present to the immune system multiple antigens in a natural conformation which mimics the bacterial environment, as well as to their intrinsic self-adjuvanticity. However, GMMA mechanism of action and the role in adjuvanticity are still unclear and need further investigation. In this review, we discuss progresses in the development of the GMMA vaccine platform, highlighting successful applications and identifying knowledge gaps and potential challenges.
Induction of Nesidioblastosis Will Reverse Diabetes in Syrian Golden Hamster (1988)

Nesidioblastosis, which is the formation of new islets and the differentiation of cells within the islets, represents part of the spectrum of hyperfunctioning states of the islets of Langerhans at the clinical level. Nesidioblastosis in the Syrian golden hamster can be induced by wrapping the head of the pancreas with cellophane tape. Ligation of the duct is not involved, and acinar cell atrophy does not occur. The purpose of this study was to determine whether the induction of nesidioblastosis could be used as a means of reversing streptozocin-induced diabetes. Outbred hamsters (n = 32), 8 wk of age, were rendered diabetic by treatment with 40 mg/kg i.p. streptozocin, administered daily for 3 days. Four days later, 16 animals chosen at random underwent laparotomy with cellophane wrapping of the pancreas. Before surgery, the serum glucose and insulin levels (means +/- SE) in the unoperated control animals (389.0 +/- 18.6, 33.9 +/- 3.8) did not differ from those in the animals awaiting the operation (373.2 +/- 18.6, 37.9 +/- 3.8). After 7 wk, 50% of the operated animals had serum glucose and insulin levels that were normal, compared to only 12% of the unoperated control animals (chi2 = 5.53, P less than .05). Islets from normoglycemic operated animals were characterized by increased numbers, including many small islets, positive immunoreactive insulin staining, and minimal vacuolation of cells. Islets from hyperglycemic operated hamsters and from the unoperated control animals were decreased in number and generally larger in size, demonstrated little or no immunoreactive insulin staining, and exhibited marked vacuolation of cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Impact of Oxygen Plasma Treatment on the Device Performance of Zinc Oxide Nanoparticle-Based Thin-Film Transistors (2012)

Thin-films of zinc oxide nanoparticles were investigated by photoluminescence spectroscopy and a broad defect-related yellow-green emission was observed. Oxygen plasma treatment was applied in order to reduce the number of defects, and the emission intensity was quenched to 4% of the initial value. Thin-film transistors that incorporate the nanoparticles as active semiconducting layers show an improved device performance after oxygen plasma treatment. The maximum drain current and the charge carrier mobility increased more than 1 order of magnitude up to a nominal value of 23 cm(2) V(-1) s(-1) and the threshold voltage was lowered.
Direct Silicon Heterostructures With Methylammonium Lead Iodide Perovskite for Photovoltaic Applications - supporting information (2020)

The research data comprises:
1. An excel file containging all x-y data points for all graphs in the main paper
2. An excel file containging all x-y data points for all graphs in the Supplementary Information

The Supplementary Information comprises:
1. Device fabrication details
2. Description of the contact structures
3. Characterisation of the materials (optical transmission, absorption coefficient, Tauc plot, photoemission determination of band edge)
4. Capacitance-voltage mathematics for one-sided and two-sided junctions
5. Capacitance-voltage results (Mott-Shottky plot) 
6. Inferred band diagrams for the heterojunction

The doi of the full paper is 10.1109/JPHOTOV.2020.2981805
Biologic determinants of uveal melanoma metastatic phenotype: role of intermediate filaments as predictive markers. (1998)

The long-range goal of our research is to develop intervention strategies based on newly discovered biologic mechanisms responsible for the invasive dissemination of metastatic uveal melanoma. To accomplish this goal, we have focused on the biologic relevance of novel marker proteins contributing to the uveal melanoma metastatic phenotype. The expression of vimentin intermediate filaments (IFs), a mesenchymal marker, is typical of melanomas, whereas carcinomas typically express keratin IFs, which are markers for epithelia. Thus, cells that coexpress both IFs are regarded as "interconverted" in that they display both mesenchymal and epithelial phenotypes. Although the biologic functions of IFs have remained enigmatic, there is substantial support to suggest that the significance of vimentin/keratin coexpression is linked with poor patient outcome in cutaneous melanoma. Our data demonstrate that human uveal melanoma cell lines (isolated from primary choroidal or ciliary body melanomas and from foci of metastatic uveal melanoma to the liver), which contain predominant populations of cells that coexpress vimentin/keratins 8 and 18 (keratins 8,18) IFs, were 6-fold more invasive through collagenous extracellular matrices in vitro, compared with uveal melanoma cells expressing vimentin only, and were 8- to 13-fold more invasive than normal uveal melanocytes. Colocalization of vimentin/keratins 8,18 in cell cultures was corroborated by immunohistochemistry in histologic sections of tumors from which the cell lines were derived. Minor populations of these cells also coexpressed keratins 13 and 17. Experimental down-regulation of the predominant keratins 8,18 in the interconverted cells, using 16-mer antisense oligonucleotides, resulted in a significant decrease in the migratory ability of the cells-similar to levels achieved by cells positive only for vimentin. These findings provide justification for additional studies of the association between coexpression of IFs vimentin/keratins 8,18 and uveal melanoma metastasis.
A paradigm shift for extracellular vesicles as small RNA carriers: from cellular waste elimination to therapeutic applications (2013)

RNA interference (RNAi) is an important avenue for target-specific gene silencing that is mainly performed by either small interfering RNAs (siRNAs) or microRNAs (miRNAs). This novel method is rapidly becoming a powerful tool for gene therapy. However, the rapid degradation of siRNAs and miRNAs and the limited duration of their action in vivo call for an efficient delivery technology. Recently, increasing attention has been paid to the use of extracellular vesicles (EVs) as delivery systems. The use of EVs as small RNA carriers has multiple advantages over conventional delivery systems. In this review, we summarize recent findings regarding the potential application of EVs as small RNA delivery systems. Moreover, we focus on some of the obstacles to EV-based therapeutics.
Pathogenic measles viruses cannot evolve to bypass vaccine-induced neutralizing antibodies (2020)

Abstract After centuries of pestilence and decades of global vaccination, measles serotypes capable of evading vaccine-induced immunity have not emerged. Here, by systematically building mutations into the H-glycoprotein of an attenuated measles strain and assaying for serum neutralization, we show that virus evolution is severely constrained by the existence of numerous codominant H-glycoprotein antigenic sites, some critical for binding to pathogenicity receptors SLAMF1 and Nectin-4. We further demonstrate the existence in serum of protective neutralizing antibodies targeting codominant F-glycoprotein epitopes. Calculations suggest that evolution of pathogenic measles viruses capable of escaping serum neutralization in vaccinated individuals is a near-zero probability scenario.
Control Strategies for Distributed Power Generation Systems Operating on Faulty Grid (2006)

The distributed power generation based on renewable energy sources such as wind and sun experiences a high penetration in the power systems around the world, having in some countries a large contribution to the total energy production. In order to protect the distribution and transmission systems, the grid operators are more and more talking about the ability of the distribution systems (mainly wind turbines WT systems) to behave as a conventional power plant. This paper discusses the possibilities of the distributed power generation systems (DPGS) to deliver power when grid disturbances are present in the utility network. The focus is set more on the control strategies for active power generation, and mainly on the creation of the reference currents which fulfill the demanded output power. Considerations about reactive power are also stated. Experimental results are presented in order to validate the theory behind the proposed control strategies on faulty grid
On Sensitivity and Robustness of Normalization Schemes to Input Distribution Shifts in Automatic MR Image Diagnosis (2023)

Magnetic Resonance Imaging (MRI) is considered the gold standard of medical imaging because of the excellent soft-tissue contrast exhibited in the images reconstructed by the MRI pipeline, which in-turn enables the human radiologist to discern many pathologies easily. More recently, Deep Learning (DL) models have also achieved state-of-the-art performance in diagnosing multiple diseases using these reconstructed images as input. However, the image reconstruction process within the MRI pipeline, which requires the use of complex hardware and adjustment of a large number of scanner parameters, is highly susceptible to noise of various forms, resulting in arbitrary artifacts within the images. Furthermore, the noise distribution is not stationary and varies within a machine, across machines, and patients, leading to varying artifacts within the images. Unfortunately, DL models are quite sensitive to these varying artifacts as it leads to changes in the input data distribution between the training and testing phases. The lack of robustness of these models against varying artifacts impedes their use in medical applications where safety is critical. In this work, we focus on improving the generalization performance of these models in the presence of multiple varying artifacts that manifest due to the complexity of the MR data acquisition. In our experiments, we observe that Batch Normalization, a widely used technique during the training of DL models for medical image analysis, is a significant cause of performance degradation in these changing environments. As a solution, we propose to use other normalization techniques, such as Group Normalization and Layer Normalization (LN), to inject robustness into model performance against varying image artifacts. Through a systematic set of experiments, we show that GN and LN provide better accuracy for various MR artifacts and distribution shifts.
A switchable digital microfluidic droplet dye-laser (2011)

Digital microfluidic devices allow the manipulation of droplets between two parallel electrodes. These electrodes can act as mirrors generating a micro-cavity, which can be exploited for a droplet dye-laser. Three representative laser-dyes with emission wavelengths spanning the whole visible spectrum are chosen to show the applicability of this concept. Sub-microlitre droplets of laser-dye solution are moved in and out of a lasing site on-chip to down-convert the UV-excitation light into blue, green and red laser-pulses.
A Roadmap for Transforming Research to Invent the Batteries of the Future Designed within the European Large Scale Research Initiative BATTERY 2030+ (2022)

Abstract This roadmap presents the transformational research ideas proposed by “BATTERY 2030+,” the European large‐scale research initiative for future battery chemistries. A “chemistry‐neutral” roadmap to advance battery research, particularly at low technology readiness levels, is outlined, with a time horizon of more than ten years. The roadmap is centered around six themes: 1) accelerated materials discovery platform, 2) battery interface genome, with the integration of smart functionalities such as 3) sensing and 4) self‐healing processes. Beyond chemistry related aspects also include crosscutting research regarding 5) manufacturability and 6) recyclability. This roadmap should be seen as an enabling complement to the global battery roadmaps which focus on expected ultrahigh battery performance, especially for the future of transport. Batteries are used in many applications and are considered to be one technology necessary to reach the climate goals. Currently the market is dominated by lithium‐ion batteries, which perform well, but despite new generations coming in the near future, they will soon approach their performance limits. Without major breakthroughs, battery performance and production requirements will not be sufficient to enable the building of a climate‐neutral society. Through this “chemistry neutral” approach a generic toolbox transforming the way batteries are developed, designed and manufactured, will be created.
Ofatumumab retreatment and maintenance in fludarabine‐refractory chronic lymphocytic leukaemia patients (2015)

There are limited data on retreatment with monoclonal antibodies (mAb) in patients with chronic lymphocytic leukaemia (CLL). In a pivotal study, ofatumumab (human anti-CD20 mAb) monotherapy demonstrated a 47% objective response rate (ORR) in fludarabine refractory CLL patients. From this study, a subset of 29 patients who had at least stable disease and then progressed were retreated with eight weekly ofatumumab infusions (induction treatment period), followed by monthly infusions for up to 2 years (maintenance treatment period). The ORR after 8 weeks of induction retreatment was 45% and 24% had continued disease control after maintenance at 52 weeks. Efficacy and safety of the retreated patients were compared with their initial results in the pivotal study. Response duration was 24.1 months vs. 6.8 months; time to next therapy was 14.8 months vs. 12.3 months; and progression-free survival was 7.4 months vs. 7.9 months (medians). Upon retreatment, 72% had infusion reactions, mostly Grade 1-2. Three patients had fatal infections. In summary, ofatumumab retreatment and maintenance therapy was feasible in patients with heavily pretreated CLL and appeared to result in more durable disease control than initial ofatumumab treatment in this subset of patients who may have a more favourable disease profile.
Hardware support for object-oriented systems (abstract) (1992)

When the performance penalty of object-oriented systems is mentioned, a common response is to blame antiquated hardware designs for not supporting object-oriented languages as they deserve, To what extent can the performance gap between conventional languages and object-oriented languages be closed using hardware? What architectural changes benefit object-oriented systems, and by how much? There have been many attempts to make hardware that better supports object-oriented programming. This tutorial describes these systems, and the extent that they have succeeded or failed in their aims. These systems include SOAR, Rekursiv and MUSHROOM, as well as some features from mainstream architectures such as SPARC. Issues covered include: choice of instruction set, design of the memory system including caches and virtual memory hardware, scaleability, use of parallelism, and hardware/software trade-offs. A common misconception is that if something is implemented in hardware then it must be fast. One aspect of the tutorial is to show that there are limits to what hardware support can achieve. However, better hardware can reduce the cost of some language features, such as dynamic binding, and can make a system more scaleable.
Genetic risk for bipolar disorder and schizophrenia predicts structure and function of the ventromedial prefrontal cortex (2021)

Our multimodal neuroimaging study linked genomic burden and brain endophenotype by demonstrating an association between polygenic risk scores for bipolar disorder and schizophrenia and the structure and function of the vmPFC. Our findings suggest that genetic factors might confer risk for psychotic disorders by influencing the integrity of the vmPFC, a brain region involved in self-referential processes and emotional regulation. Our study may also provide an imaging-genetics vulnerability marker that can be used to help identify individuals at risk for developing bipolar disorder.
Supplementary Figure 2 from EBV Is Necessary for Proliferation of Dually Infected Primary Effusion Lymphoma Cells (2023)

Supplementary Figure 2 from EBV Is Necessary for Proliferation of Dually Infected Primary Effusion Lymphoma Cells
CXCR3 and Its Ligands Participate in the Host Response toBordetella bronchisepticaInfection of the Mouse Respiratory Tract but Are Not Required for Clearance of Bacteria from the Lung (2004)

ABSTRACT Intranasal inoculation of mice with Bordetella bronchiseptica produces a transient pneumonia that is cleared over several weeks in a process known to require both neutrophils and lymphocytes. In this study, we evaluated the roles of the chemokines MIG (CXCL9), IP-10 (CXCL10), and I-TAC (CXCL11) and their common receptor, CXCR3. Following bacterial inoculation, message expression of interleukin-1 (IL-1), IL-6, and the neutrophil-attracting chemokines KC, LIX, and MIP-2 was rapidly induced, with maximal expression found at 6 h. In contrast, message expression of gamma interferon, MIG, IP-10, and I-TAC peaked at 2 days. Expression of all of these chemokines and cytokines returned to near baseline by 5 days, despite the persistence of high levels of live bacteria at this time. Induced MIG, IP-10, and I-TAC protein expression was localized in areas of inflammation at 2 to 3 days and was temporally associated with increased levels of CXCR3 + lymphocytes in bronchoalveolar lavage fluid. There was no increase in mortality in mice lacking CXCR3. However, the clearance of bacteria from the lung and trachea was delayed, and the recruitment of lymphocytes and NK cells was slightly decreased, for CXCR3 −/− mice relative to CXCR3 +/+ mice. We conclude that the CXCR3 receptor-ligand system contributes to pulmonary host defense in B. bronchiseptica infection by recruiting lymphocytes and NK cells into the lung.
CLN6 Mutations Cause Teenage-Onset Progressive Myoclonus Epilepsy (P2.183) (2014)

OBJECTIVE/ BACKGROUND: 
Progressive myoclonus epilepsy (PME) afflicts mainly teenagers. PME in young children and adults is mostly caused by neuronal ceroid lipofuscinosis (NCL). Using a whole-exome sequencing (WES) approach, we find that NCL is also a cause of teenage-onset PME.
 DESIGN/METHODS: 
A 24 year-old Pashtun Afghani man presented with myoclonus at age 15 years. Seizures and cognitive decline appeared later. Two cousins had the same disease and age of onset. Both died around age 30 with severe dementia. Investigations showed cortical myoclonus, multifocal epileptiform discharges, and generalized brain atrophy. Testing for known causes of teenage-onset PMEs were negative. Homozygosity mapping and WES, were performed to identify the disease gene.
 RESULTS: 
600,000 SNPs were genotyped in the proband and one affected cousin. Homozygosity mapping revealed two shared regions of homozygosity. WES yielded 41,597 genetic variants of which only two were exonic, novel, nonsynonymous, and located within one of the shared homozygous regions. One variant was expressed in testis. The other variant was a homozygous sequence change in the CLN6 gene. This variant segregates with the disease in the pedigree. Sequencing for it in 268 control individuals, including 176 Pashtun, revealed it in one Pashtun, in heterozygote state.
 CONCLUSIONS: 
The patients in our study closely resemble Kufs disease generally, and the teenage-onset cases of Arsov et al. in particular. Combining this with our findings that the CLN6 sequence change we identified affects a highly conserved amino acid, is the only homozygous exomic alteration in a brain-expressed gene in a shared region of homozygosity, and is not present in homozygous state in vast control sequence datasets and 176 ethnic matches, confirms that CLN6 c.768C>G (D256E) is the mutation in our family. Combined WES and homozygosity mapping in two patients from one family without a priori hypothesis led directly to the causative defect. Disclosure: Dr. Andrade has nothing to disclose. Dr. Paton has nothing to disclose. Dr. Turnbull has nothing to disclose. Dr. Klein has received personal compensation for activities with Link Medicine, and Centogene. Dr. Marshall has nothing to disclose. Dr. Scherer has nothing to disclose. Dr. Minassian has nothing to disclose.
Interaction between Light, Paper and and Color Halftones: Challenges and Modelization Approaches (2006)

We review the phenomena having an impact on the interaction between light, paper and color halftones. They comprise surface reflections and refractions at the air-paper interface, propagation of light within the paper, internal reflections at the paper-air interface, as well as ink spreading and trapping. We introduce basic notions from radiometry and optics, such as the definitions of radiant flux, irradiance, radiance, Lambert reflector, as well as collimated and diffuse light reflection and refraction. We then present classical spectral reflection models, their extension to multi-ink color halftones and the impact of different measuring devices (radiant detector, integrated sphere). Finally we briefly review ink spreading models and highlight the topics deserving further research.
Synchotron Enabled Ex-Situ and in-Situ Mechanistic Interrogation of Energy Storage Systems (2014)

A complete picture of the electrochemical processes and reaction fronts within batteries is difficult to form due to the complexities of the reactions and the difficulties of analytical interrogation of those reactions. Ex-situ measurements at various stages of reaction can provide mechanistic insight. However, configurational information is lost in the process. In-situ methods are typically hindered by the cell housing. In these studies we have used the high power NSLS synchrotron to perform in-situ EDXRD. By combining diffraction data with ex-situ methods we are able to create a more complete picture of the ongoing reactions within the cell.
Vehicle-Level Reasoning Systems: Integrating System-Wide Data to Estimate the Instantaneous Health State (2011)

At the aircraft level, a Vehicle-Level Reasoning System (VLRS) can be developed to provide aircraft with at least two significant capabilities: improvement of aircraft safety due to enhanced monitoring and reasoning about the aircrafts health state, and also potential cost savings by enabling Condition Based Maintenance (CBM). Along with the benefits of CBM, an important challenge facing aviation safety today is safeguarding against system and component failures and malfunctions. Faults can arise in one or more aircraft subsystem their effects in one system may propagate to other subsystems, and faults may interact.