gebhart/patrepeval huggingface dataset:
Immunogenicity of targeted lentivectors (2014)

To increase the safety and possibly efficacy of HIV-1 derived lentivectors (LVs) as an anti-cancer vaccine, we recently developed the Nanobody (Nb) display technology to target LVs to antigen presenting cells (APCs). In this study, we extend these data with exclusive targeting of LVs to conventional dendritic cells (DCs), which are believed to be the main cross-presenting APCs for the induction of a TH1-conducted antitumor immune response. The immunogenicity of these DC-subtype targeted LVs was compared to that of broad tropism, general APC-targeted and non-infectious LVs. Intranodal immunization with ovalbumin encoding LVs induced proliferation of antigen specific CD4+ T cells, irrespective of the LVs' targeting ability. However, the cytokine secretion profile of the restimulated CD4+ T cells demonstrated that general APC targeting induced a similar TH1-profile as the broad tropism LVs while transduction of conventional DCs alone induced a similar and less potent TH1 profile as the non-infectious LVs. This observation contradicts the hypothesis that conventional DCs are the most important APCs and suggests that the activation of other APCs is also meaningful. Despite these differences, all targeted LVs were able to stimulate cytotoxic T lymphocytes, be it to a lesser extent than broad tropism LVs. Furthermore this induction was shown to be dependent on type I interferon for the targeted and non-infectious LVs, but not for broad tropism LVs. Finally we demonstrated that the APC-targeted LVs were as potent in therapy as broad tropism LVs and as such deliver on their promise as safer and efficacious LV-based vaccines.
Supplementary Figure Legends 1-5 from Genome-Wide CpG Island Profiling of Intraductal Papillary Mucinous Neoplasms of the Pancreas (2023)

&lt;p&gt;PDF file - 68K&lt;/p&gt;
Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity (2022)

ABSTRACT Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins associated with the lysosome mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked to longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using deep proteomic profiling, we systemically profiled lysosome-associated proteins linked with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal protein dynamics to signal transduction, organelle crosstalk and organism longevity.
The role of GNAS mutation in diagnosis of mucinous pancreatic cysts. (2012)

e21048 Background: Pancreatic cysts pose a challenge in patient management primarily due to difficulties distinguishing non-mucinous cysts from potentially pre-malignant mucinous ones, and in determining the malignant potential of mucinous cysts. Mutations to the GNAS gene have been identified as a marker for intraductal papillary mucinous neoplasm (IPMN). [1,2] We evaluated the significance of GNAS mutation in diagnosis of pancreatic cysts. Methods: We retrieved archival DNA from 237 cyst fluids. 200 specimens were chosen with 100 KRAS mutant and 100 KRAS wild type in a range of CEA values. 37 specimens were chosen with a molecular diagnosis of aggressive biological behavior, to enrich for malignant IPMNs. We sequenced each fluid’s DNA from for codon 201 of GNAS. Molecular criteria for mucinous cysts included KRAS mutation, elevated DNA, or ≥2 high clonality LOH mutations. Results: Of the 237 specimens, 25 were not amplifiable due to degraded DNA, 52 (25%) had a GNAS mutation, and 160 had no GNAS mutation. Of the 52 GNAS mutated specimens, 5 were diagnosed as biologically aggressive based on significant associated mutations, 28 as statistically indolent based on associated molecular changes, and 19 as benign (no accompanying mutations). The proportion of GNAS mutations decreased with increasing molecular changes linked to malignancy. Data from [1] shows no statistical difference in frequency of GNAS mutation in side branch vs. main vs. mixed IPMNs (p= 0.46). Similarly, in our cohort, 6 cases had clear imaging features of a side branch IPMN, and of these 2 (33%) had a mutation in GNAS. Using molecular criteria for identification of mucinous cysts, 166 were mucinous and 71 non-mucinous. Incorporation of GNAS into the molecular determination of mucinous etiology identified 13 additional cases (7%). Conclusions: Use of GNAS increases sensitivity for detection of mucinous lesions. GNAS does not appear to correlate with molecular measures of biological aggressiveness. These findings confirm those in [1], that GNAS should be used in conjunction with a panel of molecular markers for evaluating the malignant potential of pancreatic cystic lesions. References 1. Sci Transl Med. 2011 Jul 20; 3:92ra66. 2. PNAS 2011 Dec 27; 108:21188-93.
Effect of VBC-1814/7J, a poly-phytocompound, on a non-infectious model of pharyngitis (2017)

Pharyngitis presents as an inflammation of the oropharynx, and clinical examination often shows evidence of nasopharyngitis. In numerous cases the condition occurs as a self-limiting illness of non-infectious aetiology, whose clinical management remains a matter for debate given the inappropriateness of antibiotics, the reported worsening following steroid use and the recent discouragement of the use of Chinese herbal medicine. The aim of the present study was thus to test VBC-1814/7J, a poly-phytocompound with known anti-inflammatory and immune-response enhancing properties, in an experimental model of non-infectious pharyngitis. Experimental non-infectious pharyngitis was induced by applying a pyridine solution to the surface of the pharyngeal mucosa in rats that were either normally fed (group A) or fed VBC-1814/7J three days prior to and three days subsequent to the induction of pharyngitis (group B). Healthy rats treated with topical saline were used as a control (group C). At time-points of 0, one hour, one day and three days sacrifices were carried out and microscopic examination, Evans blue (EB) dye extravasation and tissue concentrations of tumour necrosis factor (TNF)-α, interleukin (IL)-6 and mRNA of α- and β-defensins were studied. As compared with group C, group A showed significant microscopic damage, EB extravasation, and increases in the levels of TNF-α and IL-6, as well as in the mRNA of three defensins (P<0.001) on the third day of observation. VBC-1814/7J significantly mitigated these microscopic and inflammatory markers while allowing a prompter and wider defensin reaction (P<0.05 vs. group A). These data suggest that VBC-1814/7J, as demonstrated in earlier studies, has the potential to address non-infectious pharyngitis in clinical practice.
Revascularization of the Posterior Circulation (2005)

The primary objective of revascularization procedures in the posterior circulation is the prevention of vertebrobasilar ischemic stroke. Specific anatomical and neurophysiologic characteristics such as posterior communicating artery size affect the susceptibility to ischemia. Current indications for revascularization include symptomatic vertebrobasilar ischemia refractory to medical therapy and ischemia caused by parent vessel occlusion as treatment for complex aneurysms. Treatment options include endovascular angioplasty and stenting, surgical endarterectomy, arterial reimplantation, extracranial-to-intracranial anastomosis, and indirect bypasses. Pretreatment studies including cerebral blood flow measurements with assessment of hemodynamic reserve can affect treatment decisions. Careful blood pressure regulation, neurophysiologic monitoring, and neuroprotective measures such as mild brain hypothermia can help minimize the risks of intervention. Microscope, microinstruments and intraoperative Doppler are routinely used. The superficial temporal artery, occipital artery, and external carotid artery can be used to augment blood flow to the superior cerebellar artery, posterior cerebral artery, posterior inferior cerebellar artery, or anterior inferior cerebellar artery. Interposition venous or arterial grafts can be used to increase length. Several published series report improvement or relief of symptoms in 60 to 100% of patients with a reduction of risk of future stroke and low complication rates.
4G vision and technology development in Korea (2004)

With increasing end user demands for wider service due to the rapid growth and variety of IT (information technology) industry, the service with the data rate of 30 Mbps cannot accommodate the future mobile multimedia environment. Therefore, worldwide radio and mobile communication institutes and companies started the R & D of 4G mobile communications system prior to completing the implementation of IMT-2000 system and providing its service. ETRI is one of those organizations endeavoring for the future 4G system with capabilities beyond IMT-2000. With the establishment of R & D project for 4G radio transmission system in January of 2002, ETRI is actively working to develop 4G high-tier system, HMM (high-speed mobile Internet), and Hpi (high-speed portable Internet). In this paper, ETRI's 4G vision and enabling technologies to achieve this vision is described.
Modeling and simulation of feature-size-dependent etching of metal stacks (2001)

Aspect ratio dependent etching (ARDE) has often been observed in various etching processes. During etching of metal films in a high density plasma reactor, this phenomenon is more prominent. With a high amount of ARDE present, the narrow spaces will not be cleared unless there is enough overetch, which removes an excessive amount of the underlying layers. The main focus of this article is on the understanding of the mechanisms behind metal ARDE. The results from an extensive design of experiments on the subject were utilized for this study. SPEEDIE, the Stanford etching and deposition profile simulator, was used to develop and test appropriate models. The Langmuir adsorption model with added surface recombination of the adsorbed species, both etchants and inhibitors, was used to model the phenomenon. The added surface recombination acts as the major species loss mechanism on the feature sidewalls. The simulation results indicate that a process with inhibitors, which are highly adhesive to the metal surface and which do not like to recombine with the etchants to form volatile products, will lead to a low degree of ARDE. This is in agreement with experimental results which showed that the addition of CHF3 to the Al etch process helps to reduce the ARDE in narrow space regions.
Degradation of Visual Performance With Increasing Levels of Retinal Stray Light (2016)

Low levels of retinal stray light can cause significant increases in halo sizes, elevations in luminance detection thresholds, and reductions in contrast sensitivity whether or not a glare source is present.
Meeting report of the 4th autumn meeting of the German Society of Extracellular Vesicles (GSEV): cutting edge EV research driven by young scientists (2021)

Extracellular Vesicles and Circulating Nucleic Acids is an open access journal, focusing on extracellular vesicles and circulating nucleic acids including DNA, RNA, and miRNA and their therapeutic use.
An EREW PRAM fully-dynamic algorithm for MST (2002)

We provide an EREW PRAM fully-dynamic algorithm to maintain the minimum spanning tree (MST) of an undirected weighted graph under single edge insertions and deletions. Our approach combines the sparsification data structure with a novel parallel technique which efficiently treats edge deletions. The proposed parallel algorithm requires O(log n) time and O(n/sup 2/3/ log m/n) work, where n and m are respectively the number of nodes and edges of the given graph.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Data Figure S3 from ARX788, a Site-specific Anti-HER2 Antibody–Drug Conjugate, Demonstrates Potent and Selective Activity in HER2-low and T-DM1–resistant Breast and Gastric Cancers (2023)

&lt;p&gt;Activity of ARX788 single or fractionated dosing in breast and gastric PDX models. After single or multiple-dose administration (dotted lines) of vehicle or ARX788, mean tumor volumes ({plus minus} SEM) are shown for a subset of (A) breast or (B) gastric cancer PDX models with HER2 positive or HER2 low expression. Statistical significance (p&lt;0.05) versus vehicle was evaluated for each treatment group (n=8 mice/group).&lt;/p&gt;
Bivalent intra-spike binding provides durability against emergent Omicron lineages: Results from a global consortium (2023)

The SARS-CoV-2 Omicron variant of concern (VoC) and its sublineages contain 31-36 mutations in spike and escape neutralization by most therapeutic antibodies. In a pseudovirus neutralization assay, 66 of the nearly 400 candidate therapeutics in the Coronavirus Immunotherapeutic Consortium (CoVIC) panel neutralize Omicron and multiple Omicron sublineages. Among natural immunoglobulin Gs (IgGs), especially those in the receptor-binding domain (RBD)-2 epitope community, nearly all Omicron neutralizers recognize spike bivalently, with both antigen-binding fragments (Fabs) simultaneously engaging adjacent RBDs on the same spike. Most IgGs that do not neutralize Omicron bind either entirely monovalently or have some (22%-50%) monovalent occupancy. Cleavage of bivalent-binding IgGs to Fabs abolishes neutralization and binding affinity, with disproportionate loss of activity against Omicron pseudovirus and spike. These results suggest that VoC-resistant antibodies overcome mutagenic substitution via avidity. Hence, vaccine strategies targeting future SARS-CoV-2 variants should consider epitope display with spacing and organization identical to trimeric spike.
Promoting Connectivity of Network-Like Structures by Enforcing Region\n Separation (2020)

We propose a novel, connectivity-oriented loss function for training deep\nconvolutional networks to reconstruct network-like structures, like roads and\nirrigation canals, from aerial images. The main idea behind our loss is to\nexpress the connectivity of roads, or canals, in terms of disconnections that\nthey create between background regions of the image. In simple terms, a gap in\nthe predicted road causes two background regions, that lie on the opposite\nsides of a ground truth road, to touch in prediction. Our loss function is\ndesigned to prevent such unwanted connections between background regions, and\ntherefore close the gaps in predicted roads. It also prevents predicting false\npositive roads and canals by penalizing unwarranted disconnections of\nbackground regions. In order to capture even short, dead-ending road segments,\nwe evaluate the loss in small image crops. We show, in experiments on two\nstandard road benchmarks and a new data set of irrigation canals, that convnets\ntrained with our loss function recover road connectivity so well, that it\nsuffices to skeletonize their output to produce state of the art maps. A\ndistinct advantage of our approach is that the loss can be plugged in to any\nexisting training setup without further modifications.\n
Analysis of Interaction between Grouser and Soil Using Distinct Element Method (DEM) (2010)

When signing for tracked vehicles, which are operated on unpaved roads or soft ground, the interaction between machine and soil must be analyzed. In this research, attention was focused on the interaction under front idler, that is, traction soil by a grouser in driving system. To verify the validity of interaction analysis between a grouser and soil by using 3D DEM soil model, traction simulations and experiments were carried out. In addition, the soil model was considered particle roughness to introduce compaction effect by compression. To check the effectiveness of the soil model, compression test and shearing test were conducted. Consequently, soil behavior and porosity change were found on the tests. And comparing the results of traction simulations and experiments, soil behavior and qualitative characteristics of traction resistance were conformed. Therefore, interaction between grouser and soil could be analyzed by using the soil model considering particle roughness.
New biodegradable polymers from renewable sources: Polyester‐carbonates based on 1,3‐propylene‐co‐1,4‐cyclohexanedimethylene succinate (2001)

Abstract α,ω‐Dihydroxy‐terminated copolymeric oligomers of a 1,3‐propylene/1,4‐cyclohexanedimethylene succinate structure were obtained by the thermal polycondensation of 1,3‐propanediol/1,4‐cyclohexanedimethanol/succinic acid mixtures. They were subsequently chain‐extended via phosgene synthesis to high molecular weight aliphatic/alicyclic copolyester‐carbonates. These new polymers, besides having a biodegradable backbone, originate from two monomers, namely, 1,3‐propanediol and succinic acid, which can be obtained by renewable sources. Therefore, they have a potential as environmentally friendly materials. All synthesized materials were characterized in reference to their molecular structure by 1 H NMR and 13 C NMR. Their molecular weights and molecular weight distributions were determined by size exclusion chromatography, and their main thermal properties were measured by DSC. Spectroscopic characterizations were in full agreement with the proposed structures. 1,4‐Cyclohexanedimethanol was used as a diol comonomer to improve the overall thermal properties of poly(1,3‐propylene succinate). The results of the characterization performed show that the initial expectations were only partially satisfied. © 2001 John Wiley &amp; Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2508–2519, 2001
Real life challenges in access-control management (2009)

In this work we ask the question: what are the challenges of managing a physical or file system access-control policy for a large organization? To answer the question, we conducted a series of interviews with thirteen administrators who manage access-control policy for either a file system or a physical space. Based on these interviews we identified three sets of real-world requirements that are either ignored or inadequately addressed by technology: 1) policies are made/implemented by multiple people; 2) policy makers are distinct from policy implementers; and 3) access-control systems don't always have the capability to implement the desired policy. We present our interview results and propose several possible solutions to address the observed issues.
Practical Asynchronous Interconnect Network Design (2008)

The implementation of interconnect is becoming a significant challenge in modern integrated circuit (IC) design. Both synchronous and asynchronous strategies have been suggested to manage this problem. Creating a low skew clock tree for synchronous inter-block pipeline stages is a significant challenge. Asynchronous interconnect does not require a global clock, and therefore, it has a potential advantage in terms of design effort. This paper presents an asynchronous interconnect design that can be implemented using a standard application-specific IC flow. This design is considered across a range of IC interconnect scenarios. The results demonstrate that there is a region of the design space where the implementation provides an advantage over a synchronous interconnect by removing the need for clocked inter-block pipeline stages, while maintaining high throughput. Further results demonstrate a computer-aided design tool enhancement that would significantly increase this space. A detailed comparison of power, area, and latency of the two strategies is also provided for a range of IC scenarios.
Access Queues for Multi-Bank Register Files Enabling Enhanced Performance of Highly Parallel Processors (2006)

The proposed register access queues are used as part of a scheduler which avoids possible access conflicts for a multi-bank register file in the highly parallelized processor. From the design and implementation in 180 nm CMOS technology, a multi-bank register file with the access queue realizes 65 % smaller area and 64 % higher clock frequency when compared with a conventional multi-port-cell register file. Since the cycle-based execution performance of the processor remains practically unchanged, the higher clock frequency translates directly into higher processor performance
Stimulation of cell-mediated immunity by bestatin correlates with reduction of bacterial persistence in experimental chronic Salmonella typhimurium infection (1984)

The effect of bestatin, a low-molecular-weight immunomodulating drug isolated from Streptomyces olivoreticuli, on Salmonella typhimurium infection was elaborated. Bestatin enhanced the delayed-type hypersensitivity reaction against S. typhimurium in a dose- and time-dependent manner. Parallel to the activation of delayed-type hypersensitivity reaction, bestatin reduced the amount of persistent bacteria in livers and spleens as well as the amount of necrotic foci found in these organs. This was shown when bestatin was given either prophylactically or therapeutically. The therapeutic effect of bestatin was even seen when the drug was given in the chronic phase of the infection, i.e., 6 days after inoculation of the animals with the infectious agent. No influence of bestatin, however, could be observed on the initial multiplication rate of S. typhimurium and concomitantly on the initial mortality rate of the infected mice. As bestatin has no direct antibiotic effect on S. typhimurium, it must be concluded that the therapeutic effects of the drug on chronic infection must be solely contributed to elevation of the host's own defense mechanisms.
Semi-Supervised Learning via New Deep Network Inversion (2017)

We exploit a recently derived inversion scheme for arbitrary deep neural networks to develop a new semi-supervised learning framework that applies to a wide range of systems and problems. The approach outperforms current state-of-the-art methods on MNIST reaching $99.14\%$ of test set accuracy while using $5$ labeled examples per class. Experiments with one-dimensional signals highlight the generality of the method. Importantly, our approach is simple, efficient, and requires no change in the deep network architecture.
An n-In0.53Ga0.47As/n-InP rectifier (1981)

We report the current-voltage (I-V), capacitance-voltage (C-V), and photoresponse characteristics of n-In0.53Ga0.47 As/n-InP heterobarrier diodes. We find the conduction-band barrier is Δεc = 0.22±0.02 eV. We find thermionic emission is the dominant mechanism for carrier transport across the heterobarrier. Also, to the level of sensitivity of our measurement techniques, no interface states have been detected.
Lanthanide-halide-based nanoscintillators for portable radiological detectors (2009)

Colloidal synthesis of core/shell nanocrystals with cerium-doped lanthanum fluoride core and undoped lanthanum fluoride shell, and of core/shell nanocrystals with hygroscopic cerium-doped lanthanum bromide core and undoped lanthanum fluoride shell is reported. The nanocrystals were characterized by transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), dynamic light scattering (DLS) analysis, steady state UV-VIS optical absorption and photoluminescence spectroscopy, and by photoluminescence lifetime measurements. Scintillation tests were performed on the cerium-doped lanthanum fluoride nanocrystalline material exposed to low-level gamma irradiation.