gebhart/patrepeval huggingface dataset:
Chromosome assignment of the tumor-specific antigen of a 3-methylcholanthrene-induced mouse sarcoma. (1981)

Chemically induced sarcomas of inbred mice express antigens that are distinct and specific for each individual tumor. Chromosome assignment of tumor-specific antigens would help to elucidate the genetic basis of their diversity. Expression of the serologically defined Meth A sarcoma antigen is not suppressed in hybrid cells containing a complete foreign (Chinese hamster) genome. Chromosome and serologic analysis of microcell hybrids between Meth A sarcoma cells and Chinese hamster cells shows a clear correlation of Meth A antigen expression with the presence of the distal region of chromosome 12 (bands F1 and F2). Chromosome 16 may also be implicated. The significance of the close linkage of genes determining Meth A antigen expression with the immunoglobulin heavy chain gene cluster (on chromosome 12) and the lambda light chain genes (on chromosome 16) is discussed.
Biologics in the Treatment of Psoriasis: Clinical and Economic Overview (2009)

Background: The use of biologic medications for psoriasis is a recent therapeutic advance. Objective: To review clinical and economic data for biologic therapies in the treatment of chronic plaque psoriasis. Methods: Published meta-analyses and additional literature review identified randomized controlled trials. Analyses included the number needed to treat (NNT), the cost in Canadian dollars for the first year of treatment per the Canadian product monograph, and the estimated cost per responder achieving a 75% reduction in Psoriasis Area and Severity Index score (PASI 75). Results: Pooled NNTs were 1.3 (infliximab), 1.5 (ustekinumab 90 mg), 1.6 (adalimumab and ustekinumab 45 mg), 2.3 (etanercept), 4.1 (efalizumab), and 5.6 (alefacept). The annual treatment cost per patient was $19,825 to $37,600. The cost per patient achieving a PASI 75 response at 12 weeks ranged from $8,330 (adalimumab) to $71,371 (alefacept). Conclusion: This analysis suggests favorable cost and benefits of biologic psoriasis therapies, particularly adalimumab, infliximab, and ustekinumab.
The temporal and topological characteristics of BGP path changes (2004)

BGP has been deployed in Internet for more than a decade. However, the events that cause BGP topological changes are not well understood. Although large traces of routing updates seen in BGP operation are collected by RIPE RlS and University of Oregon RouteViews, previous work examines this data set as individual routing updates. This paper describes methods that group routing updates into events. Since one event (a policy change or peering failure) results in many update messages, we cluster updates both temporally and topologically (based on the path vector information). We propose a new approach to analyzing the update traces, classifying the topological impact of muting events, and approximating the distance to the autonomous system originating the event. Our analysis provides some insight into routing behavior: First, at least 45% path changes are caused by events on transit peerings. Second, a significant number (23-37%) of path changes are transient, in that routing updates indicate temporary path changes, but they ultimately converge on a path that is identical from the previously stable path. These observations suggest that a content provider cannot guarantee end-to-end routing stability based solely on its relationship with its immediate ISP, and that better detection of transient changes may improve routing stability.
Kinetic and Performance Studies of the Regeneration Phase of Model Pt/Ba/Rh NOx Traps for Design and Optimization (2010)

In this project a combined experimental and theoretical approach was taken to advance our understanding of lean NOx trap (LNT) technology. Fundamental kinetics studies were carried out of model LNT catalysts containing variable loadings of precious metals (Pt, Rh), and storage components (BaO, CeO{sub 2}). The Temporal Analysis of Products (TAP) reactor provided transient data under well-characterized conditions for both powder and monolith catalysts, enabling the identification of key reaction pathways and estimation of the corresponding kinetic parameters. The performance of model NOx storage and reduction (NSR) monolith catalysts were evaluated in a bench scale NOx trap using synthetic exhaust, with attention placed on the effect of the pulse timing and composition on the instantaneous and cycle-averaged product distributions. From these experiments we formulated a global model that predicts the main spatio-temporal features of the LNT and a mechanistic-based microkinetic models that incorporates a detailed understanding of the chemistry and predicts more detailed selectivity features of the LNT. The NOx trap models were used to determine its ability to simulate bench-scale data and ultimately to evaluate alternative LNT designs and operating strategies. The four-year project led to the training of several doctoral students and the dissemination of the findings as 47 presentations in conferences, catalysis societies, and academic departments as well 23 manuscripts in peer-reviewed journals. A condensed review of NOx storage and reduction was published in an encyclopedia of technology.
Protein Scaffold Engineering Towards Tunable Surface Attachment (2009)

Ringe mit Haftung: Eine selektive und einstellbare Methode zum Anbringen von Proteinen auf Metall- oder Isolatoroberflächen wird vorgestellt, bei der ein ringförmiges Protein, das innen SiO2 bindende Peptide trägt (gelb im Bild), auf einen Wechsel des Lösungsmittels hin mehrere Bindestellen präsentiert. So wird eine Monoschicht erzeugt, ohne dass die Oberfläche modifiziert werden muss. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Deep Learners Benefit More from Out-of-Distribution Examples (2011)

Recent theoretical and empirical work in statistical machine learning has demonstrated the potential of learning algorithms for deep architectures, i.e., function classes obtained by composing multiple levels of representation. The hypothesis evaluated here is that intermediate levels of representation, because they can be shared across tasks and examples from different but related distributions, can yield even more benefits. Comparative experiments were performed on a large-scale handwritten character recognition setting with 62 classes (upper case, lower case, digits), using both a multi-task setting and perturbed examples in order to obtain out-ofdistribution examples. The results agree with the hypothesis, and show that a deep learner did beat previously published results and reached human-level performance. 1
“Built‐in” PD‐1 blocker to rescue NK‐92 activity from PD‐L1–mediated tumor escape mechanisms (2021)

Success of adoptive cell therapy mainly depends on the ability of immune cells to persist and function optimally in the immunosuppressive tumor microenvironment. Although present at the cancer site, immune cells become exhausted and/or inhibited, due to the presence of inhibitory receptors such as PD-L1 on malignant cells. Novel genetic strategies to manipulate the PD1/PD-L1 axis comprise (i) PD-1 reversion where the receptor intracellular domain is replaced with an activating unit, (ii) the use of anti-PD-L1 CAR or (iii) the disruption of the PD-1 gene. We here present an alternative strategy to equip therapeutic cells with a truncated PD-1 (tPD-1) to abrogate PD-1/PD-L1 inhibition. We show that engagement of tPD-1 with PD-L1-positive tumor unleashes NK-92 activity in vitro. Furthermore, this binding was sufficiently strong to induce killing of targets otherwise not recognized by NK-92, thus increasing the range of targets. In vivo treatment with NK-92 tPD-1 cells led to reduced tumor growth and improved survival. Importantly, tPD-1 did not interfere with tumor recognition in PD-L1 negative conditions. Thus, tPD-1 represents a straightforward method for improving antitumor immunity and revealing new targets through PD-L1 positivity.
CCR5-edited CD4+ T cells augment HIV-specific immunity to enable post-rebound control of HIV replication (2021)

BackgroundWe conducted a phase I clinical trial that infused CCR5 gene-edited CD4+ T cells to determine how these T cells can better enable HIV cure strategies.MethodsThe aim of trial was to develop RNA-based approaches to deliver zinc finger nuclease (ZFN), evaluate the effect of CCR5 gene-edited CD4+ T cells on the HIV-specific T cell response, test the ability of infused CCR5 gene-edited T cells to delay viral rebound during analytical treatment interruption, and determine whether individuals heterozygous for CCR5 Δ32 preferentially benefit. We enrolled 14 individuals living with HIV whose viral load was well controlled by antiretroviral therapy (ART). We measured the time to viral rebound after ART withdrawal, the persistence of CCR5-edited CD4+ T cells, and whether infusion of 10 billion CCR5-edited CD4+ T cells augmented the HIV-specific immune response.ResultsInfusion of the CD4+ T cells was well tolerated, with no serious adverse events. We observed a modest delay in the time to viral rebound relative to historical controls; however, 3 of the 14 individuals, 2 of whom were heterozygous for CCR5 Δ32, showed post-viral rebound control of viremia, before ultimately losing control of viral replication. Interestingly, only these individuals had substantial restoration of HIV-specific CD8+ T cell responses. We observed immune escape for 1 of these reinvigorated responses at viral recrudescence, illustrating a direct link between viral control and enhanced CD8+ T cell responses.ConclusionThese findings demonstrate how CCR5 gene-edited CD4+ T cell infusion could aid HIV cure strategies by augmenting preexisting HIV-specific immune responses.REGISTRATIONClinicalTrials.gov NCT02388594.FundingNIH funding (R01AI104400, UM1AI126620, U19AI149680, T32AI007632) was provided by the National Institute of Allergy and Infectious Diseases (NIAID), the National Institute on Drug Abuse (NIDA), the National Institute of Mental Health (NIMH), and the National Institute of Neurological Disorders and Stroke (NINDS). Sangamo Therapeutics also provided funding for these studies.
Hyperhomocysteinemia potentiates diabetes-impaired EDHF-induced vascular relaxation: Role of insufficient hydrogen sulfide (2018)

Intermediate HHcy potentiated H<sub>2</sub>S reduction via CSE-downregulation in microvasculature of T2DM mice. H<sub>2</sub>S is justified as an EDHF. Insufficient H<sub>2</sub>S impaired EDHF-induced vascular relaxation via oxidative stress and IK<sub>Ca</sub> inactivation in T2DM/HHcy mice. H<sub>2</sub>S therapy may be beneficial for prevention and treatment of micro-vascular complications in patients with T2DM and HHcy.
(Invited) Flexible and Conductive Mxene/Carbon Nanotube Composite Paper for Energy Storage (2015)

Carbon nanomaterials, such as carbon nanotubes (CNTs), are attracting much attention as candidates for electrodes of energy storage devices due to their large open surfaces and high conductivity. Recently, MXenes, a new family of 2D carbides, have shown their great promise for electrodes in supercapacitors and Li-ion batteries. [1, 2] Herein, our new results show that the incorporation of CNTs into MXene films results in composite papers with much improved performance. [3] Free-standing sandwich-like MXene/CNT composite papers composed of alternating layers of MXene and CNTs were fabricated by vacuum filtration method. The resulting “papers” have good flexibility, high electrical conductivity and a structure accessible to electrolyte ions. They exhibit much better performance than pure MXene films and the randomly mixed MXene/CNT composite papers. When employed as electrodes for supercapacitors in aqueous electrolyte, capacitances of ~390 F/cm 3 were achieved. Besides, the composites showed ~75% increase in rate performance compared to pure MXene films and exhibited no capacity degradation after 10,000 cycles. The MXene/CNT composite papers can also serve as stable anodes for high-rate Li-ion batteries. Highly reversible and stable capacity of ~250 mAh/g was yielded by the titanium-based MXene/CNT composites at 0.5 C (2 hrs charge/discharge), about 10 times of that for pure MXene films. The niobium-based MXene/CNT composites achieved a high reversible capacity of ~650 mAh/g at 0.1 C (10 hrs charge/discharge). At 10 C (6 min charge/discharge), a reversible capacity of ~300 mAh/g was retained for &gt;300 cycles, indicating excellent rate performance and cycling stability. These conductive, flexible and mechnaically strong papers are promising materials that can be used in wearable or structural electrochemical energy storage and conversion systems. [1] M. Naguib, et al., MXenes: A New Family of Two-Dimensional Materials, Advanced Materials , 26 , 992-1005 (2014) [2] M. R. Lukatskaya, et al., Cation Intercalation and High Volumetric Capacitance of Two-dimensional Titanium Carbide, Science , 341 , 1502-1505 (2013) [3] M. Q. Zhao, et al. Flexible MXene/Carbon Nanotube Composite Paper with High Volumetric Capacitance, Advanced Materials , in press (2014)
Excess Power during Electrochemical Loading: Materials, Electrochemical Conditions and Techniques (2015)

The critical role of the electrode material characteristics in increasing the probability of observing excess power during electrochem- ical loading of palladium cathodes with deuterium is investigated, and excess power production obtained using palladium material with these identified characteristics is reported. Characterizations have been performed by using SEM and AFM microscopy as well as electrochemical analysis and XPS. The emerging scenario suggested by these results is that poor control in achieving the identified material status is reflected in the reproducibility of the excess heat phenomenon.
The Evolution of Selective FGFR4 Inhibitors for FGF19-Driven Malignancies (2018)

Medicinal Chemistry Reviews is an outstanding 680 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
Endogenous human cytomegalovirus gB is presented efficiently by MHC class II molecules to CD4 + CTL (2005)

Human cytomegalovirus (HCMV) infects endothelial, epithelial, and glial cells in vivo. These cells can express MHC class II proteins, but are unlikely to play important roles in priming host immunity. Instead, it seems that class II presentation of endogenous HCMV antigens in these cells allows recognition of virus infection. We characterized class II presentation of HCMV glycoprotein B (gB), a membrane protein that accumulates extensively in endosomes during virus assembly. Human CD4+ T cells specific for gB were both highly abundant in blood and cytolytic in vivo. gB-specific CD4+ T cell clones recognized gB that was expressed in glial, endothelial, and epithelial cells, but not exogenous gB that was fed to these cells. Glial cells efficiently presented extremely low levels of endogenous gB--expressed by adenovirus vectors or after HCMV infection--and stimulated CD4+ T cells better than DCs that were incubated with exogenous gB. Presentation of endogenous gB required sorting of gB to endosomal compartments and processing by acidic proteases. Although presentation of cellular proteins that traffic into endosomes is well known, our observations demonstrate for the first time that a viral protein sorted to endosomes is presented exceptionally well, and can promote CD4+ T cell recognition and killing of biologically important host cells.
User's Social Media Profile as Predictor of Empathy (2017)

The use of social media, like Facebook, Twitter and LinkedIn, is nowadays very common and quite for sure each one of us has at least a digital profile on them. The information left of these platforms such as likes, posts, tweets and photos are very informative and can be used for deducting our preferences, tendencies and behaviors. The analysis of the social media footprints has become a relevant research topic in the last decade and many works have demonstrated how to extract some traits of the user's affective sphere. In this paper, we focus on the prediction of empathic tendencies of a subject as an index of the influence of emotions during decisional processes. This value can be included in the user profile and can be relevant in some scenarios, such as music and movie recommender systems, where the emotional component is strongly delineated. We propose an approach of empathy level prediction based on a linear regression algorithm over Facebook profiles. We use a word2vec representation of the textual contents of the user's time-line posts, a LDA and SVD vector representation of the user's likes and other general descriptive data. The evaluation performed has demonstrated the validity of the approach for predicting the empathy tendency and the results have showed some relevant correlations with some specific groups of user's descriptive features.
Quantification of Mesenchymal Stem Cells (MSCs) at Sites of Human Prostate Cancer (2012)

Circulating bone marrow-derived Mesenchymal Stem Cells (BM-MSCs) have an innate tropism for tumor tissue in response to the inflammatory microenvironment present in malignant lesions. The prostate is bombarded by numerous infectious and inflammatory insults over a lifetime. Chronic inflammation is associated with CXCL12, CCL5, and CCL2, which are highly overexpressed in prostate cancer. Among other cell types, these chemoattractant stimuli recruit BM-MSCs to the tumor. MSCs are minimally defined as plastic-adhering cells characterized by the expression of CD90, CD73, and CD105 in the absence of hematopoietic markers, which can differentiate into osteoblasts, chondrocytes, and adipocytes. MSCs are immunoprivileged and have been implicated in tumorigenesis through multiple mechanisms, including promoting proliferation, angiogenesis, and metastasis, in addition to the generation of an immunosuppressive microenvironment. We have demonstrated that MSCs represent 0.01-1.1% of the total cells present in core biopsies from primary human prostatectomies. Importantly, these analyses were performed on samples prior to expansion in tissue culture. MSCs in these prostatectomy samples are FAP-, CD90-, CD73-, and CD105-positive, and CD14-, CD20-, CD34-, CD45-, and HLA-DR-negative. Additionally, like BM-MSCs, these prostate cancer-derived stromal cells (PrCSCs) were shown to differentiate into osteoblasts, adipocytes and chondrocytes. In contrast to primary prostate cancer-derived epithelial cells, fluorescently-labeled PrCSCs and BM-MSCs were both shown to home to CWR22RH prostate cancer xenografts following IV injection. These studies demonstrate that not only are MSCs present in sites of prostate cancer where they may contribute to carcinogenesis, but these cells may also potentially be used to deliver cytotoxic or imaging agents for therapeutic and/or diagnostic purposes.
Imaging of T-cells and their responses during anti-cancer immunotherapy (2019)

Immunotherapy has proven to be an effective approach in a growing number of cancers. Despite durable clinical responses achieved with antibodies targeting immune checkpoint molecules, many patients do not respond. The common denominator for immunotherapies that have successfully been introduced in the clinic is their potential to induce or enhance infiltration of cytotoxic T-cells into the tumour. However, in clinical research the molecules, cells and processes involved in effective responses during immunotherapy remain largely obscure. Therefore, <i>in vivo</i> imaging technologies that interrogate T-cell responses in patients represent a powerful tool to boost further development of immunotherapy. This review comprises a comprehensive analysis of the <i>in vivo</i> imaging technologies that allow the characterisation of T-cell responses induced by anti-cancer immunotherapy, with emphasis on technologies that are clinically available or have high translational potential. Throughout we discuss their respective strengths and weaknesses, providing arguments for selecting the optimal imaging options for future research and patient management.
SMART-I<sup>2</sup>: &#x201C;Spatial multi-user audio-visual real-time interactive interface&#x201D;, A broadcast application context (2009)

SMART-I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is a high quality 3D audio-visual interactive rendering system. In SMART-I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , the screen is also used as a multichannel loudspeaker. The spatial audio rendering is based on Wave Field Synthesis, an approach that creates a coherent spatial perception of a spatial sound scene over a large listening area. The azimuth localization accuracy of the system has been verified by a perceptual experiment. Contrary to conventional systems, SMART-I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is able to realize a high degree of 3D audio-visual integration with almost no compromise on either the audio or the graphics rendering quality. Such a system can provide benefits to a wide range of applications.
Modified control technique for Carbon Dioxide reduction, improve efficiency and power quality in small island energy network (2014)

The major objectives of a small island energy network management include the reduction of operating cost, fossil fuel dependency, Carbon Dioxide (CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) emission and improvement of price stability, operating flexibility and efficiency. In this paper a well defined control technique is proposed to regulate voltage and frequency for high penetration of renewable energy in small island system. The technique allows the improvement of efficiency and power quality indexes for critical loads while reducing CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> emissions. The standard IEEE 34 bus system is used for the small island energy network modeling. Three different cases were studied and simulated in this paper. The CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> emission, efficiency and power quality indexes have been calculated and compared for all three cases in order to verify the performance of the proposed control technique.
Influence of Si doping on the infrared reflectance characteristics of GaN grown on sapphire (1999)

Si-doped GaN films grown on sapphire are investigated by infrared reflectance. A damping behavior of the interference fringes is observed, and interpreted to be due to the presence of an interface layer between the film and the substrate. A theoretical calculation using a two-layer model to take into account the interface layer resulted in this damping in agreement with the experiment. The damping behavior and an improvement of interface properties by Si incorporation are demonstrated.