gebhart/patrepeval huggingface dataset:
Global alterations to the choroid plexus blood-CSF barrier in amyotrophic lateral sclerosis (2020)

Abstract The choroid plexus (CP) is a highly vascularized structure located in the ventricles that forms the blood-CSF barrier (BCSFB) and separates the blood from the cerebrospinal fluid (CSF). In addition to its role as a physical barrier, the CP functions in CSF secretion, transport of nutrients into the central nervous system (CNS) and a gated point of entry of circulating immune cells into the CNS. Aging and neurodegeneration have been reported to affect CP morphology and function and increase protein leakage from blood to the CSF. Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease associated with both upper and lower motor neuron loss, as well as altered proteomic and metabolomic signatures in the CSF. The role of the BCSFB and the CP in ALS is unknown. Here we describe a transcriptomic and ultrastructural analysis of BCSFB and CP alterations in human postmortem tissues from ALS and non-neurologic disease controls. ALS-CP exhibited widespread disruptions in tight junctional components of the CP epithelial layer and vascular integrity. In addition, we detected loss of pericytes around ALS blood vessels, accompanied by activation of platelet aggregation markers vWF and Fibrinogen, reminiscent of vascular injury. To investigate the immune component of ALS-CP, we conducted a comprehensive analysis of cytokines and chemokine panels in CP lysates and found a significant down-regulation of M-CSF and V-CAM1 in ALS, as well as up-regulation of VEGF-A protein. This phenotype was accompanied by an infiltration of MERTK positive macrophages into the parenchyma of the ALS-CP when compared to controls. Taken together, we demonstrate widespread structural and functional disruptions of the BCSFB in human ALS increasing our understanding of the disease pathology and identifying potential new targets for ALS therapeutic development.
Abstract 1410: TIP-1 regulates Glioma invasion through small GTPases (2011)

Abstract Therapy resistance and invasion are two common features of malignant glioma. Our previous studies showed that TIP-1 regulates sensitivity of glioma cells to ionizing radiation. It was also found that TIP-1 protein level was elevated in human malignant glioma compared to the normal brain tissue counterparts, and correlated with the malignancy of gliomas. This observation was supported with a survival study within animal models, in which TIP-1 knockdown within glioma cell lines significantly retarded progression of the intracranially implanted tumors and extended survival time of the mice. In vitro and in vivo studies indicated that it is the reduced migration and invasion capability, but not the cell proliferation rate, that contributed to the retarded tumor progression of gliomas with TIP-1 knockdown. The glioma cells with TIP-1 knockdown also showed morphological changes with reorganized cytoskeleton and reduced efficiency of reorientation in directional migration. TIP-1 was reported to associate to beta-catenin and Rhotekin, two proteins that are involved in the cell skeleton reorganization and cell migration. Their interactions are through the single PDZ domain within TIP-1 and the classic Type I PDZ-binding motifs located at the carboxyl terminus of beta-catenin and Rhotekin respectively. It was found that TIP-1 knockdown altered intracellular location of Rhotekin. Mislocalization of Rhotekin at the cell migration leading edge resulted in irregular activation of RhoA, which generally regulates cell rear body retraction. Further, we identified that beta-PIX shares a similar PDZ-binding motif and associates to TIP-1 in vitro and in vivo. Beta-PIX is recruited to the leading edge by Scribble for Rac1 or Cdc42 activation and thus regulates cell front protrusion. Knockdown of TIP-1 within the invasive glioma cells disrupted the association of beta-PIX and Scribble, resulted in mislocalization of beta-PIX and reduced Rac1 activation. Taken together, these data illustrated that TIP-1 is one critical modulator in migration of the invasive glioma through regulating two small GTPases (RhoA and Rac1), and targeting TIP-1 might represent one novel approach to treat the highly invasive and mortal glioma tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1410. doi:10.1158/1538-7445.AM2011-1410
The study of simple chemicals in animals and man: mechanisms of contact sensitivity. (2012)

When simple chemical are applied to the skin, a series of events ensues that under some conditions ultimately results in contact sensitivity (CS), a proven cell-mediated immune response (CMI). Since the discovery of CMI using picryl-Cl (PCl) in 1942, we have learned a great deal on the cellular mechanisms involved in CS, including the potential to treat warts, skin cancer, autoimmune disorders, and allergies. In this review we summarize some of the basic mechanisms of both the innate and acquired immune systems involved in CS.
Dynamic behavior of slowly-responsive congestion control algorithms (2001)

The recently developed notion of TCP-compatibility has led to a number of proposals for alternative congestion control algorithms whose long-term throughput as a function of a steady-state loss rate is similar to that of TCP. Motivated by the needs of some streaming and multicast applications, these algorithms seem poised to take the current TCP-dominated Internet to an Internet where many congestion control algorithms co-exist. An important characteristic of these alternative algorithms is that they are slowly-responsive , refraining from reacting as drastically as TCP to a single packet loss.However, the TCP-compatibility criteria explored so far in the literature considers only the static condition of a fixed loss rate. This paper investigates the behavior of slowly-responsive, TCP-compatible congestion control algorithms under more realistic dynamic network conditions, addressing the fundamental question of whether these algorithms are safe to deploy in the public Internet. We study persistent loss rates, long- and short-term fairness properties, bottleneck link utilization, and smoothness of transmission rates.
ChemInform Abstract: SPIRO(4,4)NONATETRAEN UND SPIRO(4,4)NONATRIEN‐(1,3,7) (1973)

Abstract Das Trien (II) entsteht aus dem Tosylat (I) und überschüssigem Na‐jodid (20 Std. in Aceton).
Supplemental figure 1 from Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum (2023)

&lt;p&gt;Gene promoter methylation amplification curves&lt;/p&gt;
Newcastle Disease Virus (NDV) Oncolytic Activity in Human Glioma Tumors Is Dependent on CDKN2A-Type I IFN Gene Cluster Codeletion (2020)

Glioblastoma (GBM) is the most aggressive and frequent primary brain tumor in adults with a median overall survival of 15 months. Tumor recurrence and poor prognosis are related to cancer stem cells (CSCs), which drive resistance to therapies. A common characteristic in GBM is <i>CDKN2A</i> gene loss, located close to the cluster of <i>type I IFN</i> genes at Ch9p21. Newcastle disease virus (NDV) is an avian paramyxovirus with oncolytic and immunostimulatory properties that has been proposed for the treatment of GBM. We have analyzed the <i>CDKN2A-IFN I</i> gene cluster in 1018 glioma tumors and evaluated the NDV oncolytic effect in six GBM CSCs ex vivo and in a mouse model. Our results indicate that more than 50% of GBM patients have some <i>IFN</i> deletion. Moreover, GBM susceptibility to NDV is dependent on the loss of the <i>type I IFN</i>. Infection of GBM with an NDV-expressing influenza virus NS1 protein can overcome the resistance to oncolysis by NDV of type I-competent cells. These results highlight the potential of using NDV vectors in antitumor therapies.
Whole-genome annotation by using evidence integration in functional-linkage networks (2004)

The advent of high-throughput biology has catalyzed a remarkable improvement in our ability to identify new genes. A large fraction of newly discovered genes have an unknown functional role, particularly when they are specific to a particular lineage or organism. These genes, currently labeled "hypothetical," might support important biological cell functions and could potentially serve as targets for medical, diagnostic, or pharmacogenomic studies. An important challenge to the scientific community is to associate these newly predicted genes with a biological function that can be validated by experimental screens. In the absence of sequence or structural homology to known genes, we must rely on advanced biotechnological methods, such as DNA chips and protein-protein interaction screens as well as computational techniques to assign putative functions to these genes. In this article, we propose an effective methodology for combining biological evidence obtained in several high-throughput experimental screens and integrating this evidence in a way that provides consistent functional assignments to hypothetical genes. We use the visualization method of propagation diagrams to illustrate the flow of functional evidence that supports the functional assignments produced by the algorithm. Our results contain a number of predictions and furnish strong evidence that integration of functional information is indeed a promising direction for improving the accuracy and robustness of functional genomics.
AffineGlue: Joint Matching and Robust Estimation (2023)

We propose AffineGlue, a method for joint two-view feature matching and robust estimation that reduces the combinatorial complexity of the problem by employing single-point minimal solvers. AffineGlue selects potential matches from one-to-many correspondences to estimate minimal models. Guided matching is then used to find matches consistent with the model, suffering less from the ambiguities of one-to-one matches. Moreover, we derive a new minimal solver for homography estimation, requiring only a single affine correspondence (AC) and a gravity prior. Furthermore, we train a neural network to reject ACs that are unlikely to lead to a good model. AffineGlue is superior to the SOTA on real-world datasets, even when assuming that the gravity direction points downwards. On PhotoTourism, the AUC@10° score is improved by 6.6 points compared to the SOTA. On ScanNet, AffineGlue makes SuperPoint and SuperGlue achieve similar accuracy as the detector-free LoFTR.
Growth and magnetism of Cr-doped InN (2005)

We present structural and magnetic characterization of Cr-doped InN films grown by plasma-assisted molecular beam epitaxy on c-plane sapphire substrates. Low-temperature GaN buffer layers grown by metalorganic vapor-phase epitaxy were used to accommodate the large lattice mismatch between InN and sapphire. A high n-type carrier concentration of 1.5×1020cm−3 was measured in InN films with 3% Cr doping. Films of this type, with high structural perfection, as measured in situ, with reflection high-energy electron diffraction, exhibit a well-defined in-plane magnetic hysteresis loop for temperatures varying from 5to300K. Thus, we show evidence of magnetic order in Cr-doped InN.
ChemInform Abstract: AN APPROACH TO THE ENANTIOSPECIFIC SYNTHESES OF SESBANIMIDE AND ITS ENANTIOMER FROM D‐GLUCOSE (1984)

Abstract Auf den im Formelschema beschriebenen Wegen erhält man ausgehend von Diacetonglucose (I) über die Schlüsselverbindung (IV) die enantiomeren Dithioacetale (VIII) bzw. (X).
Crystal structures of the A2A adenosine receptor and their use in medicinal chemistry (2013)

New insights into drug design are derived from the X-ray crystallographic structures of G protein-coupled receptors (GPCRs), and the adenosine receptors (ARs) are at the forefront of this effort. The 3D knowledge of receptor binding and activation promises to enable drug discovery for GPCRs in general, and specifically for the ARs. The predictability of modeling based on the X-ray structures of the A<sub>2A</sub>AR has been well demonstrated in the identification, design and modification of both known and novel AR agonists and antagonists. It is expected that structure-based design of drugs acting through ARs will provide new avenues to clinically useful agents.
Rate-Splitting Multiple Access: Unifying NOMA and SDMA in MISO VLC Channels (2020)

The increased proliferation of connected devices requires a development of innovative technologies for the next generation of wireless systems. One of the key challenges, however, is the spectrum scarcity, owing to the unprecedented broadband penetration rate in recent years. Based on this, visible light communication (VLC) has recently emerged as an effective potential solution for enabling high-speed short-range communications. Yet, despite their undoubted advantageous features, VLC systems suffer from several limitations which constraint their capabilities. As a result, several multiple access (MA) techniques, such as space-division multiple access (SDMA) and non-orthogonal multiple access (NOMA), have been considered in VLC networks as an effective approach, among others, to circumvent these limitations. However, despite their achievable multiplexing gain, their overall performance is still limited compared to the overall potential of this technology. Motivated by this, the presented article offers two contributions: firstly, we provide an overview of the key MA technologies used in VLC systems and then we introduce rate-splitting multiple access (RSMA), and discuss its capabilities and potentials in VLC systems. Secondly, through realistic system modeling and simulations of an RSMA-based two-user scenario, we illustrate the flexibility of RSMA as well as its superiority in terms of the achievable weighted sum rate over NOMA and SDMA in the context of VLC. Finally, we discuss technical challenges, open issues, and research directions, along with the offered results and insights that are expected to be useful towards the effective practical realization of RSMA in VLC configurations.
Nanometer-scale selective epitaxy of InAs quantum dots via indium segregation (2004)

We report on recent results utilizing pseudomorphic In/sub x/Ga/sub 1-x/As films in order to affect the growth, organization and structure of InAs quantum dots. Pseudomorphic InGaAs films exhibit interesting properties due to strain effects. Given time, In/sub x/Ga/sub 1-x/As films release various amounts of indium by surface segregation. This segregated layer of InAs can act to decrease the additional InAs necessary to reach the 2D to 3D transition coverage. This process enables an oxideless, single growth step of quantum dots suitable for use in quantum dot cellular automata computing and other low dimensional electronic systems.
Efficient modeling of room acoustic impulse response by segmentation into early and late components (2016)

A Room Impulse Response (RIR) has a complex time-frequency structure that can be divided into a number of discrete early reflections followed by a reverberant tail. Many acoustic signal enhancement applications, such as dereverberation and room equalization, require simple yet accurate models to represent an RIR. Parametric modeling of RIR typically approximate the overall response for a given position of a source and receiver inside a room, without considering the fundamental distinction between early reflection (modal region) and late reverberation (statistical region) of an RIR. In this paper, the RIR is estimated in two steps: first, the early reflection component is modeled utilizing fixed pole, parallel orthonormal basis functions to represent the modal behavior of the room. The late reverberation component of an RIR is more statistical in nature with exponentially decaying envelope, exhibiting different decay time constants for different frequencies. Wavelet decomposition using a multi-rate analysis filter bank is applied to model this part of the RIR. An iterative method is used to estimate the parameters of the model from a measured target RIR. The proposed hybrid method provides an accurate representation of an RIR while requiring a smaller number of parameters in comparison to existing methods.
A General Approach to Block-Based Physical Modeling with Mixed Modeling Strategies for Digital Sound Synthesis (2006)

Block-based physical modeling algorithms for sound synthesis have gained more and more interest in the past few years. They have the advantage that new models can be created by combining existing blocks and they offer the opportunity to combine different modeling techniques. We propose a general approach to creating physical models in blocks and how to connect these blocks assuring their correct physical interaction. Furthermore, we show how to implement the interconnection of these models with wave digital filter principles. The complete procedure is applied to the example application scenario of the one-dimensional wave equation. Three different modeling techniques are used. One part is implemented with a finite difference time domain approach, one with the functional transformation method, and the boundaries are implemented by wave digital filters.
Nanocomposite Ionogel Electrolytes: Nanocomposite Ionogel Electrolytes for Solid‐State Rechargeable Batteries (Adv. Energy Mater. 36/2020) (2020)

In article number 2002135, Mark C. Hersam and co-workers delineate recent advances in nanocomposite ionogel electrolytes to highlight their beneficial attributes in the context of solid-state rechargeable batteries. This work also outlines the remaining challenges and future research directions that will help guide and accelerate the incorporation of nanocomposite ionogel electrolytes in widespread practical applications.
Abstract 3703: Nanoparticle-induced targeted pro-apoptotic peptide in glioblastoma (2010)

Abstract Glioblastomas multiforme (GBM) are the most common and lethal form of intracranial tumors. They account for approximately 70% of the 22,500 new cases of malignant primary brain tumors that are diagnosed in adults in the United States each year. Although relatively uncommon, malignant gliomas are associated with disproportionately high morbidity and mortality (median survival is only 12 to 15 months). Malignant gliomas are among the most vascular of human tumors. Tumor vasculature has proven to be particularly well suited as a site for receptor-based targeting. It expresses a multitude of molecules that are not expressed in the vessels of normal tissues. Our laboratory screens phage-displayed peptide libraries in vivo and ex vivo to discover specific targets in tumor vessels. One of the peptides, CGKRK (1) binds to the blood vessels in various kinds of tumors. Initial experiments showed that intravenously injected CGKRK peptide effectively homes to lentiviral (H-RasV12-sip53)-induced glioma in mice. We coupled the CGKRK peptide to the alpha-helical amphipathic peptide D[KLAKLAK]2, which is toxic to eukaryotic cells if it internalized into the cells (2). The chimeric peptide, when added to actively growing HUVEC or U87 glioma cells colocalized with mitochondria, whereas D[KLAKLAK]2 did not. Iron oxide nanoworms (NW) coated with the chimeric D[KLAKLAK]2-CGKRK peptide were 100-200-fold more toxic to the HUVEC and U87 cells than the free peptide in vitro and specifically accumulated in the blood vessels of glioma. Treatment of lentiviral induced glioma in mice with the D[KLAKLAK]2-CGKRK-PEG-NW inhibited tumor growth and showed a significant survival increase compared to control-treated mice. 1. Hoffman, J.A., et al. Progressive vascular changes in a transgenic mouse model of squamous cell carcinoma. Cancer Cell 4, 383-391 (2003). 2. Ellerby, H.M., et al. Anti-cancer activity of targeted pro-apoptotic peptides. Nat Med 5, 1032-1038 (1999). *These authors contributed equally to this work Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3703.
Supplementary Table S9 from Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma (2023)

Supplementary Table S9 from Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma
Mutant TNF-alpha, mTNF-K90R, is a novel candidate adjuvant for a mucosal vaccine against HIV. (2010)

The development of a safe and effective mucosal vaccine adjuvant is a crucial step for the development of vaccines against human immunodeficiency virus type-1 (HIV). We have previously reported that a mutant tumor necrosis factor-alpha (TNF-alpha), mTNF-K90R, possessed strong mucosal vaccine adjuvant activities in mice. Here, we evaluated the potential of mTNF-K90R as a mucosal vaccine adjuvant for the induction of systemic and mucosal immune responses against HIV. Nasal immunization of BALB/c mice with 5 microg of an HIV gp120 env protein immunogen together with mTNF-K90R induced higher serum anti-HIV gp120 protein immunoglobulin G (IgG) responses than gp120 alone. Furthermore, mTNF-K90R induced anti-gp120 IgA responses in nasal as well as vaginal washes from immunized mice, although these were not administration sites. Again, responses with mTNF-K90R were higher than with gp120 alone. These results indicate that mTNF-K90R may be applicable as amucosal adjuvant for HIV vaccination to induce both systemic and mucosal immune responses.
ChemInform Abstract: Pseudo‐Sugars. Part 12. Synthesis of Methyl D,L‐(1,3/2,4,5)‐ and D,L‐(1,3,4/2,5)‐2,3,4,5‐Tetrahydroxycyclohexane‐1‐carboxylates. (1987)

Abstract Das aus dem Bromlacton (I) entstehende Dibromid (II) wird über die Cyclohexencarbonsäure (IIIa) in den ungesättigten Ester (IIIb) übergeführt.
Investigation of the Solution Behavior of Organosoluble Aromatic Polyimides (1997)

Abstract Two high-molecular-weight organosoluble aromatic polyimides having the same diamine, 2,2′-(trifluoromethyl)-4,4′-diaminobiphenyl diamine (PFMB), but different dianhydrides, 2,2′-bis(trifluoromethyl)-4,4′,5,5′-biphenyltetracarboxylic dianhydride (HFBPDA) and 2,2′-bis(3,4-dicarboxyphenyl)hexafluoropropane dianhydride (6FDA), were prepared via one-step polycondensation reactions. Molecular weight fractionation of these two polymers was carried out and the polyimide fractions possess successively lower weight-average molecular weights. Intrinsic viscosity data from both sets of polyimide fractions gave the Mark-Houwink-Sakurada constants of these two polyimides, which reflect differing chain rigidity in tetrahydrofuran (THF) solutions. The MHS relations are [η] = 5.24 × 10−4 M0.65 and [η] = 3.77 × 10−5 M0.97 for 6FDA-PFMB and HFBPDA-PFMB, respectively. The physical meanings of these constants are discussed using the intrinsic viscosity data of these two polyimides in varying solvents. The persistence lengths are calculated based on the viscosity and molecular weight results using Bohdanecky' s approach and they were calculated to be 6.6 and 2.0 nm for HFBPDA-PFMB and 6FDA-PFMB, respectively. The experimental results indicate that the fully aromatic HFPBDA-PFMB is more rigid in THF solutions compared with 6FDA-PFMB. However, both of these polyimides are far from possessing true rigid-rod character. Plots of the weight-average molecular weight against the elution volume depict the differences in chain stiffness, and hence in hydrodynamic volume, between samples. Examination of the hydrodynamic volume of these polymers provides evidence that they both subscribe rather well to hydrodynamic theory at high molecular weights but that the stiffer HFBPDA-PFMB shows deviation at lower values.
‘The thunder of British guns’ (2015)

Abstract This chapter focuses on the views of Nonconformists towards foreign policy. Their sympathy for oppressed peoples abroad, clashed with their belief in the need to preserve Britain's imperial power — a conflict which was complicated in the case of some Dissenters by their pacifism. The impact of the Armenian crisis of 1894–6 and the Boer War on the attitudes of Nonconformists is also discussed.