gebhart/patrepeval huggingface dataset:
Tunable morphologies from charged block copolymers (2010)

The bulk morphologies formed by a new class of charged block copolymers, 75 vol % fluorinated polyisoprene (FPI) – 25 vol% sulfonated polystyrene (PSS) with 50% sulfonation, are characterized, and the fundamental underlying forces that promote the self-assembly processes are elucidated. The results show how the bulk morphologies are substantially different from their uncharged diblock counterparts (PS-PI) and also how morphology can be tuned with volume fraction of the charged block and the casting solvent. A physical understanding based on the underlying strong electrostatic interactions between the charged block and counterions is obtained using Monte Carlo (MC) and Molecular Dynamics (MD) simulations. The 75/25 FPI-PSS shows hexagonal morphologies with the minority blocks (PSS) forming the continuous phase due to charge percolation and the FPI blocks arranged in hexagonal cylinders. Some long-range order can be sustained even if lipophobicity is increased (addition of water), albeit with lower dimensional structures. However, thermal annealing provides sufficient energy to disrupt the percolated charges and promotes aggregation of ionic sites which leads to a disordered system. Diverse and atypical morphologies are readily accessible by simply changing the number distribution of the charges on the PSS block.
Collaboration and knowledge integration for successful brain therapeutics – lessons learned from the pandemic (2022)

Brain diseases are a major cause of death and disability worldwide and contribute significantly to years of potential life lost. Although there have been considerable advances in biological mechanisms associated with brain disorders as well as drug discovery paradigms in recent years, these have not been sufficiently translated into effective treatments. This Special Article expands on Keystone Symposia's pre- and post-pandemic panel discussions on translational neuroscience research. In the article, we discuss how lessons learned from the COVID-19 pandemic can catalyze critical progress in translational research, with efficient collaboration bridging the gap between basic discovery and clinical application. To achieve this, we must place patients at the center of the research paradigm. Furthermore, we need commitment from all collaborators to jointly mitigate the risk associated with the research process. This will require support from investors, the public sector and pharmaceutical companies to translate disease mechanisms into world-class drugs. We also discuss the role of scientific publishing in supporting these models of open innovation. Open science journals can now function as hubs to accelerate progress from discovery to treatments, in neuroscience in particular, making this process less tortuous by bringing scientists together and enabling them to exchange data, tools and knowledge effectively. As stakeholders from a broad range of scientific professions, we feel an urgency to advance brain disease therapies and encourage readers to work together in tackling this challenge.
Figure S2 from Induced Telomere Damage to Treat Telomerase Expressing Therapy-Resistant Pediatric Brain Tumors (2023)

&lt;p&gt;A, Telomerase activity in HFF+hTERT cells treated with DMSO, 6-thio-dG (3 µM for 3 days), and imetelstat (IMT; 2 µM). For combination treatment, cells were pre-treated with IMT for 3 days and then with 6-thio-dG for another 3 days. (-) C, (+) C, and IC indicate negative control, positive control, and internal control respectively. Telomerase products are indicated. B-C, effect of telomerase inhibition on cell growth of HFF (B) and HFF+hTERT (C) cells treated with imetelstat (IMT; 2 µM) only, 6-thio-dG (3 µM) only, or 6-thio-dG in combination with imetelstat as described in A. Error bars represent the standard deviation generated from triplicates. P-value, **, P&lt;0.01. D, quantification showing percent cells with TIFs in HFF+hTERT cells treated with imetelstat (IMT; 2 µM) only, 6-thio-dG (3 µM for 3 days), or in combination with imetelstat as described in A. Cells counted for each treatment (n= ~50 cells). Bottom panels show representative images showing TRF2 (green), γH2AX (red), and TIFs (yellow) indicated by white arrows. DAPI (blue) indicates nucleus staining.&lt;/p&gt;
Fast image completion method using patch offset statistics (2015)

Image completion is a technique that involves repairing damaged images or filling in missing regions in a visually pleasing manner. In this work, a novel fast image completion approach is proposed, which finds the best textures to be filled into the unknown areas through internal statistics of natural images. Firstly, we create statistics from spatial offsets (relative positions) of similar patches in the image. From these statistics, a sparse representation of the most frequent offsets is derived. These offsets are then used to fill the missing region by combining a stack of shifted images using a weighted means method. Hereby, the offsets are considered in descending order in the filling routine according to their importance. Experimental results show that the proposed method yields subjective improvements compared to the state-of-the-art. Furthermore, the method synthesizes missing regions faster than existing methods.
N-Terminal Trimer Extension of Nominal CD8 T Cell Epitopes Is Sufficient to Promote Cross-Presentation to Cognate CD8 T Cells In Vivo (2007)

Cross-priming is the process in which Ag-presenting dendritic cells (DCs) acquire, process, and present Ags scavenged from other cells, and use these cells to activate naive CD8 T cells. Cross-priming of cognate CD8 cells can result in either tolerance or immunity, depending upon the activation status of the Ag-presenting DC. Previous studies have shown that nominal peptide is inefficiently cross-presented and that proteins and large polypeptides that require proteasomal processing are the main source of naturally cross-presented Ags. In this study we show that N-terminal extension of nominal peptide by as few as three residues is sufficient to produce a substrate for TAP-dependent cross-presentation that is highly efficient in cross-priming murine CD8 T cells in vivo. On a molar basis, cross-priming with 3-mer-extended peptide is 20-fold more efficient than priming with intact protein. This method of peptide extension should prove of great value in facilitating in vivo studies of CD8 immunity and tolerance that rely on cross-presentation.
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly (2023)

Resolving fundamental molecular and functional processes underlying human synaptic development is crucial for understanding normal brain function as well as dysfunction in disease. Based upon increasing evidence of species-divergent features of brain cell types, coupled with emerging studies of complex human disease genetics, we developed the first automated and quantitative high-content synaptic phenotyping platform using human neurons and astrocytes. To establish the robustness of our platform, we screened the effects of 376 small molecules on presynaptic density, neurite outgrowth, and cell viability, validating six small molecules that specifically enhanced human presynaptic density in vitro. Astrocytes were essential for mediating the effects of all six small molecules, underscoring the relevance of non-cell-autonomous factors in synapse assembly and their importance in synaptic screening applications. Bromodomain and extraterminal (BET) inhibitors emerged as the most prominent hit class and global transcriptional analyses using multiple BET inhibitors confirmed upregulation of synaptic gene expression. Through these analyses, we demonstrate the robustness of our automated screening platform for identifying potent synaptic modulators, which can be further leveraged for scaled analyses of human synaptic mechanisms and drug discovery efforts.
Optimal allocation of replicas in parallel tempering simulations (2004)

We have studied the efficiency of parallel tempering simulations for a variety of systems including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones fluid. A scheme is proposed for the optimal allocation of temperatures in these simulations. The method is compared to the existing empirical approaches used for this purpose. Accuracy associated with the computed thermodynamic quantities such as specific heat is also computed and their dependence on the trial-exchange acceptance rate is reported.
A One-Step Method to Fabricate PLLA Scaffolds With Deposition of Bioactive Hydroxyapatite and Collagen Using Ice-Based Microporogens (2009)

Scaffolding is an essential issue in tissue engineering. We have recently developed an approach to generate HA/collagen coated poly(lactic-glycolic acids) scaffolds using a porogen-leaching method [1]. The approach involves a two-step process with coating first on the paraffin microspheres and then using the coated microspheres both as the porogens and the vehicles to transfer the bioactive apatite/collagen coating. In this study, we describe an advancement of the porogen-based technology using ice-based microporogens to deposit multiple bioactive agents into the desired scaffold in a single step.
Synthetic depth-of-field with a single-camera mobile phone (2018)

Shallow depth-of-field is commonly used by photographers to isolate a subject from a distracting background. However, standard cell phone cameras cannot produce such images optically, as their short focal lengths and small apertures capture nearly all-in-focus images. We present a system to computationally synthesize shallow depth-of-field images with a single mobile camera and a single button press. If the image is of a person, we use a person segmentation network to separate the person and their accessories from the background. If available, we also use dense dual-pixel auto-focus hardware, effectively a 2-sample light field with an approximately 1 millimeter baseline, to compute a dense depth map. These two signals are combined and used to render a defocused image. Our system can process a 5.4 megapixel image in 4 seconds on a mobile phone, is fully automatic, and is robust enough to be used by non-experts. The modular nature of our system allows it to degrade naturally in the absence of a dual-pixel sensor or a human subject.
Deceleration Assistance Mitigated the Trade-off Between Sense of Agency and Driving Performance (2021)

Driving assistance technology has gained traction in recent years and is becoming more widely used in vehicles. However, drivers usually experience a reduced sense of agency when driving assistance is active even though automated assistance improves driving performance by reducing human error and ensuring quick reactions. The present study examined whether driving assistance can maintain human sense of agency during early deceleration in the face of collision risk, compared with manual deceleration. In the experimental task, participants decelerate their vehicle in a driving simulator to avoid collision with a vehicle that suddenly cut in front of them and decelerated. In the assisted condition, the system performed deceleration 100 ms after the cut-in. Participants were instructed to decelerate their vehicle and follow the vehicle that cut-in. This design ensured that the deceleration assistance applied a similar control to the vehicle as the drivers intended to, only faster and smoother. Participants rated their sense of agency and their driving performance. The results showed that drivers maintained their sense of agency and improved driving performance under driving assistance. The findings provided insights into designing driving assistance that can maintain drivers' sense of agency while improving future driving performance. It is important to establish a mode of joint-control in which the system shares the intention of human drivers and provides improved execution of control.
Facioscapulohumeral muscular dystrophy (2013)

Facioscapulohumeral muscular dystrophy (FSHD) is a progressive myopathy with a relatively late age of onset (usually in the late teens) compared with Duchenne and many other muscular dystrophies. The current FSHD disease model postulates that contraction of the D4Z4 array at chromosome 4q35 leads to a more open chromatin conformation in that region and allows transcription of the DUX4 gene. DUX4 mRNA is stable only when transcribed from certain haplotypes that contain a polyadenylation signal. DUX4 protein is hypothesized to cause FSHD by mediating cytotoxicity and impairing skeletal muscle differentiation. We recently showed in a cell culture model that DUX4 expression is regulated by telomere length, suggesting that telomere shortening during aging may be partially responsible for the delayed onset and progressive nature of FSHD. We here put our data in the context of other recent findings arguing that progressive telomere shortening may play a critical role in FSHD but is not the whole story and that the current disease model needs additional refinement.
Secondary syphilis in a 14-month-old girl and child-to-mother transmission (2023)

Syphilis cases in childhood are usually associated with congenital transmission. Acquired transmission is uncommon, and primarily related to sexual abuse or close contact/nursing with infected family members. We here describe a case of syphilis in a 14-month-old girl resulting from intrafamilial infection, with a subsequent transmission to her mother.
ChemInform Abstract: FORMATION, REACTIVITIES, AND MOLECULAR STRUCTURES OF PHOSPHINE DERIVATIVES OF TITANOCENE. ISOLATION AND CHARACTERIZATION OF A TITANIUM MONOOLEFIN Π COMPLEX (1983)

Abstract Die Photolyse einer Hexanlösung von (II) mit "O‐markierten C0‐Gruppen in Gegenwart von C150 bewirkt innerhalb von 30 min einen vollständigen Ligandenaustausch, der die Photolabilität der Carbonylliganden von (II) zeigt.
Quantitation of Pax-6 protein in ocular impression cytology samples using an electrochemiluminescence immunoassay (2022)

Paired box protein Pax-6 (oculothrombin) is a transcription factor that plays an important regulatory role in ocular, brain, and pancreatic development. Mutations of the PAX6 gene cause aniridia and Peters anomaly. Reduction in Pax-6 protein is also associated with ocular diseases such as dry eye. An electrochemiluminescence immunoassay method using the Meso Scale Discovery platform was developed to measure Pax-6 protein levels in corneal epithelial cells obtained by impression cytology. Impression cytology involves harvesting ocular epithelial cells by applying a polyethersulfone membrane patch briefly to the ocular surface using a commercially available EYEPRIM™ device. The epithelial cells that adhere to the membrane patch of the EYEPRIM™ device provide a biological sample which can be assayed for Pax-6 protein levels. Assay development identified an antibody pair capable of detecting purified recombinant Pax-6 protein produced in mammalian cells. The optimized assay has a dynamic range of 24 pg mL<sup>-1</sup> to 100,000 pg mL<sup>-1</sup> and a lower limit of quantification of 24 pg mL<sup>-1</sup>. Assay selectivity was demonstrated using either HeLa or HEK293 cells transfected with inhibitory RNA. Finally, the method was validated by measuring Pax-6 protein levels in impression cytology acquired samples obtained using the EYEPRIM™ device from rabbit cornea.
Abstract P737: Human Homologs Of Differentially Expressed Plasma MicroRNAs In Preclinical Murine Models Target Fundamental Mechanisms Of Cerebral Cavernous Malformation (2021)

Introduction: There is a current need for sensitive and specific biomarkers of Cerebral Cavernous Malformation (CCM) that can be readily translated from preclinical to human models to accurately diagnose and monitor disease states and response to novel therapeutics. MiRNAs are small non-coding RNAs that influence gene expression and whose levels can be affected by disease states. We hypothesize that there are human homologs of differentially expressed (DE) miRNA in the plasma of CCM murine models that can be identified in CCM patients. We further hypothesize that these miRNAs have gene targets within previously published CCM transcriptomes, mechanistically linking them to CCM disease. Methods: Plasma miRNAs from homozygous and heterozygous Ccm1 and Ccm3 mice, as well as their respective wild type controls were sequenced and analyzed. Putative gene targets of DE miRNAs [p&lt;0.05, false discovery rate (FDR) corrected] were queried in previously published mouse CCM transcriptomes. The human homologs of the DE miRNAs in the plasma of Ccm1 and Ccm3 mouse models were identified and assessed in the plasma of healthy controls (n=13), CCM1 (n=11), and CCM3 (n=11) patients using RT-qPCR. Results: 5 miRNAs in homozygous and 10 in heterozygous for Ccm1 , while 45 in homozygous and 2 in heterozygous for Ccm3 were DE in the plasma of mouse models (p&lt;0.05, FDR corrected), had gene targets within CCM mouse transcriptomes, and have a human homolog. Preliminary results show mmu-miR-375-3p as DE in both Ccm1 +/- and Ccm3 -/- mice. RT-qPCR assays show that plasma relative quantification values of the human homolog hsa-miR-375-3p were higher in CCM3 than in CCM1 patients ( p &lt;0.001) and in healthy controls ( p &lt;0.05). Conclusion: DE plasma miRNAs identified in mouse models with human homologs and putative gene targets mechanistically implicated in CCM disease may be used as candidate biomarkers for specific clinical contexts.
Association of plasma zinc levels with anti-SARS-CoV-2 IgG and IgA seropositivity in the general population: A case–control study (2023)

CORONA IMMUNITAS:: ISRCTN18181860.
Supplementary Dataset 1 from Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability (2023)

&lt;p&gt;Clinical data of gastric cancer patients whose genomic data was aggregrated for integrated analysis.&lt;/p&gt;
Synthesis and Discovery of Macrocyclic Polyoxygenated Bis-7-azaindolylmaleimides as a Novel Series of Potent and Highly Selective Glycogen Synthase Kinase-3β Inhibitors (2003)

Attempts to design the macrocyclic maleimides as selective protein kinase C gamma inhibitors led to the unexpected discovery of a novel series of potent and highly selective glycogen synthase kinase-3beta (GSK-3beta) inhibitors. Palladium-catalyzed cross-coupling reactions were used to synthesize the key intermediates 17 and 22 that resulted in the synthesis of novel macrocycles. All three macrocyclic series (bisindolyl-, mixed 7-azaindoleindolyl-, and bis-7-azaindolylmaleimides) were found to have submicromolar inhibitory potency at GSK-3beta with various degrees of selectivity toward other protein kinases. To gain the inhibitory potency at GSK-3beta, the ring sizes of these macrocycles may play a major role. To achieve the selectivity at GSK-3beta, the additional nitrogen atoms in the indole rings may contribute to a significant degree. Overall, the bis-7-azaindolylmaleimides 28 and 29 exhibited little or no inhibitions to a panel of 50 protein kinases. Compound 29 almost behaved as a GSK-3beta specific inhibitor. Both 28 and 29 displayed good potency in GS cell-based assay. Molecular docking studies were conducted in an attempt to rationalize the GSK-3beta selectivity of azaindolylmaleimides.
Review of terahertz and subterahertz wireless communications (2010)

According to Edholm’s law, the demand for point-to-point bandwidth in wireless short-range communications has doubled every 18 months over the last 25 years. It can be predicted that data rates of around 5–10 Gb/s will be required in ten years. In order to achieve 10 Gb/s data rates, the carrier frequencies need to be increased beyond 100 GHz. Over the past ten years, several groups have considered the prospects of using sub-terahertz (THz) and THz waves (100–2000 GHz) as a means to transmit data wirelessly. Some of the reported advantages of THz communications links are inherently higher bandwidth compared to millimeter wave links, less susceptibility to scintillation effects than infrared wireless links, and the ability to use THz links for secure communications. Our goal of this paper is to provide a comprehensive review of wireless sub-THz and THz communications.
Adult intussusceptions in descending colon (2018)

Intussusception is a rare event in adults which constitutes 1–3% of all cases of intestinal obstruction. Malignant etiology as causes of intussusception is more common in large bowel accounting for 60–65% cases. Intussusception due to colonic lipoma is rare. The present case is a 45-year-old woman who had a polypoidal growth in the descending colon. She was operated and the growth was histopathologically diagnosed as lipoma. Though rare, colonic lipoma should be considered as a probable etiology for intussusceptions.
Optically Active Allenes from an Allylic Substitution/Isomerization Sequence (2013)

It takes two to trisubstitute: A two-step procedure involving enantioselective allylic alkylation followed by 1,3 hydrogen shift enables the catalytic asymmetric synthesis of trisubstituted allenes.
The Role of Proteolytic Enzymes in the Development of Pulmonary Emphysema and Periodontal Disease (1994)

Pulmonary emphysema and periodontal disease are each characterized by the uncontrolled proteolysis of connective tissue proteins by proteinases derived from human neutrophils. Although these diseases would not appear to be related in terms of the initial insult to individual tissues, the ultimate result in each disease is the accumulation and degranulation of neutrophils at inflammatory sites, apparently as a result of frustrated phagocytosis and specific activation of these phagocytic cells. This result is easily recognized in the case of emphysema, where there is clear evidence that the primary cause of the disease is the accumulation of foreign materials in the lung (e.g., smoke condensate), followed by the recruitment of neutrophils to the organ and the release of oxidative and hydrolytic enzymes. In periodontitis, however, the problem begins with the accumulation of plaque at the base of the teeth, followed by the growth of opportunistic anaerobic bacteria below the gum line. These parasitic microbes, which are resistant to killing by both monocytes and granulocytes, secrete proteinases that can activate the kallikrein-kinin pathway, degrade clotting factors, and release the potent neutrophil chemotactic factor, C5a, from complement. It is under such conditions that neutrophils are recruited to infected sites within the periodontium. After the neutrophil-recruitment stage, the two diseases become similar in that degranulation of neutrophils occurs during attempted phagocytosis of either cigarette smoke components (emphysema) or bacteria (periodontitis), followed by inactivation of tissue proteinase inhibitors and degradation of connective tissue proteins, the ultimate result being the destruction of the alveolus or gingiva, respectively.
Microwave Dielectric Properties of Epitaxial Mn-doped Ba(Zr,Ti)O3Thin Films on LaAlO3Substrates (2013)

Environmental friendly ferroelectric relaxor Ba(Zr0.2Ti0.8)O3 thin films with an additional 2% Mn dopant were epitaxially fabricated on the (001) LaAlO3 single crystal substrates by pulsed laser deposition. Microstructure characterizations from x-ray diffraction suggest that the films are c-axis oriented with the interface relationship of [101]Mn:BZT//[100]LAO and (001)Mn:BZT //(001)LAO. The microwave dielectric property measurements (13–17.5 GHz) reveal that the films have excellent dielectric properties with large tunability, high dielectric constant, and low dielectric loss, which the average value is 25.9%, 169 and 0.054, respectively. It is indicated that the additional 2% Mn doped Ba(Zr0.2Ti0.8)O3 thin films can be used for the development of the room temperature tunable microwave elements and related device applications.