gebhart/patrepeval huggingface dataset:
Maturation and circuit integration of transplanted human cortical organoids (2022)

Self-organizing neural organoids represent a promising in vitro platform with which to model human development and disease<sup>1-5</sup>. However, organoids lack the connectivity that exists in vivo, which limits maturation and makes integration with other circuits that control behaviour impossible. Here we show that human stem cell-derived cortical organoids transplanted into the somatosensory cortex of newborn athymic rats develop mature cell types that integrate into sensory and motivation-related circuits. MRI reveals post-transplantation organoid growth across multiple stem cell lines and animals, whereas single-nucleus profiling shows progression of corticogenesis and the emergence of activity-dependent transcriptional programs. Indeed, transplanted cortical neurons display more complex morphological, synaptic and intrinsic membrane properties than their in vitro counterparts, which enables the discovery of defects in neurons derived from individuals with Timothy syndrome. Anatomical and functional tracings show that transplanted organoids receive thalamocortical and corticocortical inputs, and in vivo recordings of neural activity demonstrate that these inputs can produce sensory responses in human cells. Finally, cortical organoids extend axons throughout the rat brain and their optogenetic activation can drive reward-seeking behaviour. Thus, transplanted human cortical neurons mature and engage host circuits that control behaviour. We anticipate that this approach will be useful for detecting circuit-level phenotypes in patient-derived cells that cannot otherwise be uncovered.
Mid-infrared chirped-pulse upconversion with four-wave difference frequency generation in gases (2013)

Chirped-pulse upconversion of sub-single-cycle mid-infrared pulses with gaseous media has been realized. Single-shot detection of mid-infrared spectra from 250 to 5500 cm−1 with 5 cm−1 resolution was demonstrated.
Similarity-Based Multimodal Regression (2022)

Abstract To better understand complex human phenotypes, large-scale studies have increasingly collected multiple data modalities across domains such as imaging, mobile health, and physical activity. The properties of each data type often differ substantially and require either separate analyses or extensive processing to obtain comparable features for a combined analysis. Multimodal data fusion enables certain analyses on matrix-valued and vector-valued data, but it generally cannot integrate modalities of different dimensions and data structures. For a single data modality, multivariate distance matrix regression provides a distance-based framework for regression accommodating a wide range of data types. However, no distancebased method exists to handle multiple complementary types of data. We propose a novel distance-based regression model, which we refer to as Similarity-based Multimodal Regression (SiMMR), that enables simultaneous regression of multiple modalities through their distance profiles. We demonstrate through simulation, imaging studies, and longitudinal mobile health analyses that our proposed method can detect associations in multimodal data of differing properties and dimensionalities, even with modest sample sizes. We perform experiments to evaluate several different test statistics and provide recommendations for applying our method across a broad range of scenarios.
Internal strain monitoring in composite materials with embedded photonic crystal fiber Bragg gratings (2014)

The possibility of embedding optical fiber sensors inside carbon fiber reinforced polymer (CFRP) for structural health monitoring purposes has already been demonstrated previously. So far however, these sensors only allowed axial strain measurements because of their low sensitivity for strain in the direction perpendicular to the optical fiber’s axis. The design flexibility provided by novel photonic crystal fiber (PCF) technology now allows developing dedicated fibers with substantially enhanced sensitivity to such transverse loads. We exploited that flexibility and we developed a PCF that, when equipped with a fiber Bragg grating (FBG), leads to a sensor that allows measuring transverse strains in reinforced composite materials, with an order of magnitude increase of the sensitivity over the state-of-the-art. In addition it allows shear strain sensing in adhesive bonds, which are used in composite repair patches. This is confirmed both with experiments and finite element simulations on such fibers embedded in CFRP coupons and adhesive bonds. Our sensor brings the achievable transverse strain measurement resolution close to a target value of 1 &mu;strain and could therefore play an important role for multi-dimensional strain sensing, not only in the domain of structural health monitoring, but also in the field of composite material production monitoring. Our results thereby illustrate the added value that PCFs have to offer for internal strain measurements inside composite materials and structures.
Automated localization of periventricular and subcortical white matter lesions (2007)

It is still unclear whether periventricular and subcortical white matter lesions (WMLs) differ in etiology or clinical consequences. Studies addressing this issue would benefit from automated segmentation and localization of WMLs. Several papers have been published on WML segmentation in MR images. Automated localization however, has not been investigated as much. This work presents and evaluates a novel method to label segmented WMLs as periventricular and subcortical. The proposed technique combines tissue classification and registration-based segmentation to outline the ventricles in MRI brain data. The segmented lesions can then be labeled into periventricular WMLs and subcortical WMLs by applying region growing and morphological operations. The technique was tested on scans of 20 elderly subjects in which neuro-anatomy experts manually segmented WMLs. Localization accuracy was evaluated by comparing the results of the automated method with a manual localization. Similarity indices and volumetric intraclass correlations between the automated and the manual localization were 0.89 and 0.95 for periventricular WMLs and 0.64 and 0.89 for subcortical WMLs, respectively. We conclude that this automated method for WML localization performs well to excellent in comparison to the gold standard.
FIDO rover field trials as rehearsal for the NASA 2003 Mars Exploration Rovers mission (2003)

This paper describes recent extended field trials performed using the FIDO (Field Integrated Design & Operations) rover, an advanced NASA technology development platform and research prototype for the next planned rover mission to Mars. Realistic physical simulation of the NASA 2003 Mars Exploration Rovers mission was achieved through collaborative efforts of roboticists, planetary scientists, and mission operations personnel. An overview of the objectives, approach, and results is reported.
Nucleoprotein‐specific nonneutralizing antibodies speed up <scp>LCMV</scp> elimination independently of complement and <scp>F</scp>cγ<scp>R</scp> (2013)

CD 8 + T cells have an essential role in controlling lymphocytic choriomeningitis virus ( LCMV ) infection in mice. Here, we examined the contribution of humoral immunity, including nonneutralizing antibodies ( A bs), in this infection induced by low virus inoculation doses. Mice with impaired humoral immunity readily terminated infection with the slowly replicating LCMV strain A rmstrong but showed delayed virus elimination after inoculation with the faster replicating LCMV strain WE and failed to clear the rapidly replicating LCMV strain D ocile, which is in contrast to the results obtained with wild‐type mice. Thus, the requirement for adaptive humoral immunity to control the infection was dependent on the replication speed of the LCMV strains used. Ab transfers further showed that LCMV ‐specific I g G A bs isolated from LCMV immune serum accelerated virus elimination. These A bs were mainly directed against the viral nucleoprotein ( NP ) and completely lacked virus neutralizing activity. Moreover, m A bs specific for the LCMV NP were also able to decrease viral titers after transfer into infected hosts. Intriguingly, neither C 3 nor F cγ receptors were required for the antiviral activity of the transferred A bs. In conclusion, our study suggests that rapidly generated nonneutralizing A bs specific for the viral NP speed up virus elimination and thereby may counteract T ‐cell exhaustion.
X-ray study of anisotropically shaped metal halide perovskite nanoparticles in tubular pores (2018)

Recently, we have reported that metal halide perovskite nanoparticles formed in nanoporous alumina and silicon thin films exhibit blue shifted photoluminescence due to spatial confinement, thus allowing for color tuning of the emission by varying the pore size. While perovskite nanoparticles grown in nanoporous alumina films have been integrated into LEDs, similar approaches have failed with silicon. Here, we report the results of investigating the structure of the alumina pore system and the perovskite crystallites forming within. We use two x-ray diffraction techniques, namely, small-angle x-ray scattering (SAXS) and high-energy microbeam wide-angle x-ray scattering (WAXS). SAXS reveals that the alumina pore system diffracts like regularly arranged tubes with the average diameter and nearest neighbor distance of 12 nm and 20 nm, respectively. High-energy microbeam WAXS shows that perovskite nanoparticles within the nanoporous alumina have a distinctly anisotropic shape with the average particle length along and perpendicular to the pore axis of 26 nm and 13 nm, respectively. In contrast, no shape anisotropy has been detected for nanoparticles inside the silicon pores in a previous study. This suggests that utilizing nanoporous alumina has a twofold advantage. First, the tubular alumina pores, spanning the entire insulating film, offer percolated paths for the perovskite to fill. Second, the elongation of the nanoparticles in the tubular alumina pores can be expected to aid device performance as the length of the nanoparticles approaches the active layer thickness (ca. 40 nm) of LEDs, while the small diameter of the crystallites accounts for the observed blue shifted emission.
ChemInform Abstract: A Cascade of Reactions Involving Anchimeric Assistance Leads to a Highly “Crowded” Hexa(alkylcarboxy)benzene. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The biological efficacy profile of <scp>BAX</scp> 855, a <scp>PEG</scp>ylated recombinant factor <scp>VIII</scp> molecule (2014)

Summary Prophylaxis prevents joint and other bleeding episodes in patients with haemophilia A. Development of new factor concentrates with longer circulating half‐lives may encourage patients to start, continue or resume prophylaxis. The aim of this study was to compare the pharmacodynamic effect of a PEGylated full‐length recombinant factor VIII ( rFVIII ) concentrate with that of an unmodified rFVIII concentrate with respect to the duration of prophylactic efficacy in a murine model of haemophilic joint bleeding. Mice were pretreated with BAX 855 or unmodified rFVIII at specified times before right knee puncture to induce haemarthrosis; left knee joints served as controls. Joint bleeding was evaluated using a combination of visual and histological assessments. Administration of a single dose of unmodified rFVIII before joint puncture prevented haemarthrosis in mice up to 24 h, whereas pretreatment with BAX 855 protected the joint from bleeding up to 48 h. This pharmacodynamic study showed prolonged efficacy of BAX 855 compared to ADVATE in a haemophilia A mouse joint bleeding model. This finding supports the possibility of using BAX 855 to increase FVIII trough levels and/or extend the dosing interval in patients with haemophilia A on prophylaxis, which may potentially improve prophylactic efficacy and long‐term adherence.
CD70 antibody‐drug conjugate: A potential novel therapeutic agent for ovarian cancer (2021)

This study aimed to investigate the cytotoxicity of a cluster of differentiation 70 antibody-drug conjugate (CD70-ADC) against ovarian cancer in in vitro and in vivo xenograft models. CD70 expression was assessed in clinical samples by immunohistochemical analysis. Western blotting and fluorescence-activated cell sorting analyses were used to determine CD70 expression in the ovarian cancer cell lines A2780 and SKOV3, and in the cisplatin-resistant ovarian cancer cell lines A2780cisR and SKOV3cisR. CD70 expression after cisplatin exposure was determined in A2780 cells transfected with mock- or nuclear factor (NF)-κB-p65-small interfering RNA. We developed an ADC with an anti-CD70 monoclonal antibody linked to monomethyl auristatin F and investigated its cytotoxic effect. We examined 63 ovarian cancer clinical samples; 43 (68.3%) of them expressed CD70. Among patients with advanced stage disease (n = 50), those who received neoadjuvant chemotherapy were more likely to exhibit high CD70 expression compared to those who did not (55.6% [15/27] vs 17.4% [4/23], P < .01). CD70 expression was confirmed in A2780cisR, SKOV3, and SKOV3cisR cells. Notably, CD70 expression was induced after cisplatin treatment in A2780 mock cells but not in A2780-NF-κB-p65-silenced cells. CD70-ADC was cytotoxic to A2780cisR, SKOV3, and SKOV3cisR cells, with IC<sub>50</sub> values ranging from 0.104 to 0.341 nmol/L. In A2780cisR and SKOV3cisR xenograft models, tumor growth in CD70-ADC treated mice was significantly inhibited compared to that in the control-ADC treated mice (A2780cisR: 32.0 vs 1639.0 mm<sup>3</sup> , P < .01; SKOV3cisR: 232.2 vs 584.9 mm<sup>3</sup> , P < .01). Platinum treatment induced CD70 expression in ovarian cancer cells. CD70-ADC may have potential therapeutic implications in the treatment of CD70 expressing ovarian cancer.
Channel modelling of human tissues at terahertz band (2016)

In this paper, the channel model is proposed to compute the path loss, delay and noise at THz band of interest (0.5 THz ~ 1.5 THz). The results shows that THz band channel is strongly dependent on both the type of the medium and the distance while the concentration of water have a lot of influence because it not only causes attenuation to the THz wave but also introduces non-white noise. Therefore, the proposed model paves the way to the further studies considering more body structures and tissue properties.
Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy (2018)

The development of effective strategies for the comprehensive identification and quantification of proteoforms in complex systems is a critical challenge in proteomics. Proteoforms, the specific molecular forms in which proteins are present in biological systems, are the key effectors of biological function. Thus, knowledge of proteoform identities and abundances is essential to unraveling the mechanisms that underlie protein function. We recently reported a strategy that integrates conventional top-down mass spectrometry with intact-mass determinations for enhanced proteoform identifications and the elucidation of proteoform families and applied it to the analysis of yeast cell lysate. In the present work, we extend this strategy to enable quantification of proteoforms, and we examine changes in the abundance of murine mitochondrial proteoforms upon differentiation of mouse myoblasts to myotubes. The integrated top-down and intact-mass strategy provided an increase of ∼37% in the number of identified proteoforms compared to top-down alone, which is in agreement with our previous work in yeast; 1779 unique proteoforms were identified using the integrated strategy compared to 1301 using top-down analysis alone. Quantitative comparison of proteoform differences between the myoblast and myotube cell types showed 129 observed proteoforms exhibiting statistically significant abundance changes (fold change >2 and false discovery rate <5%).
velink - A Blockchain-based Shared Mobility Platform for Private and Commercial Vehicles utilizing ERC-721 Tokens (2021)

Transportation of people and goods is important and crucial in the context of smart cities. The trend in regard of people's mobility is moving from privately owned vehicles towards shared mobility. This trend is even stronger in urban areas, where space for parking is limited, and the mobility is supported by the public transport system, which lowers the need for private vehicles. Several challenges and barriers of currently available solutions retard a massive growth of this mobility option, such as the trust problem, data monopolism, or intermediary costs. Decentralizing mobility management is a promising approach to solve the current problems of the mobility market, allowing to move towards a more usable internet of mobility and smart transportation. Leveraging blockchain technology allows to cut intermediary costs, by utilizing smart contracts. Important in this ecosystem is the proof of identity of participants in the blockchain network. To proof the possession of the claimed identity, the private key corresponding to the wallet address is utilized, and therefore essential to protect. In this paper, a blockchain-based shared mobility platform is proposed and a proof-of-concept is shown. First, current problems and state-of-the-art systems are analyzed. Then, a decentralized concept is built based on ERC-721 tokens, implemented in a smart contract, and augmented with a Hardware Security Module (HSM) to protect the confidential key material. Finally, the system is evaluated and compared against state-of-the-art solutions.
Targeting Extracellular Matrix Remodeling Restores BRAF Inhibitor Sensitivity in BRAFi-resistant Melanoma (2020)

BRAF inhibition results in a selective pressure toward higher expression of MT1-MMP. MT1-MMP is pivotal to an ECM-based signaling pathway that confers resistance to BRAFi therapy.
Intelligent Synthesis of Smart Ceramic Materials (2002)

Abstract This article is focus on the hydrothermal synthesis of smart ceramic materials that have a perovskite‐type structure. Perovskite compounds have the general formula ABO 3 , where the A cation is relatively large and of low valence and the B cation is relatively small. Hydrothermal synthesis involves numerous simultaneous reactions between dissolved and solid species in an aqueous system to form anhydrous multicomponent oxides. Hydrothermal media may provide an effective reaction environment for synthesizing numerous smart ceramic materials from a variety of precursor reagents (e.g., water‐soluble salts, hydroxides, oxides) in the form of polycrystalline solids, thin films, and single crystals. In particular, phase‐pure ceramic materials that have controlled stoichiometry and morphology can be hydrothermally synthesized in a single experimental step from simple and inexpensive precursors at moderate temperatures and pressures far below those required for conventional techniques. It is important to select a precursor system that is both reactive and cost‐effective. However, the reactivity of a precursor system can be judged only by optimizing the processing variables such as reagent (precursor) concentrations and ratios, pH, temperature, and pressure, which can be extremely time‐consuming due to the large number of variables involved. To improve the efficiency of evaluating a precursor system, a comprehensive thermodynamic model that simulates hydrothermal reactions has been developed. This model is a part of the OLI software. The simulation approach discussed here has been validated for numerous perovskite‐type multicomponent oxide systems, which include alkaline‐earth titanates and zirconates, lead titanate, various solid solutions of lead zirconate titanate, lead magnesium niobate, and lead zinc niobate. In this article, modeling and experimental validation of selected hydrothermal systems are presented.
ChemInform Abstract: Acid‐Catalyzed Rearrangements of 1‐Hydroxy‐2,3,4,4a‐tetrahydro‐9H‐xanthen‐9‐ones: Synthesis and Cycloaddition Reactions of 3,4‐Dihydro‐9H‐xanthen‐9‐ones. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Inactivation of myostatin by photooxygenation using functionalized <scp>d</scp>-peptides (2023)

Inhibition of myostatin is an attractive strategy for the treatment of muscular atrophic diseases such as muscular dystrophy. For the efficient inhibition of myostatin, functionalized peptides were developed by the conjugation of a 16-mer myostatin-binding d-peptide with a photooxygenation catalyst. These peptides induced myostatin-selective photooxygenation and inactivation under near-infrared irradiation, and were associated with little cytotoxicity or phototoxicity. The peptides are resistant to enzymatic digestion due to their d-peptide chains. These properties could contribute to the <i>in vivo</i> use of photooxygenation-based inactivation strategies targeting myostatin.
Thermal limitations of volume Bragg gratings used in lasers for spectral control (2013)

In this paper we present experiments and calculations of the property changes of a highly reflecting volume Bragg grating (VBG) when it is used as a laser cavity mirror. A small absorption of the reflected laser beam resulted in a laser output power roll-off, increased coupling through the VBG, and a change of the spectrum from a single to a double peak at high power. The simulations revealed that an inhomogeneous temperature distribution deformed the grating such that the diffraction efficiency was reduced and the light penetrated deeper into the VBG, which accelerated the deteriorating effects. We extrapolated the power limit found in our investigations for various beam radii and absorption coefficients.
Erratum. The Women’s Leadership Gap in Diabetes: A Call for Equity and Excellence. Diabetes Care 2021;44:1734–1743 (2022)

In the Results and Fig. 2B of article cited above, the percentage of female American Diabetes Association (ADA) Presidents of Medicine and Science was given as 9%; the correct percentage is 11%. This work undercounted one female individual serving in this leadership capacity. This miscalculation occurred as the specialized program (https://gender-api.com/) utilized to determine the most probable gender of each name provided an errant assignment. As noted in the methods, manual quality control was performed for names with accuracy scores &amp;lt;95. The software provided male gender for the individual in question, with an accuracy score of 97 that did not hit the threshold for further verification. Therefore, the article Results section, second paragraph in closing, should have stated: “Since the 1970s, 83% of persons appointed as ADA President of Health Care and Education have been women (Fig. 2A), but only 11% of those appointed as ADA President of Medicine and Science have been female (Fig. 2B).” The authors apologize for the error. The online version of the article (https://doi.org/10.2337/dci21-0015) has been updated to correct the error in the text and figure.
An Influenza Virus Hemagglutinin Computationally Optimized Broadly Reactive Antigen Elicits Antibodies Endowed with Group 1 Heterosubtypic Breadth against Swine Influenza Viruses (2020)

Computationally optimized broadly reactive antigens (COBRA) designed for different influenza virus subtypes (H1N1, H3N2, and H5N1) elicit a subtype-specific broad antibody (Ab) response in naive as well as in preimmune influenza virus animal models (1–9).