gebhart/patrepeval huggingface dataset:
Self-Assembly of Amphiphilic Dendritic Dipeptides into Helical Pores (2004)

Abstract Natural pore-forming proteins act as viral helical coats1 and transmembrane channels2, 3, 4, exhibit antibacterial activity5 and are used in synthetic systems, such as for reversible encapsulation6 or stochastic sensing7. These diverse functions are intimately linked to protein structure1, 2, 3, 4. The close link between protein structure and protein function makes the design of synthetic mimics a formidable challenge, given that structure formation needs to be carefully controlled on all hierarchy levels, in solution and in the bulk. In fact, with few exceptions8, 9, synthetic pore structures capable of assembling into periodically ordered assemblies that are stable in solution and in the solid state10, 11, 12, 13 have not yet been realized. In the case of dendrimers, covalent14 and non-covalent15 coating and assembly of a range of different structures15, 16, 17 has only yielded closed columns18. Here we describe a library of amphiphilic dendritic dipeptides that self-assemble in solution and in bulk through a complex recognition process into helical pores. We find that the molecular recognition and self-assembly process is sufficiently robust to tolerate a range of modifications to the amphiphile structure, while preliminary proton transport measurements establish that the pores are functional. We expect that this class of self-assembling dendrimers will allow the design of a variety of biologically inspired systems with functional properties arising from their porous structure.
Generative Attribute Controller with Conditional Filtered Generative Adversarial Networks (2017)

We present a generative attribute controller (GAC), a novel functionality for generating or editing an image while intuitively controlling large variations of an attribute. This controller is based on a novel generative model called the conditional filtered generative adversarial network (CFGAN), which is an extension of the conventional conditional GAN (CGAN) that incorporates a filtering architecture into the generator input. Unlike the conventional CGAN, which represents an attribute directly using an observable variable (e.g., the binary indicator of attribute presence) so its controllability is restricted to attribute labeling (e.g., restricted to an ON or OFF control), the CFGAN has a filtering architecture that associates an attribute with a multi-dimensional latent variable, enabling latent variations of the attribute to be represented. We also define the filtering architecture and training scheme considering controllability, enabling the variations of the attribute to be intuitively controlled using typical controllers (radio buttons and slide bars). We evaluated our CFGAN on MNIST, CUB, and CelebA datasets and show that it enables large variations of an attribute to be not only represented but also intuitively controlled while retaining identity. We also show that the learned latent space has enough expressive power to conduct attribute transfer and attribute-based image retrieval.
Nanotwinned metal MEMS films with unprecedented strength and stability (2017)

Silicon-based microelectromechanical systems (MEMS) sensors have become ubiquitous in consumer-based products, but realization of an interconnected network of MEMS devices that allows components to be remotely monitored and controlled, a concept often described as the "Internet of Things," will require a suite of MEMS materials and properties that are not currently available. We report on the synthesis of metallic nickel-molybdenum-tungsten films with direct current sputter deposition, which results in fully dense crystallographically textured films that are filled with nanotwins. These films exhibit linear elastic mechanical behavior and tensile strengths exceeding 3 GPa, which is unprecedented for materials that are compatible with wafer-level device fabrication processes. The ultrahigh strength is attributed to a combination of solid solution strengthening and the presence of dense nanotwins. These films also have excellent thermal and mechanical stability, high density, and electrical properties that are attractive for next-generation metal MEMS applications.
Effect of UV wavelength on the hardening process of porogen-containing and porogen-free ultralow-k plasma-enhanced chemical vapor deposition dielectrics (2011)

The effect of narrow-band 172 nm and broad-band &amp;gt;200 nm UV sources in the new curing scheme of the plasma-enhanced chemical vapor deposition (PECVD) dielectrics is studied. The new curing scheme is based on porogen removal (organic sacrificial phase introduced to generate open porosity) from PECVD dielectric before its final UV curing. The results are compared with the PECVD films fabricated in the conventional scheme in which porogen is still present during the UV curing. The same curing time of porogen-containing conventional PECVD films with 172 nm and &amp;gt;200 nm UV sources results in only 10% difference in their Young’s modulus (YM): 5.84 and 5.32 GPa, respectively. However, the porogen-free films cured with 172 nm UV source show a YM of 6.64 GPa (k100 kHz∼2.2, 44% open porosity), approximately twice as large as those cured with &amp;gt;200 nm UV having a YM of 3.38 GPa (k100 kHz∼2.0, 48% open porosity). The mechanical properties, optical properties in the range of 150–800 nm, dielectric constants at 100 kHz and 4 GHz, porosities, pore size distributions, and bonding structure are evaluated. The impact of porogen on optical characteristics and, therefore, on the photochemical UV-hardening mechanism is discussed. The achieved mechanical properties are explained on a basis of the percolation of rigidity theory and random network concepts.
Humorale Immunreaktion von Patienten mit Lungenkarzinom gegen TPTE (Transmembrane Phosphatase with TEnsin homology) (2018)

Das cancer/testis – Antigen Transmembrane Phosphatase with TEnsin homology (TPTE) wird aberrant auf den Zellen zahlreicher Tumorentitäten und auch beim Lungenkarzinom exprimiert. In dieser Studie analysierten wir den prognostischen Wert von Autoantikörpern gegen das Antigen-TPTE im Serum von Patienten mit Lungenkarzinom.
The performance analysis of a multi-carrier CDMA system using DQPSK modulation for frequency selective fading channels (2002)

In this paper, we present a multi-carrier CDMA system using differential QPSK modulation in urban mobile environment. From the analysis and simulation results, we find that the performance of the multi-carrier CDMA system is improved with the aid of guard interval, especially in the case of existing strong interference from other users. Compared with the traditional DQPSK-DS-CDMA system, the advantage of multi-carrier CDMA is also evident.
Type II restriction modification system methylation subunit of Alicyclobacillus acidocaldarius (2023)

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering recombination inside or outside of a cell using isolated and/or purified polypeptides and/or nucleic acid sequences from Alicyclobacillus acidocaldarius.
7.5 Cellular 4G LTE Aeronautical Mobile Telemetry Flight Test Results (2020)

Flight test results on a novel approach to Aeronautical Mobile Telemetry (AMT) employing 4G Long Term Evolution (LTE) Cellular Technology are presented. In this system, Doppler shifts are handled by an appliqu providing a front-end to a Commercial-Off-The-Shelf (COTS) LTE modem. The appliqu performs Doppler compensation via real time analysis of LTE signals and allows seamless operation of LTE signaling, including connection setup and handover events. The flight test results clearly demonstrate the capability of the system to sustain an uninterrupted LTE connection at varying aircraft speeds that produce Doppler shifts that are significantly higher than what typical commercial LTE systems can handle. In these tests, the radio link delivered substantial bi-directional data rates up to a maximum range of 60km, while the combination of Doppler compensation and handovers at the TA provided an uninterrupted radio link in both directions. Overall, the flight test confirmed that an airborne COTS LTE transceiver in combination with a Doppler compensation appliqu can successfully operate at high aircraft speeds. This proof-of-concept flight test also forms a basis from which to further refine AMT solutions based on 4G, and the emerging 5G technologies.
The Top 10 oomycete pathogens in molecular plant pathology (2014)

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
Inflammation, Endoplasmic Reticulum Stress, Autophagy, and the Monocyte Chemoattractant Protein-1/CCR2 Pathway (2012)

Numerous inflammatory cytokines have been implicated in the pathogenesis of cardiovascular diseases. Monocyte chemoattractant protein (MCP)-1/CCL2 is expressed by mainly inflammatory cells and stromal cells such as endothelial cells, and its expression is upregulated after proinflammatory stimuli and tissue injury. MCP-1 can function as a traditional chemotactic cytokine and also regulates gene transcription. The recently discovered novel zinc-finger protein, called MCPIP (MCP-1-induced protein), initiates a series of signaling events that causes oxidative and endoplasmic reticulum (ER) stress, leading to autophagy that can result in cell death or differentiation, depending on the cellular context. After a brief review of the basic processes involved in inflammation, ER stress, and autophagy, the recently elucidated role of MCP-1 and MCPIP in inflammatory diseases is reviewed. MCPIP was found to be able to control inflammatory response by inhibition of nuclear factor-κB activation through its deubiquitinase activity or by degradation of mRNA encoding a set of inflammatory cytokines through its RNase activity. The potential inclusion of such a novel deubiquitinase in the emerging anti-inflammatory strategies for the treatment of inflammation-related diseases such as cardiovascular diseases and type 2 diabetes is briefly discussed.
Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro (2023)

The 3C-like protease (3CLpro) is an essential enzyme for the replication of SARS-CoV-2 and other coronaviruses and thus is a target for coronavirus drug discovery. Nearly all inhibitors of coronavirus 3CLpro reported so far are covalent inhibitors. Here, we report the development of specific, noncovalent inhibitors of 3CLpro. The most potent one, WU-04, effectively blocks SARS-CoV-2 replications in human cells with EC<sub>50</sub> values in the 10-nM range. WU-04 also inhibits the 3CLpro of SARS-CoV and MERS-CoV with high potency, indicating that it is a pan-inhibitor of coronavirus 3CLpro. WU-04 showed anti-SARS-CoV-2 activity similar to that of PF-07321332 (Nirmatrelvir) in K18-hACE2 mice when the same dose was administered orally. Thus, WU-04 is a promising drug candidate for coronavirus treatment.
Antibodies to a cell surface histone-like protein protect against Histoplasma capsulatum (2003)

A protective role for antibodies has not previously been described for host defense against the pathogenic fungus Histoplasma capsulatum (Hc). Mouse mAb's were generated from mice immunized with Hc yeast that binds the cell surface of Hc. Administration of mAb's before Hc infection reduced fungal burden, decreased pulmonary inflammation, and prolonged survival in a murine infection model. Protection mediated by mAb's was associated with enhanced levels of IL-4, IL-6, and IFN-γ in the lungs of infected mice. The mAb's increased phagocytosis of yeast by J774.16 cells through a CR3-dependent process. Ingestion of mAb-opsonized Hc by J774.16 macrophage-like cells was associated with yeast cell growth inhibition and killing. The mAb's bound to a 17-kDa antigen expressed on the surface of Hc. The antigen was identified as a histone H2B–like protein. This study establishes that mAb's to a cell surface protein of Hc alter the intracellular fate of the fungus and mediate protection in a murine model of lethal histoplasmosis, and it suggests a new candidate antigen for vaccine development.
π-Conjugated multiporphyrin box via self-assembly of an ethynylene-bridged zinc porphyrin dimer (2003)

An ethynylene-bridged zinc porphyrin dimer bearing metal-coordinating groups, such as bis[{5-(4-pyridyl)-15-(3,5-didodecyloxyphenyl)porphyrinato}zinc] Z2, self-assembles in CHCl 3 to form a rectangular-shaped supramolecular nano box, in which all the Z2 units preferentially adopt a planar conformation with a syn-parallel geometry as for the pyridyl groups.
Inhaled short interfering RNA as a promising approach to the therapy of viral respiratory infections (2005)

Respiratory viruses, exemplified by respiratory syncytial virus (RSV), influenza virus and parainfluenza virus (PIV), are major serial killers, claiming millions of human lives annually worldwide. Respiratory infection byRSV and PIV is the most prevalent cause of pediatric hospitalization in industrialized Western nations. In the U.S. alone, it leads to > 90,000 admissions per year at a cost of about $300 million. The lack of a reliable vaccine or drugs against these viruses, in part due to the high mutation rate of the viral RNA genomes, has led to a desperate search for novel strategies for intervention, the most recent of which is RNA interference (RNAi). Studies within the past 4 years have established RNAi as a reliable technology to silence viral gene expression via post-transcriptional mechanisms. In exciting recent results, intranasally applied short interfering RNA (siRNA) provided protection, as well as cure, against both RSV and PIV in a mouse model, supporting inhaled siRNA as a highly promising antiviral drug of the future. This review summarizes the delivery, function and pharmacology of inhaled siRNA.
Novel prognostic prediction models for patients with stage IV colorectal cancer after concurrent curative resection (2016)

We developed novel and reliable personalised prognostic models, integrating tumour, node, metastasis (TNM) factors as well as the preoperative serum carcinoembryonic antigen level, tumour location and metastatic lesions, to predict patients' prognosis following surgically curative resection. This individualised prediction model may help clinicians in the treatment of postoperative stage IV CRC following surgically curative resection.
Imaging radial distribution functions of complex particles by relayed dynamic nuclear polarization (2023)

Raw data and Matlab scripts from the publication at https://doi.org/10.1021/jacs.3c01279 All codes are provided free of charge and come with no warranty. Future use (original or modified) is required to cite: Zenedo data deposit at DOI 10.5281/zenodo.7756308 Berruyer P., Cibaka-Ndaya C. , Pinon A., Sanchez C., Drisko G. L., and Emsley L.. Imaging radial distribution functions of complex particles by relayed dynamic nuclear polarization. <em>J. Am. Chem. Soc.</em> <strong>2023.</strong> https://doi.org/10.1021/jacs.3c01279 The data are organized in two separated folders, each corresponding to two different samples (<strong>A</strong> and <strong>B</strong>) analyzed in the aforementioned manuscript. Below “<em>i”</em> denoted for “SampleA” or “SampleB”, depending on the considered samples. <em>i</em>_0_raw_nmr_data.zip is a ZIP folder that contains all the raw NMR data in topspin format for sample <em>i</em>. These data are transferred into Matlab using the script <em>i</em>_1_extract_nmr_data_from_topspin.m. The latter Matlab script eventually saved the NMR data within a Matlab MAT-file <em>i</em>_2_extracted_nmr_data.mat. The Matlab script <em>i</em>_3_RDNP_imaging.m used the extracted NMR data saved within the <em>i</em>_2_extracted_nmr_data.mat file. Note that this script uses parallel computing capabilities of Matlab and it is recommended to run it with a high performance computing (HPC) facilities. It performs the data fitting to obtain the final internal composition of the studied particles. Once the program converged, the data are automatically saved as a Matlab MAT-file under the name <em>i</em>_4_composition_fitted.mat. Finally, the internal structure is plotted using the Matlab script <em>i</em>_5_plot_from_fit.m.
Conformation as a Protecting Group: A Regioselective Aromatic Bromination En Route to Complex π-Electron Systems (2008)

A new strategy to achieve regioselective functionalization of a sterically congested aromatic system driven by conformational demands is described. Electrophilic substitution occurs at the more planarizable subunit without undesired chemistry at mutually reactive sites and without the need for protecting or masking groups that must be manipulated later. Model studies are described to understand this selectivity, and possibilities for the construction of orthogonal, differentially substituted pi-systems of relevance for molecular electronics are demonstrated.
Importance of tyrosine phosphorylation for transmembrane signaling in plants (2021)

Reversible protein phosphorylation is a widespread post-translational modification fundamental for signaling across all domains of life. Tyrosine (Tyr) phosphorylation has recently emerged as being important for plant receptor kinase (RK)-mediated signaling, particularly during plant immunity. How Tyr phosphorylation regulates RK function is however largely unknown. Notably, the expansion of protein Tyr phosphatase and SH2 domain-containing protein families, which are the core of regulatory phospho-Tyr (pTyr) networks in choanozoans, did not occur in plants. Here, we summarize the current understanding of plant RK Tyr phosphorylation focusing on the critical role of a pTyr site ('VIa-Tyr') conserved in several plant RKs. Furthermore, we discuss the possibility of metazoan-like pTyr signaling modules in plants based on atypical components with convergent biochemical functions.
Bidirectional Photoinduced Energy Transfer in Nanoassemblies of Quantum Dots and Luminescent Metal Complexes (2014)

This work describes the synthesis and photophysical characterization of Ir(III) and Ru(II) complexes bearing terminal amino groups, which act as anchoring units for the attachment to quantum dots, QDs. The photophysical properties of the metal complexes in combination with different types of QDs, allows directional photoinduced processes in the assemblies. In particular, we show photoinduced energy transfer from the luminescent excited Ir(III) unit to the CdTe nanocrystals, with an efficiency of 40%. The directionality was then inverted by employing an emitting Ru(II) complex as energy acceptor, in combination with photoluminescent CdSe/ZnS quantum dots. The efficiency of the photoinduced energy transfer from the nanocrystals to the Ru(II) center was estimated to be as high as 75%. This work provides model systems for nanoassemblies based on quantum dots and metal complexes for optoelectronic applications, and as active light-harvesting systems.
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys (2022)

The SARS-CoV-2 Omicron variant has very high levels of transmission, is resistant to neutralization by authorized therapeutic human monoclonal antibodies (mAb) and is less sensitive to vaccine-mediated immunity. To provide additional therapies against Omicron, we isolated a mAb named P2G3 from a previously infected vaccinated donor and showed that it has picomolar-range neutralizing activity against Omicron BA.1, BA.1.1, BA.2 and all other variants tested. We solved the structure of P2G3 Fab in complex with the Omicron spike using cryo-electron microscopy at 3.04 Å resolution to identify the P2G3 epitope as a Class 3 mAb that is different from mAb-binding spike epitopes reported previously. Using a SARS-CoV-2 Omicron monkey challenge model, we show that P2G3 alone, or in combination with P5C3 (a broadly active Class 1 mAb previously identified), confers complete prophylactic or therapeutic protection. Although we could select for SARS-CoV-2 mutants escaping neutralization by P2G3 or by P5C3 in vitro, they had low infectivity and 'escape' mutations are extremely rare in public sequence databases. We conclude that this combination of mAbs has potential as an anti-Omicron drug.
Natural Killer (NK) Cell Activating Factor Produced by a Human T‐Cell Hybridoma (1991)

A human T-cell hybridoma (KC8-1.10), whose culture supernatant augments peripheral blood lymphocytes (PBL)-mediated spontaneous cytotoxicity against K562 cells, was established. This activity [natural killer (NK) cell activating activity] appears to be not due to interferon-gamma (IFN-gamma) and interleukin-2 (IL-2) for the following reasons: 1) KC8-1.10 produced negligible or small amounts of IFNs and IL-2. 2) The NK cell activating activity in the KC8-1.10 culture supernatant was not neutralized by anti-IFN-gamma antiserum and stable even after pH 2 treatment for 24 hr, which is known to destroy IFN-gamma activity. 3) IL-2-dependent cell line absorbed IL-2 more efficiently than it absorbed the NK cell activating activity, and the latter activity was not retained by Blue Sepharose column in contrast with IL-2. The NK cell activating factor in the KC8-1.10 culture supernatant appears to be a glycoprotein, because the activity was abolished with pronase treatment or with boiling for 5 min and because the activity was retained by concanavalin A- and Pisum sativum agglutinin-agarose. Finally it was found that the NK cell activating activity requires Leu 11b+ cells to exert its effect.
The Persistent Müllerian Duct Syndrome: An Update Based Upon a Personal Experience of 157 Cases (2017)

Male sex differentiation is driven by 2 hormones, testosterone and anti-müllerian hormone (AMH), responsible for the regression of müllerian ducts in male fetuses. Mutations inactivating AMH or its receptor AMHRII lead to the persistent müllerian duct syndrome (PMDS) in otherwise normally virilized 46,XY males. Our objective was to review the clinical, anatomical, and molecular features of PMDS based upon a review of the literature and upon 157 personal cases. Three clinical presentations exist: bilateral cryptorchidism, unilateral cryptorchidism with contralateral hernia, and transverse testicular ectopia. Abnormalities of male excretory ducts are frequent. Testicular malignant degeneration occurs in 33% of adults with the disorder, while cancer of müllerian derivatives is less frequent. Fertility is rare but possible if at least one testis is scrotal and its excretory ducts are intact. Eighty families with 64 different mutations of the AMH gene have been identified, mostly in exons 1, 2, and 5. AMHRII gene mutations representing 58 different alleles have been discovered in 75 families. The most common mutation, a 27-bp deletion in the kinase domain, was found in 30 patients of mostly Northern European origin. In 12% of cases, no mutation of AMH or AMHRII has been detected, suggesting a disruption of other pathways involved in müllerian regression.