gebhart/patrepeval huggingface dataset:
Size-based sorting of hydrogel droplets using inertial microfluidics (2018)

Hydrogel droplets encapsulating cells and molecules provide a unique platform in biochemistry, biology, and medicine, including single-cell and single-molecule analysis, directed molecular evolution, and detection of cellular secretions. The ability to prepare hydrogel droplets with high monodispersity can lead to synchronization of populations, more controlled biomaterials, and more quantitative assays. Here, we present an inertial microfluidic device for passive, continuous, and high-throughput sorting of hydrogel droplets by size. The sorting is achieved due to size-dependent lateral inertial equilibrium positions: hydrogel droplets of different sizes have different equilibrium positions under the combined effects of shear-gradient lift and wall-effect lift forces. We apply this separation technique to isolate smaller hydrogel droplets containing microalgal colonies from larger empty droplets. We found that hydrogel droplets containing microalga Euglena gracilis (E. gracilis) shrink as cells grow and divide, while empty hydrogel droplets retain their size. Cell-laden hydrogel droplets were collected with up to 93.6% purity, and enrichment factor up to 5.51. After sorting, we were able to recover cells from hydrogel droplets without significantly affecting cell viability.
Comprehensive analysis of human hookworm secreted proteins using a proteogenomic approach (2018)

Summary The human hookworm Necator americanus infects more than 400 million people worldwide, contributing substantially to the poverty in these regions. Adult stage N. americanus live in the small intestine of the human host where they inject excretory/secretory (ES) products into the mucosa. ES products have been characterized at the proteome level for a number of animal hookworm species, but until now, the difficulty in obtaining sufficient live N. americanus has been an obstacle in characterizing the secretome of this important human pathogen. Herein we describe the ES proteome of N. americanus and utilize this information to conduct the first proteogenomic analysis of a parasitic helminth, significantly improving the available genome and thereby generating a robust description of the parasite secretome. The genome annotation resulted in a a revised prediction of 3,425 fewer genes than initially reported, accompanied by a significant increase in the number of exons and introns, total gene length and the percentage of the genome covered by genes. Almost 200 ES proteins were identified by LC-MS/MS with SCP/TAPS proteins, ‘hypothetical’ proteins and proteases among the most abundant families. These proteins were compared to commonly used model species of human parasitic infections, including Ancylostoma caninum, Nippostrongylus brasiliensis and Heligmosomoides polygyrus . Our findings provide valuable information on important families of proteins with both known and unknown functions that could be instrumental in host-parasite interactions, including protein families that might be key for parasite survival in the onslaught of robust immune responses, as well as vaccine and drug targets.
Microcontact Printing: Ultrathin Sticker‐Type ZnO Thin Film Transistors Formed by Transfer Printing via Topological Confinement of Water‐Soluble Sacrificial Polymer in Dimple Structure (Adv. Funct. Mater. 11/2013) (2013)

Sticker-type electronics give electronic functions to unconventional substrates. On page 1375 Heung Cho Ko and co-workers demonstrate an advanced methodology to guarantee both stability in device fabrication and high-efficiency transfer printing of final devices to enable such a stick-and-play system. They employ a water-soluble sacrificial layer on a dimpled handling substrate, which enables the topological confinement of the ultrathin substrate.
Supplementary Figure 4 from Constitutive Activation of Signal Transducers and Activators of Transcription Predicts Vorinostat Resistance in Cutaneous T-Cell Lymphoma (2023)

Supplementary Figure 4 from Constitutive Activation of Signal Transducers and Activators of Transcription Predicts Vorinostat Resistance in Cutaneous T-Cell Lymphoma
30GHz Ge electro-absorption modulator integrated with 3μm silicon-on-insulator waveguide (2011)

We demonstrate a compact waveguide-based high-speed Ge electro-absorption (EA) modulator integrated with a single mode 3 µm silicon-on-isolator (SOI) waveguide. The Ge EA modulator is based on a horizontally-oriented p-i-n structure butt-coupled with a deep-etched silicon waveguide, which transitions adiabatically to a shallow-etched single mode large core SOI waveguide. The demonstrated device has a compact active region of 1.0 × 45 µm(2), a total insertion loss of 2.5-5 dB and an extinction ratio of 4-7.5 dB over a wavelength range of 1610-1640 nm with -4V(pp) bias. The estimated Δα/α value is in the range of 2-3.3. The 3 dB bandwidth measurements show that the device is capable of operating at more than 30 GHz. Clear eye-diagram openings at 12.5 Gbps demonstrates large signal modulation at high transmission rate.
The rapid desensitization of glucagon-stimulated adenylate cyclase is a cyclic AMP-independent process that can be mimicked by hormones which stimulate inositol phospholipid metabolism (1987)

Treatment of intact hepatocytes with glucagon, TH-glucagon [( 1-N-alpha-trinitrophenylhistidine, 12-homoarginine]glucagon), angiotensin or vasopressin led to a rapid time- and dose-dependent loss of the glucagon-stimulated response of the adenylate cyclase activity seen in membrane fractions isolated from these cells. Intracellular cyclic AMP concentrations were only elevated with glucagon. All ligands were capable of causing both desensitization/loss of glucagon-stimulated adenylate cyclase activity and stimulation of inositol phospholipid metabolism in the intact hepatocytes. Maximally effective doses of angiotensin precluded any further inhibition/desensitizing action when either glucagon or TH-glucagon was subsequently added to these intact cells, as has been shown previously for the phorbol ester TPA (12-O-tetradecanoylphorbol 13-acetate) [Heyworth, Wilson, Gawler & Houslay (1985) FEBS Lett. 187, 196-200]. Treatment of intact hepatocytes with these various ligands caused a selective loss of the glucagon-stimulated adenylate cyclase activity in a washed membrane fraction and did not alter the basal, GTP-, NaF- and forskolin-stimulated responses. Angiotensin failed to inhibit glucagon-stimulated adenylate cyclase activity when added directly to a washed membrane fraction from control cells. Glucagon GR2 receptor-stimulated adenylate cyclase is suggested to undergo desensitization/uncoupling through a cyclic AMP-independent process, which involves the stimulation of inositol phospholipid metabolism by glucagon acting through GR1 receptors. This action can be mimicked by other hormones which act on the liver to stimulate inositol phospholipid metabolism. As the phorbol ester TPA also mimics this process, it is proposed that protein kinase C activation plays a pivotal role in the molecular mechanism of desensitization of glucagon-stimulated adenylate cyclase. The site of the lesion in desensitization is shown to be at the level of coupling between the glucagon receptor and the stimulatory guanine nucleotide regulatory protein Gs, and it is suggested that one or both of these components may provide a target for phosphorylation by protein kinase C.
Energy independence of energy trading system in microgrid (2017)

In recent years, interest in smart grids has increased globally along with the trend to reduce greenhouse gas emissions. One of the smart grid research area actively being done is energy trading in a microgrid. In particular, an energy trading system in the microgrid within an island should consider the own energy independence of the microgrid very seriously. In this paper, we propose a new metric to evaluate the energy independence of an energy trading system in a microgrid. The energy independence is discussed through energy trading simulation, which is first performed in this paper. Furthermore, we numerically present the proper energy trading cycle under various conditions with an existing energy trading mechanism.
Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses (2021)

The SARS-CoV-2 proteome shares regions of conservation with endemic human coronaviruses (CoVs), but it remains unknown to what extent these may be cross-recognized by the antibody response. Here, we study cross-reactivity using a highly multiplexed peptide assay (PepSeq) to generate an epitope-resolved view of IgG reactivity across all human CoVs in both COVID-19 convalescent and negative donors. PepSeq resolves epitopes across the SARS-CoV-2 Spike and Nucleocapsid proteins that are commonly targeted in convalescent donors, including several sites also recognized in some uninfected controls. By comparing patterns of homologous reactivity between CoVs and using targeted antibody-depletion experiments, we demonstrate that SARS-CoV-2 elicits antibodies that cross-recognize pandemic and endemic CoV antigens at two Spike S2 subunit epitopes. We further show that these cross-reactive antibodies preferentially bind endemic homologs. Our findings highlight sites at which the SARS-CoV-2 response appears to be shaped by previous CoV exposures and which have the potential to raise broadly neutralizing responses.
Molecular Targeting of HDM-2 Oncoprotein in Human Stem-Like Colonic Epithelium-Derived Progenitor and Stem-Like Colon Cancer Cells (2017)

Morano, William F. MD; Shaikh, Mohammad F. MD; Love, Patrice; Platoff, Rebecca M.; Simoncini, Michaela N. MD; Gleeson, Elizabeth M. MD, MPH; Shay, Jerry PhD; Pincus, Matthew R. MD, PhD; Bowne, Wilbur B. MD, FACS Author Information
Two structurally diverse Zn-based coordination polymers with excellent antibacterial activity (2018)

Two novel Zn-based coordination polymers with unique structural properties display an exceptional antibacterial activity against Gram-positive and Gram-negative bacteria.
Processus morphogénétiques (2018)

Enseignement Le cours n’a pas eu lieu. Colloque – What’s new in adult neurogenesis? La génération et la différenciation de certains neurones chez les vertébrés adultes, y compris chez les mammifères et chez sapiens, est un phénomène désormais clairement établi. De nombreuses questions restent cependant ouvertes quant à la régulation de cette neurogenèse adulte et à sa fonction physiologique. Intervenants : – Fiona Doetsch, Biozentrum, Bâle, Suisse ; – Pierre-Marie Lledo, Institut Pasteur, Par...
Regulation of CD8 + T Cell Development by Thymus-Specific Proteasomes (2007)

Proteasomes are responsible for generating peptides presented by the class I major histocompatibility complex (MHC) molecules of the immune system. Here, we report the identification of a previously unrecognized catalytic subunit called beta5t. beta5t is expressed exclusively in cortical thymic epithelial cells, which are responsible for the positive selection of developing thymocytes. Although the chymotrypsin-like activity of proteasomes is considered to be important for the production of peptides with high affinities for MHC class I clefts, incorporation of beta5t into proteasomes in place of beta5 or beta5i selectively reduces this activity. We also found that beta5t-deficient mice displayed defective development of CD8(+) T cells in the thymus. Our results suggest a key role for beta5t in generating the MHC class I-restricted CD8(+) T cell repertoire during thymic selection.
Microwave‐Assisted Suzuki Reactions for the Preparation of the Antifungal 3‐Aryl‐5‐methyl‐2,5‐dihydrofuran‐2‐ones. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Magnetic Resonance Measurements of Renal Blood Flow and Disease Progression in Autosomal Dominant Polycystic Kidney Disease (2006)

Whether changes in renal blood flow (RBF) are associated with and possibly contribute to cystic disease progression in autosomal dominant polycystic kidney disease (ADPKD) has not been ascertained. The Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP) was created to develop imaging techniques and analyses to evaluate progression. A total of 131 participants with early ADPKD had measurements of RBF and total kidney (TKV) and cyst (TCV) volumes by magnetic resonance and of GFR by iothalamate clearance at baseline and 1, 2, and 3 yr. The effects of age, gender, body mass index, hypertension status, mean arterial pressure (MAP), TKV, TCV, RBF, renal vascular resistance (RVR), GFR, serum uric acid, HDL and LDL cholesterol, 24-h urine volume, sodium (UNaE) and albumin (UAE) excretions, and estimated protein intake were examined at baseline on TKV, TCV, and GFR slopes. TKV and TCV increased, RBF decreased, and GFR remained stable. TKV, TCV, RVR, serum uric acid, UAE, UNaE, age, body mass index, MAP, and estimated protein intake were positively and RBF and GFR negatively correlated with TKV and TCV slopes. TKV, RBF, UNaE, and UAE were independent predictors of TKV and TCV slopes (structural disease progression). TKV, TCV, RVR, and MAP were negatively and RBF positively correlated with GFR slopes. Regression to the mean confounded the analysis of GFR slopes. TKV and RBF were independent predictors of GFR decline (functional disease progression). In ADPKD, RBF reduction (1) parallels TKV increase, (2) precedes GFR decline, and (3) predicts structural and functional disease progression.
Title Symmetric UL/DL diversity permutations for OFDMA PHY Date Submitted 2005-1-27 (2005)

Purpose Notice This document has been prepared to assist IEEE 802.16. It is offered as a basis for discussion and is not binding on the contributing individual(s) or organization(s). The material in this document is subject to change in form and content after further study. The contributor(s) reserve(s) the right to add, amend or withdraw material contained herein. Release The contributor grants a free, irrevocable license to the IEEE to incorporate material contained in this contribution, and any modifications thereof, in the creation of an IEEE Standards publication; to copyright in the IEEE’s name any IEEE Standards publication even though it may include portions of this contribution; and at the IEEE’s sole discretion to permit others to reproduce in whole or in part the resulting IEEE Standards publication. The contributor also acknowledges and accepts that this contribution may be made public by IEEE 802.16.
SARS‐CoV‐2‐associated neuropathology in non‐human primates (2021)

SARS‐CoV‐2 infection impacts multiple organ systems, including the central nervous system (CNS). Multiple reports have described a variety of neurological manifestations associated with infection that may contribute to worsening COVID‐19. The neuropathology of SARS‐CoV‐2 is not well understood, necessitating the development of relevant animal models for investigation. Here, we report marked neuropathology but with limited virus in the CNS of two non‐human primate models (NHPs) of SARS‐CoV‐2 infection. Adult male and female purpose‐bred Rhesus macaques (RMs; n = 4) and wild‐caught African green monkeys (AGMs; n = 4) were inoculated with the 2019‐nCoV/USA‐WA1/2020 strain of SARS‐CoV‐2 via multi‐route mucosal or aerosol challenge. SARS‐CoV‐2 nucleocapsid (SARS‐N) mRNA was detected in nasal swabs within the first week of inoculation, demonstrating infection of all study animals. All animals were euthanized at the study endpoint of 4 weeks post‐inoculation, with the exception of two AGMs that reached humane endpoints at 8‐ and 22‐days post‐challenge. Seven regions of the CNS were investigated for pathology and virus infection. Archival brain tissues from two non‐infected adult female RMs were used as aged‐matched controls. Mild, but chronic, hypoxemia with impaired gas exchange were suggested by SpO 2 values that stayed at or below 95% and elevated blood CO 2 in the majority of the study animals. Neuroinflammation was seen throughout the brain and brainstem but with limited virus detection by immunohistochemistry and RNAscope of fixed tissues and viral RNA detection using a highly sensitive CRISPR‐fluorescent detection system on RNA extracted from sectioned brain lysates. In addition, neuronal injury and death were suggested by pyknotic and karyolytic nuclei and cellular blebbing. Limited myelin vacuolation was revealed in two infected animals through Luxol Fast Blue staining. Neuronal cleaved caspase 3 positivity was seen at a greater frequency in infected animals compared to controls, suggesting increased apoptosis in infection. Microhemorrhages were larger and more frequent among infected NHPs, as compared to controls. Neuroinflammation, neuronal injury and death, and microhemorrhages were seen in animals that did not develop severe respiratory disease and may suggest neuropathology contributes to on‐going symptoms of convalesced patients. Our findings in NHPs are in agreement with human autopsy and neuroimaging studies and demonstrate this is a relevant animal model for investigating neuropathological changes associated with COVID‐19. Our results also suggest that hypoxic‐ischemic events leading to energy failure and neuronal injury, contribute to the neuropathological consequences of COVID‐19. Further studies are warranted to elucidate the mechanisms of SARS‐CoV‐2 neuropathogenesis.
Temperature dependency of x -cut LiNbO 3 modulator DC drift (2000)

The activation energy (Ea) for DC drifts of x-cut LiNbO3 (LN) modulators was obtained to be 1.4 ± 0.2 eV based on statistical consideration of long-term biased aging test data at 100 and 120°C. Ea = 1.4 eV means that 20 years of device life at 65°C – common system requirements – can be promptly tested by 9 days&apos; aging at 120°C.
Helicobacter pyloriInduces RANTES through Activation of NF-κB (2003)

Helicobacter pylori-infected gastric mucosa displays a conspicuous infiltration of mononuclear cells and neutrophils. RANTES (short for "regulated upon activation, normal T cell expressed and secreted") is a chemoattractant cytokine (chemokine) important in the infiltration of T lymphocytes and monocytes. RANTES may therefore contribute to the cellular infiltrate in the H. pylori-infected gastric mucosa. The aim of this study was to analyze the molecular mechanism responsible for H. pylori-mediated RANTES expression. We observed that gastric epithelial cells produced RANTES upon coculture with H. pylori. In addition, H. pylori induced RANTES mRNA expression and an increase in luciferase activity in cells which were transfected with a luciferase reporter construct derived from the RANTES promoter, in gastric epithelial cells, indicating that the induction of RANTES production occurred at the transcriptional level. Induction of RANTES was dependent on an intact cag pathogenicity island. Activation of the RANTES promoter by H. pylori occurred through the action of NF-kappa B. Transfection of kinase-deficient mutants of I kappa B kinase (IKK) and NF-kappa B-inducing kinase (NIK) inhibited H. pylori-mediated RANTES activation. In contrast, tumor necrosis factor alpha- or interleukin-1/Toll-like receptor signaling molecules-such as mitogen-activated protein kinase/extracellular signal-regulated kinase kinase 1, MyD88, and interleukin-1 receptor-associated kinase-did not play a role in RANTES activation by H. pylori. Collectively, H. pylori induced NF-kappa B activation through an intracellular signaling pathway that involved IKK and NIK, leading to RANTES gene transcription. RANTES induction by H. pylori may play an important role in gastric inflammation.
The use of heparin/polycation coacervate sustain release system to compare the bone regenerative potentials of 5 BMPs using a critical sized calvarial bone defect model (2022)

Nonunion following bone fracture and segmental bone defects are challenging clinical conditions. To combat this clinical dilemma, development of new bone tissue engineering therapies using biocompatible materials to deliver bone growth factors is desirable. This aim of this study is to use a heparin/polycation coacervate sustained-release platform to compare 5 bone morphogenetic proteins (BMPs) for promoting bone defect healing in a critical sized calvarial defect model. The in vitro 3D osteogenic pellet cultures assays demonstrated that BMPs 2, 4, 6, 7 and 9 all enhanced mineralization in vitro compared to the control group. BMP2 resulted in higher mineralized volume than BMP4 and BMP6. All BMPs and the control group activated the pSMAD5 signaling pathway and expressed osterix (OSX). The binding of BMP2 with coacervate significantly increased the coacervate average particle size. BMP2, 4, 6, & 7 bound to coacervate significantly increased the Zeta potential of the coacervate while BMP9 binding showed insignificant increase. Furthermore, using a monolayer culture osteogenic assay, it was found that hMDSCs cultured in the coacervate BMP2 osteogenic medium expressed higher levels of RUNX2, OSX, ALP and COX-2 compared to the control and BMPs 4, 6, 7 & 9. Additionally, the coacervate complex can be loaded with up to 2 μg of BMP proteins for sustained release. In vivo, when BMPs were delivered using the coacervate sustained release system, BMP2 was identified to be the most potent BMP promoting bone regeneration and regenerated 10 times of new bone than BMPs 4, 6 & 9. BMP7 also stimulated robust bone regeneration when compared to BMPs 4, 6 & 9. The quality of the newly regenerated bone by all BMPs delivered by coacervate is equivalent to the host bone consisting of bone matrix and bone marrow with normal bone architecture. Although the defect was not completely healed at 6 weeks, coacervate sustain release BMPs, particularly BMP2 and BMP7, could represent a new strategy for treatment of bone defects and non-unions.
Study on amorphous SiOχ film anode prepared by reactive evaporation for lithium-ion batteries (2017)

京都大学
Interaction of Sapphyrin with Phosphorylated Species of Biological Interest (1996)

A model for the interaction of the water-soluble sapphyrin derivative 1 with a variety of nucleic acid species is presented. Three modes of interaction are described: The first mode, seen with all the nucleic acid species, is that of “phosphate chelation”. This mode is exemplified by a solid state structure of the complex formed between the monobasic form of cAMP and the sapphyrin species [2H·2]2+. It involves the specific chelation of the oxyanion of a phosphorylated nucleotide or nucleic acid species with the protonated core of sapphyrin via Coulombic interactions that include H-bonding interactions. Spectroscopically, this interaction is characterized by a visible absorption at 422 nm and corresponds to complexes formed between the dimeric form of 1 and phosphorylated nucleotides. In the case of double-stranded DNA, this mode of binding shows a preference for the more flexible copolymer [poly(dA-dT)]2 over [poly(dG-dC)]2. The second mode involves a hydrophobic interaction with the nucleobases present in both monomeric and single-stranded polymeric nucleotides. Spectroscopically, this nucleotide-dependent interaction is characterized by the absorption of the monomeric species of 1 at ca. 450 nm. The third mode involves the highly ordered aggregation of 1 on the surface of certain double-stranded, helical nucleic acids at low phosphate ester to sapphyrin (P/S) ratios and is templated by the higher order structure of these nucleic acid polymers. Spectroscopically, this mode is characterized by a visible absorption at ca. 400 nm and a large, conservative induced CD signal for 1.