gebhart/patrepeval huggingface dataset:
Effective Encapsulation of Proteins into Size‐Controlled Phospholipid Vesicles Using Freeze‐Thawing and Extrusion (2003)

We are aiming to improve the encapsulation efficiency of proteins in a size-regulated phospholipid vesicle using an extrusion method. Mixed lipids (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), cholesterol, 1,5-dipalmitoyl-l-glutamate-N-succinic acid (DPEA), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[monomethoxy poly(ethylene glycol) (5,000)] (PEG-DSPE) at a molar ratio of 5, 5, 1, and 0.033 were hydrated with a NaOH solution (7.6 mM) to obtain a polydispersed multilamellar vesicle dispersion (50 nm to 30 microm diameter). The polydispersed vesicles were converted to smaller vesicles having an average diameter of ca. 500 nm with a relatively narrow size distribution by freeze-thawing at a lipid concentration of 2 g dL(-)(1) and cooling rate of -140 degrees C min(-1). The lyophilized powder of the freeze-thawed vesicles was rehydrated into a concentrated protein solution (carbonyl hemoglobin solution, 40 g dL(-1)) and retained the size and size distribution of the original vesicles. The resulting vesicle dispersion smoothly permeated through the membrane filters during extrusion. The average permeation rate of the freeze-thawed vesicles was ca. 30 times faster than that of simple hydrated vesicles. During the extrusion process, proteins were encapsulated into the reconstructed vesicles with a diameter of 250 +/- 20 nm.
Erratum: PIK3CA oncogenic mutations represent a major mechanism of resistance to trastuzumab in HER2/neu overexpressing uterine serous carcinomas (2015)

Correction to: British Journal of Cancer (2015) 113, 1020–1026. doi:10.1038/bjc.2015.306 It has been brought to our attention that there is an error in Figure 3 of the above paper published in advance online on 1 September 2015. The original label above the figure reads as ‘ARK-2 E93Q’. It should becorrected to ‘ARK-2 R93Q’.
Convergence of the iterativewater-filling algorithm with sequential updates in spectrum sharing scenarios (2011)

Spectrum sharing between two independent, co-existing transmit-receive pairs (TRPs) is formulated as a non-cooperative game with the TRPs as players, their individual link rates as payoffs and power allocation over the utilized spectral bands as the strategy. A Nash Equilibrium (NE) corresponds to the outcome of such a game and TRPs iteratively use the water-filling algorithm according to an agreed order for achieving the NE. Dynamics of this distributed algorithm is studied to determine the conditions for convergence and characterize the resulting NE. A sufficient condition on global convergence is derived and is shown to be tighter than existing ones. Further, a novel characterization of the globally achievable NE based on necessary conditions is presented. Some of these results are also extended to multiple NE scenarios where local convergence is exhibited.
Wire-Based Additive Manufacturing of Stainless Steel Components (2020)

Three different wire-fed additive manufacturing (AM) processes were employed to evaluate differences between laser, arc, and electron beam heat sources used for high-deposition-rate AM on the order of 1 kg/h. Optimum weld and build parameters were developed independently to match the characteristics of each heat source using 308L stainless steel welding wire as the feedstock. Laser-wire AM was made with the lowest energy per unit length of weld and had the best control of the melt pool and surface finish. Wire arc-based AM had an intermediate energy per unit length of weld of approximately 5× that of the laser process, while electron beam wire AM had the highest energy per unit length of weld at approximately 10× that of the laser process. Analysis of the parts that were built included evaluation of mechanical properties and microstructures, and these properties are discussed with respect to the difference in input energy and cooling rates. Results show that all three processes build parts with properties that exceed those of annealed 304L wrought stainless steel. How-ever, significant differences exist between the processes, and the results presented here can be used to help select the best wire-fed process for a given high-deposition-rate application.
A retrospective study for investigating the relationship between old and new staging systems with prognosis in ovarian cancer using gynecologic cancer registry of Japan Society of Obstetrics and Gynecology (JSOG): disparity between serous carcinoma and clear cell carcinoma (2020)

The results suggest that changes in classification for stage III and stage IV are appropriate, but the subclassification for stage IC might be too detailed. There was a discrepancy of prognosis by histological type between stage IA and IC1.
Presumed Vascular Traction-Associated Recurrence of Retinal Detachment in Patients With Myopic Macular Hole (2009)

Optical coherence tomography (OCT) and OCT-ophthalmoscopic examinations were consecutively performed in two patients with focal retinal redetachment despite previously successful repair of the myopic macular hole-related retinal detachment by vitrectomy with removal of the internal limiting membrane. A microfold developed on the redetached retinal surface in both eyes soon after surgery. C-scan analysis by OCT-ophthalmoscope showed that the retinal microfolds coincided with a retinal artery adjacent to the preexisting macular hole. OCT revealed the focal retinal detachment was most prominent beneath the retinal microfold in both study eyes and did not reach the macular hole in one eye. The retinal microfold was most marked at the initiation of the recurrence and then attenuated with the elevation of the detached retina. Inward vascular tractional force appearing as a retinal microfold can be a critical trigger of recurrent retinal detachment in patients with myopic macular hole.
Sirt1 enhances skeletal muscle insulin sensitivity in mice during caloric restriction (2011)

Skeletal muscle insulin resistance is a key component of the etiology of type 2 diabetes. Caloric restriction (CR) enhances the sensitivity of skeletal muscle to insulin. However, the molecular signals within skeletal muscle linking CR to improved insulin action remain largely unknown. Recently, the mammalian ortholog of Sir2, sirtuin 1 (Sirt1), has been identified as a potential transducer of perturbations in cellular energy flux into subsequent metabolic adaptations, including modulation of skeletal muscle insulin action. Here, we have demonstrated that CR increases Sirt1 deacetylase activity in skeletal muscle in mice, in parallel with enhanced insulin-stimulated phosphoinositide 3-kinase (PI3K) signaling and glucose uptake. These adaptations in skeletal muscle insulin action were completely abrogated in mice lacking Sirt1 deacetylase activity. Mechanistically, Sirt1 was found to be required for the deacetylation and inactivation of the transcription factor Stat3 during CR, which resulted in decreased gene and protein expression of the p55α/p50α subunits of PI3K, thereby promoting more efficient PI3K signaling during insulin stimulation. Thus, these data demonstrate that Sirt1 is an integral signaling node in skeletal muscle linking CR to improved insulin action, primarily via modulation of PI3K signaling.
The gene for the APC-binding protein β-catenin (CTNNB1) maps to chromosome 3p22, a region frequently altered in human malignancies (1995)

beta-Catenin is one of the E-cadherin associated proteins involved in the process of cellular adhesion. It has recently been shown to interact with the APC protein whose gene is known to be mutated in the germline of familial adenomatous polyposis patients. This interaction implies that beta-catenin is a potential regulator of the APC gene. The localization of the human beta-catenin gene (CTNNB1) to chromosome 3p22, by fluorescent in situ hybridization (FISH), has linked the gene to a region that is frequently altered in several human malignancies. The location of the gene and the protein interactions suggest the importance of beta-catenin in the etiology of various human cancers.
The Dhcp Handbook (2002)

From the Publisher:
The Dynamic Host Configuration Protocol (DHCP) provides a way to automate and manage the network configurations of devices that use the TCP/IP protocol suite. Without DHCP, network administrators must manually enter in IP addresses for each computer and network device and then manually change that address each time the device is moved to a different part of the network. The DHCP Handbook, Second Edition is a complete reference for understanding DHCP, deploying and managing DHCP services, and debugging problems with DHCP clients and servers. Chapters devoted to failover, authentication, Windows 2000, DHCPv6, and DHCP/DNS interaction reflect the recent updates to the standard and issues that are most pertinent to network planners and administrators. Throughout the book, the authors are careful to balance conceptual discussions of DHCP with detailed implementation examples and practical advice.
Simultaneous mRNA, protein, and immune-repertoire profiling of thousands of single cells (2019)

Abstract High-throughput single cell RNA-seq (scRNA-seq) has transformed our understanding of heterogenous immune populations. Advances in scRNA-seq, such as oligo-conjugated antibody technologies that enable protein expression profiling alongside mRNA, are expanding the range of molecules that can be profiled at the single cell level. Although sequencing the T-cell and B-cell immune repertoire can provide crucial insights into the complexities of the adaptive immune system, thus advancing discoveries in immunology and immune-oncology, the ability to extract this information from single cells requires new technology to profile regions of the mRNA missed by conventional 3′ scRNA-seq. Here we demonstrate a novel approach using the BD Rhapsody™ system to extract immune-repertoire information in addition to gene-expression information from the same cells. In a single workflow, we profiled a panel of 400 mRNA targets and 40 protein markers as well as the CDR3 region of T- and B-cell receptors in thousands of human PBMCs. After using the mRNA and protein information to robustly annotate different lymphocyte populations, we examined the T- and B-cell repertoires for differences in their clonal diversity. We were able to identify clonally expanded T cells and B cells and examine how their gene-expression profiles differ from that of non-expanded cells. This study demonstrates the power of combining mRNA, protein, and immune repertoire analysis at the single cell level to answer complex and important biological and clinical questions. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.
Estimation of waveguide phase error in silica-based waveguides (1997)

A new estimation method is proposed in order to clarify waveguide phase error factors. Using the proposed method, it is possible to analyze such factors as core size error and refractive index error, which cause optical phase error in waveguides. This method is applied to silica-based waveguides to estimate the waveguide phase error. This revealed an average core size error of 2.1/spl times/10/sup -3/ /spl mu/m and an average refractive index error of 1.9/spl times/10/sup -6/. Finally, based on the measured phase error values, the optimum arrayed-waveguide grating (AWG) configuration is considered with a view to achieving low crosstalk.
Hepatitis C Virus Improves Human Tregs Suppressive Function and Promotes Their Recruitment to the Liver (2019)

Direct interaction between HCV and Tregs represents a newly defined mechanism that could potentiate HCV immune evasion and favor intratumoral recruitment contributing to HCC progression.
Macrocycles from Perhalogenated Heterocycles (2003)

Perhalogenated heteroaromatic systems, such as trichloro-s-triazine and pentafluoropyridine, are multifunctional "building blocks" that react with a number of appropriate difunctional nucleophiles to provide access to a variety of macrocyclic and even cage-like molecular architectures. Unusual structural and complexation characteristics of the systems reported so far, such as the recognition of anions, provide a further stimulus for the development of this area.
Direct detection of superoxide anion generated in C60-photosensitized oxidation of NADH and an analogue by molecular oxygen (2002)

Visible-light irradiation of poly(vinylpyrrolidone) (PVP)-solubilized C60 in water in the presence of NADH (dihydronicotinamide adenine dinucleotide) and molecular oxygen (O2) results in formation of superoxide anion (O2˙−). Formation of O2˙− having a characteristic g‖ value of 2.18 was evidenced by the direct observation with use of a low-temperature EPR technique at 77 K. Photoinduced O2˙− formation was also observed for an N-methyl-2-pyrrolidone (NMP) solution of C60 and 1-benzyl-1,4-dihydronicotinamide (BNAH) in the presence of O2, whereas C60 radical anion (C60˙−) was formed in the absence of O2 under otherwise the same experimental conditions. These results suggest that C602− formed in the photoinduced electron-transfer reduction of C60 by BNAH acts as an electron donor to O2 to give O2˙− in NMP.
Contrasting Perspective on Asphaltene Molecular Weight. This Comment vs the Overview of A. A. Herod, K. D. Bartle, and R. Kandiyoti (2008)

Asphaltene molecular weight (Asphaltenes, Heavy Oils and Petroleomics; Springer: New York, 2007) continues to be the subject of a longstanding debate in the literature. A paper (Energy Fuels 2007, 21, 2176−2203) recently published (referred to as HBK) claims that asphaltene molecular weights are bimodal with one component in the roughly megadalton range and a second component in the roughly 5 kDa range. These claims are in sharp contrast to results published from a variety of measurements with the overall conclusions that asphaltene molecular weights are monomodal with a most probable 750 Da (±200) with a fwhm 500–1000 Da. In this report, we provide a summary of the four molecular diffusion techniques and seven mass spectral techniques from many groups around the world that are all in accord with the 750 Da most probable mass. Moreover, here we discuss why HBK reported anomalously large asphaltene molecular weights along with the unique claim of a bimodal distribution. In particular, the size exclusion chromatography (SEC) results that yield megadalton masses were performed with the solvent N-methylpyrrolidinone which is known to flocculate up to 50% of the asphaltenes. The megadalton mass is likely large asphaltene aggregates or flocs. In a previous referenced paper from the HBK labs, the better solvent for asphaltenes, tetrahydrofuran, did not give the megadalton peak in their SEC experiments as they stated; we suspect because the asphaltenes were suitably dissolved (although still with some aggregation). The corresponding discussion treats the known hierarchy of asphaltene aggregation at very low concentration in a good solvent, toluene. In addition, the mass spectral method used in HBK, laser desorption ionization, is shown herein and in the literature to yield anomalously large molecular weights for asphaltenes and polycyclic aromatic hydrocarbons due to gas phase aggregation if (1) the laser power is too high, (2) the surface concentration of asphaltenes is too high, or (3) if the ions are collected too quickly (i.e., from a dense plasma). Properly accounting for these potential pitfalls, one obtains the same most probable ~750 Da molecular weight as from all of the other techniques. Finally, ESI MS is shown herein and in ample literature to be readily able to detect large masses (the primary reason ESI led to a Nobel Prize); the absence of large mass species in ESI MS of asphaltenes is because they are not present. The congruence of so many molecular diffusion techniques and mass spectral techniques is a powerful advance for asphaltene science.
An algorithm for iterative decoding and channel estimation of space-time coded FH systems (2003)

This paper proposes an algorithm for joint decoding and channel estimation (JDE) of frequency-hopping (FH) system employing space-time (ST) codes. The channel is modeled as a block fading channel, where the fade is constant during each hop and independent from other hops. The algorithm is based on quantizing the fading process, such as done in Markov fading models. The algorithm is semiblind, where initial estimation of the channel is obtained using orthogonal pilot sequence insertion (OPSI). Unlike existing JDE algorithms, the algorithm exploits soft information from the decoder to improve the channel estimation iteratively. The performance of the algorithm approaches the performance of the system where all signals in the frame are assumed to be known with probability one, i.e. acting as pilots.
Physical Interaction of Histone Deacetylase 6 (HDAC6) with STAT3 Regulates IL-10 Gene Expression and Immune Tolerance Mediated by Antigen-Presenting Cells (APCs) (2012)

Abstract Abstract 829 APCs are critical in T-cell activation and in the induction of T-cell tolerance. Epigenetic modifications of specific genes in the APC play a key role in this process, and among them, histone deacetylases (HDACs) have emerged as key participants. HDAC6 is a 131 KDa protein with preferential cytoplasmic localization where it regulates the acetylation of proteins involved in cytoskeleton, cell-cell interaction and cell migration. Emerging evidence also implicates HDAC6 in regulation of immune responses, in particular at the level of the APC/T cell immune synapse1 and in the suppressive function of regulatory T-cells2. Expanding upon these immunoregulatory properties, here we show for the first time that HDAC6 physically interacts with STAT3, a transcriptional activator of IL-10 gene expression. By co-immunoprecipitation studies and confocal studies we found that HDAC6 co-localize with STAT3 in the cytoplasm and nuclei of macrophages. Furthermore, by using several HDAC6 and STAT3 mutants we have identified that the aminoacids 503–840 of HDAC6 and the STAT3 domain comprising aminoacids 465–585 are required for this interaction. Functionally, knocking down HDAC6 in a macrophage cell line (RAW264.7-HDAC6KD) resulted in inhibition of STAT3 phosphorylation, decreased recruitment of STAT3 to the IL-10 gene promoter and abrogation of IL-10 production by these cells in response to either LPS or IL-10. Similar results were observed in dendritic cells (DCs) or macrophages isolated from HDAC6 knock-out (KO) mice. Furthermore, HDAC6KD clones or APCs from HDAC6 KO mice displayed an enhanced expression of the co-stimulatory molecule B7.2 and are better activators of antigen-specific CD4+ T-cell responses in vitro. More importantly, these APCs are able of restoring the responsiveness of anergic T-cells from lymphoma-bearing mice. Pharmacologic inhibition of HDAC6 in APCs with Tubastatin A, an isotype-selective HDAC6 inhibitor, yielded similar enhancement of APC and T-cell function in vitro. Further support for HDAC6 as an appealing target in cancer immunotherapy has been recently provided by the significant delay in tumor growth observed in either HDAC6 KO mice or in wild type mice treated with Tubastatin A. In summary, we have shown for the first time that HDAC6 interacts physically with STAT3 and such an interaction is necessary for STAT3 phosphorylation and IL-10 gene expression in APCs. Disrupting the HDAC6/STAT3/IL-10 axis in APCs with selective HDAC6 inhibitors represents a novel approach to overcome tolerogenic pathways in these cells and tip the balance towards effective antitumor immune responses. Disclosures: No relevant conflicts of interest to declare.
A Versatile and Practical Synthesis of Bis(indolyl)methanes/Bis(indolyl)glycoconjugates Catalyzed by Trichloro‐1,3,5‐triazine. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Highly efficient cycloreversion of photochromic dithienylethene compounds using visible light-driven photoredox catalysis (2014)

Photochromic cis-1,2-dithienylethene (DTE) compounds are the most suitable to the application in reversible molecular memories and switches, but imbalance in the quantum yields for the chromic interconversion limits the full potentials. We have demonstrated and investigated photoelectrocatalytic cycloreversion of DTE compounds. A series of cyclometalated Ir(III) complexes served as photoredox catalysts to achieve one order of magnitude enhancement in the cycloreversion quantum yields. The mechanism, involving photoinduced oxidation of DTE, electrocatalytic ring opening and reductive termination, has been thoroughly investigated. Nanosecond transient spectroscopic techniques were employed to directly monitor bidirectional electron transfer between DTE and the photoredox catalyst. It was found that the oxidative photoinduced electron transfer was diffusion-controlled and located in the Marcus-normal region, whereas the competing back electron transfer occurred in the Marcus-inverted region. This novel discovery establishes that synthetic control over back electron transfer, rather than photoinduced electron transfer, can improve the performance of the photoelectrocatalysis. Combined studies, including the kinetic investigations with the use of variable-temperature stopped-flow UV-vis absorption spectroscopy and quantum chemical calculations based on time-dependent density functional theory, further enabled identification of the radical intermediate that underwent thermal, electrocatalytic cycloreversion. Finally, analyses based on the Marcus theory of electron transfer suggested regeneration of the excited-state catalyst in the termination step to initiate dark-state electrocatalytic cycloreversion. The results obtained in this work established novel principles to maximizing quantum yields for photoinduced cycloreversion of DTEs. It is envisioned that our findings will provide novel guidance to the future application of the truly reversible photochromism to a broad range of molecular photonic systems.
De Novo Mutations Causing Shwachman-Diamond Syndrome and a Founder Mutation in SBDS in the (2014)

We summarize the molecular findings in a patient cohort with Shwachman-Diamond syndrome that underwent genetic diagnostic testing. We could confirm a molecular diagnosis in 81 individuals. Our data is consistent with previous findings that the most common mutations in SBDS are recurrent gene conversion mutations in exon 2, c.258+2T>C or c.183_184delinsCT. The patients diagnosed either had two recurrent mutations (78%), or one recurrent mutation and a rare family-specific mutation (22%). We identified six unrelated individuals with SDS of French Canadian decent with the c.120del (p.Arg39fsX) mutation. Molecular analysis revealed that this mutation occurs with a founder haplotype. The opposing SBDS mutation present in these individuals was the common c.258+2T>C mutation, which was on a different haplotype in all five families. In addition, we estimated that approximately 9% (5 out of a subset of 54 patients with parent information) of the SDS individuals had a de novo mutation on one allele and an inherited mutation on the other allele. The de novo mutations were either recurrent gene conversion mutations (n=3) or rare point mutations (n=2). The occurrence of de novo mutation requires that parental carrier testing be performed for accurate familial risk assessment.