gebhart/patrepeval huggingface dataset:
A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm (2020)

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.
Synthesis of Titanium Complexes That Contain Triamido−Amine Ligands (1996)

We report the synthesis of a variety of titanium complexes that contain (Et3SiNCH2CH2)3N, (C6F5NCH2CH2)3N, or (Me3SiNCH2CH2CH2)3N ligands. Complexes in the first category include [(Et3SiNCH2CH2)3N]TiCl, [(Et3SiNCH2CH2)3N]Ti(OTf), and [(Et3SiNCH2CH2)3N]Ti(t-Bu). Complexes in the second category include [(C6F5NCH2CH2)3N]TiX (X = Cl, Br, I, OTf) and [(C6F5NCH2CH2)3N]TiR (R = Me, Et). Complexes in the third category include [(Me3SiNCH2CH2CH2)3N]TiCl and [(Me3SiNCH2CH2CH2)3N]TiCH3. In an X-ray study [(Me3SiNCH2CH2CH2)3N]TiCl was shown to contain a coordinated amino nitrogen and TiN2C3 rings that were puckered in a pseudocyclohexane chair form. The TiN2C3 rings are proposed to “flip” via dissociation of the amino nitrogen donor in the methyl complex, but the flipping rate is slow on the NMR time scale in [(Me3SiNCH2CH2CH2)3N]TiCl as a consequence of the greater electrophilicity of the metal.
[P3–082]: IMMUNOHISTOCHEMICAL CHARACTERISATION OF NOVEL TAU ANTIBODIES IN TRANSGENIC ANIMALS (2017)

Amyloid plaques and neurofibrillary tangles are key pathological events associated with Alzheimer's disease (AD). To date, considerable efforts have identified a variety of potential novel therapeutics focussed on removing and/or preventing amyloid deposition by either inhibiting the β site amyloid precursor protein cleaving enzyme (BACE) or targeted anti-amyloid antibodies. More recently, directed discovery efforts have focussed on preventing the deposition and spreading of neurofibrillary tangles which are comprised of hyperphosphorylated tau. Here we report on the immunohistochemistry characterisation of multiple antibodies raised against different epitopes of tau, including phospho- and non-phospho epitopes. The focus was to delineate the immunoreactivity signature of these antibodies in tau transgenic mouse models to gain an insight into the CNS distribution of tau. Brains from different mouse models, including wild type, MAPT knockout and Tau transgenic mouse (+/- injection of Tau fibrils), were collected, fixed and paraffin embedded. Immunohistochemistry was performed using the tau antibodies of interest, followed by imaging. Special attention was paid to the time between sacrifice of the animals and fixation to minimalize post-mortem dephosphorylation. Reference antibodies were included in the study. Non-phosphorylated tau is known to be present mainly in axons and not in neuronal cell bodies of wild type mice. In transgenic models, Tau1 immunoreactivity is observed both in axons and the somatodendritic compartment. Phosphorylated tau on the other hand is a major component of aggregates present in the brains of P301S and P301L animals and is virtually absent from normal neurons. However, by the use of high-affinity phosphorylation-dependent antibodies and by minimising post-mortem delay, phosphorylated tau could be detected in wild type brains. In contrast to dephosphorylated tau, phosphorylated tau was mainly observed in neuronal somata and dendrites. Until recently, it was generally accepted that phosphorylated tau is scarce in healthy neurons. However, this study clearly identifies the presence of phosphorylated tau in the somatodendritic compartment of neurons under physiological circumstances. This opens up the idea that accumulation of hyperphosphorylated tau is not necessarily triggered by increased kinase or decreased phosphatase activity, but could start from the existing pool of phosphorylated tau.
A BJT-based temperature-to-digital converter with ±60mK (3σ) inaccuracy from −70°C to 125°C in 160nm CMOS (2016)

This paper presents the most accurate BJT-based CMOS temperature-to-digital converter (TDC) ever reported, with an inaccuracy of ±60mK (3σ) from -70°C to 125°C. This is 2× better than the state-of-the-art, despite being implemented in a process (160nm) that only offers low-β <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> (<;5) PNPs. It is also the most energy-efficient ever reported, with a resolution FOM of 7.3pJ°C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . This level of performance is achieved by an improved β <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> -compensation scheme, the use of dynamic error correction techniques to suppress non-BJT related errors and the use of an energy-efficient zoom-ADC based on current-reuse OTAs. These techniques also result in very low power-supply sensitivity (12mK/V), thus maintaining TDC accuracy for supply voltages ranging from 1.5V to 2V.
Supplementary Figure 1 from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients (2023)

&lt;p&gt;PDF file - 2015K, Injection site reaction in patient M21&lt;/p&gt;
Polymerization of Polar Vinyl Monomers with Novel Cobalt-based Catalyst (1999)

Abstract Cobalt-based complex CH3C(CH2PPh2)3Co(BH4) (1) polymerized polar vinyl monomers like acrylonitrile (AN) and methyl methacrylate (MMA) without any cocatalysts. The molecular weight of the poly(AN) was fairly high at around 500 × 103. It was concluded that the polymerizations did not proceed with radical polymerization mechanism based on the copolymerization results with styrene. The obtained poly(AN) had an atactic structure.
Differential specificity of cereal promoters in homologous and heterologous cereals (2007)

Improving the cereal grain using a transgenic approach would require the use of specific gene/s but also the use of specific promoter elements to control the spatial and temporal expression of the gene/s. We have studied several seed-specific cereal promoters to investigate if promoter strength and specificity is maintained from a homologous to a heterologous system. Transgenic rice, wheat and barley were generated to study promoters of the bifunctional alpha-amylase subtilisin inhibitor gene (Isa) form barley, the Em gene from wheat and a number of storage protein promoters from barley, rice and wheat. The isa promoter from barley show differential control of reporter gene expression in grains of transgenic wheat and rice. The wheat Em promoter shows comparable reporter gene expression in transgenic wheat, barley and rice. The seed-specific promoters from wheat, barley and rice directed seed-specific reporter gene expression in a homologous system. However, in a heterologous system the storage protein promoters either maintained seed-specific reporter gene expression, or showed differential control of reporter gene expression, or failed to direct any reporter gene expression. Analysis of transgenic rice and barley seeds is ongoing and data reflecting promoter strength will be discussed. Possible reasons for this differential control of reporter gene expression between homologous and heterologous systems, and implications for using cereal promoters across other cereal species for transgenic breeding will be discussed.
IEEE ACCESS Special Section Editorial: Energy Efficient Wireless Communications With Energy Harvesting and Wireless Power Transfer (2018)

With technological advancements, future wireless communications networks are expected to incorporate densely deployed base stations serving tens of billions of low-power wireless devices, in order to enable emerging Internet-of-Things (IoT) applications. However, this leads to a dramatic increase in energy cost at the wireless network, and makes it a difficult task to efficiently power massive wireless devices. Therefore, how to reduce the energy cost at the network side and also provide sustainable energy supply at the wireless device side become two increasingly important issues for the success of IoT. Recently, energy harvesting (EH) from ambient sources (e.g., solar and wind) and dedicated wireless power transfer (WPT) via radio frequency (RF) signals have emerged as appealing solutions to power base stations and low-power wireless devices. Such techniques have several promising advantages over the traditional grid/battery-powered systems, such as improved energy efficiency, reduced energy and maintenance costs, prolonged lifetime, and even perpetual and uninterrupted operations. Hence, EH wireless communications and wireless powered communications have attracted signifficant interests recently from both academia and industry.
Size-Dependent Dynamics of Nanoparticles in Unentangled Polyelectrolyte Solutions (2015)

The mobility of polystyrene nanoparticles ranging in diameter from 300 nm to 2 μm was measured in dilute and semidilute solutions of partially hydrolyzed polyacrylamide. In this model system, the ratio of particle to polymer size controls the long-time diffusivity of nanoparticles. The particle dynamics transition from subdiffusive on short time scales to Fickian on long time scales, qualitatively similar to predictions for polymer dynamics using a Rouse model. The diffusivities extracted from the long-time Fickian regime, however, are larger than those predicted by the Stokes-Einstein equation and the bulk zero-shear viscosity and moreover do not collapse according to hydrodynamic models. The size-dependent deviations of the long-time particle diffusivities derive instead from the coupling between the dynamics of the particle and the polymer over the length scale of the particle. Although the long-time diffusivities collapse according to predictions, deviations of the short-time scaling exponents and the crossover time between subdiffusive and Fickian dynamics indicate that the particles are only partially coupled to the relaxation modes of the polymer.
Homomorphic Computation of Edit Distance. (2015)

These days genomic sequence analysis provides a key way of understanding the biology of an organism. However, since these sequences contain much private information, it can be very dangerous to reveal any part of them. It is desirable to protect this sensitive information when performing sequence analysis in public. As a first step in this direction, we present a method to perform the edit distance algorithm on encrypted data to obtain an encrypted result. In our approach, the genomic data owner provides only the encrypted sequence, and the public commercial cloud can perform the sequence analysis without decryption. The result can be decrypted only by the data owner or designated representative holding the decryption key. In this paper, we describe how to calculate edit distance on encrypted data with a somewhat homomorphic encryption scheme and analyze its performance. More precisely, given two encrypted sequences of lengths n and m, we show that a somewhat homomorphic scheme of depth O((n+m)loglog(n+m)) can evaluate the edit distance algorithm in O(nmlog(n+m)) homomorphic computations. In the case of n=m, the depth can be brought down to O(n) using our optimization technique. Finally, we present the estimated performance of the edit distance algorithm and verify it by implementing it for short DNA sequences.
Altered biodistribution of deglycosylated extracellular vesicles through enhanced cellular uptake (2020)

Extracellular vesicles (EVs) from cancer are delivered both proximal and distal organs. EVs are highly glycosylated at the surface where EVs interact with cells and therefore has an impact on their properties and biological functions. Aberrant glycosylation in cancer is associated with cancer progression and metastasis. However, the biological function of glycosylation on the surface of EV is uncovered. We first demonstrated differential glycosylation profiles of EVs and their originated cells, and distinct glycosylation profiles in a brain-metastatic subline BMD2a from its parental human breast cancer cell line, MDA-MB-231-luc-D3H2LN by lectin blot. We then investigated the roles of surface glycoconjugates on EV uptake. N- and/or O-glycosylation removal of fluorescent-labelled BMD2a EVs enhanced cellular uptake to endothelial cells, suggesting that surface glycosylation has inhibitory effects on cellular uptake. Biodistribution of glycosylation-deprived BMD2a EVs administrated intravenously into mice was further analysed ex vivo using near-infrared lipophilic dye. EVs treated with O-deglycosylation enzymes enhanced the accumulation of EVs to the lungs after 24 h from the injection, while N-deglycosylation did not markedly alter biodistribution. As the lungs are first organs in which intravenous blood flows, we suggest that surface glycosylation of cancer-derived EVs avoid promiscuous adhesion to proximal tissues to be delivered to distant organs.
Using BNC as Bioplasmonic Sensors (2022)

This study aimed to find a technique for using BNC (bacterial nanocellulose) as a plasmonic biosensor with a hot spot localized surface. A template protein (Hb) was imprinted on Au nanorods and was followed with the polymerization of APTMS and TMPS. The protein was then removed to leave an artificial receptor, which enabled protein rebinding. We were successful in developing a procedure for this study, and in the future we will be developing a technique that will allow multiple detection of proteins.
Metabolomics enables precision medicine: “A White Paper, Community Perspective” (2016)

Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its "Precision Medicine and Pharmacometabolomics Task Group", with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.
[CONTROVERSIES REGARDING THE ACCURACY AND LIMITATIONS OF FROZEN SECTION IN THYROID PATHOLOGY: AN EVIDENCE-BASED ASSESSMENT]. (2015)

Palpable thyroid nodules are present clinically in 4-7% of the population and their prevalence increases to 50%-67% when using high-resolution neck ultrasonography. By contrast, thyroid carcinoma (TC) represents only 5-20% of these nodules, which underlines the need for an appropriate approach to avoid unnecessary surgery. Frozen section (PS) has been used for more than 40 years in thyroid surgery to establish the diagnosis of malignancy. However, a controversy persists regarding the accuracy of FS and its place in thyroid pathology has changed with the emergence of fine-needle aspiration (FNA). A PubMed Medline and SpringerLink search was made covering the period from January 2000 to June 2012 to assess the accuracy of ES, its limitations and indications for the diagnosis of thyroid nodules. Twenty publications encompassing 8.567 subjects were included in our study. The average value of TC among thyroid nodules in analyzed studies was 15.5 %. ES ability to detect cancer expressed by its sensitivity (Ss) was 67.5 %. More than two thirds of the authors considered PS useful exclusively in the presence of doubtful ENA and for guiding the surgical extension in cases confirmed as malignant by FNA; however, only 33% accepted FS as a routine examination for the management of thyroid nodules. The influence of FS on surgical reintervention rate in nodular thyroid pathology was considered to be negligible by most studies, whereas 31 % of the authors thought that FS has a favorable benefit by decreasing the number of surgical re-interventions. In conclusion, the role of FS in thyroid pathology evolved from a mandatory component for thyroid surgery to an optional examination after a pre-operative FNA cytology. The accuracy of FS seems to provide no sufficient additional benefit and most experts support its use only in the presence of equivocal or suspicious cytological features, for guiding the surgical extension in cases confirmed as malignant by FNA and for the identification of other potentially confusing intraoperative findings.
ChemInform Abstract: Using the Pummerer Cyclization—Deprotonation—Cycloaddition Cascade of Imidosulfoxides for Alkaloid Synthesis. (2000)

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.
High Potency and Broad-Spectrum Antimicrobial Peptides Synthesized via Ring-Opening Polymerization of α-Aminoacid-N-carboxyanhydrides (2009)

Antimicrobial peptides (AMPs), particularly those effective against methicillin-resistant Staphylococcus aureus ( S. aureus ) and antibiotic-resistant Pseudomonas aeruginosa ( P. aeruginosa ), are important alternatives to antibiotics. Typical peptide synthesis methods involving solid-phase sequential synthesis are slow and costly, which are obstacles to their more widespread application. In this paper, we synthesize peptides via ring-opening polymerization of alpha-amino acid N-carboxyanhydrides (NCA) using a transition metal initiator. This method offers high potential for inexpensive synthesis of substantial quantities of AMPs. Lysine (K) was chosen as the hydrophilic amino acid and alanine (A), phenylalanine (F), and leucine (L) as the hydrophobic amino acids. We synthesized five series of AMPs (i.e., P(KA), P(KL), P(KF), P(KAL), and P(KFL)), varied the hydrophobic amino acid content from 0 to 100%, and determined minimal inhibitory concentrations (MICs) against clinically important Gram-negative and Gram-positive bacteria and fungi (i.e., Escherichia coli ( E. coli ), P. aeruginosa , Serratia marcescens ( S. marcescens ), and Candida albicans ( C. albicans ). We found that P(K(10)F(7.5)L(7.5)) and P(K(10)F(15)) show the broadest activity against all five pathogens and have the lowest MICs against these pathogens. For P(K(10)F(7.5)L(7.5)), the MICs against E. coli , P. aeruginosa , S. marcescens , S. aureus , and C. albicans are 31 microg/mL, 31 microg/mL, 250 microg/mL, 31 microg/mL, and 62.5 microg/mL, while for P(K(10)F(15)) the respective MICs are 31 microg/mL, 31 microg/mL, 250 microg/mL, 31 microg/mL, and 125 microg/mL. These are lower than the MICs of many naturally occurring AMPs. The membrane depolarization and SEM assays confirm that the mechanism of microbe killing by P(K(10)F(7.5)L(7.5)) copeptide includes membrane disruption, which is likely to inhibit rapid induction of AMP-resistance in pathogens.
<title>High Resolution Lithography Of Charge Coupled Devices (CCDS) Using Projection Printing</title> (1978)

A four phase transparent gate CCD has been fabricated using 1:1 projection printing on all photo-lithographic processes which required resist resolution in the 2-4 µm range on many of the masking levels. The photolithographic processes and techniques used will be described and presented.
Polydopamine Thin Films as Protein Linker Layer for Sensitive Detection of Interleukin-6 by Surface Plasmon Enhanced Fluorescence Spectroscopy (2016)

Polydopamine (PDA) thin films are introduced to the surface modification of biosensor surfaces utilizing surface plasmon enhanced fluorescence spectroscopy (SPFS) as the linker layer of capture antibody on to the sensor surfaces. The capture antibody can be directly attached to the sensor surface without using any coupling agent by functionalizing the gold sensor surface with PDA thin films. The PDA coating is performed by a single-step preparation process by applying the dopamine solution on the sensor surface, which requires an extremely short incubation time (10 min). The real-time in situ measurement of the adsorption kinetics of the capture antibody onto the PDA-coated sensor surface is studied by surface plasmon resonance (SPR) spectroscopy. It reveals that the immobilization of capture antibody immediately occurs after introduction of a solution containing capture antibody, and the sensor surface is fully covered with the capture antibody. The sensitive detection of the cytokine marker interleukin-6 (IL-6) is performed by SPFS using a sandwich assay format with fluorescently labeled detection antibody. The sensor chips functionalized by PDA chemistry exhibited sensitive sensor responses with low nonspecific adsorption of the detection antibody onto the sensor surface. The detection limit of IL-6 with the developed SPFS biosensor is determined to be 2 pg/mL (100 fM), which is within the range of the diagnostic criteria. Our observation elucidates the remarkable utility of PDA coatings for chemical modification of the metallic sensor surfaces by a simple, brief, and inexpensive manner.