gebhart/patrepeval huggingface dataset:
Mixing discrete block co‐oligomers: When does it behave like a disperse sample? (2022)

Abstract Blends of block copolymers (BCPs) have great potential for applications in nanotechnology as the desired dimensions and complex nanopatterns can be designed upon mixing BCPs with other BCPs or homopolymers. Recently, we explored the synthesis of a series of discrete oligo(dimethylsiloxane) block co‐oligomers (BCOs) and studied their phase behavior. Here, we disclose our results on blending oligomers of different lengths of discrete hydrazone end‐functionalized oligo(dimethylsiloxanes) to study the effect of mixing on the morphological order. These mixtures possess a certain dispersity ( Ð ) as a result of the composition of the mixture. We have found that a distinct boundary exists between a good and poor morphological order at Ð ~ 1.10. As a result, the domain spacings of the low dispersity mixtures can be tuned by the molecular composition of the mixture, creating a wider spectrum of morphologies. Furthermore, we compare a hydrazone end‐functionalized siloxane with a dispersity as a result of mixing with its analog having a similar dispersity but resulting from traditional polymerization. Finally, a discrete BCO was mixed with a disperse BCO of similar size and composition. The discrete BCO is immiscible in the disperse BCO which emphasizes the differences in interactions within disperse and discrete oligomers. These results demonstrate that the entropic and enthalpic contributions to nanoscale order in a system composed of discrete components are different compared to disperse BCPs and BCOs.
A New Dibenzofuran from the Barks of Sorbus commixta (2017)

A new dibenzofuran derivative, 1,2,4-trimethoxydibenzofuran-3,9-diol (7), was isolated from the ethyl acetate fraction of Sorbus commixta barks, along with six known compounds, lupeol (1), betulin (2), betulinic acid (3), ursolic acid (4), -sitosterol (5) and -pyrufuran (6). Their structures were determined by NMR spectroscopic analysis, including of 1 H and 13 C NMR, 1 H-1 H COSY, HSQC and HMBC spectra data. Cytotoxic activities of seven compounds were evaluated in five cancer cell lines, HEp-2, A549, MCF-7, PC-3 and SKOV-3 at the concentrations ranging from 10 to 100 M.
Low complexity space-time MMSE equalization in WCDMA systems (2006)

In this paper we propose a low complexity frequency-domain method for finding the minimum mean square error (MMSE) equalizer. Special properties of circulant matrices are exploited in the method. Simulations show that only a minor performance loss is experienced compared to time-domain processing. We also compare joint space-time processing to decoupled equalization and spatial combining. The complexity reduction due to the decoupled processing is evident, while the performance loss remains small. Consequently, the proposed low complexity frequency-domain method can also be used with multiple receive antennas with tolerable performance loss compared to joint space time equalization. Additionally, different MMSE equalizer definitions for multiple receive antennas are considered, and their performance is studied in simulation using estimated channels. Simulations are carried out in high data rate WCDMA system model.
CYP53A15 of Cochliobolus lunatus, a Target for Natural Antifungal Compounds (2008)

A novel cytochrome P450, CYP53A15, was identified in the pathogenic filamentous ascomycete Cochliobolus lunatus. The protein, classified into the CYP53 family, was capable of para hydroxylation of benzoate. Benzoate is a key intermediate in the metabolism of aromatic compounds in fungi and yet basically toxic to the organism. To guide functional analyses, protein structure was predicted by homology modeling. Since many naturally occurring antifungal phenolic compounds are structurally similar to CYP53A15 substrates, we tested their putative binding into the active site of CYP53A15. Some of these compounds inhibited CYP53A15. Increased antifungal activity was observed when tested in the presence of benzoate. Some results suggest that CYP53A15 O-demethylation activity is important in detoxification of other antifungal substances. With the design of potent inhibitors, CYP53 enzymes could serve as alternative antifungal drug targets.
Spinal cord injury: a systematic review and meta-analysis of microRNA alterations (2023)

Abstract Spinal cord injury (SCI) often results in life-long disability, lost wages, reduced quality of life, and high economic burden. A bottle neck in the performance of clinical trials exists, in part, due to a lack of diagnostic and prognostic markers of injury severity and neurologic recovery. In addition, while many interventions show promise in preclinical animal models, there are currently no neurorestorative treatments for SCI patients. The development of objective biological markers (biomarkers) and molecular targets for novel treatments for SCI represent two urgent unmet clinical needs. MicroRNAs (miRNAs) represent promising molecules as objective and informative molecules of injury severity and recovery and as potential therapeutic targets. miRNAs are small, stable, regulatory RNA molecules that are evolutionarily conserved across species. miRNAs represent powerful predictors of pathology, particularly with respect to neurologic disorders. Here, we present a systematic review and meta-analysis investigating the conserved inter- and intra-species miRNA changes that occur post-SCI and provide a comprehensive resource for the SCI community. Our analysis identifies a robust set of miRNAs that are involved in the pathophysiologic processes activated in response to SCI.
Neurologic signs and symptoms in fibromyalgia (2009)

This blinded, controlled study demonstrated neurologic physical examination findings in persons with FM. The FM group had more neurologic symptoms than did the controls, with moderate correlation between symptoms and signs. These findings have implications for the medical evaluation of patients with FM.
Positive allosteric modulation of metabotropic glutamate receptor 5 modulates Akt and GSK3β signaling <i>in vivo</i> (2019)

Abstract Background Positive allosteric modulators (PAMs) of metabotropic glutamate receptor 5 (mGlu 5 ) have behavioral effects predictive of antipsychotic activity in experimental models such as amphetamine-induced hyperlocomotion (AHL). However, the signaling mechanisms that contribute to the antipsychotic-like properties of mGlu 5 PAMs are not well understood. Methods Because the Akt/GSK3β pathway has been implicated in schizophrenia and is modulated by known antipsychotic drugs, we evaluated the effects of systemic administration of two mGlu 5 PAMs on Akt and GSK3β signaling using western blot analysis in both naïve and amphetamine-treated adult male rats. Results In the dorsal striatum, the mGlu 5 -selective PAM VU0092273 (30 mg/kg) significantly increased Akt phosphorylation at residues associated with enhanced kinase activity, Thr308 and Ser473. Inhibitory phosphorylation of GSK3β at Ser9 was also increased. Similar effects were observed with a second mGlu 5 PAM, VU0360172 (56.6 mg/kg). VU0092273 increased Akt phosphorylation levels in amphetamine-treated rats. Effects on Akt/GSK3β signaling were not limited to the striatum, as VU0092273 also increased Akt/GSK3β phosphorylation in the medial prefrontal cortex. Conclusions These findings suggest that mGlu 5 PAMs that have antipsychotic-like efficacy in rats affect signaling pathways that are modulated by known antipsychotics, and raise the possibility that inhibition of GSK3β might contribute to the antipsychotic-like effects of mGlu 5 PAMs.
Click Chemistry Hydrogels for Extrusion Bioprinting: Progress, Challenges, and Opportunities (2022)

The emergence of 3D bioprinting has allowed a variety of hydrogel-based "bioinks" to be printed in the presence of cells to create precisely defined cell-loaded 3D scaffolds in a single step for advancing tissue engineering and/or regenerative medicine. While existing bioinks based primarily on ionic cross-linking, photo-cross-linking, or thermogelation have significantly advanced the field, they offer technical limitations in terms of the mechanics, degradation rates, and the cell viabilities achievable with the printed scaffolds, particularly in terms of aiming to match the wide range of mechanics and cellular microenvironments. Click chemistry offers an appealing solution to this challenge given that proper selection of the chemistry can enable precise tuning of both the gelation rate and the degradation rate, both key to successful tissue regeneration; simultaneously, the often bio-orthogonal nature of click chemistry is beneficial to maintain high cell viabilities within the scaffolds. However, to date, relatively few examples of 3D-printed click chemistry hydrogels have been reported, mostly due to the technical challenges of controlling mixing during the printing process to generate high-fidelity prints without clogging the printer. This review aims to showcase existing cross-linking modalities, characterize the advantages and disadvantages of different click chemistries reported, highlight current examples of click chemistry hydrogel bioinks, and discuss the design of mixing strategies to enable effective 3D extrusion bioprinting of click hydrogels.
Recent topics in fibrodysplasia ossificans progressiva (2012)

Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant disorder characterized by progressive heterotopic bone formation in skeletal muscle tissue. Patients with FOP show malformed digits, osteochondroma, and other skeletal abnormalities due to abnormal patterning during development. Heterozygous mutations in the Activin A receptor type I (ACVR1) gene, which encodes the bone morphogenetic protein (BMP) type I receptor ALK2, have been identified in not only typical FOP patients but also patients with unusually mild or severe clinical features. The serine/threonine kinase activity of ALK2 may be constitutively activated by mutations in the GS domain or the kinase domain. Based on these findings, selective small chemical inhibitors and allele-specific RNAi approaches for mutant ALK2 have been developed for preventing heterotopic bone formation in FOP. Other novel treatments have also been reported to block heterotopic bone formation in patients with FOP. These findings open the door to the next step in FOP treatment and related research.
First Demonstration of 10G-EPON and GE-PON Co-existing System Employing Dual-rate Burst-mode 3R Transceiver (2010)

Novel 10G-EPON dual-rate burst-mode 3R transceiver with receiver sensitivity of −31.2dBm for 10.3Gb/s and −35.6dBm for 1.25Gb/s was developed. 10G-EPON and GE-PON coexisting system of 32× ONUs with loss budget of 33.5dB was successfully demonstrated.
WLC45-6: A Family of Low Complexity Adaptive Binary Linear Block Codes (2006)

A family of linear binary block codes is constructed from ordinary block repetition codes using cyclic shifts of the input information vector which greatly simplifies encoding. These codes have variable block length and variable minimum Hamming distance. Several sets of cyclic shifts are defined to constrain the search for good codes. Codeword enumeration strategies are discussed. The proposed codes are shown to be good candidates for adaptive coding, turbo product coding, retransmission schemes and multihop routing, and block differential encoding. A generic parallel encoder structure well suited to OFDM systems, and a non-recursive block differential encoder capable of arbitrarily increasing the code rate with the block length, for given minimum Hamming distance, are proposed. Numerical examples compare the bit-error rate assuming iterative soft- decision decoding and the union bound.
Estradiol Suppresses MCP-1 Expression In Vivo (1998)

The mechanisms by which 17beta-estradiol retards atherogenesis are not known. The adhesion of monocytes to endothelial cells followed by the migration of monocytes into the artery wall are key cellular events that occur throughout the entire atherogenic process and may be responsive to estradiol. Monocyte chemoattractant protein-1 (MCP-1), a chemokine that is expressed in atherosclerotic lesions, is thought to play a major role in stimulating the migration of blood monocytes into developing atherosclerotic lesions. We therefore assessed the effects of estradiol in vivo on MCP-1 protein and mRNA expression in the descending thoracic aorta of rabbits fed a cholesterol-enriched (0.5%) diet for 6 weeks and in animals fed normal chow. MCP-1 protein was quantified by Western blot analysis and monocyte chemotaxis bioassay, and reverse transcription-polymerase chain reaction was used to ascertain the level of MCP-1 mRNA expression. We observed that in both ovary-intact and ovariectomized (OVX) animals, MCP-1 protein and mRNA expression were significantly increased by 6 weeks in animals fed a high-cholesterol diet. The cholesterol-induced increase in MCP-1 protein and mRNA expression was significantly attenuated in OVX rabbits supplemented with estradiol pellets (1.5- and 10.0-mg 60-day-release pellets), which yielded a range of estradiol concentrations encompassing the physiological levels. MCP-1 protein and mRNA expression were increased in normocholesterolemic OVX rabbits compared with normocholesterolemic ovary-intact animals, and this increase was prevented in OVX animals supplemented with estradiol pellets. Our observations indicate that both basal and hypercholesterolemia-induced increases in MCP-1 protein are modulated by physiological concentrations of estradiol.
Microfluidic model with air-walls reveals fibroblasts and keratinocytes modulate melanoma cell phenotype, migration, and metabolism (2021)

Melanoma evolution is a complex process. The role epidermal keratinocytes and dermal fibroblasts play in this process and the mechanisms involved in tumor-stroma interactions remain poorly understood. Here, we used a microfluidic platform to evaluate the cross-talk between human primary melanoma cells, keratinocytes and dermal fibroblasts. The microfluidic device included multiple circular chambers separated by a series of narrow connection channels. The microdevice design allowed us to develop a new cell patterning method based on air-walls, removing the need for hydrogel barriers, porous membranes, or external equipment. Using this method, we co-cultured melanoma cells in the presence of keratinocytes and/or dermal fibroblasts. The results demonstrated that the presence of dermal fibroblasts and keratinocytes led to changes in melanoma cell morphology and growth pattern. Molecular analysis revealed changes in the chemokine secretion pattern, identifying multiple secreted factors involved in tumor progression. Finally, optical metabolic imaging showed that melanoma cells, fibroblasts, and keratinocytes exhibited different metabolic features. Additionally, the presence of stromal cells led to a metabolic shift in melanoma cells, highlighting the role the skin microenvironment on melanoma evolution.
Motion boundary response domains in awake monkey V2 (2012)

In the primate visual system, motion information is mainly processed in the dorsal visual pathway (V1 - MT). Recent findings of direction maps in areas V2 and V4, however, suggest that these areas may also play a significant role in motion perception. Perceptually, relative motion is an important source for detection of object boundaries as well as its 3D shape. In this study, we tested the hypothesis that area V2 is involved in detection of motion boundaries and their orientation at a population level. Monkeys were trained to perform a simple eye fixation task. Cortical activities were imaged through a chronic optical window over the visual areasV1 and V2. A motion boundary was created by two random dot patches within which dots were drifting coherently in opposite directions. By comparing cortical responses to horizontal and vertical motion boundaries, we found that there are domains within V2 that are preferentially activated by specific orientation of the motion boundaries. These orientation domains co-localize with regular luminance orientation domains. In comparison, V1 does not have a clear orientation response pattern to the motion boundaries, although pixel-averaged quantification does indicate some weak response in V1. Results from control stimuli indicate that such differences between V1 and V2 were not due to their differences in spatial frequency preferences and point to a V2 locus of motion boundary detection. Such second-order orientation detection mechanism shares the same functional architectures as the luminance orientation maps in V2. Meeting abstract presented at VSS 2012
ChemInform Abstract: LiCuIIxCuIIIyMnIII,IV(2‐(x+y))O4: 5 V Cathode Materials. (1997)

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.
COVID-19 severity is predicted by earlier evidence of accelerated aging (2020)

With no known treatments or vaccine, COVID-19 presents a major threat, particularly to older adults, who account for the majority of severe illness and deaths. The age-related susceptibility is partly explained by increased comorbidities including dementia and type II diabetes [1]. While it is unclear why these diseases predispose risk, we hypothesize that increased biological age, rather than chronological age, may be driving disease-related trends in COVID-19 severity with age. To test this hypothesis, we applied our previously validated biological age measure (PhenoAge) [2] composed of chronological age and nine clinical chemistry biomarkers to data of 347,751 participants from a large community cohort in the United Kingdom (UK Biobank), recruited between 2006 and 2010. Other data included disease diagnoses (to 2017), mortality data (to 2020), and the UK national COVID-19 test results (to May 31, 2020) [3]. Accelerated aging 10-14 years prior to the start of the COVID-19 pandemic was associated with test positivity (OR=1.15 per 5-year acceleration, 95% CI: 1.08 to 1.21, p=3.2×10<sup>-6</sup>) and all-cause mortality with test-confirmed COVID-19 (OR=1.25, per 5-year acceleration, 95% CI: 1.09 to 1.44, p=0.002) after adjustment for demographics including current chronological age and pre-existing diseases or conditions. The corresponding areas under the curves were 0.669 and 0.803, respectively. Biological aging, as captured by PhenoAge, is a better predictor of COVID-19 severity than chronological age, and may inform risk stratification initiatives, while also elucidating possible underlying mechanisms, particularly those related to inflammaging.
SSCQE (Single Stimulus Continuous Quality Evaluation): A New Subjective Assessment Method Introduced in ITU-R Recommendation 500-7: Presentation and Results (1996)

Based on the work undertaken within the European Commission's project RACE MOSAIC to overcome specific digital picture quality issues (e.g. content-dependent encoding performance, codec cascading, dynamic statistical multiplexing), a new methodology was designed to allow subjective assessment of both picture and service quality in conditions closer to the actual home environment. This paper gives a description of this new method, recently introduced in ITU-R Recommendation 500 under the label “SSCQE” for Single Stimulus Continuous Quality Evaluation, including test results.
An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays (2013)

New technologies in genomics and proteomics have influenced the emergence of proteogenomics, a field at the confluence of genomics, transcriptomics, and proteomics. First generation proteogenomic toolkits employ peptide mass spectrometry to identify novel protein coding regions. We extend first generation proteogenomic tools to achieve greater accuracy and enable the analysis of large, complex genomes. We apply our pipeline to Zea mays, which has a genome comparable in size to human. Our pipeline begins with the comparison of mass spectra to a putative translation of the genome. We select novel peptides, those that match a region of the genome that was not previously known to be protein coding, for grouping into refinement events. We present a novel, probabilistic framework for evaluating the accuracy of each event. Our calculated event probability, or eventProb, considers the number of supporting peptides and spectra, and the quality of each supporting peptide-spectrum match. Our pipeline predicts 165 novel protein-coding genes and proposes updated models for 741 additional genes.
The Raman Active Vibrational Modes of Anthraquinones (2022)

Anthraquinones are a family of natural products with useful bioactivity and optical properties. An anthraquinone called parietin is produced by extremophiles to protect against solar ultraviolet B radiation, so it is a potential biosignature in astrobiology. Raman spectroscopy, which is now used in space environments, can detect molecules such as parietin based on molecular vibrations. In this study, we show that time-dependent density functional theory (TDDFT) can accurately calculate the Raman spectra of three dihydroxyanthraquinones: parietin, emodin, and chrysophanol. By comparing calculated spectra to measured Raman spectra from purified powders, 10 vibrational modes are identified. The detailed molecular motions of these fused ring vibrations are described, and vibrations modes that are common to all three molecules are highlighted. In addition to powder spectra, Raman measurements from the thallus of <i>Xanthoria parietina,</i> a lichen that produces parietin, are reported, with excellent agreement to both the parietin powder and calculated Raman spectra. These results show that TDDFT calculations could make significant contributions to spectral analysis in the search for biotic organic materials beyond Earth.
Fully Integrated Wideband Doherty PA with Additive-Voltage Supported Load-Modulation in CMOS 130nm (2019)

This work introduces the first CMOS integrated Doherty power amplifier (DPA) with additive-voltage supported continuous load-modulation. Key features of the architecture are the wideband behaviour and low AM-PM distortion. Owing to the transformer based architecture, it is area efficient and highly suitable for integrated technologies. A prototype has been implemented in CMOS 130 nm. The complete chip size including input matching and the proposed load modulation network is less than 1.2 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Measured peak output power of 25 dBm is reached at 2.4 GHz with 27.6 % power added efficiency (PAE) and 24 % PAE at 6 dB backoff. The DPA delivers more than 24 dBm output power from 2.2 GHz to 3 GHz and thus, covers 31 % of bandwidth. Measured AM-PM distortion of less than 3° is obtained.
Should We Be Applying Warfarin Pharmacogenetics to Clinical Practice? No, Not Now (2009)

The U.S. Food and Drug Administration modified warfarin labeling in 2007 to suggest, but not mandate, pharmacogenetic testing. Genetic analysis is now commercially available. However, results predict only one third of all dosing variation, the value of testing in reducing bleeding and thrombosis rates remains unproved, and cost-effectiveness is not established. Careful consideration of clinical factors that influence dosing, conscientious prothrombin time monitoring, and sage dosage adjustment remain paramount in warfarin management. Further study is required before routine warfarin pharmacogenetic testing can be recommended.