gebhart/patrepeval huggingface dataset:
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes (2009)

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.
Arsenic selenide dielectric metasurfaces (2019)

Arsenic triselenide (As<sub>2</sub>Se<sub>3</sub>) is of interest for use in dielectric metasurfaces for several reasons: It has a high linear refractive index, <i>n</i>=2.8, enabling high index contrast with its surrounding medium; it has an exceptionally high optical nonlinearity (<i>n</i><sub>2</sub> &lt; 900 &times; that of silica) making it a good candidate for nonlinear metasurfaces; and its band gap of 1.8 eV and wide transmission window, spanning from approximately 1.5-14 &mu;m, make it useful for applications in the shortwave infrared into the long-wave infrared. We discuss recent results in which we showed that unpassivated As<sub>2</sub>Se<sub>3</sub> films degrade significantly under ambient conditions in the presence of light. We discuss the mechanism of this degradation and show that deposition of a thin (~10 nm) Al<sub>2</sub>O<sub>3</sub> passivation layer, deposited via atomic layer deposition, together with preventing exposure to below-band gap light inhibits degradation. Finally, we fabricate initial As<sub>2</sub>Se<sub>3</sub>-based dielectric metasurfaces by writing features via a laser direct write system. For mid-wave to long-wave infrared applications, features with relevant sizes can be written using this technique. We measure resonances for these structures and compare to theoretical results.
Methoxyethyl-Modified Intercellular Adhesion Molecule-1 Antisense Phosphorothiateoligonucleotides Inhibit Allograft Rejection, Ischemic-Reperfusion Injury, and Cyclosporine-Induced Nephrotoxicity (2005)

ME/PS-modified ICAM-1 antisense oligo is very effective in inhibiting the ICAM-1-dependent mechanism of graft infiltration and tissue damage involved in allograft rejection, ischemic-reperfusion injury, and CsA-induced nephrotoxicity.
The Nociceptin Pharmacophore Site for Opioid Receptor Binding Derived from the NMR Structure and Bioactivity Relationships (2005)

Nociceptin, a 17 amino acid opioid-like peptide that has an inhibitory effect on synaptic transmission in the nervous system, is involved in learning, memory, attention, and emotion and is also implicated in the perception of pain and visual, auditory, and olfactory functions. In this study, we investigated the NMR solution structure of nociceptin in membrane-like environments (trifluoroethanol and SDS micelles) and found it to have a relatively stable helix conformation from residues 4-17 with functionally important N-terminal residues being folded aperidoically on top of the helix. In functional assays for receptor binding and calcium flux, alanine-scanning variants of nociceptin indicated that functionally important residues generally followed helix periodicity, consistent with the NMR structural model. Structure-activity relationships allowed identification of pharmacophore sites that were used in small molecule data base searches, affording hits with demonstrated nociceptin receptor binding affinities.
Antimicrobial and toxicological activities of some depsides and depsidones (2012)

The Journal of the National Science Foundation of Sri Lanka publishes the results of research in all aspects of Science and Technology. The journal also has a website at http://www.nsf.gov.lk/. 2020 Impact Factor: 0.515The JNSF provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge.
Capacity of hyperthermophilic Crenarchaeota for decomposition of refractory proteins (α- and β-keratins) (2014)

Anaerobic thermophilic archaea of the genera Thermogladius and Desulfurococcus capable of a- and P3-keratin decomposition were isolated from hot springs of Kamchatka and Kunashir Island. For two of them (strains 2355k and 3008g), the presence of high-molecular mass, cell-bound endopeptidases active against nonhydrolyzed and partially hydrolyzed proteins at high values of temperature and pH was shown. Capacity for β-keratin decomposition was also found in collection strains (type strains of Desulfurococcus amylolyticus subsp. amylolyticus, D. mucosus subsp. mobilis, and D. fermentans).
Genetic and pharmacological reduction of CDK14 mitigates α-synuclein pathology in human neurons and in rodent models of Parkinson’s disease (2022)

Abstract Parkinsona’s disease (PD) is a debilitating neurodegenerative disease characterized by the loss of midbrain dopaminergic neurons (DaNs) and the abnormal accumulation of α-Synuclein (α-Syn) protein. Currently, no treatment can slow nor halt the progression of PD. Multiplications and mutations of the α-Syn gene ( SNCA ) cause PD-associated syndromes and animal models that overexpress α-Syn replicate several features of PD. Decreasing total α-Syn levels, therefore, is an attractive approach to slow down neurodegeneration in patients with synucleinopathy. We previously performed a genetic screen for modifiers of α-Syn levels and identified CDK14, a kinase of largely unknown function as a regulator of α-Syn. To test the potential therapeutic effects of CDK14 reduction in PD, we ablated Cdk14 in the α-Syn preformed fibrils (PFF)-induced PD mouse model. We found that loss of Cdk14 mitigates the grip strength deficit of PFF-treated mice and ameliorates PFF-induced cortical α-Syn pathology, indicated by reduced numbers of pS129 α-Syn-containing cells. In primary neurons, we found that Cdk14 depletion protects against the propagation of toxic α-Syn species. We further validated these findings on pS129 α-Syn levels in PD patient neurons. Finally, we leveraged the recent discovery of a covalent inhibitor of CDK14 to determine whether this target is pharmacologically tractable in vitro and in vivo . We found that CDK14 inhibition decreases total and pathologically aggregated α-Syn in human neurons, in PFF- challenged rat neurons and in the brains of α-Syn-humanized mice. In summary, we suggest that CDK14 represents a novel therapeutic target for PD-associated synucleinopathy.
A method to assess endocardial regional longitudinal curvature of the left ventricle (1995)

Knowledge of the instantaneous geometry of the left ventricular (LV) chamber is necessary to calculate LV function and wall stresses. We describe a method utilizing myocardial markers that does not rely on any a priori assumptions of global LV geometry. Five dogs underwent placement of 25 endocardial and 3 epicardial miniature LV markers. Six weeks later, the animals were studied during conscious closed-chest conditions. The three-dimensional coordinates of the LV markers were used to compute longitudinal fitted curves for LV walls and septum during steady-state conditions; endocardial radii of curvature (rcurv) were then computed for each region at the midequatorial (rcurv-eq) and apical levels. There was a uniform decrease in rcurv in each LV wall during systole (compared with diastole, P < 0.01); at end systole, rcurv was regionally heterogeneous between opposing walls, e.g., anterior and posterior rcurv-eq values were 17.2 +/- 2.0 and 17.7 +/- 1.8 (SD) cm, respectively (P < 0.05). At end diastole, only septal-lateral rcurv-eq was different (16.9 +/- 2.1 vs. 18.7 +/- 1.3 cm: P < 0.05). Normalization of rcurv (to instantaneous LV volume) removed the systolic-diastolic differences, but a similar pattern of regional heterogeneity persisted. The data presented pertain to the LV endocardial surface, but the method described can be applied to the epicardial surface as well; this new method offers promise in assessing dynamic changes in longitudinal LV endocardial curvature.
Differently Selected d -Enantiomeric Peptides Act on Different Aβ Species (2009)

Aging is the most significant risk factor for Alzheimer disease (AD). The pathological hallmark of AD is the accumulation of aggregated amyloid-beta (Abeta) forms and insoluble plaques, mainly composed of Abeta, in the brain of the patient. Recently, we reported on the selection of D-enantiomeric, Abeta-binding peptides D1 and D3. D1 was selected against aggregated Abeta species to address diagnosis by in vivo imaging of amyloid plaques, whereas D3 was selected using low-molecular-weight Abeta species, therefore addressing therapeutical studies. Here, we use a surface plasmon resonance method to confirm that both peptides show the desired binding specificities.
Concise synthesis of calystegines B2 and B3via intramolecular Nozaki–Hiyama–Kishi reaction (2016)

The key step in the concise syntheses of calystegine B2 and its C-2 epimer calystegine B3 was the construction of cycloheptanone 8via an intramolecular Nozaki-Hiyama-Kishi (NHK) reaction of 9, an aldehyde containing a Z-vinyl iodide. Vinyl iodide 9 was obtained by the Stork olefination of aldehyde 10, derived from carbohydrate starting materials. Calystegines B2 (3) and B3 (4) were synthesized from d-xylose and l-arabinose derivatives respectively in 11 steps in excellent overall yields (27% and 19%).
Roundoff noise in floating point state space digital filters (2003)

The roundoff noise properties of floating-point state-space digital filters are examined. It is shown that the roundoff noise behavior of these filters is related to their coefficient sensitivity. Expressions for the variance of the output roundoff noise are derived when the input to the filter is a zero-mean, wide-sense stationary random process. These expressions, as expected, depend on the input signal statistics along with the filter parameters, in particular the controllability and observability grammians.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Homicide by schizophrenic patients in Israel (1999)

Thirty-three schizophrenic inpatients aged 45.3 +/- 13.5 years who had been found not guilty of homicide by reason of insanity were compared with 28 schizophrenic patients matched for age, sex and duration of disease who had not committed any crime. Statistical analysis revealed a high rate in the study group of individual factors associated with aggression, such as alcohol abuse, previous contact with the police, aggressive behavior and threats (P < 0.05). Significantly more of them were also immigrants (P < 0.05). There was no between-group difference in familial factors. These findings support earlier studies indicating that schizophrenic patients with the profile of alcoholism, aggressiveness and foreign country of origin are at high risk of homicidal behavior.
Realization of a salt bridge-free microfluidic reference electrode (2012)

We report on the design of a microfluidic electrochemical cell with a true Ag/AgCl reference electrode that does not rely on a physical barrier or salt bridge, but instead takes advantage of slow diffusion times in micro-channels. The device concept is demonstrated in PDMS using the Ir(+IV)/Ir(+III) redox couple as an example. A scaling analysis provides limits of operation for the device.
Towards a generic, service oriented framework for distributed real-time systems. (2012)

Abstract—Continuously increasing complexity and scale of distributed real-time systems have exposed the limitations of their existing development methodologies. This fact is evident by the unsustainable rate of increase in the development and maintenance costs of such systems. In this paper, we present a generic, service-oriented framework for distributed real-time systems. The proposed framework can potentially serve as the basis for a widely applicable, cross-domain toolset, thus, decreasing the development and maintenance costs for distributed real-time systems. The proposed framework consists of a generic, service-oriented deployment platform that abstracts away the details of implementation platform and an associated development methodology. The proposed framework makes extensive use of the existing service-oriented technologies such as Web Services. However, it also extends these technologies for application to distributed real-time systems by introducing QoS-aware service deployment and service monitoring phases. This paper presents the details of the proposed framework as well as a case-study of the application of the proposed framework to the domain of smart grid. Keywords-real-time systems; service-oriented computing; smart grid; cyber-physical systems; web services I.
ChemInform Abstract: Synthesis of Aminomethylated 4‐Fluoropiperidines and 3‐Fluoropyrrolidines. (2010)

Abstract Key step of the title synthesis is the regioselective bromofluorination of methylenepiperidines and ‐pyrrolidines (I) with NBS and Et 3 N·3HF.
Thermodynamics of glucagon aggregation (1979)

Heats of dilution of concentrated glucagon solutions have been measured calorimetrically at 10 and 25 degrees C in 0.2 M potassium phosphate buffer of pH 10.6. Analysis of the data in terms of a monomer-trimer equilibrium gives the following thermodynamic parameters for the association reaction at 25 degrees C: delta G degrees = 7.34 kcal/mol of trimer, delta H degrees = -31.2 kcal/mol, deltaS degrees = -80 cal/(K mol), deltaCp = 430 cal/(K mol). The sensitivity of heat of dilution data to the association constant and stoichiometry of the reaction is discussed.
ERYTHROPOIETIN ATTENUATES INFLAMMATORY AND PROTHROMBOGENIC RESPONSES IN EXPERIMENTAL SEPSIS. (2005)

Copyright © by 2005 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.
A ubiquitous chromatin opening element prevents transgene silencing in pluripotent stem cells and their differentiated progeny (2013)

Methylation-induced gene silencing represents a major obstacle to efficient transgene expression in pluripotent cells and thereof derived tissues. As ubiquitous chromatin opening elements (UCOE) have been shown to prevent transgene silencing in cell lines and primary hematopoietic cells, we hypothesized a similar activity in pluripotent cells. This concept was investigated in the context of cytidine deaminase (CDD) gene transfer, an approach to render hematopoietic cells resistant to the chemotherapeutic agent Ara-C. When murine induced pluripotent stem cells (iPSC)/embryonic stem cells (ESCs) were transduced with self-inactivating lentiviral vectors using housekeeping (truncated elongation factor 1α; EFS) or viral (spleen focus-forming virus; SFFV) promoters, incorporation of an heterogeneous nuclear ribonucleoproteins A2 B1/chromobox protein homolog 3 locus-derived UCOE (A2UCOE) significantly increased transgene expression and Ara-C resistance and effectively prevented silencing of the SFFV-promoter. The EFS promoter showed relatively stable transgene expression in naïve iPSCs, but rapid transgene silencing was observed upon hematopoietic differentiation. When combined with the A2UCOE, however, the EFS promoter yielded stable transgene expression in 73% ± 6% of CD41(+) hematopoietic progeny, markedly increased CDD expression levels, and significantly enhanced Ara-C resistance in clonogenic cells. Bisulfite sequencing revealed protection from differentiation-induced promoter CpG methylation to be associated with these effects. Similar transgene promoting activities of the A2UCOE were observed during murine neurogenic differentiation, in naïve human pluripotent cells, and during nondirected multilineage differentiation of these cells. Thus, our data provide strong evidence that UCOEs can efficiently prevent transgene silencing in iPS/ESCs and their differentiated progeny and thereby introduce a generalized concept to circumvent differentiation-induced transgene silencing during the generation of advanced iPSC/ESC-based gene and cell therapy products.
Photolysis of Substituted Benzenediazonium Salts: Spin-Selective Reactivity of Aryl Cations (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotolysis of Substituted Benzenediazonium Salts: Spin-Selective Reactivity of Aryl CationsSusan M. Gasper, C. Devadoss, and Gary B. SchusterCite this: J. Am. Chem. Soc. 1995, 117, 19, 5206–5211Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/ja00124a004https://doi.org/10.1021/ja00124a004research-articleACS PublicationsRequest reuse permissionsArticle Views658Altmetric-Citations60LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Rigid Amphipathic Fusion Inhibitor dUY11 Acts through Photosensitization of Viruses (2013)

Rigid amphipathic fusion inhibitors (RAFIs) are lipophilic inverted-cone-shaped molecules thought to antagonize the membrane curvature transitions that occur during virus-cell fusion and are broad-spectrum antivirals against enveloped viruses (Broad-SAVE). Here, we show that RAFIs act like membrane-binding photosensitizers: their antiviral effect is dependent on light and the generation of singlet oxygen ((1)O(2)), similar to the mechanistic paradigm established for LJ001, a chemically unrelated class of Broad-SAVE. Photosensitization of viral membranes is a common mechanism that underlies these Broad-SAVE.
Identifying Subtypes of Alzheimer’s Disease: An analysis of possible cognitive subgroups through the life span (2022)

Abstract Background Typical Alzheimer’s disease (AD) is linked to memory impairment and medial temporal lobe atrophy. However, different patterns of cognitive decline in individuals with AD have been described in the literature (e.g., Murray et al., 2011; Lam et al., 2013; Scheltens et al., 2015). The variability of AD is also observed throughout the life span, as aging processes develop (Ferreira et al., 2017), which highlights the importance of investigating changes over time and establishing possible stages and therapeutic windows. Method The Toronto Cognitive Assessment (TorCA) was used to provide a characterization of cognitive profiles including orientation, immediate recall, delayed recall, delayed recognition, visuospatial function, executive control and language in 609 individuals with possible AD. Normative data for the TorCA (Freedman et al., 2018) suggest different levels of impairment can be identified depending on age groups. The present study investigated 27 neuropsychological subtests within the TorCA. Scores were summed based on cognitive domains and transformed into z‐scores. Further, the dataset was split into 4 age groups (Group 1 = less than 59; Group 2 = 60 to 69; Group 3 = 70 to 79; and Group 4 = over 80 years of age). The scores were analyzed with latent profile analyses (LPA) to identify cluster memberships among subjects. Result Different AD subtypes were identified in each age group characterized by patterns of cognitive impairment as follows: a) Group 1: 1. Cluster 1: mild; 2. Cluster 2: amnestic; 3. Cluster 3: executive; 4. Cluster 4: moderate diffuse. b) Group 2: 1. Cluster 1: mild diffuse; 2. Cluster 2: executive / visuospatial; 3. Cluster 3: moderate with preserved orientation and visuospatial c) Group 3: 1. Cluster 1: moderate executive; 2. Cluster 2: mild diffuse; 3. Cluster 3: amnestic; 4. Cluster 4: moderate diffuse. d) Group 4: 1. Cluster 1: severe diffuse; 2. Cluster 2: mild diffuse. Conclusion These findings suggest that different subtypes of AD can be identified throughout the life span. Further investigation of these differences will aid in the development of clinical tools to diagnose and treat subgroups, in the development of protocols that stratify this population for better research recruitment, and establishing relevant neuropsychological and clinical tools.
ConSLAM: Construction Data Set for SLAM (2023)

This paper presents a data set collected periodically on a construction site. The data set aims to evaluate the performance of simultaneous localization and mapping (SLAM) algorithms used by mobile scanners or autonomous robots. It includes ground-truth scans of a construction site collected using a terrestrial laser scanner along with five sequences of spatially registered and time-synchronized images, lidar scans, and inertial data coming from our prototypical handheld scanner. We also recover the ground-truth trajectory of the mobile scanner by registering the sequential lidar scans to the ground-truth scans and show how to use a popular software package to measure the accuracy of SLAM algorithms against our trajectory automatically. To the best of our knowledge, this is the first publicly accessible data set consisting of periodically collected sequential data on a construction site.