gebhart/patrepeval huggingface dataset:
Viz3D: effective exploratory visualization of large multidimensional data sets (2004)

We propose a multidimensional visualization technique, named Viz3D, that creates a 3D representation of n-dimensional data that may be interactively manipulated by users to handle visual cluttering and object occlusion. The projection performed in Viz3D is comparable in quality with the 3D projections obtained with well-known dimensionality reduction techniques, at a lower complexity cost. While a 3D projection conveys more information, giving the user more control of the visual representation and an additional dimension, as compared to 2D, visual cluttering and object occlusion are still a problem in handling large multidimensional data sets. To produce more effective visualizations, two strategies are introduced. Dimensionality is handled with a similarity clustering of attributes prior to projection. Data set size is handled with a new strategy of visualizing data densities, rather than individual data records. Both the direct and density Viz3D visualizations provide the basis for a user driven visual clustering approach applicable to high-dimensional data sets that is very simple, intuitive and effective.
Modeling the Pressure-Density Relationship in Thin Films at Asperity Contacts in Mixed Lubrication (2005)

In mixed lubricated contact, the asperity contact regions may be separated by a thin layer of lubricant film. Simulations of mixed lubrication often use empirical formulae to describe the change of density with pressure in the lubricated areas. However, these models may not be applicable to molecularly thin films at asperity contact regions. We present a molecular simulation approach for density characterization of the fluid at asperity contact regions in mixed lubrication. The resultant density-pressure relationship is compared to the traditional Dowson-Higginson model. It is found that the two models predict comparable densities at low pressures but diverge at higher pressures.
Ophthalmology and Therapy: Reflecting on 2020 and Embracing the Challenges of 2021 (2021)

2020 will forever be marked as a year that brought with it an unprecedented number of challenges for the healthcare community. COVID-19 had monumental effects on all fields, including ophthalmology. Considering this we are truly thankful for all of the support we have received, despite the pressures brought about by the pandemic. We are very grateful to our Editorial and Advisory boards who have continued to offer their advice, to our authors for working with us to help publish their work, and to our readers for engaging with our content. The Editorial below has been authored by Ophthalmology and Therapy's EU Editor-in-Chief Professor Tariq Aslam. Professor Aslam writes about his aspirations for the healthcare and ophthalmology community in 2021, and how the journal hopes to play its part in facing these challenges.
Polarized localization and borate-dependent degradation of the Arabidopsis borate transporter BOR1 in tobacco BY-2 cells (2013)

In Arabidopsis the borate transporter BOR1, which is located in the plasma membrane, is degraded in the presence of excess boron by an endocytosis-mediated mechanism. A similar mechanism was suggested in rice as excess boron decreased rice borate transporter levels, although in this case whether the decrease was dependent on an increase in degradation or a decrease in protein synthesis was not elucidated. To address whether the borate-dependent degradation mechanism is conserved among plant cells, we analyzed the fate of GFP-tagged BOR1 (BOR1-GFP) in transformed tobacco BY-2 cells. Cells expressing BOR1-GFP displayed GFP fluorescence at the plasma membrane, especially at the membrane between two attached cells. The plasma membrane signal was abolished when cells were incubated in medium with a high concentration of borate (3 to 5 mM). This decrease in BOR1-GFP signal was mediated by a specific degradation of the protein after internalization by endocytosis from the plasma membrane. Pharmacological analysis indicated that the decrease in BOR1-GFP largely depends on the increase in degradation rate and that the degradation was mediated by a tyrosine-motif and the actin cytoskeleton. Tyr mutants of BOR1-GFP, which has been shown to inhibit borate-dependent degradation in Arabidopsis root cells, did not show borate-dependent endocytosis in tobacco BY-2 cells. These findings indicate that the borate-dependent degradation machinery of the borate transporter is conserved among plant species.
Präzise Leistungen ab dem ersten Versuch: Das Berliner Brain-Computer-Interface (2007)

Einleitung: Nicht-invasive Brain-Computer-Interfaces (BCI) übersetzen den Willen eines Probanden oder Patienten in technische Steuersignale ohne die Benutzung von peripheren Nerven oder Muskeln. Dabei haben sich willentlich zu beeinflussende Modulationen sensor-motorischer Rhythmen als besonders geeignete ableitbare Gehirn-Aktivität herausgestellt.
Fine-tuning of the Hsc70-based Human Protein Disaggregase Machinery by the Distinctive C-terminal Extension of Apg2 (2022)

Apg2, one of the three cytosolic Hsp110 chaperones in humans, supports reactivation of unordered and ordered protein aggregates by Hsc70 (HspA8). Together with DnaJB1, Apg2 serves to nucleate Hsc70 molecules into sites where productive entropic pulling forces can be developed. During aggregate reactivation, Apg2 performs as a specialized nucleotide exchange factor, but the origin of its specialization is poorly defined. Here we report on the role of the distinctive C-terminal extension present in Apg2 and other metazoan homologs. We found that the first part of this Apg2 subdomain, with propensity to adopt α-helical structure, interacts with the nucleotide binding domain of Hsc70 in a nucleotide-dependent manner, contributing significantly to the stability of the Hsc70:Apg2 complex. Moreover, the second intrinsically disordered segment of Apg2 C-terminal extension plays an important role as a downregulator of nucleotide exchange. An NMR analysis showed that the interaction with Hsc70 nucleotide binding domain modifies the chemical environment of residues located in important functional sites such as the interface between lobe I and II and the nucleotide binding site. Our data indicate that Apg2 C-terminal extension is a fine-tuner of human Hsc70 activity that optimizes the substrate remodeling ability of the chaperone system.
Tumor-Associated Macrophages Are Related to Volumetric Growth of Vestibular Schwannomas (2013)

This study demonstrates that M2-type macrophages in vestibular schwannomas relate to angiogenesis and volumetric tumor growth. These results imply that the M2-type macrophage infiltrate contributes to progressive tumor growth, making it a potential target for pharmacologic therapy.
The Response to Chemotherapy of Serum Mycobacterium Leprae-Specific Antigen in Multibacillary Leprosy Patients (1991)

We have examined the Mycobacterium leprae phenolic glycolipid-I (PG-I) antigen levels in the sera of 45 multibacillary leprosy patients commencing chemotherapy. The PG-I antigen levels correlated with the bacterial and morphological indices, but not with the serum IgM anti-PG-I antibody levels. Antigen levels were significantly higher in patients with diffuse skin infiltration, but did not vary significantly with other parameters reflecting the duration and extent of untreated disease. The PG-I antigen levels in 27 patients examined serially decreased consistently over the first year of multidrug therapy.
Development of the Innervation and Airway Smooth Muscle in Human Fetal Lung (1999)

Human and porcine fetal airways have been shown to contract spontaneously from the first trimester, the latter also contracting in response to neural stimulation. Our object was to map immunohistochemically the innervation and its relationship to the airway smooth muscle (ASM) in the human fetal lung from early gestation to the postnatal period. Whole mounts of the bronchial tree were stained with antibodies to the pan-neuronal marker protein gene product 9.5, the Schwann cell marker S-100, and the ASM contractile protein alpha-actin, and imaged using confocal microscopy. By the end of the embryonic period (53 d gestation), the branching epithelial tubules in the primordial lung were covered with ASM to the base of the terminal sacs. An extensive plexus of nerve trunks containing nerve bundles, forming ganglia, and Schwann cells ensheathed the ASM. By 16 wk (canalicular stage), maturation of the innervation was advanced with two major nerve trunks running the length of the bronchial tree, giving rise to varicosed fibers lying on the ASM. An extensive nerve plexus in the mucosa was also present. The distal airways of infants who had died of Sudden Infant Death Syndrome were also covered with smooth muscle and were well innervated. Thus, an essentially complete coat of ASM and an abundant neural plexus ensheathing the airways are an integral part of the branching epithelial tubules from early in lung development.
Mice lacking N-acetylglucosaminyltransferase I activity die at mid-gestation, revealing an essential role for complex or hybrid N-linked carbohydrates. (1994)

Eukaryotic cells require N-linked carbohydrates for survival. However, the biosynthetic intermediate Man5GlcNAc2Asn, in place of mature N-linked structures, allows glycoprotein synthesis and somatic cell growth to proceed normally. To determine whether the same would be true in a complex biological situation, the gene Mgat-1 was disrupted by homologous recombination in embryonic stem cells and transmitted to the germ line. The Mgat-1 gene encodes N-acetylglucosaminyltransferase I [GlcNAc-TI; alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase; UDP-N-acetyl-D-glucosamine:glycoprotein (N-acetyl-D-glucosamine to alpha-D-mannosyl-1,3-(R1)-beta-D-mannosyl-R2) beta-1,2-N-acetyl-D-glucosaminyltransferase, EC 2.4.1.101], the transferase that initiates synthesis of hybrid and complex N-linked carbohydrates from Man5GlcNAc2Asn. Mice lacking GlcNAc-TI activity did not survive to term. Biochemical and morphological analyses of embryos from 8.5 to 13.5 days of gestation showed that Mgat-1-/-embryos are developmentally retarded, most noticeably in neural tissue, and die between 9.5 and 10.5 days of development.
Data from The Effect of Corticosteroids on Prostate Cancer Outcome Following Treatment with Enzalutamide: A Multivariate Analysis of the Phase III AFFIRM Trial (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The clinical impact of concurrent corticosteroid use (CCU) on enzalutamide-treated patients with metastatic castration-resistant prostate cancer (mCRPC) is unknown. We investigated the association of CCU with overall survival (OS), radiographic progression-free survival (rPFS), and time to prostate-specific antigen progression (TTPP) in post-chemotherapy, enzalutamide-treated patients with mCRPC.&lt;/p&gt;Patients and Methods:&lt;p&gt;&lt;i&gt;Post hoc&lt;/i&gt; analysis of AFFIRM (NCT00974311) with patients (&lt;i&gt;n&lt;/i&gt; = 1,199) randomized 2:1 to enzalutamide 160 mg/day or placebo. Treatment group, CCU, and known prognostic factors were evaluated for impact on OS, rPFS, and TTPP using a multivariate Cox proportional hazards model. CCU was defined as “baseline” (use started at baseline) or “on-study” (baseline plus use that was started during the trial).&lt;/p&gt;Results:&lt;p&gt;Enzalutamide significantly improved OS, rPFS, and TTPP independent of baseline CCU but was associated with inferior clinical outcomes when compared with no baseline CCU, including a shorter OS [10.8 months vs. not reached (NR); HR for use vs. no use, 2.13; 95% confidence interval (CI), 1.79–2.54], rPFS (5.2 months vs. 8.0 months; HR, 1.49; 95% CI, 1.29–1.72], and TTPP (4.6 months vs. 5.7 months; HR, 1.50; 95% CI, 1.25–1.81). These findings held in a multivariate analysis adjusting for baseline prognostic factors wherein baseline CCU was independently associated with decreased OS (HR, 1.71; 95% CI, 1.43–2.04; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and rPFS (HR, 1.28; 95% CI, 1.11–1.48; &lt;i&gt;P&lt;/i&gt; = 0.0007).&lt;/p&gt;Conclusions:&lt;p&gt;Patients with mCRPC benefited from enzalutamide treatment independent of CCU, but CCU was associated with worse baseline prognostic factors and outcomes.&lt;/p&gt;&lt;/div&gt;
The Univentricular Atrioventricular Connections (1985)

The authors examined nine autopsied hearts with univentricular atrioventricular&#13;\nconnection (UAVC), and described the important pathologic findings of each cardiac segment.&#13;\nThe classification of our cases was based on the morphology of main chamber and the status&#13;\nof atrioventricular connection. Left ventricular type was seen in five cases; one case of double&#13;\ninlet, three cases of absent right atrioventricular connection and one absent left atrioventricular&#13;\nconnection. Of four cases of right ventricular type, two were double inlet, one absent right&#13;\natrioventricular connection and one absent left connection. The pattern of the apical trabeculation&#13;\nof main chamber, the relationship between the septum and the crux cordis, and the&#13;\npresence and position of rudimentary chamber were the essence in determining the type of&#13;\nUAVc. The distribution pattern of delimiting arteries may be used as a guide to determine the&#13;\nventricular loop when the anatomical position of the rudimentary chamber is equivocal, In the&#13;\ncases of absent atrioventricular connection the ventricular loop can be determined by the&#13;\nventricular type of the main chamber and the site of absent connection.
Sourcerer (2006)

We present Sourcerer, a search engine for open-source code. Sourcerer extracts fine-grained structural information from the code and stores it in a relational model. This information is used to implement a basic notion of CodeRank and to enable search forms that go beyond conventional keyword-based searches.
Perceptive Locomotion Through Nonlinear Model-Predictive Control (2023)

Dynamic locomotion in rough terrain requires accurate foot placement, collision avoidance, and planning of the underactuated dynamics of the system. Reliably optimizing for such motions and interactions in the presence of imperfect and often incomplete perceptive information is challenging. We present a complete perception, planning, and control pipeline, which can optimize motions for all degrees of freedom of the robot in real time. To mitigate the numerical challenges posed by the terrain, a sequence of convex inequality constraints is extracted as local approximations of foothold feasibility and embedded into an online model-predictive controller. Steppability classification, plane segmentation, and a signed distance field are precomputed per elevation map to minimize the computational effort during the optimization. A combination of multiple-shooting, real-time iteration, and a filter-based line search is used to solve the formulated problem reliably and at high rate. We validate the proposed method in scenarios with gaps, slopes, and stepping stones in simulation and experimentally on the ANYmal quadruped platform, resulting in state-of-the-art dynamic climbing.
Impaired Function of HDAC6 Slows Down Axonal Growth and Interferes with Axon Initial Segment Development (2010)

The development of morphological neuronal polarity starts by the formation and elongation of an axon. At the same time the axon initial segment (AIS) is generated and creates a diffusion barrier which differentiate axon and somatodendritic compartment. Different structural and functional proteins that contribute to the generation of neuronal action potential are concentrated at the axon initial segment. While axonal elongation is controlled by signalling pathways that regulate cytoskeleton through microtubule associated proteins and tubulin modifications, the microtubule cytoskeleton under the AIS is mostly unknown. Thus, understanding which proteins modify tubulin, where in the neuron and at which developmental stage is crucial to understanding how morphological and functional neuronal polarity is achieved. In this study performed in mice and using a well established model of murine cultured hippocampal neurons, we report that the tubulin deacetylase HDAC6 is localized at the distal region of the axon, and its inhibition with TSA or tubacin slows down axonal growth. Suppression of HDAC6 expression with HDAC6 shRNAs or expression of a non-active mutant of HDAC6 also reduces axonal length. Furthermore, HDAC6 inhibition or suppression avoids the concentration of ankyrinG and sodium channels at the axon initial segment (AIS). Moreover, treatment of mouse cultured hippocampal neurons with detergents to eliminate the soluble pool of microtubules identified a pool of detergent resistant acetylated microtubules at the AIS, not present at the rest of the axon. Inhibition or suppression of HDAC6 increases acetylation all along the axon and disrupts the specificity of AIS cytoskeleton, modifying the axonal distal gradient localization of KIF5C to a somatodendritic and axonal localization. In conclusion, our results reveal a new role of HDAC6 tubulin deacetylase as a regulator of microtubule characteristics in the axon distal region where axonal elongation takes place, and allowing the development of acetylated microtubules microdomains where HDAC6 is not concentrated, such as the axon initial segment.
Date Syrup and Baker's Yeast Production (2002)

Date syrup might be considered as one of the innovative and attractive byproducts in date processing for the habitants in west and southwest Asia. Date syrup, which is an important byproduct of dates, was obtained by water extraction and evaluated as a substrate for baker's yeast production, in a batch laboratory-scale fermentation. Saccharomyces cerevisiae was cultivated in the date syrup (20 g/L) based medium. Batch growth was studied in shaken flasks. The diauxic growth was observed with two specific growth rates, 0.22 and 0.035 h-1, where the first relates to date sugar consumption and the second to ethanol uptake. Addition of a corn steep liquor (CSL) increased the dry cell mass, and a maximum yield was observed at 7% CSL in culture media. The effects of different carbon sources on biomass and yield indicated that date syrup could be evaluated as a favorable carbon source in baker's yeast production.
Construction of a Well-Defined Multifunctional Dendrimer for Theranostics (2011)

A dendrimer-based building block for theranostics was designed. The multifunctional dendrimer is polyamide-based and contains nine azide termini, nine amine termini, and fifty-four terminal acid groups. Orthogonal functionalization of the multifunctional dendrimer with a near-infrared (NIR) cyanine dye afforded the final dendrimer that shows fluorescence in the NIR region and no toxicity toward T98G human cells. The synthetic strategy described here might be promising for fabricating the next generation of materials for theranostics.
ChemInform Abstract: ESR Studies of Radicals Derived from 1,3,2‐Benzodioxaboroles. (1986)

Abstract The reactions of photochemically generated ethoxyl and t‐butoxyl radicals with the dioxaboroles (I)‐(III) are studied in solution using ESR spectroscopy.
CT-Guided Sacroiliac Joint Injections (1999)

Confusion surrounding low back pain syndrome may partially be resolved in a select small group of patients by instituting a provocative intraarticular injection of a combination of a local anesthetic and a steroid. This approach enables one to determine whether the sacroiliac joint (SIJ) is the site of origin of the low back pain syndrome. We carried out a study of 71 computed tomography (CT)-guided injections in 58 patients with noninflammatory etiology. The injection was confirmatory to the SIJ abnormalities in 64 (90.1%) joints. The effect wore off in 2-14 days in 90% of the patients. We conclude that CT guidance is the best method of precise needle placement, and thus CT-guided anesthetic injection is the most specific confirmatory test for diagnosing the SIJ arthritis. In addition, in noninflammatory conditions, the role of intraarticular injection is primarily for diagnostic purposes and it has little or no therapeutic benefit.
Combining Models with Code: A Tale of Two Languages (2014)

In the pure model-driven view of software engineering, models are the sole artifacts to be created and maintained and executable source code is entirely generated from the models. However, due to the variety of modern platforms and the complexity of capturing them correctly in models, this vision has not yet been fully realized. In this paper, we propose an approach that allows combining high-level models with low-level code into an executable system. The approach is based on two modeling languages, one presenting a common abstraction of modeling and programming languages, and the other allowing to express the bridge between the model and code. We illustrate our approach using a running example of an invoicing system for which the business logic requirements are captured by an executable model and the requirements on the graphical user interface are directly mocked up using a GUI designer tool that generates Java code.
Low-Grade Inflammation and Ambulatory Blood Pressure Response to Antihypertensive Treatment: The ALPHABET Study (2013)

Baseline low-grade inflammation in patients with hypertension was associated with a poor ambulatory BP response, especially with losartan/HCTZ treatment. Initial measurement of hsCRP could be useful for selection of an appropriate antihypertensive drug.
Structures of C7H10 Valence Tautomers as Determined by Electron Diffraction (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructures of C7H10 Valence Tautomers as Determined by Electron DiffractionJoseph F. Chiang and S. H. BauerCite this: J. Am. Chem. Soc. 1966, 88, 3, 420–425Publication Date (Print):February 1, 1966Publication History Published online1 May 2002Published inissue 1 February 1966https://pubs.acs.org/doi/10.1021/ja00955a007https://doi.org/10.1021/ja00955a007research-articleACS PublicationsRequest reuse permissionsArticle Views58Altmetric-Citations37LEARN 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