gebhart/patrepeval huggingface dataset:
Engineering 3D Bio-Artificial Heart Muscle (2014)

Current therapies in left ventricular systolic dysfunction and end-stage heart failure include mechanical assist devices or transplant. The development of a tissue-engineered integrative platform would present a therapeutic option that overcomes the limitations associated with current treatment modalities. This study provides a foundation for the fabrication and preliminary viability of the acellular ventricular extracellular matrix (AVEM) model. Acellular ventricular extracellular matrix was fabricated by culturing 4 million rat neonatal cardiac cells around an excised acellular ventricular segment. Acellular ventricular extracellular matrix generated a maximum spontaneous contractile force of 388.3 μN and demonstrated a Frank-Starling relationship at varying pretensions. Histologic assessment displayed cell cohesion and adhesion within the AVEM as a result of passive cell seeding.
Frequency domain post-processing technique based on POCS (2003)

A novel post-processing technique in the DCT domain, based on the theory of the projection onto convex sets (POCS), to reduce the blocking artifacts in the block discrete cosine transform (BDCT)-coded images, is proposed. Computer simulation results indicate that the proposed scheme performs better than conventional post-processing algorithms. Furthermore, the proposed algorithm can be implemented without DCT/IDCT operations. Estimates of computation savings vary between 41 and 64% depending on the task.
Expediting expertise (2014)

In this paper, we present Expediting Expertise, a system designed to provide structured support to the otherwise informal process of social learning in the enterprise. It employs a data-driven approach where online content is automatically analyzed and categorized into relevant topics, topic-specific user expertise is calculated by comparing the models of individual users against those of the experts, and personalized recommendation of learning activities is created accordingly to facilitate expertise development. The system's UI is designed to provide users with ongoing feedback of current expertise, progress, and comparison with others. Learning recommendation is visualized with an interactive treemap which presents estimated return on investment and distance to current expertise for each recommended learning activity. Evaluation of the system showed very positive results.
ChemInform Abstract: A STEREOCONTROLLED PARTIAL SYNTHESIS OF 1α‐HYDROXY VITAMIN D3 (1982)

Abstract Es wird eine neue stereokontrollierte Partialsynthese für l‐a‐Hydroxyvitamin‐D3 beschrieben, die von 7‐Dehydrocholesterin (Ia) ausgeht.
NeuroPath2Path: Classification and elastic morphing between neuronal\n arbors using path-wise similarity (2019)

The shape and connectivity of a neuron determine its function. Modern imaging\nmethods have proven successful at extracting such information. However, in\norder to analyze this type of data, neuronal morphology needs to be encoded in\na graph-theoretic method. This encoding enables the use of high throughput\ninformatic methods to extract and infer brain function. The application of\ngraph-theoretic methods to neuronal morphological representation comes with\ncertain difficulties. Here we report a novel, effective method to accomplish\nthis task.\n The morphology of a neuron, which consists of its overall size, global shape,\nlocal branch patterns, and cell-specific biophysical properties, can vary\nsignificantly with the cell's identity, location, as well as developmental and\nphysiological state. Various algorithms have been developed to customize shape\nbased statistical and graph related features for quantitative analysis of\nneuromorphology, followed by the classification of neuron cell types using the\nfeatures. Unlike the classical feature extraction based methods from imaged or\n3D reconstructed neurons, we propose a model based on the rooted path\ndecomposition from the soma to the dendrites of a neuron and extract\nmorphological features on each path. We hypothesize that measuring the distance\nbetween two neurons can be realized by minimizing the cost of continuously\nmorphing the set of all rooted paths of one neuron to another. To validate this\nclaim, we first establish the correspondence of paths between two neurons using\na modified Munkres algorithm. Next, an elastic deformation framework that\nemploys the square root velocity function is established to perform the\ncontinuous morphing, which, in addition, provides an effective visualization\ntool. We experimentally show the efficacy of NeuroPath2Path, NeuroP2P, over the\nstate of the art.\n
Automatic Form Filling with Form-BERT (2021)

Digital-forms are commonly used for collecting structured information from users. However, filling digital-forms that include a large number of fields is tedious and error-prone. Auto-filling form fields for the user is highly beneficial for improving user experience and potentially collecting more valuable information (in cases where not all fields are mandatory). Online E-commerce marketplaces quite often utilize such forms to collect listing attributes from sellers. In this work, we describe Form-BERT -- a Transformer-based model which is optimized for auto-filling listing attributes given the following inputs: free-text, list of known attribute names, and zero or more attribute values. Form-BERT can be further used iteratively to leverage filled out attributes as the form filling progresses.
Recognition of Guanine−Guanine Mismatches by the Dimeric Form of 2-Amino-1,8-naphthyridine (2001)

Dimeric 2-amino-1,8-naphthyridine selectively binds to a G−G mismatch with high affinity (Kd = 53 nM). We have investigated a binding mechanism of naphthyridine dimer 2 to a G−G mismatch by spectroscopic studies, thermodynamic analysis, and structure−activity studies for the thermal stabilization of the mismatch. 1H NMR spectra of a complex of 2 with 9-mer duplex d(CATCGGATG)2 containing a G−G mismatch showed that all hydrogens in two naphthyridine rings of 2 were observed upfield compared to those of 2 in a free state. The 2D-NOESY experiments showed that each naphthyridine of 2 binds to a guanine in the G−G mismatch within the π-stack. In CD spectra, a large conformational change of the G−G mismatch-containing duplex was observed upon complex formation with 2. Isothermal calorimetry titration of 2 binding to the G−G mismatch showed that the stoichiometry for the binding is about 1:1 and that the binding is enthalpy-controlled. It is clarified by structure−activity studies that show (i) the linker connecting two naphthyridine rings was essential for the stabilization of the G−G mismatch, (ii) the binding efficiency was very sensitive to the linker structure, and (iii) the binding of two naphthyridines to each one of two Gs in the G−G mismatch is essential for a strong stabilization. These results strongly supported the intercalation of both naphthyridine rings of 2 into DNA base pairs and the formation of a hydrogen bonded complex with the G−G mismatch.
ChemInform Abstract: Alternative Routes to the Acylphloroglucinol Rhodomyrtone. (2016)

ChemInformVolume 47, Issue 20 Natural Products ChemInform Abstract: Alternative Routes to the Acylphloroglucinol Rhodomyrtone. Marius Morkunas, Marius Morkunas Inst. Org. Chem., Eberhard-Karls-Univ., D-72076 Tuebingen, GermanySearch for more papers by this authorMartin E. Maier, Martin E. Maier Inst. Org. Chem., Eberhard-Karls-Univ., D-72076 Tuebingen, GermanySearch for more papers by this author Marius Morkunas, Marius Morkunas Inst. Org. Chem., Eberhard-Karls-Univ., D-72076 Tuebingen, GermanySearch for more papers by this authorMartin E. Maier, Martin E. Maier Inst. Org. Chem., Eberhard-Karls-Univ., D-72076 Tuebingen, GermanySearch for more papers by this author First published: 27 April 2016 https://doi.org/10.1002/chin.201620212Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume47, Issue20April, 2016 RelatedInformation
Subtalar Arthroereisis as Adjunct Treatment for Type II Posterior Tibial Tendon Deficiency (2006)

Type II posterior tibial tendon deficiency (PTTD) represents a wide spectrum of disease and may be treated with a variety of corrective surgical procedures. Recent reports suggest that treatment may vary based on severity of flexible flatfoot deformity. Mild flexible flatfoot may be corrected with combined flexor digitorum longus transfer and medializing calcaneal osteotomy, whereas additional measures may be needed to correct more severe flexible flatfoot. Subtalar arthroereisis is an adjunct procedure that holds promise for patients with both the mild and more severe variants. In milder presentations of type II PTTD, subtalar arthroereisis may aid in the correction of hindfoot deformity and protect soft tissue reconstruction. In more severe type II PTTD, subtalar arthroereisis may further normalize parameters undercorrected with the initial procedure. In this article, we describe the background and surgical technique for subtalar arthroereisis with a Maxwell-Brancheau titanium arthroereisis sinus tarsi implant (KMI, Carlsbad, CA) combined with flexor digitorum longus transfer and medializing calcaneal osteotomy for treatment of type II PTTD.
A High-Power-Density High-Efficiency Three-Level Buck Converter for Cellphone Battery Charging Applications (2018)

This paper introduces a high-power-density low-profile high-efficiency three-level buck converter for cellphone battery charging applications. This converter is designed to deliver up to 40 W across a 4:1 input voltage range, as enabled by the latest USB standard. A comprehensive methodology based on augmented state-space modeling is used to accurately predict the converter's waveforms and optimize its design. The converter's inductor is realized using a custom-shaped low-profile ferrite core., with its winding and core losses minimized using 3D finite-element analysis. To maximize efficiency, the converter is designed to achieve zero-voltage switching (ZVS) at light-to-medium loads. A prototype three-level buck converter with a PCB area of 358 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , component height of 1 mm, an input voltage range of 5 V-20 V, an output voltage range of 3 V-4.2 V, and a maximum output current of 10 A is built and tested. The prototype converter achieves a peak efficiency of 98.5% at 2:1 conversion ratio, maintains high efficiency across its entire operating range, and achieves a power density of 704 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
Recovering Kinetic Energy Using Electric Motors (2016)

Presented during the Three Minute Thesis (3MT™) Competition on November 15, 2016 in the LeCraw Auditorium, Scheller College of Business at Georgia Tech.
Mapping single-cell atlases throughout Metazoa unravels cell type evolution (2020)

Abstract Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.
Benefits of Sustained Upregulated Unimolecular GLP-1 and CCK Receptor Signalling in Obesity-Diabetes (2021)

Combined activation of GLP-1 and CCK1 receptors has potential to synergistically augment the appetite-suppressive and glucose homeostatic actions of the individual parent peptides. In the current study, pancreatic beta-cell benefits of combined GLP-1 and CCK1 receptor upregulation were established, before characterising bioactivity and antidiabetic efficacy of an acylated dual-acting GLP-1/CCK hybrid peptide, namely [Lys<sup>12</sup>Pal]Ex-4/CCK. Both exendin-4 and CCK exhibited (p<0.001) proliferative and anti-apoptotic effects in BRIN BD11 beta-cells. Proliferative benefits were significantly (p<0.01) augmented by combined peptide treatment when compared to either parent peptide alone. These effects were linked to increases (p<0.001) in GLUT2 and glucokinase beta-cell gene expression, with decreased (p<0.05-p<0.001) expression of NFκB and BAX. [Lys<sup>12</sup>Pal]Ex-4/CCK exhibited prominent insulinotropic actions <i>in vitro</i>, coupled with beneficial (p<0.001) satiety and glucose homeostatic effects in the mice, with bioactivity evident 24 h after administration. Following twice daily injection of [Lys<sup>12</sup>Pal]Ex-4/CCK for 28 days in diabetic high fat fed (HFF) mice with streptozotocin (STZ)-induced compromised beta-cells, there were clear reductions (p<0.05-p<0.001) in energy intake and body weight. Circulating glucose was returned to lean control concentrations, with associated increases (p<0.001) in plasma and pancreatic insulin levels. Glucose tolerance and insulin secretory responsiveness were significantly (p<0.05-p<0.001) improved by hybrid peptide therapy. In keeping with this, evaluation of pancreatic histology revealed restoration of normal islet alpha- to beta-cell ratios and reduction (p<0.01) in centralised islet glucagon staining. Improvements in pancreatic islet morphology were associated with increased (p<0.05) proliferation and reduced (p<0.001) apoptosis of beta-cells. Together, these data highlight the effectiveness of sustained dual GLP-1 and CCK1 receptor activation by [Lys<sup>12</sup>Pal]Ex-4/CCK for the treatment of obesity-related diabetes.
Dysfunctional telomeres trigger cellular senescence mediated by cyclic GMP-AMP synthase (2020)

Defective DNA damage response (DDR) signaling is a common mechanism that initiates and maintains the cellular senescence phenotype. Dysfunctional telomeres activate DDR signaling, genomic instability, and cellular senescence, but the links among these events remains unclear. Here, using an array of biochemical and imaging techniques, including a highly regulatable CRISPR/Cas9 strategy to induce DNA double strand breaks specifically in the telomeres, ChIP, telomere immunofluorescence, fluorescence <i>in situ</i> hybridization (FISH), micronuclei imaging, and the telomere shortest length assay (TeSLA), we show that chromosome mis-segregation due to imperfect DDR signaling in response to dysfunctional telomeres creates a preponderance of chromatin fragments in the cytosol, which leads to a premature senescence phenotype. We found that this phenomenon is caused not by telomere shortening, but by cyclic GMP-AMP synthase (cGAS) recognizing cytosolic chromatin fragments and then activating the stimulator of interferon genes (STING) cytosolic DNA-sensing pathway and downstream interferon signaling. Significantly, genetic and pharmacological manipulation of cGAS not only attenuated immune signaling, but also prevented premature cellular senescence in response to dysfunctional telomeres. The findings of our study uncover a cellular intrinsic mechanism involving the cGAS-mediated cytosolic self-DNA-sensing pathway that initiates premature senescence independently of telomere shortening.
Abstract 091: Improved Blood Pressure Control and High Adherence to a Novel Management Model of Hypertension Care in a West African Population (2017)

Background: Logistic and socioeconomic barriers limit effective blood pressure (BP) control in many parts of Sub-Saharan Africa, including the Republic of Ghana. We tested a novel hypertension management model of care designed for resource-limited settings. Methods and Results: The “Akoma Pa” model was developed using human-centered design methodology involving patients, physicians, and nurses. The model consisted of a mobile tablet, BP machine and a novel software application in a unique platform to allow for longitudinal patient management. Patients were provided with a tailored hypertension management plan based on their enrollment comorbidities and risk factors. A cohort of 150 hypertensive patients (57±8 years; 73% female) accessed regular blood pressure assessments at a local pharmacy and received real-time automated feedback based on their individualized plan. On the mobile application, clinicians were able to view patient data, provide patients with feedback via SMS on their condition, and write electronic prescriptions which could be accessed by participating pharmacies. Average baseline BP was 135±18/84±10 mmHg in the overall cohort and 153±13/90±11 mmHg in the subgroup with uncontrolled hypertension (n=58). After 6 months of voluntary weekly monitoring, systolic blood pressure decreased significantly (p&lt;0.01) in the overall cohort (-4.7±18.7 mmHg) and in the uncontrolled subgroup (-15.2±17.6mmHg). Systolic blood pressure remained constant in the sub group with controlled pressure at baseline. The proportion of the population with uncontrolled hypertension decreased from 39% to 27% (p=0.01). Patient compliance with weekly BP assessments was 61% and 2,855 BP assessments were conducted. During 33 of the 2,855 BP assessments (1% of pharmacy visits), the software application directly referred patients to a health facility (33 visits in 25 patients). Improvement in overall health awareness was reported in 82% of the participants and 95% of participants indicated a desire to continue using this model in the future. Conclusions: Compliance and satisfaction with this multifaceted hypertension care model were high and led to significant and sustained decreases in blood pressure in this West African hypertensive population.
Electronic Structures, Spectroscopy, and Electrochemistry of [M(diimine)(CN-BR3)4]2– (M = Fe, Ru; R = Ph, C6F5) Complexes (2020)

Complexes with the formula [M(diimine)(CN-BR<sub>3</sub>)<sub>4</sub>]<sup>2-</sup>, where diimine = bipyridine (bpy), phenanthroline (phen), 3,5-trifluoromethylbipyridine (flpy), R = Ph, C<sub>6</sub>F<sub>5</sub>, and M = Fe<sup>II</sup>, Ru<sup>II</sup>, were synthesized and characterized by X-ray crystal structure analysis, UV-visible spectroscopy, IR spectroscopy, and voltammetry. Three highly soluble complexes, [Fe<sup>II</sup>(bpy)(CN-B(C<sub>6</sub>F<sub>5</sub>)<sub>3</sub>)<sub>4</sub>]<sup>2-</sup>, [Ru<sup>II</sup>(bpy)(CN-B(C<sub>6</sub>F<sub>5</sub>)<sub>3</sub>)<sub>4</sub>]<sup>2-</sup>, and [Ru<sup>II</sup>(flpy)(CN-B(C<sub>6</sub>F<sub>5</sub>)<sub>3</sub>)<sub>4</sub>]<sup>2-</sup>, exhibit electrochemically reversible redox reactions, with large potential differences between the bpy<sup>0/-</sup> or flpy<sup>0/-</sup> and M<sup>III/II</sup> couples of 3.27, 3.52, and 3.19 V, respectively. CASSCF+NEVPT2 calculations accurately reproduce the effects of borane coordination on the electronic structures and spectra of cyanometallates.
Supplementary Figure 1 from Mammographic Breast Density and Breast Cancer: Evidence of a Shared Genetic Basis (2023)

&lt;p&gt;PDF file - 275K, Significance of the mammographic breast density polygenic risk score (PRS) for the prediction of breast cancer risk, according to percent cut-off of SNPs used in the PRS: sensitivity analysis using imputed case:control genotype dosages.&lt;/p&gt;
In-vitro evaluation of drugs proposed as chondroprotective agents. (1992)

Three proposed chondroprotective agents (CP), namely glucosamine sulfate (GAS), chondroitin sulfate (CS) and glycosaminoglycan-peptide complex (GP-C), were tested on differentiated human articular chondrocytes cultured in clusters. Chondrocyte productions of proteoglycans (PG), type II collagen (coll. II) and prostaglandin E2 (PGE2) were established by specific radioimmunoassays applied to the culture medium (CM) and in chondrocyte clusters (CC). Collagenolytic activity was assayed in CM. DNA synthesis, studied by measuring 3H-thymidine incorporation, was unaffected by CS and GAS. GP-C, at low concentration, stimulated DNA synthesis. GP-C, at higher doses, induced a high increase in PG and coll. II productions. GAS and CS induced a stimulatory effect limited to PG production. None of the CP tested here affected the basal PGE2 production by human chondrocytes.
A Refined Model for the TSG-6 Link Module in Complex with Hyaluronan (2014)

Tumor necrosis factor-stimulated gene-6 (TSG-6) is an inflammation-associated hyaluronan (HA)-binding protein that contributes to remodeling of HA-rich extracellular matrices during inflammatory processes and ovulation. The HA-binding domain of TSG-6 consists solely of a Link module, making it a prototypical member of the superfamily of proteins that interacts with this high molecular weight polysaccharide composed of repeating disaccharides of D-glucuronic acid and N-acetyl-D-glucosamine (GlcNAc). Previously we modeled a complex of the TSG-6 Link module in association with an HA octasaccharide based on the structure of the domain in its HA-bound conformation. Here we have generated a refined model for a HA/Link module complex using novel restraints identified from NMR spectroscopy of the protein in the presence of 10 distinct HA oligosaccharides (from 4- to 8-mers); the model was then tested using unique sugar reagents, i.e. chondroitin/HA hybrid oligomers and an octasaccharide in which a single sugar ring was (13)C-labeled. The HA chain was found to make more extensive contacts with the TSG-6 surface than thought previously, such that a D-glucuronic acid ring makes stacking and ionic interactions with a histidine and lysine, respectively. Importantly, this causes the HA to bend around two faces of the Link module (resembling the way that HA binds to CD44), potentially providing a mechanism for how TSG-6 can reorganize HA during inflammation. However, the HA-binding site defined here may not play a role in TSG-6-mediated transfer of heavy chains from inter-α-inhibitor onto HA, a process known to be essential for ovulation.
Kinetics of carbon nanotubeoxidation (2006)

Carbon nanotubes, graphite and amorphous carbon are structurally different, which is reflected in their reactivity and the resistance to oxidation. This paper reports the stability of single- and multi-walled nanotubes, and their true oxidation rates based on conversion to CO2 when heated in the presence of oxygen. Non-isothermal techniques were employed to determine the kinetic parameters for the oxidation of nanotubes, amorphous carbon and graphite. Single-walled nanotubes were found to be the most reactive, followed by multi-walled nanotubes, amorphous carbon and graphite. The oxidation rates of different single-walled tubes samples containing different residual catalysts were also found to vary significantly.
Single Molecule Chemistry with Polymers and Colloids: A Way to Handle Complex Reactions and Physical Processes? (2001)

Incorporation of polymers in compartments slightly larger than their size allows chemistry and physics on single entities, for example the formation of single-chain polymer crystals by single-molecule chemistry. Recent results and possibilities are discussed.