gebhart/patrepeval huggingface dataset:
A cell-centred finite volume formulation of geometrically-exact\n Simo-Reissner beams with arbitrary initial curvatures (2021)

This paper presents a novel total Lagrangian cell-centred finite volume\nformulation of geometrically exact beams with arbitrary initial curvature\nundergoing large displacements and finite rotations. The choice of rotation\nparametrisation, the mathematical formulation of the beam kinematics, conjugate\nstrain measures and the linearisation of the strong form of governing equations\nis described. The finite volume based discretisation of the computational\ndomain and the governing equations for each computational volume are presented.\nThe discretised integral form of the equilibrium equations are solved using a\nblock-coupled Newton-Raphson solution procedure. The efficacy of the proposed\nmethodology is presented by comparing the simulated numerical results with\nclassic benchmark test cases available in the literature. The objectivity of\nstrain measures for the current formulation and mesh convergence studies for\nboth initially straight and curved beam configurations are also discussed.\n
ChemInform Abstract: ASYMMETRIC 9‐HYDROXYLATION OF ANTHRACYCLINONES. TOTAL SYNTHESIS OF (+)‐4‐DEMETHOXYDAUNOMYCINONE (1984)

Abstract Die beiden Daunomycinderivate (I) werden zu (II) bromiert und zu den Olefinen (III) debromiert.
Short residence time hydropyrolysis of coal. Technical progress report, 1 July-31 September 1980 (1980)

In this quarterly report we update the status of the program to gather kinetic data for the pyrolysis and hydropyrolysis of coal and the combined theoretical and experimental effort to understand the role of plasticity in these processes.
A SYNERGISTIC MODEL FOR REPRESENTING AND INTERPRETING HUMAN ACTIVITIES AND EVENTS FROM VIDEO (2003)

This paper describes a new and innovative and approach for representing, recognizing and interpreting human activity from video, contributing to an automated system capable of recognition of complex human behaviors. This technology is directly applicable for monitoring public safety and law enforcement, and capturing of activities is crucial for supporting virtual collaborations between citizens, and between citizens and government. Digital video stores of terabytes are now common, and will continue to increase until they dominate stored data. The government of the future will have to manage, organize, recall, and interpret information from this resource, This paper addresses one important facet of this. The approach presented here is a model based on the hierarchical synergy of three other models: the Local/Global (L-G) graph, the Stochastic Petri Net (SPN) graph and a neural network (NN) model. The application focus is the description of activity of actors in a video (or multi-sensor) scene, from the snapshot state description through higher levels of organization into events. The concept of importance is the distinction and interaction between structural knowledge, or knowledge about physical state, and functional knowledge, knowledge about change and events. The L-G graph provides a powerful description of the structural image features presented in an event, and the SPN model offers a description of the functional behavior. The NN (or other adaptive) model provides the capability of leaning behavioral patterns for classification of posture and activity, and forecasting possible events in a free environment.
Elaborating 5-(4-chlorophenyl)-1,3,4-thiadiazole scaffold with a p-tolyl sulfonamide moiety enhances cytotoxic activity: Design, synthesis, in vitro cytotoxicity evaluation, radiolabelling, and in vivo pharmacokinetic study (2022)

Novel 1,3,4-thiadiazole derivatives (3-5) were designed, synthesized, and screened for cytotoxic activity. Compound 3 bearing substituted benzenesulfonamide scaffold exhibited remarkable potency against breast cancer (MCF-7), hepatoma (HepG2), colon cancer (HCT116), and lung cancer (A549) cells and lower potency on the normal cells (WI-38), as well as, it possesses higher anticancer activity than starting 5-(4-chlorophenyl)-1,3,4-thiadiazole-2-amine (2) and the positive control Staurosporine. The anticancer activity of compound 3 is at least partly attributed to the inhibition of the tumor-associated human carbonic anhydrase isoforms IX and XII. The high selectivity of compound 3 for cancer cells over normal cells and for tumor-associated CA isoforms IX and XII over the off-target cytosolic isoform II reflects its safety. Pharmacokinetic study of compound 3 was evaluated in a normal mice model based on a radiopharmaceutical chemistry approach.
Fractal features of a crumpling network in randomly folded thin matter and mechanics of sheet crushing (2013)

We study the static and dynamic properties of networks of crumpled creases formed in hand crushed sheets of paper. The fractal dimensionalities of crumpling networks in the unfolded (flat) and folded configurations are determined. Some other noteworthy features of crumpling networks are established. The physical implications of these findings are discussed. Specifically, we state that self-avoiding interactions introduce a characteristic length scale of sheet crumpling. A framework to model the crumpling phenomena is suggested. Mechanics of sheet crushing under external confinement is developed. The effect of compaction geometry on the crushing mechanics is revealed.
Creation of Optical Cat and GKP States Using Shaped Free Electrons (2023)

A new approach to generating quantum states of light most suitable for robust quantum computing draws on one of the most basic interactions in physics---the interaction between free electrons and photons.
Vibrations and Waves (1972)

The M.I.T. Introductory Physics Series is the result of a program of careful study, planning, and development that began in 1960. The Education Research Center at the Massachusetts Institute of Technology (formerly the Science Teaching Center) was established to study the process of instruction, aids thereto, and the learning process itself, with special reference to science teaching at the university level. Generous support from a number of foundations provided the means for assembling and maintaining an experienced staff to co-operate with members of the Institute's Physics Department in the examination, improvement, and development of physics curriculum materials for students planning careers in the sciences. After careful analysis of objectives and the problems involved, preliminary versions of textbooks were prepared, tested through classroom use at M.I.T. and other institutions, re-evaluated, rewritten, and tried again. Only then were the final manuscripts undertaken.
Predicting Protein Function from Structure—The Roles of Short-chain Dehydrogenase/Reductase Enzymes in Bordetella O-antigen Biosynthesis (2007)

The pathogenic bacteria Bordetella parapertussis and Bordetella bronchiseptica express a lipopolysaccharide O antigen containing a polymer of 2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. The O-antigen cluster contains three neighbouring genes that encode proteins belonging to the short-chain dehydrogenase/reductase (SDR) family, wbmF, wbmG and wbmH, and we aimed to elucidate their individual functions. Mutation and complementation implicate each gene in O-antigen expression but, as their putative sugar nucleotide substrates are not currently available, biochemical characterisation of WbmF, WbmG and WbmH is impractical at the present time. SDR family members catalyse a wide range of chemical reactions including oxidation, reduction and epimerisation. Because they typically share low sequence conservation, however, catalytic function cannot be predicted from sequence analysis alone. In this context, structural characterisation of the native proteins, co-crystals and small-molecule soaks enables differentiation of the functions of WbmF, WbmG and WbmH. These proteins exhibit typical SDR architecture and coordinate NAD. In the substrate-binding domain, all three enzymes bind uridyl nucleotides. WbmG contains a typical SDR catalytic TYK triad, which is required for oxidoreductase function, but the active site is devoid of additional acid-base functionality. Similarly, WbmH possesses a TYK triad, but an otherwise feature-poor active site. Consequently, 3,5-epimerase function can probably be ruled out for these enzymes. The WbmF active site contains conserved 3,5-epimerase features, namely, a positionally conserved cysteine (Cys133) and basic side chain (His90 or Asn213), but lacks the serine/threonine component of the SDR triad and therefore may not act as an oxidoreductase. The data suggest a pathway for synthesis of the O-antigen precursor UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid and illustrate the usefulness of structural data in predicting protein function.
PSI-18 Adiponectin serum concentrations in late pregnancy and early lactation in primiparous and multiparous Holstein dairy cows. (2018)

The peripartal decrease of insulin sensitivity in peripheral tissues other than the mammary gland facilitates draining of glucose towards the mammary gland at that time. Adiponectin is an insulin-sensitizing adipokine; its concentrations decrease around parturition in dairy cows. Based on the different metabolic stress in primiparous (PP) and multiparous (MP) cows (PP are still growing, MP have more milk), we hypothesized that the serum concentrations of adiponectin in the dry period and subsequent lactation will be greater in PP than in MP cows. Blood was sampled -50, -14, 8, 28, and 100 days relative to calving from 201 PP and 456 MP Holstein cows on three experimental farms, i.e. a subset from the optiKuh project*. Individual feed intake and milk yield were recorded daily, milk composition was analyzed weekly, and energy balance (EB) was calculated on a weekly basis assuming 10% of bodyweight at calving as body gain for PP. Serum adiponectin concentrations were measured with an in-house developed bovine-specific ELISA. For statistical analyses the linear mixed model was used (SPSS 25; fixed effects: time, parity, farm, all interactions; random effects: cow). Due to a significant time*parity interaction for adiponectin, further analyses were performed separately for the pre- and postpartum period. Results are presented as means ±SEM. Prepartum, PP had lower adiponectin concentrations (23.3 ± 0.37 µg/mL) and EB (10.6 ± 1.29 MJ NEL/day) than MP (Adiponectin: 26.7 ± 0.26 µg/mL; p<0.001; EB: 16.9 ± 1.41 MJ NEL/day; p=0.014). Postpartum, PP had higher adiponectin concentrations (26 ± 0.25µg/mL) than MP (24.4 ± 0.18 µg/mL; p=0.002) but EB did not differ (p=0.2) although MP yielded more milk (39.1 ± 0.28 kg/day) than PP (29.2 ± 0.29 kg/day; p<0.001). The higher adiponectin concentrations and assumingly greater insulin sensitivity postpartum in PP would allow for further body growth beside lactation. *funded by the German Federal Ministry of Food and Agriculture.
Sub-surface Serial Block Face Scanning Electron Microscopy (2015)

Journal Article Sub-surface Serial Block Face Scanning Electron Microscopy Get access Q He, Q He National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892 Search for other works by this author on: Oxford Academic Google Scholar MA Aronova, MA Aronova National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892 Search for other works by this author on: Oxford Academic Google Scholar DC Joy, DC Joy Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 Search for other works by this author on: Oxford Academic Google Scholar G Zhang, G Zhang National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892 Search for other works by this author on: Oxford Academic Google Scholar RD Leapman RD Leapman National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892 Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 21, Issue S3, 1 August 2015, Pages 1267–1268, https://doi.org/10.1017/S1431927615007126 Published: 23 September 2015
BMP7-based peptide agonists of BMPR1A protect the left ventricle against pathological remodeling induced by pressure overload (2022)

Aortic stenosis (AS) exposes the left ventricle (LV) to pressure overload leading to detrimental LV remodeling and heart failure. In animal models of cardiac injury or hemodynamic stress, bone morphogenetic protein-7 (BMP7) protects LV against remodeling by counteracting TGF-β effects. BMP receptor 1A (BMPR1A) might mediate BMP7 antifibrotic effects. Herein we evaluated BMP7-based peptides, THR123 and THR184, agonists of BMPR1A, as cardioprotective drugs in a pressure overload model. We studied patients with AS, mice subjected to four-week transverse aortic constriction (TAC) and TAC release (de-TAC). The LV of AS patients and TAC mice featured Bmpr1a downregulation. Also, pSMAD1/5/(8)9 was reduced in TAC mice. Pre-emptive treatment of mice with THR123 and THR184, during the four-week TAC period, normalized pSMAD1/5/(8)9 levels in the LV, attenuated overexpression of remodeling-related genes (Col 1α1, β-MHC, BNP), palliated structural damage (hypertrophy and fibrosis) and alleviated LV dysfunction (systolic and diastolic). THR184 administration, starting fifteen days after TAC, halted the ongoing remodeling and partially reversed LV dysfunction. The reverse remodeling after pressure overload release was facilitated by THR184. Both peptides diminished the TGF-β1-induced hypertrophic gene program in cardiomyocytes, collagen transcriptional activation in fibroblasts, and differentiation of cardiac fibroblasts to myofibroblasts. Molecular docking suggests that both peptides bind with similar binding energies to the BMP7 binding domain at the BMPR1A. The present study results provide a preclinical proof-of-concept of potential therapeutic benefits of BMP7-based small peptides, which function as agonists of BMPR1A, against the pathological LV remodeling in the context of aortic stenosis.
Collective phenomena in cold indirect excitons (2016)

Due to their long lifetimes, indirect excitons can cool to below the temperature of quantum degeneracy. This gives an opportunity to experimentally study cold composite bosons. Both theoretically predicted phenomena and phenomena that have not been anticipated were observed in a cold gas of indirect excitons. In this contribution, we overview our studies of cold indirect excitons over the past decade, presenting spontaneous coherence and condensation of excitons, spatially modulated exciton state, long-range spin currents and spin textures, and exciton localization–delocalization transitions.
Compression of neural signals using discriminative coding for wireless applications (2009)

One of the most critical tasks when designing a portable wireless neural recording system is to limit power consumption. This paper proposes a new compression technique applied to neuronal recordings in real-time. The signal is compressed before transmission using a discriminative vector quantization algorithm and then it is reconstructed on the receiver side. Results show that power consumption is decreased while more efficiently using the limited bandwidth. A discriminative Linde-Buzo-Gray algorithm (DLBG) preserves action potential regions of the neuronal signal where information is contained while efficiently filtering background activity. The compression algorithm has been tested in real time on a hardware platform (PICO DSP [3]) that has a Digital Signal Processor (DSP) which performs the algorithm before sending the compressed data to a wireless transmitter. The compression ratios obtained range between 20:1 and 70:1 depending on the embedding size of the signal and the number of code-vectors used.
Carbon nanotube self-assembly with lipids and detergent: a molecular dynamics study (2008)

The dispersion of carbon nanotubes (CNTs) in aqueous media is of potential importance in a number of biomedical applications. CNT solubilization has been achieved via the non-covalent adsorption of lipids and detergent onto the tube surface. We use coarse-grained molecular dynamics to study the self-assembly of CNTs with various amphiphiles, namely a bilayer-forming lipid, dipalmitoylphosphatidylcholine (DPPC), and two species of detergent, dihexanoylphosphatidylcholine (DHPC) and lysophosphatidylcholine (LPC). We find that for a low amphiphile/CNT ratio, DPPC, DHPC and LPC all wrap around the CNT. Upon increasing the number of amphiphiles, a transition in adsorption is observed: DPPC encapsulates the CNT within a cylindrical micelle, whilst both DHPC and LPC adsorb onto CNTs in hemimicelles. This study highlights differences in adsorption mechanism of bilayer-forming lipids and detergents on CNTs which may in the future be exploitable to enable enhancement of CNT solubilization whilst minimizing perturbation of cell membrane integrity.
The Vibrio harveyi master quorum‐sensing regulator, LuxR, a TetR‐type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters (2008)

Quorum sensing is the process of cell-to-cell communication by which bacteria communicate via secreted signal molecules called autoinducers. As cell population density increases, the accumulation of autoinducers leads to co-ordinated changes in gene expression across the bacterial community. The marine bacterium, Vibrio harveyi, uses three autoinducers to achieve intra-species, intra-genera and inter-species cell-cell communication. The detection of these autoinducers ultimately leads to the production of LuxR, the quorum-sensing master regulator that controls expression of the genes in the quorum-sensing regulon. LuxR is a member of the TetR protein superfamily; however, unlike other TetR repressors that typically repress their own gene expression and that of an adjacent operon, LuxR is capable of activating and repressing a large number of genes. Here, we used protein binding microarrays and a two-layered bioinformatics approach to show that LuxR binds a 21 bp consensus operator with dyad symmetry. In vitro and in vivo analyses of two promoters directly regulated by LuxR allowed us to identify those bases that are critical for LuxR binding. Together, the in silico and biochemical results enabled us to scan the genome and identify novel targets of LuxR in V. harveyi and thus expand the understanding of the quorum-sensing regulon.
Biological Responsiveness in Observing Sexual Attractiveness of Woman (2017)

In this paper, we investigate the change of biometric signal for sexual attractiveness. Eye camera system and electrocardiograph was used in our experiment to evaluate the change of pupil diameter and heart rate variability (HRV). Five young male students participated in our experiment that was attempted by the observation of the 10 female portraits belonging to the final selection of beauty contest. An interesting result that top two and bottom two entries appeared at the both ends was obtained by the measurement of HRV represented in Poincaré plot. This polarization in attractive patterns was implied by the emotional change of individual difference between the attractiveness for beauty or cuteness.
A 20-Mb Region of Chromosome 4 Controls TNF-α-Mediated CD8+ T Cell Aggression Toward β Cells in Type 1 Diabetes (2006)

Identification of candidate genes and their immunological mechanisms that control autoaggressive T cells in inflamed environments, may lead to novel therapies for autoimmune diseases, like type 1 diabetes (T1D). In this study, we used transgenic NOD mice that constitutively express TNF-alpha in their islets from neonatal life (TNF-alpha-NOD) to identify protective alleles that control T1D in the presence of a proinflammatory environment. We show that TNF-alpha-mediated breakdown in T cell tolerance requires recessive NOD alleles. To identify some of these recessive alleles, we crossed TNF-alpha-NOD mice to diabetes-resistant congenic NOD mice having protective alleles at insulin-dependent diabetes (Idd) loci that control spontaneous T1D at either the preinsulitis (Idd3.Idd5) or postinsulitis (Idd9) phases. No protection from TNF-alpha-accelerated T1D was afforded by resistance alleles at Idd3.Idd5. Lack of protection was not at the level of T cell priming, the efficacy of islet-infiltrating APCs to present islet peptides, nor the ability of high levels of CD4+ Foxp3+ T cells to accumulate in the islets. In contrast, protective alleles at Idd9 significantly increased the age at which TNF-alpha-NOD mice developed T1D. Disease delay was associated with a decreased ability of CD8+ T cells to respond to islet Ags presented by islet-infiltrating APCs. Finally, we demonstrate that the protective region on chromosome 4 that controls T1D in TNF-alpha-Idd9 mice is restricted to the Idd9.1 region. These data provide new evidence of the mechanisms by which selective genetic loci control autoimmune diseases in the presence of a strong inflammatory assault.
New developments in automated PrepLCMS extends the robustness and utility of the method for compound library analysis and purification (1998)

New developments in the high throughput purification of combinatorial libraries by automated preparative LC-MS is presented. To facilitate high speed purifications at the multimilligram level, short columns operated at ultra high flow rates were incorporated. In order to match the linear velocity of the short analytical columns for high speed separations (operated at 4.0 mL/min), it was required to operate the preparative columns at flow rates in excess of 70 mL/min. For chromatographically well-behaved compounds, analytical LC-MS analyses and preparative LC-MS analyses could be achieved in as little as 5 min. For compounds exhibiting poor chromatographic peak shapes and/or for compound mixtures requiring higher resolution separations, slightly longer preparative LC-MS analysis times were required (8-10 min/sample).
Direct Entry to Peptidyl Ketones via SmI2-Mediated C−C Bond Formation with Readily Accessible N-Peptidyl Oxazolidinones (2007)

In this work, a new method for the preparation of peptidyl ketones is presented employing a SmI(2)/H(2)O-mediated coupling of N-peptidyl oxazolidinones with electron-deficient alkenes. The requisite peptide imides were easily prepared by solution-phase peptide synthesis starting from an N-acyl oxazolidinone derivative of an amino acid. Importantly, they could be used directly in the C-C bond-forming step without the need for further functionalization. Coupling of these peptide derivatives with a second peptide possessing an N-terminal acryloyl group leads to ketomethylene isosteres of glycine-containing peptides. This method represents an alternative means for ligating two small peptides through a C-C bond-forming step.