gebhart/patrepeval huggingface dataset:
Arbitrary surface structuring of amorphous silicon films based on femtosecond-laser-induced crystallization (2006)

The arbitrary surface structuring of amorphous silicon (a-Si) films was performed by applying the Fourier-transform (FT) method to the femtosecond-laser-induced crystallization. In order to realize the arbitrary structuring, the logo q-Psi was produced in the a-Si film by the FT of a computer-generated hologram. The crystallization of a-Si was performed using the near-infrared femtosecond-laser pulses. By micro-Raman spectroscopy, scanning-electron microscopy, and transmission-electron microscopy, it was found that the femtosecond-laser pulses induced a localized phase transformation from the amorphous to the crystalline phase, and the spatially selected crystallization of the a-Si was responsible for the formation of the two-dimensional pattern.
Faster sequential universal coding via block partitioning (2006)

Rissanen provided a sequential universal coding algorithm based on a block partitioning scheme, where the source model is estimated at the beginning of each block. This approach asymptotically approaches the entropy at the fastest possible rate of 1/2log(n) bits per unknown parameter. We show that the complexity of this algorithm is /spl Omega/(nlog(n)), which is comparable to existing sequential universal algorithms. We provide a sequential O(nlog(log(n))) algorithm by modifying Rissanen's block partitioning scheme. The redundancy with our approach is greater than with Rissanen's block partitioning scheme by a multiplicative factor 1+O(1/log(log(n))), hence it asymptotically approaches the entropy at the fastest possible rate.
Pre-existing and machine learning-based models for cardiovascular risk prediction (2021)

Predicting the risk of cardiovascular disease is the key to primary prevention. Machine learning has attracted attention in analyzing increasingly large, complex healthcare data. We assessed discrimination and calibration of pre-existing cardiovascular risk prediction models and developed machine learning-based prediction algorithms. This study included 222,998 Korean adults aged 40-79 years, naïve to lipid-lowering therapy, had no history of cardiovascular disease. Pre-existing models showed moderate to good discrimination in predicting future cardiovascular events (C-statistics 0.70-0.80). Pooled cohort equation (PCE) specifically showed C-statistics of 0.738. Among other machine learning models such as logistic regression, treebag, random forest, and adaboost, the neural network model showed the greatest C-statistic (0.751), which was significantly higher than that for PCE. It also showed improved agreement between the predicted risk and observed outcomes (Hosmer-Lemeshow χ<sup>2</sup> = 86.1, P < 0.001) than PCE for whites did (Hosmer-Lemeshow χ<sup>2</sup> = 171.1, P < 0.001). Similar improvements were observed for Framingham risk score, systematic coronary risk evaluation, and QRISK3. This study demonstrated that machine learning-based algorithms could improve performance in cardiovascular risk prediction over contemporary cardiovascular risk models in statin-naïve healthy Korean adults without cardiovascular disease. The model can be easily adopted for risk assessment and clinical decision making.
Expanding the potential of in vivo cell therapy with tLNP-RNAs (targeted lipid nanoparticle-RNA) (2023)

The application of lipid nanoparticles (LNPs) as a non-viral delivery system for advanced therapies, in conjunction with RNA-based medicines, is set to revolutionize the field. David McCall, Senior Editor, BioInsights, speaks to Adrian Bot, Chief Scientific Officer and Executive Vice President of R&amp;D, Capstan Therapeutics, about the potential of these tools to drive the burgeoning in vivo cell therapy space in particular, and the broader gene medicine field in general.
Data from Apogossypol derivatives as antagonists of antiapoptotic Bcl-2 family proteins (2023)

&lt;div&gt;Abstract&lt;p&gt;Guided by a combination of nuclear magnetic resonance binding assays and computational docking studies, we synthesized a library of 5,5′ substituted Apogossypol derivatives as potent Bcl-X&lt;sub&gt;L&lt;/sub&gt; antagonists. Each compound was subsequently tested for its ability to inhibit Bcl-X&lt;sub&gt;L&lt;/sub&gt; in an &lt;i&gt;in vitro&lt;/i&gt; fluorescence polarization competition assay and exert single-agent proapoptotic activity in human cancer cell lines. The most potent compound BI79D10 binds to Bcl-X&lt;sub&gt;L&lt;/sub&gt;, Bcl-2, and Mcl-1 with IC&lt;sub&gt;50&lt;/sub&gt; values of 190, 360, and 520 nmol/L, respectively, and potently inhibits cell growth in the H460 human lung cancer cell line with an EC&lt;sub&gt;50&lt;/sub&gt; value of 680 nmol/L, expressing high levels of Bcl-2. BI79D10 also effectively induces apoptosis of the RS11846 human lymphoma cell line in a dose-dependent manner and shows little cytotoxicity against &lt;i&gt;bax&lt;/i&gt;&lt;sup&gt;−/−&lt;/sup&gt;&lt;i&gt;bak&lt;/i&gt;&lt;sup&gt;−/−&lt;/sup&gt; mouse embryonic fibroblast cells, in which antiapoptotic Bcl-2 family proteins lack a cytoprotective phenotype, implying that BI79D10 has little off-target effects. BI79D10 displays &lt;i&gt;in vivo&lt;/i&gt; efficacy in transgenic mice, in which Bcl-2 is overexpressed in splenic B cells. Together with its improved plasma and microsomal stability relative to Apogossypol, BI79D10 represents a lead compound for the development of novel apoptosis-based therapies for cancer. [Mol Cancer Ther 2009;8(4):904–13]&lt;/p&gt;&lt;/div&gt;
Beam steering via peak power decay in nonlinear waveguide arrays (2013)

We report the experimental observation and theoretical analysis of a novel beam-steering effect in periodic waveguide arrays that arises from the interplay between discrete diffraction, Kerr nonlinearity and any mechanism that effectively weakens the nonlinear part of the beam. In this regime the propagation direction shows increased sensitivity to the input angle and for a certain angular range around normal incidence a nonlinear beam may be guided to a direction opposite to that initially inserted. For continuous wave beams the role of this mechanism is played by absorption of any kind, such as three photon absorption, two photon absorption or even linear absorption. For pulsed beams we show that the same dynamics can arise due to strong normal temporal dispersion, while absorption is not necessary and can be a further enhancing or alternative factor. This observation falls under a more general dissipation-assisted beam velocity control mechanism in nonlinear optical lattices, which is also theoretically predicted by the effective particle approach.
Androgen Receptor Counteracts Doxorubicin-Induced Cardiotoxicity in Male Mice (2010)

Doxorubicin (Dox) has been used as a potent anticancer agent, but serious cardiotoxicity precludes its use in a wide range of patients. We have reported that the androgen-androgen receptor (AR) system plays important roles in cardiac growth and protection from angiotensin II-induced cardiac remodeling. The present study was undertaken to clarify whether the androgen-AR system exerts a cardioprotective effect against Dox-induced cardiotoxicity. Male AR knockout (ARKO) and age-matched littermate male wild-type (WT) mice at 25 wk of age were given ip injections of Dox (20 mg/kg) or a vehicle. The survival rate and left ventricular function in Dox-treated male ARKO mice were reduced compared with those in Dox-treated male WT mice. Electron microscopic study showed prominent vacuole formation of myocardial mitochondria in Dox-treated male ARKO mice. Cardiac oxidative stress and apoptosis of cardiomyocytes were increased more prominently by Dox treatment in male ARKO mice than in male WT mice. In addition, Dox-induced reduction in the expression of cardiac mitochondria transcription factor A (Tfam) and phosphorylation of serine-threonine kinase (Akt) was more pronounced in male ARKO mice than in male WT mice. In cardiac myoblast cells, testosterone up-regulated Akt phosphorylation and Tfam expression and exerted an antiapoptotic effect against Dox-induced cardiotoxicity. Collectively, the results demonstrate that Dox-induced cardiotoxicity is aggravated in male ARKO mice via exacerbation of mitochondrial damage and superoxide generation, leading to enhanced apoptosis of cardiomyocytes. Thus, the androgen-AR system is thought to counteract Dox-induced cardiotoxicity partly through activation of the Akt pathway and up-regulation of Tfam to protect cardiomyocytes from mitochondrial damage and apoptosis.
n-Pentenyl Furanosides and Related Glycosyl Donors for the Synthesis of Archaeol Glycolipid Analogues (1996)

An efficient synthesis of archaeol glycoglycerolipid diethers is described: peracetylated pentenylfuranosides produced in a one-pot procedure from Glc, Gal or Man react efficiently with glycerol diether 5 to furnish 1,2-trans glycolipids in high yields and excellent stereoselectivities whereas direct glycosidation of D-glucurone gave after lactone opening the uronamide glycolipid 13.
Role for Cell-Surface Collagen of Streptococcus pyogenes in Infections (2020)

Group A <i>Streptococcus</i> (GAS) displays cell-surface proteins that resemble human collagen. We find that a fluorophore-labeled collagen mimetic peptide (CMP) labels GAS cells but not <i>Escherichia coli</i> or <i>Bacillus subtilis</i> cells, which lack such proteins. The CMP likely engages in a heterotrimeric helix with endogenous collagen, as the nonnatural d enantiomer of the CMP does not label GAS cells. To identify a molecular target, we used reverse genetics to "knock-in" the GAS genes that encode two proteins with collagen-like domains, Scl1 and Scl2, into <i>B. subtilis</i>. The fluorescent CMP labels the cells of these <i>B. subtilis</i> strains. Moreover, these strains bind tightly to a surface of mammalian collagen. These data are consistent with streptococcal collagen forming triple helices with damaged collagen in a wound bed and thus have implications for microbial virulence.
Results of a 5-Year Multicenter Trial of a New Generation Cooled High Energy Transurethral Microwave Thermal Therapy Catheter for Benign Prostatic Hyperplasia (2011)

Cooled, high energy transurethral microwave thermal therapy using a new generation treatment catheter produced safe, durable, clinically relevant results in men with lower urinary tract symptoms caused by benign prostatic hyperplasia for 5 years after treatment with acceptable medical and surgical re-treatment rates.
Copper(II) Binding to the Intrinsically Disordered C-Terminal Peptide of SARS-CoV-2 Virulence Factor Nsp1 (2022)

The first encoded SARS-CoV-2 protein (Nsp1) binds to the human 40S ribosome and blocks synthesis of host proteins, thereby inhibiting critical elements of the innate immune response. The final 33 residues of the natively unstructured Nsp1 C-terminus adopt a helix-turn-helix geometry upon binding to the ribosome. We have characterized the fluctuating conformations of this peptide using circular dichroism spectroscopy along with measurements of tryptophan fluorescence and energy transfer. Tryptophan fluorescence decay kinetics reveal that copper(II) binds to the peptide at micromolar concentrations, and electron paramagnetic resonance spectroscopy indicates that the metal ion coordinates to the lone histidine residue.
On Data-Driven Modeling and Simulation of Aero-Thermo-Mechanically Degrading Nonlinear Continuum Systems (2006)

Recent advances on data-driven application systems, sensor and computational technologies as well as long-term needs for efficient and accurate systemic behavior prediction monitoring in the context of realistic system design and maintenance, have brought degrading continuum systems modeling and simulation in the forefront of our activities. This paper outlines the initial steps of a methodology for applying a data-driven inverse-problem approach on the area of modeling mass-conserving degrading thermo-mechanical multi-domain nonlinear continuum structural and material systems. The methodology is applied for composite materials under simultaneous mechanical and thermal multi-field excitation and is based on mechatronic and computational automation. Furthermore, the multi-domain multiphysics modeling necessary for addressing the fluid-structure interaction involved in such systems is also discussed in the context of jet platforms with aerodynamically induced heating. Finally, simulation demonstrations are presented for the F-16 fighter jet and for a sensor-driven data solution reconstruction of an aircraft wing to demonstrate the potential for developing a material and structural health monitoring system based on he concept of dissipated energy density as a material health metric.
Economics of tandem flat plate photovoltaic modules (2016)

Tandem modules, formed by stacking two PV cells, either monolithically or mechanically, can offer higher solar conversion efficiency than modules that use only one type of PV cell. Such modules necessarily cost more per unit area than either single-junction alternative, but the increased efficiency leverages area-related costs to potentially reduce system cost per watt. High-efficiency, low-cost tandems could arise if the cost of III-V cells is reduced to approach the cost of silicon cells, or if stable large-area perovskite cells are demonstrated with efficiency approaching that of today's best laboratory devices. Within the scope given by these optimistic assumptions, future costs and performance still have a substantial range of uncertainty. A probabilistic Monte Carlo model is presented that generates a large number of cost and performance scenarios based on a range of values for each input parameter. The results can be used to assign a probability, within the scope of the assumptions, that the tandem will be more cost-effective than either single-junction alternative. Four types of tandem modules are analyzed: (1) III-V on silicon, (2) III-V on thin film, (3) perovskite on silicon, and (4) perovskite on thin film. All of these tandems have a reasonable chance (>10%) of providing slightly lower cost per watt for residential systems, and the two thin-film options might also slightly benefit utility-scale systems. Achieving a substantial cost benefit is less likely. Only the perovskite on thin film tandem has a reasonable chance of reducing system cost per watt by more than 10% for residential systems, or of reducing system cost per watt by more than 5% for utility-scale systems.
Population Differences in Antifreeze/Cryoprotectant Accumulation Patterns in an Antarctic Insect (1983)

The freezing tolerant antarctic midge Belgica antarctica Jacobs accumulates a three component cryoprotectant system during the period of seasonal transition (February-March). Separate populations produce qualitatively identical cryoprotectants (erythritol, glucose and trehalose), but with quantitative variations that may yield a doubling in levels of one or more individual cryoprotectants. These quantitative variations occur under identical thermal and photic conditions. The protective potential of cryoprotectants when represented as a combined indicator of concentration (hydroxyl equivalents) is essentially equal among populations as hardening is maximized. Supercooling points elevate from austral summer lows of -10.2 to winter highs of -5.0TC. The accumulation of cryoprotectants occurs concomitantly with the gradual decrease in microhabitat temperatures (0.20 to 0.25TC d1). It is suggested that enhanced hardening is not alone triggered by temperature, but may be associated with other environmental stressors or development programming.
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations (2020)

Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochemical efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves parallel monitoring of the noncovalent recognition elements and the covalent reactivity of the molecules to avoid potential idiosyncratic side effects. This challenge calls for special design protocols, including a variety of computational chemistry methods. Covalent inhibition proceeds through multiple steps, and calculating free energy changes of the subsequent binding events along the overall binding process would help us to better control the design of drug candidates. Inspired by the recent success of free energy calculations on reversible binders, we developed a complex protocol to compute free energies related to the noncovalent and covalent binding steps with thermodynamic integration and hybrid quantum mechanical/molecular mechanical (QM/MM) potential of mean force (PMF) calculations, respectively. In optimization settings, we examined two therapeutically relevant proteins complexed with congeneric sets of irreversible cysteine targeting covalent inhibitors. In the selectivity paradigm, we studied the irreversible binding of covalent inhibitors to phylogenetically close targets by a mutational approach. The results of the calculations are in good agreement with the experimental free energy values derived from the inhibition and kinetic constants (<i>K</i><sub>i</sub> and <i>k</i><sub>inact</sub>) of the enzyme-inhibitor binding. The proposed method might be a powerful tool to predict the potency, selectivity, and binding mechanism of irreversible covalent inhibitors.
Synthesis and cytotoxic activity of indolyl thiazoles (1997)

A number of indolyl thiazoles have been prepared and evaluated for their antitumor properties. The compounds were synthesized from the appropriate indole, building up the thiazole ring using the Hantzsch reaction. Cytotoxic activity was measured in the human breast cancer cell line SKBr3 using the MTT assay.
Sensory Deviancy Detection Measured Directly Within the Human Nucleus Accumbens (2015)

Rapid changes in the environment evoke a comparison between expectancy and actual outcome to inform optimal subsequent behavior. The nucleus accumbens (NAcc), a key interface between the hippocampus and neocortical regions, is a candidate region for mediating this comparison. Here, we report event-related potentials obtained from the NAcc using direct intracranial recordings in 5 human participants while they listened to trains of auditory stimuli differing in their degree of deviation from repetitive background stimuli. NAcc recordings revealed an early mismatch signal (50-220 ms) in response to all deviants. NAcc activity in this time window was also sensitive to the statistics of stimulus deviancy, with larger amplitudes as a function of the level of deviancy. Importantly, this NAcc mismatch signal also predicted generation of longer latency scalp potentials (300-400 ms). The results provide direct human evidence that the NAcc is a key component of a network engaged in encoding statistics of the sensory environmental.
Painful diabetic peripheral neuropathy: consensus recommendations on diagnosis, assessment and management (2011)

Painful diabetic peripheral neuropathy (DPN) is common, is associated with significant reduction in quality of life and poses major treatment challenges to the practising physician. Although poor glucose control and cardiovascular risk factors have been proven to contribute to the aetiology of DPN, risk factors specific for painful DPN remain unknown. A number of instruments have been tested to assess the character, intensity and impact of painful DPN on quality of life, activities of daily living and mood. Management of the patient with DPN must be tailored to individual requirements, taking into consideration the co-morbidities and other factors. Pharmacological agents with proven efficacy for painful DPN include tricyclic anti-depressants, the selective serotonin and noradrenaline re-uptake inhibitors, anti-convulsants, opiates, membrane stabilizers, the anti-oxidant alpha-lipoic acid and topical agents including capsaicin. Current first-line therapies for painful DPN include tricyclic anti-depressants, the serotonin and noradrenaline re-uptake inhibitor duloxetine and the anti-convulsants pregabalin and gabapentin. When prescribing any of these agents, other co-morbidities and costs must be taken into account. Second-line approaches include the use of opiates such as synthetic opioid tramadol, morphine and oxycodone-controlled release. There is a limited literature with regard to combination treatment. In extreme cases of painful DPN unresponsive to pharmacotherapy, occasional use of electrical spinal cord stimulation might be indicated. There are a number of unmet needs in the therapeutic management of painful DPN. These include the need for randomized controlled trials with active comparators and data on the long-term efficacy of agents used, as most trials have lasted for less than 6 months. Finally, there is a need for appropriately designed studies to investigate non-pharmacological approaches.
Antenna Placement and Performance Tradeoffs with Hand Blockage in Millimeter Wave Systems (2019)

The ongoing commercial deployment of millimeter wave systems brings into focus a number of practical issues in form factor user equipment (UE) design. With wavelengths becoming smaller, antenna gain patterns becoming directional, and link budgets critically dependent on beamforming, it becomes imperative to use a number of antenna modules at different locations of the UE for good performance. While more antennas/modules can enhance beamforming array gains, it comes with the tradeoff of higher component cost, power consumption of the associated radio frequency circuitry, and a beam management overhead in learning the appropriate beam weights. Thus, the goal of a good UE design is to provide robust spherical coverage corresponding to good array gains over the entire sphere around the UE with a low beam management overhead, complexity, and cost. The scope of this paper is to study the implications of two popular commercial millimeter wave UE designs (a face and an edge design) on spherical coverage. We show that analog beam codebooks can result in good performance for both the designs, and the edge design provides a better tradeoff in terms of robust performance (with hand blockage), beam management overhead, implementation complexity from an antenna placement standpoint and cost.
C4BP-IgM protein as a therapeutic approach to treat Neisseria gonorrhoeae infections (2019)

Gonorrhea is a sexually transmitted infection with 87 million new cases per year globally. Increasing antibiotic resistance has severely limited treatment options. A mechanism that Neisseria gonorrhoeae uses to evade complement attack is binding of the complement inhibitor C4b-binding protein (C4BP). We screened 107 porin B1a (PorB1a) and 83 PorB1b clinical isolates randomly selected from a Swedish strain collection over the last 10 years and noted that 96/107 (89.7%) PorB1a and 16/83 (19.3%) PorB1b bound C4BP; C4BP binding substantially correlated with the ability to evade complement-dependent killing (r = 0.78). We designed 2 chimeric proteins that fused C4BP domains to the backbone of IgG or IgM (C4BP-IgG; C4BP-IgM) with the aim of enhancing complement activation and killing of gonococci. Both proteins bound gonococci (KD C4BP-IgM = 2.4 nM; KD C4BP-IgG 980.7 nM), but only hexameric C4BP-IgM efficiently outcompeted heptameric C4BP from the bacterial surface, resulting in enhanced complement deposition and bacterial killing. Furthermore, C4BP-IgM substantially attenuated the duration and burden of colonization of 2 C4BP-binding gonococcal isolates but not a non-C4BP-binding strain in a mouse vaginal colonization model using human factor H/C4BP-transgenic mice. Our preclinical data present C4BP-IgM as an adjunct to conventional antimicrobials for the treatment of gonorrhea.