gebhart/patrepeval huggingface dataset:
An experimentally supported model for the origin of charge transport barrier in Zn(O,S)/CIGSSe solar cells (2016)

Zinc oxysulfide buffer layers with [O]:[S] of 1:0, 6:1, 4:1, 2:1, and 1:1 ratios were deposited by atomic layer deposition on Cu(In,Ga)(S,Se)2 absorbers and made into finished solar cells. We demonstrate using Time-Resolved Photoluminescence that the minority carrier lifetime of Zn(O,S) buffered solar cells is dependent on the sulfur content of the buffer layer. τ1 for devices with [O]:[S] of 1:0–4:1 are &amp;lt;10 ns, indicating efficient charge separation in devices with low sulfur content. An additional τ2 is observed for relaxed devices with [O]:[S] of 2:1 and both relaxed and light soaked devices with [O]:[S] of 1:1. Corroborated with one-dimensional electronic band structure simulation results, we attribute this additional decay lifetime to radiative recombination in the absorber due to excessive acceptor-type defects in sulfur-rich Zn(O,S) buffer layer that causes a buildup in interface-barrier for charge transport. A light soaking step shortens the carrier lifetime for the moderately sulfur-rich 2:1 device when excess acceptors are passivated in the buffer, reducing the crossover in the dark and illuminated I-V curves. However, when a high concentration of excess acceptors exist in the buffer and cannot be passivated by light soaking, as with the sulfur-rich 1:1 device, then cell efficiency of the device will remain low.
A conductive hydrogel based on alginate and carbon nanotubes for probing microbial electroactivity (2018)

Some bacteria can act as catalysts to oxidize (or reduce) organic or inorganic matter with the potential of generating electrical current. Despite their high value for sustainable energy, organic compound production and bioremediation, a tool to probe the natural biodiversity and to select most efficient microbes is still lacking. Compartmentalized cell culture is an ideal strategy for achieving such a goal but the appropriate compartment allowing cell growth and electron exchange must be tailored. Here, we develop a conductive composite hydrogel made of a double network of alginate and carbon nanotubes. Homogeneous mixing of carbon nanotubes within the polyelectrolyte is obtained by a surfactant assisted dispersion followed by a desorption step for triggering electrical conductivity. Dripping the mixture in a gelling bath through simple extrusion or a double one allows the formation of either plain hydrogel beads or liquid core hydrogel capsules. The process is shown to be compatible with the bacterial culture (Geobacter sulfurreducens). Bacteria can indeed colonize the outer wall of plain beads or the inner wall of the conductive capsules' shell that function as an anode from which electrons produced by the cells are collected.
Physiological modulation of BiP activity by trans-protomer engagement of the interdomain linker (2015)

DnaK/Hsp70 chaperones form oligomers of poorly understood structure and functional significance. Site-specific proteolysis and crosslinking were used to probe the architecture of oligomers formed by the endoplasmic reticulum (ER) Hsp70, BiP. These were found to consist of adjacent protomers engaging the interdomain linker of one molecule in the substrate binding site of another, attenuating the chaperone function of oligomeric BiP. Native gel electrophoresis revealed a rapidly-modulated reciprocal relationship between the burden of unfolded proteins and BiP oligomers and slower equilibration between oligomers and inactive, covalently-modified BiP. Lumenal ER calcium depletion caused rapid oligomerization of mammalian BiP and a coincidental diminution in substrate binding, pointing to the relative inertness of the oligomers. Thus, equilibration between inactive oligomers and active monomeric BiP is poised to buffer fluctuations in ER unfolded protein load on a rapid timescale attainable neither by inter-conversion of active and covalently-modified BiP nor by the conventional unfolded protein response.
Learning Optimal Parametric Hydrodynamic Database for Vortex-Induced Crossflow Vibration Prediction (2021)

The Vortex-induced vibration (VIV) prediction of long flexible cylindrical structures relies on the accuracy of the hydrodynamic database constructed via rigid cylinder forced vibration experiments. However, to create a comprehensive hydrodynamic database with tens of input parameters including vibration amplitudes and frequencies and Reynolds number, surface roughness and so forth is technically challenging and virtually impossible due to the large number of experiments required. The current work presents an alternative approach to approximate the crossflow (CF) hydrodynamic coefficient database in a carefully chosen parameterized form. The learning of the parameters is posed as a constraint optimization, where the objective function is constructed based on the error between the experimental response and theoretical prediction assuming energy balance between fluid and structure. Such a method yields the optimal estimation of the CF parametric hydrodynamic database and produces the VIV response prediction based on the updated hydrodynamic database. The method then was tested on several experiments, including freely-mounted rigid cylinder in large Reynolds number with combined crossflow and inline vibrations and large-scale flexible cylinder test in the Norwegian Deepwater Program, and the result is shown to robustly and significantly reduce the error in predicting cylinder VIVs.
Figure S2 from Thymidine Kinase 1 Loss Confers Trifluridine Resistance without Affecting 5-Fluorouracil Metabolism and Cytotoxicity (2023)

&lt;p&gt;The effect of siRNA against TK1 and TK2 on FTD activation.&lt;/p&gt;
Reactivity and Structural Diversity in the Reaction of Guanidine 1,5,7‐Triazabicyclo[4.4.0]dec‐5‐ene with CO<sub>2</sub>, CS<sub>2</sub>, and Other Heterocumulenes (2016)

The guanidine 1,5,7‐triazabicyclo[4.4.0]dec‐5‐ene (TBD) reacted with the heterocumulenes CO 2 , CS 2 , i Pr 2 NCN i Pr 2 , p ‐tolylNCO, and p ‐tolylNCS to give three types of products: TBD–CO 2 ( 1 ) and TBD– p ‐tolylNCS ( 5 ), resulting from the addition of the cumulene to TBD, TBD(–H)({ i PrNH}–C=N{ i Pr}) ( 3 ) and TBD(–H)( p ‐tolylNHCO) ( 4 ), resulting from addition of the N–H bond of TBD to the C=N bond of the cumulene, and the dithiocarbamate salt [TBDH][TBD(–H)CS 2 ] ( 2 ) after transfer of a proton to a second molecule of TBD. Competition reactions indicated that the stability of the compounds decreases in the order 4 &gt; 5 &gt; 1 &gt; 2 &gt; 3 . DFT calculations showed that the relative stabilities of the products are governed by both the Lewis acidity of the heterocumulene and the Brønsted basicity of the TBD(–H)–cumulene anion, whereas their distinct structures are determined by the latter, with the most basic site governing the geometry of the final product.
Fluorescent (Blue Light) Cystoscopy Improved 3-Year Recurrence-Free Survival Rates of Recurrent Bladder Tumor Patients (2017)

Downs, Tracy M. MD, FACS; Rushmer, Timothy J.; Abel, Jason E. MD, FACS; Damodaran, Shiva MD; Richards, Kyle A. MD; Jarrard, David F. MD Author Information
Cytokinesis machinery promotes cell dissociation from collectively migrating strands in confinement (2022)

Supplementary code - Cytokinesis machinery promotes cell dissociation from collectively migrating strands in confinement<br> - Robert A. Law, Alexander Kiepas, Habben E. Desta, Emiliano Perez Ipiña**, Maria Parlani, Se Jong Lee, Chris L. Yankaskas, Runchen Zhao, Panagiotis Mistriotis, Nianchao Wang, Zhizhan Gu, Petr Kalab1, Peter Friedl, Brian A. Camley**, Konstantinos Konstantopoulos.<br> <br> **Corresponding authors for codes and model <br> These codes are shared to allow replication of our results and further exploration. Our codes were not developed with the goal of being efficient or easy to read, nor do they follow standard notations and conventions. We cannot guarantee that they will work as predicted if you try to change things without understanding them. In this sense, they are released in the spirit of the CRAPL license. <br> Requirements:<br> - All python code runs in python 3, specifically we used Python 3.9.5.<br> - The Jupyter notebook version is 6.4.6 and was installed using the default Anaconda installation.<br> - To install all required packages run 'pip install -r requirements.txt'.<br> - Stan library requires c++ installed.<br> <br> NOTE: If the versions of the libraries are different from those used in our study, we cannot guarantee that the software will operate successfully.<br> We advise utilizing conda (https://conda.io/), setting up a fresh environment, and installing the versions of the study's libraries.
Retinal Vascular and Oxygen Temporal Dynamic Responses to Light Flicker in Humans (2017)

Mathematical modeling revealed considerable differences in the time courses of changes among metrics during flicker, indicating flicker duration should be considered separately for each metric. Future application of this method may be useful to elucidate alterations in temporal dynamic responses to light flicker due to retinal diseases.
First-line pembrolizumab in advanced urothelial carcinoma: Clinical parameters associated with efficacy in the phase 2 KEYNOTE-052 and phase 3 KEYNOTE-361 trials. (2022)

521 Background: First-line treatment with pembrolizumab (pembro) monotherapy has shown durable clinical activity in selected patients (pts) with advanced/unresectable or metastatic urothelial carcinoma (UC). In a pooled population of pts with advanced UC from the single-arm phase 2 KEYNOTE-052 (NCT02335424) and the randomized, open-label, phase 3 KEYNOTE-361 (NCT02853305) studies, this exploratory analysis evaluated the relationship between baseline characteristics and clinical outcomes of first-line pembro monotherapy. Methods: Cisplatin-ineligible pts with advanced UC were enrolled in KEYNOTE-052 and chemotherapy-naive pts with advanced UC were enrolled in KEYNOTE-361. For analysis of predictive factors for ORR and OS in pembro-treated pts, the purposeful selection method was used to build the multivariable logistic regression model (ORR) and multivariable Cox model (OS), beginning with a univariable analysis of each independent variable. Any variable in the univariate model with P &lt; 0.10 was a candidate for the multivariate model. The stepwise selection method was used to select the variables in the final model. Significance of the final model was set at P &lt; 0.05. Data cutoff dates were September 26, 2020 (KEYNOTE-052) and April 29, 2020 (KEYNOTE-361). Results: This pooled analysis included 681 pts treated with pembro monotherapy (KEYNOTE-052, N = 374; KEYNOTE-361, N = 307 [170 were cisplatin ineligible]). Median follow-up was 51.9 mo (range, 22.0-65.3). ORR was 29.4% (95% CI, 26.0-32.9; 69 CRs, 131 PRs), and median DOR was 33.2 mo (range, 1.4+ to 60.7+). Median OS was 12.5 mo (95% CI, 11.0-14.6). By multivariate analysis, independent factors significantly associated with higher ORR were PD-L1 status (combined positive score [CPS] ≥10 vs CPS &lt; 10; odds ratio [OR], 1.90 [95% CI, 1.33-2.71]; P = 0.0004), site of metastasis (lymph node only vs visceral disease; OR, 1.66 [95% CI, 1.06-2.59]; P = 0.0265), liver involvement (absent vs present; OR, 1.75 [95% CI, 1.06-2.89]; P = 0.0294), and baseline hemoglobin level ≥10 vs &lt; 10 g/dL; OR, 2.17 [95% CI, 1.09-4.31]; P = 0.0276). Multivariate analysis of OS is displayed in the Table. Conclusions: This exploratory multivariate analysis identified numerous factors, including PD-L1–positive status (CPS ≥10), lymph node only metastasis, and lower ECOG PS score, associated with improved clinical outcomes in pts with advanced UC treated with first-line pembro monotherapy. Clinical trial information: NCT02335424 and NCT02853305. [Table: see text]
EDAM: Earthquake damage assessment communication system using smartphones (2014)

On May 20th and 29th, 2012 two earthquakes of 5.9Mw and 5.8Mw respectively have struck the Emilia Romagna region in Italy, causing 27 deaths and widespread damage. The epicenters were between Finale Emilia and Medolla. The damage assessment after the earthquake was managed from the Italian Emergency Authority, using printed forms (AeDES) which were filled by specialists on site. Since the use of smartphones is becoming more and more spread among the population, its utilization within the field reconnaissance has been proposed in this paper. An application that can be run by normal citizens on smartphones was developed, to give an initial damage evaluation of the area, which is going to be very useful when resources (e.g. the number of specialist is limited). A simplified version of the application was tested for the first time during 2012 Emilia earthquake to enhance the emergency response, showing the efficiency of the proposed method
Performance of polyethyleneimine–silica adsorbent for post-combustion CO2 capture in a bubbling fluidized bed (2014)

The high performance of polyethyleneimine (PEI)-based solid adsorbent for CO2 capture has been well recognized in thermogravimetric analysis (TGA) and small-scale fixed bed reactors through the measurements of their equilibrium capacities but has not been really demonstrated on larger scales towards practical utilization. In the present study, a laboratory-scale bubbling fluidized bed reactor loaded with a few kg adsorbent is used to evaluate the adsorption performance of PEI–silica adsorbent under different working conditions including with/without the presence of moisture, different gas–solid contact times, initial bed temperatures, and CO2 partial pressures. The adsorption capacities have shown a clear degradation tendency under dry condition. However, they can be stabilized at a high level of 10.6–11.1% w/w over 60 cycles if moisture (ca. 8.8 vol%) is present in the gas flow during adsorption and desorption. Breakthrough capacities can be stabilized at the level of 7.6–8.2% w/w with the gas–solid contact time of 13 s. The adsorption capacities for the simulated flue gases containing 5% CO2 are only slightly lower than those for the simulated flue gases containing 15% CO2, indicating that the PEI–silica adsorbent is suitable for CO2 capture from flue gases of both coal-fired and natural gas-fired combined cycle power plants. The exothermal heat of adsorption is estimated by the energy balance in the fluidized bed reactor and found to be close (within 10%) to the measured value by TG-DSC. The regeneration heat for the as-prepared PEI–silica adsorbent is found to be 2360 kJ/kgCO2 assuming 75% recovery of sensible heat which is well below the values of 3900–4500 kJ/kgCO2 for a typical MEA scrubbing process with 90% recovery of sensible heat.
Learning Optimization Friendly Comfort Model for HVAC Model Predictive Control (2015)

Heating, Ventilation and Air Conditioning(HVAC) systems perform environmental regulations to provide thermal comfort and acceptable indoor air quality. Recently optimization based Model Predictive Control (MPC) has shown promising results to improve energy efficiency of HVAC system in smart buildings. However rigorous studies on incorporating data driving comfort requirement into the MPC framework are lacking. Previous research on comfort learning usually ignores the restrictions of the downstream control and merely focuses on utilizing existing machine learning tools, which induce undesirable non-linear coupling in decision variables. In this work, we adopt a novel "learning for application" scheme. The idea is to describe user comfort zone by a Convex Piecewise Linear Classifier (CPLC), which is directly pluggable for the optimization in MPC. We analyze the theoretical generalization performance of the classifier and propose a cost sensitive large margin learning formulation. The learning problem is then solved by online stochastic gradient descent with Mixed Integer Quadratic Program (MIQP) initialization. Experimental results on publicly available comfort data set validates the performance of CPLC and the training algorithm. HVAC MPC case studies show that the proposed method enables much better exploitation and seamless integration of individual comfort requirement in the MPC framework.
Mechanistic Characterization of (Xantphos)Ni(I)-Mediated Alkyl Bromide Activation: Oxidative Addition, Electron Transfer, or Halogen-Atom Abstraction (2019)

Ni(I)-mediated single-electron oxidative activation of alkyl halides has been extensively proposed as a key step in Ni-catalyzed cross-coupling reactions to generate radical intermediates. There are four mechanisms through which this step could take place: oxidative addition, outer-sphere electron transfer, inner-sphere electron transfer, and concerted halogen-atom abstraction. Despite considerable computational studies, there is no experimental study to evaluate all four pathways for Ni(I)-mediated alkyl radical formation. Herein, we report the isolation of a series of (Xantphos)Ni(I)-Ar complexes that selectively activate alkyl halides over aryl halides to eject radicals and form Ni(II) complexes. This observation allows the application of kinetic studies on the steric, electronic, and solvent effects, in combination with DFT calculations, to systematically assess the four possible pathways. Our data reveal that (Xantphos)Ni(I)-mediated alkyl halide activation proceeds via a concerted halogen-atom abstraction mechanism. This result corroborates previous DFT studies on (terpy)Ni(I)- and (py)Ni(I)-mediated alkyl radical formation, and contrasts with the outer-sphere electron transfer pathway observed for (PPh<sub>3</sub>)<sub>4</sub>Ni(0)-mediated aryl halide activation. This study of a model system provides insight into the overall mechanism of Ni-catalyzed cross-coupling reactions and offers a basis for differentiating electrophiles in cross-electrophile coupling reactions.
The IGF1R/INSR Inhibitor BI 885578 Selectively Inhibits Growth of IGF2-Overexpressing Colorectal Cancer Tumors and Potentiates the Efficacy of Anti-VEGF Therapy (2017)

Abstract Clinical studies of pharmacologic agents targeting the insulin-like growth factor (IGF) pathway in unselected cancer patients have so far demonstrated modest efficacy outcomes, with objective responses being rare. As such, the identification of selection biomarkers for enrichment of potential responders represents a high priority for future trials of these agents. Several reports have described high IGF2 expression in a subset of colorectal cancers, with focal IGF2 amplification being responsible for some of these cases. We defined a novel cut-off value for IGF2 overexpression based on differential expression between colorectal tumors and normal tissue samples. Analysis of two independent colorectal cancer datasets revealed IGF2 to be overexpressed at a frequency of 13% to 22%. An in vitro screen of 34 colorectal cancer cell lines revealed IGF2 expression to significantly correlate with sensitivity to the IGF1R/INSR inhibitor BI 885578. Furthermore, autocrine IGF2 constitutively activated IGF1R and Akt phosphorylation, which was inhibited by BI 885578 treatment. BI 885578 significantly delayed the growth of IGF2-high colorectal cancer xenograft tumors in mice, while combination with a VEGF-A antibody increased efficacy and induced tumor regression. Besides colorectal cancer, IGF2 overexpression was detected in more than 10% of bladder carcinoma, hepatocellular carcinoma and non-small cell lung cancer patient samples. Meanwhile, IGF2-high non-colorectal cancer cells lines displayed constitutive IGF1R phosphorylation and were sensitive to BI 885578. Our findings suggest that IGF2 may represent an attractive patient selection biomarker for IGF pathway inhibitors and that combination with VEGF-targeting agents may further improve clinical outcomes. Mol Cancer Ther; 16(10); 2223–33. ©2017 AACR.
Supplementary Figure 4 from Real-time Raman Spectroscopy for &lt;i&gt;In Vivo&lt;/i&gt; Skin Cancer Diagnosis (2023)

&lt;p&gt;PDF file - 38K, ROC curve for discriminating biopsied skin cancers (MM, BCC, SCC, n = 200) from biopsied non-skin cancer lesions (AN, BN, CN, IN, JN, SK, AK, n =91).&lt;/p&gt;
Considerations for routinely testing for high lipoprotein(a) (2022)

Lp(a) should be measured in every patient at least once to identify patients with very high Lp(a) levels. These patients could benefit from Lp(a) lowering therapies when approved. In the meantime, therapy in high Lp(a) patients should focus on further reducing LDL-C and other ASCVD risk factors.
The copper–nicotinamide complex: sustainable applications in coupling and cycloaddition reactions (2014)

The copper(<sc>ii</sc>)–nicotinamide complex catalyzes the C–S, C–N bond forming and cycloaddition reactions under a variety of sustainable reaction conditions.
Optimal secure partial-repair in distributed storage systems (2017)

Consider a distributed storage system where parts of the source file fragments in storage nodes are lost. We denote a storage node that lost a part of its fragments as a faulty storage node and a storage node that lost non of its fragment as a complete storage node. In a process, termed as partial repair, a set of storage nodes (among faulty and complete storage nodes) transmit repairing fragments to other faulty storage nodes to recover the lost fragments. We first investigate the optimal partial repair in which the required bandwidth for recovering the lost fragments is minimal. Next, we assume that an eavesdropper wiretaps a subset of links connecting storage nodes, and overhears a number of repairing fragments. We then study optimal secure partial-repair in which the partial-repair bandwidth is minimal and the eavesdropper obtains no information about the source file by overhearing the repairing fragments. We propose optimal secure codes for exact partial-repair in a special scenario.
¿De qué hablamos cuando hablamos de innovación en periodismo? (2022)

The news media are constantly introducing innovations in their presentation formats, transforming as they do journalistic genres and creating entirely new ways of telling and consuming news. These changes are also closely reflected in academic research on journalism. This article carries out a systematic review of the literature analyzing the following new journalistic formats: structured journalism, immersive journalism, 360° video reports, virtual reality and augmented reality applied to journalism, newsgames and docugames. To do so, the scientific production examining these formats is first analyzed to determine the academic impact of these studies, while identifying their characteristics and tracking their evolution over time. Second, the leading researchers in this field are identified and interviewed to ascertain their opinion about the future of journalism and changing trends in journalistic formats. The results show that the number of academic publications about journalistic innovation peaked in 2019, above all in the three journals – Digital Journalism, Journalism Practice and Profesional de la Información – that lead the way in this discipline. The 23 academics interviewed reported that innovation impacts primarily on four aspects of journalism: information and content; audience; methods and resources and news media companies.