gebhart/patrepeval huggingface dataset:
A Multidisciplinary Approach to Probing Enthalpy–Entropy Compensation and the Interfacial Mobility Model (2011)

In recent years, interfacial mobility has gained popularity as a model with which to rationalize both affinity in ligand binding and the often observed phenomenon of enthalpy-entropy compensation. While protein contraction and reduced mobility, as demonstrated by computational and NMR techniques respectively, have been correlated to entropies of binding for a variety of systems, to our knowledge, Raman difference spectroscopy has never been included in these analyses. Here, nonresonance Raman difference spectroscopy, isothermal titration calorimetry, and X-ray crystallography were utilized to correlate protein contraction, as demonstrated by an increase in protein interior packing and decreased residual protein movement, with trends of enthalpy-entropy compensation. These results are in accord with the interfacial mobility model and lend additional credence to this view of protein activity.
A novel rate-distortion optimization method of H.264/AVC intra coder (2011)

In H.264/AVC, the concept of rate-distortion optimization (RDO) mode decision has proven to be an important coding tool. But the complexity and computation load of RDO technique is extremely high. In this paper, we propose an enhanced low complexity cost function for H.264/AVC intra 4x4 mode selections. The enhanced cost function uses sum of absolute Hadamard-transformed differences (SATD) and variance of the residual block to estimate distortion part of the cost function. A threshold based large coefficients count is also used for estimating the bit-rate part. The proposed method improves the rate-distortion (RD) performance of the conventional fast cost functions while maintaining low complexity requirement.
UNION RATES OF HUMERAL SHAFT FRACTURES TREATED WITH FUNCTIONAL BRACING (2013)

The aim of this audit was to assess the union rate of humeral shaft fractures treated conservatively in a functional brace in our unit, compared to a “gold standard” of 98% as reported by Sarmiento (JBJS 1977). A retrospective clinical and radiographic review of 155 closed humeral shaft fractures managed with a humeral brace from 2005–2012 was performed. Pathological fractures and patients under 18 were excluded. The mean age was 60 (18–94) with 45 males and 72 females. 15 (10%) patients under 18 and 8 (5%) pathological fractures were excluded; 15 (10%) patients were lost to follow up. Of the remaining 117 fractures, 83 (71%) went on to union and 34 (29%) developed a non-union. Mean time to union was 131 days (47–622). 80% of distal fractures and 75% of midshaft fractures united but only 58% of proximal fractures went on to unite. There was no significant difference in union rates between multi fragmentary (> 3 parts) and simple fracture patterns (69% vs 71% respectively). Our study suggests that a lower threshold for operative intervention of proximal third humeral shaft fractures may be required.
ChemInform Abstract: Novel and Flexible Entries into Prostaglandins and Analogues Based on Ring Closing Alkyne Metathesis or Alkyne Cross Metathesis. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pre-Select Static Caching and Neighborhood Ordering for BFS-like Algorithms on Disk-based Graph Engines (2019)

Many important graph algorithms are based on the breadth first search (BFS) approach, which builds itself on recursive vertex traversal. We classify algorithms that share this characteristic into what we call a BFS-like algorithm. In this work, we first analyze and study the I/O request patterns of BFS-like algorithms executed on disk-based graph engines. Our analysis exposes two shortcomings in executing BFS-like algorithms. First, we find that the use of the cache is ineffective. To make use of the cache more effectively, we propose an in-memory static cache, which we call BFS-Aware Static Cache or Basc, for short. Basc is static as its contents, which are edge lists of vertices that are pre-selected before algorithm execution, do not change throughout the execution of the algorithm. Second, we find that state-of-the-art ordering method for graphs on disks is ineffective with BFS-like algorithms. Thus, based on an I/O cost model that estimates the performance based on the ordering of graphs, we develop an efficient graph ordering called Neighborhood Ordering or Norder. We provide extensive evaluations of Basc and Norder on two well-known graph engines using five real-world graphs including Twitter that has 1.9 billion edges. Our experimental results show that Basc and Norder, collectively have substantial performance impact.
Data from MRI-Based Digital Models Forecast Patient-Specific Treatment Responses to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Triple-negative breast cancer (TNBC) is persistently refractory to therapy, and methods to improve targeting and evaluation of responses to therapy in this disease are needed. Here, we integrate quantitative MRI data with biologically based mathematical modeling to accurately predict the response of TNBC to neoadjuvant systemic therapy (NAST) on an individual basis. Specifically, 56 patients with TNBC enrolled in the ARTEMIS trial (NCT02276443) underwent standard-of-care doxorubicin/cyclophosphamide (A/C) and then paclitaxel for NAST, where dynamic contrast-enhanced MRI and diffusion-weighted MRI were acquired before treatment and after two and four cycles of A/C. A biologically based model was established to characterize tumor cell movement, proliferation, and treatment-induced cell death. Two evaluation frameworks were investigated using: (i) images acquired before and after two cycles of A/C for calibration and predicting tumor status after A/C, and (ii) images acquired before, after two cycles, and after four cycles of A/C for calibration and predicting response following NAST. For Framework 1, the concordance correlation coefficients between the predicted and measured patient-specific, post-A/C changes in tumor cellularity and volume were 0.95 and 0.94, respectively. For Framework 2, the biologically based model achieved an area under the receiver operator characteristic curve of 0.89 (sensitivity/specificity = 0.72/0.95) for differentiating pathological complete response (pCR) from non-pCR, which is statistically superior (&lt;i&gt;P&lt;/i&gt; &lt; 0.05) to the value of 0.78 (sensitivity/specificity = 0.72/0.79) achieved by tumor volume measured after four cycles of A/C. Overall, this model successfully captured patient-specific, spatiotemporal dynamics of TNBC response to NAST, providing highly accurate predictions of NAST response.&lt;/p&gt;Significance:&lt;p&gt;Integrating MRI data with biologically based mathematical modeling successfully predicts breast cancer response to chemotherapy, suggesting digital twins could facilitate a paradigm shift from simply assessing response to predicting and optimizing therapeutic efficacy.&lt;/p&gt;&lt;/div&gt;
Ultrafast reclamation of fracking effluents using surface-engineered nanosilicon sponges (2021)

Effluents from the fracking process are typically discharged at elevated temperatures and are a major environmental concern. We applied a surface-engineered sponge (SEnS) with thermal stability up to 220 ºC to reclaim emulsified oily wastewater at discharge temperatures between 30-100 ºC. The sponge achieved 92-96% removal efficiency within 5 minutes, where speed increased by 27% by melting waxes. The adsorbed oil from the SEnS was also recovered within 1-2 minutes by diluent wash. These performance metrics suggest that SEnS could emerge as a practical solution to achieve fracking water reclamation processes’ Net-Zero goals.
Developing professional caregivers’ empathy and emotional competencies through mindfulness-based stress reduction (MBSR): results of two proof-of-concept studies (2018)

The programme was feasible and acceptable. It was associated with a significant signal on the following outcomes: perspective taking, the identification of one's own emotions and emotional acceptance, thus, justifying moving towards efficacy trials using these outcomes.
Code-division-multiplexing using orthogonal codes for fast electrical impedance tomography (2014)

Electrical impedance tomography (EIT) is used to determine the spatial conductivity distribution of a measurement environment, what involves several applications in the area of process engineering or medical science. In common systems a measurement environment is usually stimulated by defined current patterns in a serial time-multiplexing manner. Higher measurement rates can be achieved with code-multiplexed (CDM) excitations for parallel measurements. In order to optimize channel separation and dynamic range, orthogonal Walsh-Hadamard codes have been implemented on a fast EIT system. The crosstalk between different channels has been analyzed for 9 parallel coded excitation signals. Furthermore reconstructed conductivity distributions have been compared to reconstruction results obtained from frequency-multiplexed (FDM) measurements (root mean square difference of 0.02%).
Single Cell Analysis of Factor VIII-specific T Cells in Hemophilic Mice after Treatment with Human Factor VIII (2002)

A multi-parameter flow-cytometry assay was established suitable for analyzing T-cell-specific cell surface markers (CD3, CD4) together with intracellular cytokines on a single cell level. This assay was used to identify the frequency and the kinetic of different populations of factor VIII (FVIII)-specific CD4+ T cells in hemophilic E-17 mice after treatment with human FVIII. A clear temporal correlation was found between the appearance of FVIII-specific CD4+ T cells in the spleen and the detection of anti-FVIII antibodies in plasma. These cells and antibodies were detectable in all experiments after two doses of FVIII and in a few even after a single dose. The IFN-gamma-producing T cells were the most prominent type of FVIII-specific T cells suggesting Th1-type T cells have an important role in regulating the anti-FVIII immune response in E-17 mice. IL-10-producing T cells were the second most dominant type. They were detectable after two doses of FVIII and increased in frequency after four. Cytokine co-expression studies analyzing IL-10 and IFN-gamma in the same cell indicated that there might be at least two types of IL-10 positive T cells, those cells that produce IL-10 only and in addition cells that produce IL-10 and IFN-gamma. Furthermore, FVIII-specific T cells producing IL-2 were found in all experiments after two doses of FVIII. In a few experiments IL-4-producing T cells were seen but in most experiments they were not detectable. In contrast, IL-4 could be found in supernatants of in vitro restimulated CD8- spleen cells.
Terminal Transferase as a Predictor of Initial Responsiveness to Vincristine and Prednisone in Blastic Chronic Myelogenous Leukemia (1978)

We undertook a prospective trial to evaluate terminal deoxynucleotidyl transferase activity as a predictor of responsiveness to vincristine and prednisone in 22 Philadelphia-chromosome-positive patients with blastic chronic myelogenous leukemia. Thirteen patients were transferase positive, and nine negative. None of the nine negative patients responded, whereas eight of the 13 positive (P = 0.004) responded with complete clearing of peripheral blood blast cells and a return of normal marrow cellularity with less than 5 per cent blast cells. Among transferase-positive patients under 50 years of age the response rate was 78 per cent. Blast-cell morphology (i.e., lymphoblastic versus myeloblastic) had no significant correlation with either responsiveness or terminal transferase activity. The results of this study suggest that responsiveness to vincristine and prednisone in blastic chronic myelogenous leukemia is confined to patients whose leukemic cells are transferase positive.
Table S1 from Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer (2023)

&lt;p&gt;Supplementary Table 1: List of the compounds in the epigenetic inhibitor library.&lt;/p&gt;
Ultra-High Quality Video Frame Synchronous Audio Coding (2003)

Two methods of coding and delivering ultra-high-quality audio are presented. Both methods are video frame synchronous and editable at common video frame rates (23.98, 24, 25, 29.97, and 30 frames per second) without the use of sample-rate converters. The first is an ultra-high-quality audio coder that exceeds 4.8 on the ITU-R five-point audio impairment scale at a bit rate of 256 kbit/s per channel and at up to three generations of encoding/decoding. The second is an enhanced method of video frame synchronous PCM packing. Specifically the problem of transmitting 48-kHz audio in 29.97-Hz frames is examined.
In situ quantification of temperature and strain within photovoltaic modules through optical sensing (2022)

Abstract The ability to quantify internal strain levels within a photovoltaic (PV) laminate is essential to aid in the development of reliable and sustainable PV modules. This need is even greater for emerging applications with a high degree of integration such as vehicle and infrastructure integrated PV. Within this work, we demonstrate a scalable optical sensing solution, which allows for the in situ thermo‐mechanical strain and temperature monitoring of photovoltaic modules. Using a combination of two optic fibers with fiber Bragg gratings (FBGs) with a different packaging, an absolute in‐laminate temperature accuracy of 0.3°C has been achieved along with the ability to detect changes in strain as low as 0.248 μϵ. The sensor solution provides the potential to monitor and quantify various failure modes or degradation at various stages in the development process up to in‐field monitoring. Furthermore, it provides a platform for the direct validation of physics‐based simulations.
Supplemental Methods from AGS16F Is a Novel Antibody Drug Conjugate Directed against ENPP3 for the Treatment of Renal Cell Carcinoma (2023)

&lt;p&gt;Supplemental Methods&lt;/p&gt;
Stationary analysis of the “Shortest Queue First” service policy: The asymmetric case (2017)

The Shortest Queue First service discipline is analyzed for two asymmetric queues. For Poisson job arrivals and exponentially distributed service times, we first show that the Laplace transform of workloads in each queue is related to the solution M of a two-dimensional functional equation with given matrices Q1, Q2 and vector L, where each function h1 and h2 is algebraically defined on a rational cubic curve. The solution M is then represented by a series expansion involving the semi-group generated by the pair of functions h1 and h2. This series expansion together with analytic continuation properties of the solution M enables us to calculate the empty queue probabilities, the mean queue occupancies and to characterize the tail behavior of the workload distribution at each queue.Regarding the application to congestion control in telecommunication networks, our analysis shows that, without explicit marking, the SQF discipline yields a good performance in terms of mean waiting time for flows with a small contribution to the global load; this discipline may, however, have adverse effects for very large values of the waiting time, with tail asymptotics similar to that for the lowest priority flow of an HoL system.
A convenient synthesis of 1,3,6‐dioxazocine, 1,3,7‐dioxazonine, 1,3,8‐dioxazecine and 1,3‐dioxa‐6,10‐diazadodecane (1988)

Abstract A series of perhydro heterocycles of eight to ten ring members containing one nitrogen and two oxygen atoms has been prepared. These include four 1,3,6‐dioxazocines, and 1,3,7‐dioxazonine and one 1,3,8‐dioxazecine. A twelve‐membered ring containing two oxygen and two nitrogen atoms was also prepared. An X‐ray structure of one of the 1,3,6‐dioxazocines, 5 , was determined. This compound crystallized in the orthorhomic space group Pccn with a = 25.922(15)Å, b = 12.150(4)Å and C = 9.342(4)Å. Two of the 1,3,6‐dioxazocines have the benzylidine acetal structure which will hydrolyze to give benzaldehyde.
Nematic nanoparticle arrays with angle-selective emissivity in the near-IR (2015)

Metamaterial emitters based on electromagnetic band-gap (EBG) structures have previously been studied for controlling the angle and polarization of near-IR emissivity from a surface. Here, we investigate PEC backed nematic nanoparticle arrays that can be tailored to have custom angle-selective emissivity in the near-IR. Compared with structures requiring top-down fabrication methods, nanoparticle arrays have the potential to offer low-cost fabrication for large area coatings. A genetic algorithm is employed to synthesize a Pd nanorod array in a dielectric host medium that possesses low emissivity normal to the surface and high emissivity at a targeted oblique angle.
Endoskopisk sleeve-gastroplastik behandlingsalternativ vid obesitas (2021)

Obesity is a growing health problem and challenge to the health care systems in the western world. Available treatment is limited to lifestyle modifications, cognitive therapy, drugs and bariatric surgery. On one hand, lifestyle changes and pharmacological treatment have very limited long-term effects on obesity. On the other hand, bariatric surgery is effective to maintain long-term weigh reduction but is associated with complications and reaches less than 2 % of patients with indication for surgery. Thus, there is a gap in the management of patients with obesity, and endoscopic bariatric therapies might fill that gap by providing effective, repeatable and reversible alternatives for selected patients with obesity. This article introduces endoscopic methods to achieve weight loss with special focus on endoscopic sleeve gastroplasty (ESG). Data in the literature demonstrates that ESG is effective in reducing total and excessive body weight up to two years after the procedure as well as reducing obesity-related co-morbidity. The challenge is that ESG requires advanced endoscopic skills and is not yet available at many centres. A structured training program is needed to disseminate ESG and offer selected patients with obesity an alternative to bariatric surgery in Europe.
Optimization of an Immobilized-Cell Biocatalyst for Production of 4-Cyanopentanoic Acid (2002)

Optimization of microbial cell immobilization, catalyst specific activity, and volumetric productivity were required for scale-up of the nitrilase-catalyzed hydrolysis of 2-methylglutaronitrile to 4-cyanopentanoic acid, an intermediate in the preparation of 1,5-dimethyl-2-piperidone. As an alternative to the immobilization of Acidovorax facilis 72W cells in carrageenan, immobilization in alginate, followed by cross-linking with glutaraldehyde and polyethylenimine, produced a catalyst which was stable in reaction mixtures containing high concentrations of 4-cyanopentanoic acid ammonium salt. Immobilization in alginate produced catalysts with a higher nitrilase specific activity than was achieved in carrageenan, and volumetric productivity of 4-cyanopentanoic acid was increased from 19 to 49 g/L/h. Substituting alginate for carrageenan also eliminated one process step in the immobilization. A further increase in volumetric productivity to 79 g/L/h was achieved by using an immobilized Escherichia coli transformant which expresses A. facilis 72W nitrilase.
A Practical Asymmetric Synthesis of Enantiomerically Pure 3-Substituted Pyroglutamic Acids and Related Compounds (2000)

DBU-catalyzed Michael addition reactions were shown to occur at room temperature between a nickel(II) complex of the Schiff base of glycine 1 and (S)- or (R)-N-(E-enoyl)-4-phenyl-3-oxazolidin-2-ones (2, see scheme). This reaction, which has an almost completely stereoselective outcome, provides a practical and generalized approach to a family of glutamic/pyroglutamic acids. R=alkyl, aryl. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2000/z14093_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Data from IL13-Mediated Dectin-1 and Mannose Receptor Overexpression Promotes Macrophage Antitumor Activities through Recognition of Sialylated Tumor Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Macrophage-mediated cytotoxicity is controlled by surface receptor expression and activation. Despite the numerous studies documenting the role of macrophage C-type lectin receptors (CLR) in pathogen elimination, little is known about their contribution to antitumor responses. Here, we report that IL13 inhibits T-cell lymphoma and ovarian adenocarcinoma development in tumor-bearing mice through the conversion of tumor-supporting macrophages to cytotoxic effectors, characterized by a CLR signature composed of dectin-1 and mannose receptor (MR). We show that dectin-1 and MR are critical for the recognition of tumor cells through sialic acid–specific glycan structure on their surface and for the subsequent activation of macrophage tumoricidal response. Finally, we validated that IL13 antitumor effect mediated by dectin-1 and MR overexpression on macrophages can extend to various types of human tumors. Therefore, these results identify these CLRs as potential targets to promote macrophage antitumor response and represent an attractive approach to elicit tumor-associated macrophage tumoricidal properties.&lt;/p&gt;&lt;/div&gt;
Top-down fabrication of AlGaN/GaN nanoribbons (2011)

Lateral AlGaN/GaN nanoribbons (NRs) have been fabricated through a top-down technology on planar AlGaN/GaN samples grown on a silicon substrate. Electron-beam lithography and Cl2-based dry etching were used to define the NRs with widths in the 70–145 nm range. The electrical and structural properties of the AlGaN/GaN NRs have been measured and compared to standard planar structures fabricated on the same chip. External mechanical stress and adequate surface passivation have an important effect on the NR’s performance. A 50% improvement in the current density of SixNy passivated AlGaN/GaN NRs was obtained with respect to planar samples.
Bioinspired Programming of Resistive Memory Devices for Implementing Spiking Neural Networks (2017)

In this work, we will focus on the role that non-volatile resistive memory technologies (RRAM) can play for modeling key features of biological synapses. We will present an architecture and a reading/programming strategy to emulate both Short and Long Term Plasticity (STP, LTP) rules using non-volatile OxRAM arrays. A visual-pattern extraction application is discussed using spiking neural networks. We demonstrated that Long-Term plasticity allows the neural networks to learn patterns and the Short Term plasticity allows to improve accuracy (reduction of the false positive events generated by white noise in the input data) in presence of significant background noise in the input data.