gebhart/patrepeval huggingface dataset:
RF-emission device safety testing using MRI (2013)

Radiofrequency (RF) emitting wireless devices such as mobile phones are required to undergo standardized safety testing prior to entering the consumer market. Strict regulations are imposed on the amount of RF energy these devices are allowed to emit to prevent excessive deposition of RF energy into the body. In this work, a novel safety evaluation test for wireless devices using magnetic resonance thermometry is proposed.
Surgical treatment options for ureteric stones (2017)

Technologic improvements in extracorporeal lithotripters, digital endoscopy, and holmium laser lithotripters allow most ureteric stones to be treated with a minimally invasive approach—specifically shock wave lithotripsy (SWL) or ureteroscopy (URS). This chapter will review the essential techniques, efficacy, and complications of SWL and URS in the management of ureteric calculi. The role of percutaneous anterograde ureteroscopy in management of selected ureteric stones will be reviewed as well. As ureteral stent placement can be used as an adjunct to surgical management of selected ureteral stones, indications for stent placement, and the impact of stent design and application on patient comfort will be discussed. In 2016, the European Association of Urology (EAU) , the American Urological Association (AUA) and the Endourological Society Nephrolithiasis Guidelines reviewed all relevant literature examining the efficacy and complications for management of ureteral stones. These and other evidence-based guidelines will also be reviewed.
Characterization of the ultrafast nonlinear response of new organic compounds (2020)

Here, we present our development of several experimental methods, which, when applied together, can provide a thorough characterization of the nonlinear refraction and absorption properties of materials. We focus mainly on time-resolved methods for studying both transient absorption and refraction that reveal molecular dynamics including excited-state absorption, singlet-triplet transfer, instantaneous electronic nonlinear refraction, and molecular reorientation. In particular, we will describe our recent studies of new materials including organometallic compounds and organic solvents such as Tetrachloroethylene (C<sub>2</sub>Cl<sub>4</sub>).
ChemInform Abstract: Preparation of 2‐Amino‐2′‐hydroxy‐1,1′‐binaphthyl and N‐Arylated 2‐Amino‐1,1′‐binaphthyl Derivatives via Palladium‐Catalyzed Amination. (1999)

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.
Transcription Factors as Molecular Targets: Molecular Mechanisms of Decoy ODN and their Design (2003)

Recent progress in cellular and molecular research has provided a new technique to inhibit target gene expression based on DNA technology such as antisense oligonucleotides (ODN) or decoy ODN. Especially, application of an antisense strategy to regulate the transcription of disease-related genes in vivo has important therapeutic potential to treat or cure a variety of diseases and abnormal physiological conditions. On the other hand, recently, a successful ODN-based approach termed decoy ODN has used synthetic ODN containing an enhancer element that can penetrate cells, to bind to sequence-specific DNA-binding proteins and interfere with transcription in vitro and in vivo. Transfection of cis-element double-stranded decoy ODN has been reported as a new powerful tool in a new class of anti-gene strategies to treat various diseases as gene therapy or as a research tool to examine the molecular mechanisms of expression of a specific gene. Transfection of double-stranded ODN corresponding to the cis-sequence will result in attenuation of the authentic cis-trans interaction, leading to removal of trans-factors from the endogenous cis-elements with subsequent modulation of gene expression. To date, we have chosen several target transcription factors such as NFkappaB (nuclear factor-kappaB) and E2F to prevent the progression of diseases, and negative regulatory element (NRE) for the renin gene and angiotensinogen gene-activating element (AGE) for the angiotensinogen gene to examine the molecular mechanisms of gene expression. In this section, we introduce the principles of the decoy strategy and how to design decoy ODN.
Genome-wide analysis of allelic imbalance in prostate cancer using the Affymetrix 50K SNP mapping array (2007)

Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous cancer in male subjects in Western countries. The widespread use of prostate-specific antigen (PSA) has increased the detection of this cancer form in earlier stages. Moreover, it has increased the need for new diagnostic procedures to be developed for patient stratification based on risk of progression. We analysed laser-microdissected prostate tumour tissue from 43 patients with histologically verified PCa, using the new high-resolution Affymetrix Mapping 50K single-nucleotide polymorphism array. The results showed six major loss of heterozygosity regions at chromosomes 6q14-16, 8p23-11, 10q23, 13q13-21 and 16q21-24 and a novel region at chromosome 21q22.2, all of which reveal concomitant copy number loss. Tumour development was further characterised by numerous novel genomic regions almost exclusively showing copy number loss. However, tumour progression towards a metastatic stage, as well as poor differentiation, was identified by specific patterns of copy number gains of genomic regions located at chromosomes 8q, 1q, 3q and 7q. Androgen ablation therapy was further characterised by copy gain at chromosomes 2p and 10q. In conclusion, patterns of allelic imbalance were discovered in PCa, consisting allelic loss as an early event in tumour development, and distinct patterns of allelic amplification related to tumour progression and poor differentiation.
Energetic considerations of ciliary beating and the advantage of metachronal coordination (1999)

The internal mechanism of cilia is among the most ancient biological motors on an evolutionary scale. It produces beat patterns that consist of two phases: during the effective stroke, the cilium moves approximately as a straight rod, and during the recovery stroke, it rolls close to the surface in a tangential motion. It is commonly agreed that these two phases are designed for efficient functioning: the effective stroke encounters strong viscous resistance and generates thrust, whereas the recovery stroke returns the cilium to starting position while avoiding viscous resistance. Metachronal coordination between cilia, which occurs when many of them beat close to each other, is believed to be an autonomous result of the hydrodynamical interactions in the system. Qualitatively, metachronism is perceived as a way for reducing the energy expenditure required for beating. This paper presents a quantitative study of the energy expenditure of beating cilia, and of the energetic significance of metachronism. We develop a method for computing the work done by model cilia that beat in a viscous fluid. We demonstrate that for a single cilium, beating in water, the mechanical work done during the effective stroke is approximately five times the amount of work done during the recovery stroke. Investigation of multicilia configurations shows that having neighboring cilia beat metachronally is energetically advantageous and perhaps even crucial for multiciliary functioning. Finally, the model is used to approximate the number of dynein arm attachments that are likely to occur during the effective and recovery strokes of a beat cycle, predicting that almost all of the available dynein arms should participate in generating the motion.
N,N-Acetals as N-Acyliminium Ion Precursors: Synthesis and Absolute Stereochemistry of Epiquinamide (2008)

A stereoselective synthesis of (+)-epiquinamide is presented in combination with determination of the absolute configuration of the natural product. Key steps in the sequence involved chemoenzymatic formation of an enantiomerically pure cyanohydrin, reductive cyclization to the corresponding cyclic N,N-acetal, and subsequent conversion into a suitable N-acyliminium ion precursor to enable construction of the second ring.
Magnetite ferrofluids stabilized by sulfonato-calixarenes (2007)

Magnetite (Fe304) nanoparticles stabilised by sulfonatocalixarene macrocycles are readily accessible by a rapid in situ co-precipitation, and exhibit ferro-fluidic and superparamagnetic behaviour.
Author response: NaLi-H1: A universal synthetic library of humanized nanobodies providing highly functional antibodies and intrabodies (2016)

Antibodies are proteins that form part of an animal’s immune system and can identify and help eradicate infections. These proteins are also needed at many stages in biological research and represent one of the most promising tools in medical applications, from diagnostics to treatments. Traditionally, antibodies have been collected from animals that had been previously injected with a target molecule that the antibodies must recognize. An alternative strategy that uses bacteria and bacteria-infecting viruses instead of animals was developed several decades ago and allows researchers to obtain antibodies more quickly. However, the majority of the scientific community view these “in vitro selected antibodies” as inferior to those produced via the more traditional approach. Moutel, Bery et al. set out to challenge this widespread opinion, using a smaller kind of antibody known as nanobodies. The proteins were originally found in animals like llamas and camels and are now widely used in biological research. One particularly stable nanobody was chosen to form the backbone of the in vitro antibodies, and the DNA that encodes this nanobody was altered to make the protein more similar to human antibodies. Moutel, Bery et al. then changed the DNA sequence further to make billions of different versions of the nanobody, each one slightly different from the next in the region that binds to the target molecules. Transferring this DNA into bacteria resulted in a library (called the NaLi-H1 library) of bacterial clones that produce the nanobodies displayed at the surface of bacteria-infecting viruses. Moutel, Bery et al. then screened this library against various target molecules, including some from tumor cells, and showed that the fully in vitro selected antibodies worked just as well as natural antibodies in a number of assays. The in vitro antibodies could even be used to track, or inactivate, proteins within living cells. The NaLi-H1 library will help other researchers obtain new antibodies that bind strongly to their targets. The approaches developed to create the library could also see more people decide to create their own synthetic libraries, which would accelerate the identification of new antibodies in a way that is cheaper and requires fewer experiments to be done using animals. These in vitro selected antibodies could help to advance both fundamental and medical research.
ChemInform Abstract: Total Syntheses of (‐)‐Macrolactin A, (+)‐Macrolactin E, and (‐)‐Macrolactinic Acid: An Exercise in Stille Cross‐Coupling Chemistry. (1998)

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.
Ga–Pt supported catalytically active liquid metal solutions (SCALMS) prepared by ultrasonication – influence of synthesis conditions onn-heptane dehydrogenation performance (2023)

Supported catalytically active liquid metal solution (SCALMS) materials represent a recently developed class of heterogeneous catalysts, where the catalytic reaction takes place at the highly dynamic interface of supported liquid alloys. Ga nuggets were dispersed into nano-droplets in propan-2-ol using ultrasonication followed by the addition of Pt in a galvanic displacement reaction - either directly into the Ga/propan-2-ol dispersion (<i>in situ</i>) or consecutively onto the supported Ga droplets (<i>ex situ</i>). The <i>in situ</i> galvanic displacement reaction between Ga and Pt was studied in three different reaction media, namely propan-2-ol, water, and 20 vol% water containing propan-2-ol. TEM investigations reveal that the Ga-Pt reaction in propan-2-ol resulted in the formation of Pt aggregates on top of Ga nano-droplets. In the water/propan-2-ol mixture, the desired incorporation of Pt into the Ga matrix was achieved. The <i>ex situ</i> prepared Ga-Pt SCALMS were tested in <i>n</i>-heptane dehydrogenation. Ga-Pt SCALMS synthesized in pure alcoholic solution showed equal dehydrogenation and cracking activity. Ga-Pt SCALMS prepared in pure water, in contrast, showed mainly cracking activity due to oxidation of Ga droplets. The Ga-Pt SCALMS material prepared in water/propan-2-ol resulted in high activity, <i>n</i>-heptene selectivity of 63%, and only low cracking tendency. This can be attributed to the supported liquid Ga-Pt alloy where Pt atoms are present in the liquid Ga matrix at the highly dynamic catalytic interface.
Identifying, Characterizing, and Engineering a Phenolic Acid-Responsive Transcriptional Factor from Bacillus amyloliquefaciens (2023)

Transcriptional factors-based biosensors are commonly used in metabolic engineering for inducible control of gene expression and related applications such as high-throughput screening and dynamic pathway regulations. Mining for novel transcriptional factors is essential for expanding the usability of these toolsets. Here, we report the identification, characterization, and engineering of a phenolic acid responsive regulator PadR from <i>Bacillus amyloliquefaciens</i> (BaPadR). This BaPadR-based biosensor system showed a unique ligand preference and exhibited a high output strength comparable to that of commonly used inducible expression systems. Through engineering the DNA binding region of BaPadR, we further enhanced the dynamic range of the biosensor system. The DNA sequences that are responsible for BaPadR recognition were located by promoter truncation and hybrid promoter building. To further explore the tunability of the sensor system, base substitutions were performed on the BaPadR binding region of the phenolic acid decarboxylase promoter (P<sub>padC</sub>) and the hybrid promoter. This novel biosensor system can serve as a valuable tool in future synthetic biology applications.
Advances in the Study of Chronic Active Epstein-Barr Virus Infection: Clinical Features Under the 2016 WHO Classification and Mechanisms of Development (2019)

Chronic active Epstein-Barr virus infection (CAEBV) is one of the Epstein-Barr virus (EBV)-positive T- or NK-lymphoproliferative diseases. It is considered rare and geographically limited to Japan and East Asia. However, CAEBV is drawing international attention, and the number of case reported worldwide is increasing, after its classification in the EBV-positive T- or NK-cell neoplasms, in the 2016 WHO classification. In this article, I review current advances in the study of CAEBV under the new definition and show future directions. In CAEBV, EBV-infected T or NK cells clonally proliferate and infiltrate multiple organs, leading to their failure. These characteristics define CAEBV as a lymphoid neoplasm. However, the main symptom of CAEBV is inflammation. Recently, the mechanisms underlying the development of CAEBV have gradually become clearer. EBV infection of T or NK cells can occur during the acute phase of primary infection with a high EBV load in the peripheral blood. In addition, it was reported that cytotoxic T cells decreased in numbers or showed dysfunction in CAEBV. These findings suggest that undetermined immunosuppressive disorders may underlie persistent infection of T or NK cells. Furthermore, EBV itself contributes to the survival of host cells. <i>In vitro</i> EBV infection of T cells induced intercellular survival-promoting pathways. Constitutive activation of NF-kB and STAT3 was observed in EBV-positive T or NK cells in CAEBV, promoting not only cell survival but also CAEBV development. During the disease course, CAEBV can lead to two lethal conditions: hemophagocytic lymphohistiocytosis and chemotherapy-resistant lymphoma. It is necessary to start treatment before these conditions develop. At present, the only effective treatment strategy for eradicating EBV-infected T or NK cells is allogeneic stem cell transplantation (allo-HSCT). However, patients with an active disease, in which the condition is accompanied by fever, liver dysfunction, progressive skin lesions, vasculitis, or uveitis, had worse outcomes after allo-HSCT, than patients with an inactive disease had. Unfortunately, current chemotherapies are insufficient to improve the activity of CAEBV. Based on the molecular mechanisms for the development of the disease, the NF-kB, or JAK/STAT mediating pathways are attractive candidate targets for new treatments.
Lipases Immobilization for Effective Synthesis of Biodiesel Starting from Coffee Waste Oils (2013)

Immobilized lipases were applied to the enzymatic conversion of oils from spent coffee ground into biodiesel. Two lipases were selected for the study because of their conformational behavior analysed by Molecular Dynamics (MD) simulations taking into account that immobilization conditions affect conformational behavior of the lipases and ultimately, their efficiency upon immobilization. The enzymatic synthesis of biodiesel was initially carried out on a model substrate (triolein) in order to select the most promising immobilized biocatalysts. The results indicate that oils can be converted quantitatively within hours. The role of the nature of the immobilization support emerged as a key factor affecting reaction rate, most probably because of partition and mass transfer barriers occurring with hydrophilic solid supports. Finally, oil from spent coffee ground was transformed into biodiesel with yields ranging from 55% to 72%. The synthesis is of particular interest in the perspective of developing sustainable processes for the production of bio-fuels from food wastes and renewable materials. The enzymatic synthesis of biodiesel is carried out under mild conditions, with stoichiometric amounts of substrates (oil and methanol) and the removal of free fatty acids is not required.
Spectral tuning > 25 nm from GaN nanowire lasers using hydrostatic pressure. (2014)

Abstract not provided.
Monitoring PD-L1 expression on circulating tumor cells (CTCs) in patients with NSCLC treated with PD1 inhibitors. (2018)

147 Background: Inhibitors of the immune checkpoint PD-1/PD-L1 have become a standard of care in NSCLC. Patient selection, currently based on PD-L1 expression in tumor tissue, is limited by its temporal and spatial heterogeneity. We hypothesized that monitoring PD-L1 staining of circulating tumor cells (CTCs) could represent a valuable non-invasive biomarker. Methods: Up to 3 blood samples were prospectively collected from patients with advanced NSCLC: i) pretreatment (nivolumab), ii) first follow-up, iii) progression. CTCs were isolated from 10 mL of blood using cell size-based technology (ISET, Rarecells). PD-L1 expression was assessed by immunofluorescence on CTCs and immunohistochemistry on tissue. Results: 162 samples from 96 patients were collected. PD-L1 expression could be assessed pretreatment on tissue and CTCs in 72% and 93%, respectively; and was ≥1% in 37% and 83%; ≥5% in 35% and 79%, respectively. No correlation between tissue and CTCs PD-L1 expressions was observed (Spearman coefficient correlation = 0.04, p = 0.77). At baseline, each 10/7.5 ml increase in CTCs count was associated with increased risk of death and progression (HR[95%CI]: 1.06 [1.005;1.117] p = 0.03 for OS and HR[95%CI]: 1.05 [1.01;1.10] p = 0.02 for PFS). The presence of PD-L1(+)CTC (≥1%) had no prognostic impact (OS: p = 0.89 and PFS: p = 0.55), but pretreatment PD-L1(+)CTCs were more frequent in the “non-responders” group (PFS &lt; 6 months) (p = 0.04). Median CTC count was 30 (n = 96), 68.3 (n = 44) and 50.3 (n = 22) pretreatment, at the first follow-up and at progression, respectively. The changes in CTC count at the first follow-up had no impact on PFS (p = 0.45) or OS (p = 0.68). 96% of patients had PD-L1(+)CTCs at progression. Further analyses are ongoing to assess the prognostic value of the persistence of CTCs and PD-L1(+)CTCs at the first follow up and at progression. Conclusions: Analysis of PD-L1 expression on CTCs is highly feasible. PD-L1 expressions on tissue and CTCs are discordant, CTCs being more likely positives, suggesting false negatives occurring in small biopsies. Further analyses of the kinetics of this biomarker throughout ICI treatment, along with other circulating biomarkers, are ongoing. Clinical trial information: NCT02827344.
A synthesizable datapath-oriented embedded FPGA fabric (2007)

We present an architecture for a synthesizable datapath-oriented Field Programmable Gate Array (FPGA) core which can be used to provide post-fabrication flexibility to a System-on-Chip (SoC). Our architecture is optimized for bus-based operations that are common in signal processing and computation intensive applications. It employs a directional routing architecture, which allows it to be synthesized using standard ASIC design tools and flows. We also describe a proof-of-concept layout of our core. It is shown that the proposed architecture is significantly more area efficient than the best previously reported synthesizable programmable logic core.
ChemInform Abstract: Liquid Crystals with Restricted Molecular Topologies: Supermolecules and Supramolecular Assemblies (1998)

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.
Nanocomposites: The Role of Interfaces in Polyethylene/Metal‐Oxide Nanocomposites for Ultrahigh‐Voltage Insulating Materials (Adv. Mater. 4/2018) (2018)

In article number 1703624, Amir Masoud Pourrahimi, Mikael S. Hedenqvist, and Richard T. Olsson discuss the role of interfaces in polyethylene/metal oxide nanocomposites, which, in future, may be used in insulating materials for highvoltage transmission lines. The most recent and cutting-edge developments in both materials and experimental characterizations from the molecular scale to the macroscale are considered. Image design: Amir Pourrahimi.
Phasing Locking of High Power Fiber Amplifier Arrays (2010)

We report locking the phase of a five element 725-W amplifier array and in addition we report phase locking off the backscatter from a remote object. The rms phase error was measured to be λ/60.
Emission Characteristics Based on Nanocolumn Photonic Crystal Effect of Orderly Arrayed InGaN/GaN Nanocolumns (2014)

In this paper, we discuss the emission characteristics based on the nanocolumn photonic crystal effect. The GaN nanocolumn arrays, at the top region of which InGaN/GaN MQWs were integrated, were optically pumped resulting in lasing oscillation, as shown in Fig. 2. Clear thresholds were observed in the light intensity vs. excitation density characteristics (see Fig.2 (c)). The lasing wavelength changed from 492.3 to 501.1 nm with increasing the column diameter (D) from 183 to 205 nm at the lattice constant (L) of 245 nm, as the result of the photonic band edge shift. Figure 3 shows the photonic band diagram of a nanocolumn system; note that the experimental lasing wavelength corresponded to the photonic band edge at Γ11. The normalized band edge wavelength L/λ is expressed as a function of the structural parameter of D/L 13) as shown in Fig. 4 (a), where the experimental lasing wavelength are plotted by circles.