gebhart/patrepeval huggingface dataset:
Inorganic polyphosphate as an energy source in tumorigenesis (2020)

Cancer cells have high demands for energy to maintain their exceedingly proliferative growth. However, the mechanism of energy expenditure in cancer is not well understood. We hypothesize that cancer cells might utilize energy-rich inorganic polyphosphate (polyP), as energetic reserve. PolyP is comprised of orthophosphates linked by phosphoanhydride bonds, as in ATP. Here, we show that polyP is highly abundant in several types of cancer cells, including brain tumor-initiating cells (BTICs), i.e., stem-like cells derived from a mouse brain tumor model that we have previously described. The polymer is avidly consumed during starvation of the BTICs. Depletion of ATP by inhibiting glycolysis and mitochondrial ATP-synthase (OXPHOS) further decreases the levels of polyP and alters morphology of the cells. Moreover, enzymatic hydrolysis of the polymer impairs the viability of cancer cells and significantly deprives ATP stores. These results suggest that polyP might be utilized as a source of phosphate energy in cancer. While the role of polyP as an energy source is established for bacteria, this finding is the first demonstration that polyP may play a similar role in the metabolism of cancer cells.
Improving communication skills through project-based learning (2007)

Communication skills are an essential part of engineering education in order to prepare students to be competent for engineering industry. This paper described a project-based learning activity that integrated communication through lab reports to improve students' higher level engineering skills and increase their communication skills. By guiding students to answer questions about observations and results using examples and a detailed grading rubric, we were able to see a great improvement in their technical writing. We also found that practicing the lab report format for the individual labs made the final lab report easier to compile, and the students were less overwhelmed and able to understand the big picture. Additionally, having a TA available for personal questions on grading comments helped those who needed more explanation or who had questions outside the scope of the rubric and examples.
Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning (2015)

Adaptive immunity in bacteria involves RNA-guided surveillance complexes that use CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target invasive nucleic acids for degradation. Whereas type I and type II CRISPR-Cas surveillance complexes target double-stranded DNA, type III complexes target single-stranded RNA. Near-atomic resolution cryo-electron microscopy reconstructions of native type III Cmr (CRISPR RAMP module) complexes in the absence and presence of target RNA reveal a helical protein arrangement that positions the crRNA for substrate binding. Thumblike β hairpins intercalate between segments of duplexed crRNA:target RNA to facilitate cleavage of the target at 6-nucleotide intervals. The Cmr complex is architecturally similar to the type I CRISPR-Cascade complex, suggesting divergent evolution of these immune systems from a common ancestor.
ChemInform Abstract: Ene Approach for Concurrent Control Over the Chiral Centres at C‐20 and C‐22 of Steroid Side Chains: A Highly Stereocontrolled Synthesis of (20S,22R)‐(erythro)‐22‐Hydroxy‐23,24‐acetylenic Steroid Side Chains. (1989)

Abstract The steroidal alkene (I) is coupled with the acetylenic aldehydes (IIa) ‐ (IIc), forming the erythro‐alcohols (III) as the main products.
Far-Field Radiation Properties of Impedance-Loaded Loop Antennas from RF to Optical Frequencies (2018)

Impedance loading of antennas has been of&#13;\ninterest for more than half a century due to its ability to fundamentally change an antenna’s operating characteristics. Variable reactive loading can be employed for configurability&#13;\nof the frequency response, polarization and far-field properties of an antenna. Closed-form expressions for the current and input impedance of a thin-wire loop antenna with loads in the periphery were derived in the RF and optical regimes in 1965&#13;\nand 2017, respectively. Meanwhile, closed-form far-field&#13;\nradiation properties of circular loop antennas in the RF and optical regimes were derived in 1996 and 2017. This paper&#13;\nextends this theory to provide closed-form analytical&#13;\nexpressions for the far-field radiation properties of impedance loaded&#13;\nloop antennas valid from the RF to the optical regimes.&#13;\nThe expressions are validated by comparison with commercial&#13;\nsimulation tools. In addition, a beam steering example is&#13;\npresented as a potential application of the theory.
Snapshots of cytochrome c folding (2005)

Dansyl-to-heme distance distributions [P(r)] during folding have been determined in five variants of Saccharomyces cerevisiae iso-1 ferricytochrome c (labeled at mutant Cys residues 4, 39, 50, 66, and 99) by analysis of fluorescence energy-transfer kinetics. Moment analysis of the P(r) distributions clearly indicates that cytochrome c refolding is not a simple two-state process. After 1 ms of folding, the polypeptide ensemble is not uniformly collapsed and there are site variations in the relative populations of collapsed structures. P(r) distributions reveal structural features of the multiple intermediate species and evolution of the polypeptide ensemble.
Disassembly of Nanospheres with a PEG Shell upon Adsorption onto PEGylated Substrates (2019)

Polymeric nanospheres have the ability to encapsulate drugs and are therefore widely used in drug delivery applications. Structural transformations that affect drug release from nanospheres are governed by the surrounding environment. To understand these effects, we investigated the adsorption behavior of three types of nanospheres onto model surfaces using quartz crystal microbalance with dissipation (QCM-D) and by atomic force microscopy (AFM). Substrates were prepared from polymers with different degrees of PEGylation (0, 1, and 15%). Nanospheres were prepared via self-assembly of block copolymers. Tyrosine-derived nanospheres are A-B-A triblock copolymers with methoxy poly(ethylene glycol) (PEG) as the A-blocks and an alternating copolymer of desaminotyrosyl-tyrosine octyl ester and suberic acid oligo(DTO-SA) as the B-block. On non-PEGylated substrates, these nanospheres assembled into a close-packed structure; on PEGylated substrates, the adsorbed nanospheres formed a continuous film, thinner than the size of the nanospheres suggesting unraveling of the PEG corona and disassembly of the nanospheres. Also, the adsorption was concentration-dependent, the final thickness being attained at exponentially longer times at lower concentrations. Such substrate- and concentration-dependent behavior was not observed with Pluronic F-127 and PEG-poly(caprolactone) (PCL) nanospheres. Since the essential difference among the three nanospheres is the composition of the core, we conclude that the core influences the adsorption characteristics of the nanospheres as a consequence of their disassembly upon adsorption. These results are expected to be useful in designing nanospheres for their efficient transport across vascular barriers and for delivering drugs to their targets.
Correlates of protection against symptomatic and asymptomatic SARS-CoV-2 infection (2021)

The global supply of COVID-19 vaccines remains limited. An understanding of the immune response that is predictive of protection could facilitate rapid licensure of new vaccines. Data from a randomized efficacy trial of the ChAdOx1 nCoV-19 (AZD1222) vaccine in the United Kingdom was analyzed to determine the antibody levels associated with protection against SARS-CoV-2. Binding and neutralizing antibodies at 28 days after the second dose were measured in infected and noninfected vaccine recipients. Higher levels of all immune markers were correlated with a reduced risk of symptomatic infection. A vaccine efficacy of 80% against symptomatic infection with majority Alpha (B.1.1.7) variant of SARS-CoV-2 was achieved with 264 (95% CI: 108, 806) binding antibody units (BAU)/ml: and 506 (95% CI: 135, not computed (beyond data range) (NC)) BAU/ml for anti-spike and anti-RBD antibodies, and 26 (95% CI: NC, NC) international unit (IU)/ml and 247 (95% CI: 101, NC) normalized neutralization titers (NF<sub>50</sub>) for pseudovirus and live-virus neutralization, respectively. Immune markers were not correlated with asymptomatic infections at the 5% significance level. These data can be used to bridge to new populations using validated assays, and allow extrapolation of efficacy estimates to new COVID-19 vaccines.
A study for the bias control of indium–tin–oxide films synthesized by cesium assisted radio frequency magnetron sputtering (2003)

In order to synthesize low resistive and high transparent indium–tin–oxide (ITO) films at room temperature, cesium assisted rf plasma sputtering was performed with additional substrate bias. We tried to control positive ions by negative substrate bias and negative ions by positive substrate bias. Plasma parameters, such as plasma density and electron temperature, were also controlled by the addition of cesium. The lowest specific resistivity of 4.4×10−4 Ω cm and high preferred oriented plane of (400) spectra from x-ray diffraction were obtained at the deposition condition of −100 V substrate bias. Our method proves to be very effective in low temperature growth of high quality ITO films.
On linear balancing sets (2009)

Let n be an even positive integer and F be the field GF(2). A word in F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> is called balanced if its Hamming weight is n/2. A subset C ¿ F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> is called a balancing set if for every word y ¿ F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> there is a word x ¿ C such that y + x is balanced. It is shown that most linear subspaces of F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> of dimension slightly larger than 3/2 log <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> n are balancing sets. An application of linear balancing sets is presented for designing efficient error-correcting coding schemes in which the codewords are balanced.
Human adenosine A3 receptor as selective target of new 2-aralkynyl-N6-methyl-MECA derivatives (2010)

Adenosine A3 receptor (AA3R) is involved in a variety of key physiological processes such as release of inflammatory mediators and inhibition of tumour necrosis factor-α production. Its activation is suggested to take part in immunosuppression and in the protection from brain and heart ischaemia. Recent studies suggest that AA3R agonists could be employed as therapeutic agents for the treatment of rheumatoid arthritis, dry eye disorders, asthma, as antiinflammatory agents, and in cancer therapy as cytostatic and chemoprotective compounds [1]. Hence, the design and synthesis of potent and selective AA3R agonists could help to provide tools for the further characterization of the physiopathological role of this receptor and for the development of new drugs. Our group has previously published the synthesis and biological evaluation of 2-(ar)alkynyl-N6-methoxyadenosine and corresponding 5′-N-methylcarboxamidoadenosine (MECA) derivatives, which demonstrated to possess different degrees of affinity and selectivity for the human AA3R [2]. In particular, some MECA derivatives bearing an aromatic ring directly linked to the 2-ethynyl group showed the best profile for this receptor subtype, with low nanomolar affinity and selectivity from 1,600- to 22,000-fold. As previously, we had demonstrated that also the introduction of a methyl group in N6-position of 2-phenylethynyladenosine favoured the interaction with the human AA3R [3], we designed and synthesised 2-aralkynyl-N6-methyl MECA analogues with the aim at improving AA3R affinity and selectivity. The synthesised compounds were evaluated in radioligand binding studies and in functional assays performed in CHO cells stably transfected with human ARs. Functional studies were carried out using a new Eu-GTP assay which exploits the unique fluorescence properties of lanthanide chelates and provides a powerful alternative to assays that utilise radioisotopes. Results proved that the new compounds possess sub-nanomolar AA3R affinity and remarkable selectivity versus the other AR subtypes. Functional studies demonstrated also that the new derivatives behave as full agonists resulting to be among the most potent and selective AA3R ligands reported so far [4]. A molecular modelling study was performed to analyse the particular pharmacological behaviour of the presented molecules for the four AR subtypes. In particular, we made an attempt to get a rationalisation of the high selectivities of the presented molecules for the human AA3R using the recently solved AA2AR crystal structure as template for homology modelling studies and by carrying out docking experiments at the four AR binding sites.
D104 UVP Measurement of Taylor-Couette Vortex Flow with Axial Flow (2010)

Recently, a new chemical extraction method using Taylor-Couette vortex flow (T-CVF) is expected, because the extraction agent's contact and dispersion efficiency can be improved by use of T-CVF. Using this method, the amount of solvent and extraction agent can be reduced compared with the conventional methods, and environmental degradation and cost reduction are expected. For realizing the practical usage of this method, it is important to investigate T-CVF characteristics with axial flow including the inlet and the outlet. Therefore, in this study, we investigated the effects of axial flow on T-CVF structure using an Ultrasonic Velocity Profile monitor (UVP) can measure flow dynamic characteristics. From the measurement result, in the case with axial flow, the lift up phenomenon of T-CVF was confirmed.
Prevalence of shiga toxin producing Escherichia coli, Salmonella enterica, and Listeria monocytogenes at public access watershed sites in a California Central Coast agricultural region (2014)

Produce contaminated with enteric pathogens is a major source of foodborne illness in the United States. Lakes, streams, rivers, and ponds were sampled with Moore swabs bi-monthly for over 2 years at 30 locations in the vicinity of a leafy green growing region on the Central California Coast and screened for Shiga toxin producing Escherichia coli (STEC), Salmonella enterica, and Listeria monocytogenes to evaluate the prevalence and persistence of pathogen subtypes. The prevalence of STEC from 1386 samples was 11%; 110 samples (8%) contained E. coli O157:H7 with the highest prevalence occurring close to cattle operations. Non-O157 STEC isolates represented major clinical O-types and 57% contained both shiga toxin types 1 and 2 and intimin. Multiple Locus Variable Number Tandem Repeat Analysis of STEC isolates indicated prevalent strains during the period of study. Notably, Salmonella was present at high levels throughout the sampling region with 65% prevalence in 1405 samples resulting in 996 isolates with slightly lower prevalence in late autumn. There were 2, 8, and 14 sites that were Salmonella-positive over 90, 80, and 70% of the time, respectively. The serotypes identified most often were 6,8:d:-, Typhimurium, and Give. Interestingly, analysis by Pulsed Field Gel Electrophoresis indicated persistence and transport of pulsotypes in the region over several years. In this original study of L. monocytogenes in the region prevalence was 43% of 1405 samples resulting in 635 individual isolates. Over 85% of the isolates belonged to serotype 4b with serotypes 1/2a, 1/2b, 3a, 4d with 4e representing the rest, and there were 12 and 2 sites that were positive over 50 and 80% of the time, respectively. Although surface water is not directly used for irrigation in this region, transport to the produce can occur by other means. This environmental survey assesses initial contamination levels toward an understanding of transport leading to produce recalls or outbreaks.
Trafficking (2007)

In this paper, we report, first of all, the discovery of a particular kind of emerging social practice involving the exchange of multimedia content on mobiles that we label 'trafficking'. Second, the iteration of a design solution to extend these practices to include the trafficking of broadcast TV content 'segments'. Third, the implications this had for basic assumptions in the interaction design afforded by the two primary OS's in the mobile handset domain. And, fourth, the legal and business inhibitors-enablers that affected not only this research but which are likely to affect all attempts to stretch the capacity of mobile devices and mobile interaction design to afford new ways of 'trafficking' multimedia content.
Comparison of Patient Acceptance of Polyurethane vs. Silicone Indwelling Ureteral Stents (1990)

The symptomatic effects and positional stability of four types of ureteral stents—double-pigtail polyurethane, double figure-four silicone, double-pigtail silicone, and double-J blended polyurethane—were compared in 66 patients. The most common complaint was urinary frequency (more than once every 3 hours), which occurred in 18 of the 20 patients with double-pigtail polyurethane stents, 16 of 19 with double figure-four silicone stents, 13 of 17 with double-pigtail silicone stents, and 6 of 8 with double-J blended polyurethane stents. Nocturia was somewhat less common (13,12,4, and 3, respectively). Urgency (17,14, 9, and 3) and occasional urge incontinence (3, 2, 0, and 0) were reported. Approximately half of the patients with the polyurethane stents vs. one fourth to one third of those with silicone stents had dysuria. There was no significant correlation between the length of stent in the bladder and the symptoms, although the stents with the shortest intravesical portions were associated with the fewest irritative symptoms and the stent with the largest renal pelvic segment (double figure four) carried the highest incidence of flank discomfort. Stent migration was dependent on tip configuration, with pigtail and figure-four stents remaining in place and double-J stents tending to migrate either proximally or distally. The authors prefer to use silicone double-pigtail stents and note that patients should be told to expect irritative symptoms.
Tumor‐derived transforming growth factor‐β1 and interleukin‐6 are chemotactic for lymphokine‐activated killer cells (1994)

Adherent lymphokine-activated killer (A-LAK) cells are purified IL-2 activated natural killer (NK) cells with potent anti-tumor cytotoxic activity. They have been used in the adoptive immunotherapy of metastatic cancers. However, it has been shown that intravenously transferred LAK cells have a poor homing capacity to tumor sites. For the present study, the effects of tumor-derived factors on the in vitro migratory capacity of A-LAK cells was investigated. In a micropore migration assay the conditioned medium from 3LL Lewis lung carcinoma cell cultures was found to exert a strong chemotactic, but not chemokinetic effect on A-LAK cells. This effect was partially inhibited by neutralizing antibodies against the cytokines TGF-beta 1 and IL-6. A combination of the 2 antibodies completely suppressed the chemotactic activity of tumor-cell-conditioned medium. Purified TGF-beta 1 and recombinant IL-6 were chemotactic for A-LAK cells. Biological activities of both cytokines were detectable in the tumor-cell-conditioned medium. The in vivo relevance of these findings, with respect to tissue infiltration of NK cells and LAK cells in inflammation or cancer, remains to be elucidated.
Proteus system architecture and organization (2002)

The Proteus architecture is a highly parallel MIMD, multiple instruction multiple data, machine optimized for large granularity tasks such as machine vision and image processing. The system can achieve 20 G-flops (80 G-flops peak). It accepts data via multiple serial links at a rate of up to 640 megabytes/second. The system employs hierarchical reconfigurable interconnection network with the highest level being a circuit switched enhanced hypercube serial interconnection network for internal data transfers. The system is designed to use 256 to 1.024 risc processors. The processors use 1 M byte external read/write allocating caches for reduced multiprocessor contention. The system detects, locates and replaces faulty subsystems using redundant hardware to facilitate fault tolerance. The parallelism is directly controllable trough an advanced software system for partitioning, scheduling and development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In Vitro Heavy-Atom Effect of Palladium(II) and Platinum(II) Complexes of Pyrrolidine-Fused Chlorin in Photodynamic Therapy (2009)

Introduction of a heavy atom into photosensitizers generally facilitates intersystem crossing and improves the quantum yield (Phi(Delta)) of singlet oxygen ((1)O(2)), which is a key species in photodynamic therapy (PDT). However, little information is available about the physiological importance of this heavy-atom effect. The aim of this study is to examine the heavy-atom effect in simple metallochlorins in vitro at the cellular level. 1,3-Dipolar cycloaddition of azomethine ylide to 5,10,15,20-tetrakis(pentafluorophenyl)porphyrinato palladium(II) and platinum(II) afforded metallochlorins 4b and 4c in yields of 17.1 and 12.9%, respectively. The Phi(Delta) values increased in the order of 4a (0.28) < 4b (0.89) < 4c (0.92) in C(6)D(6). The photocytotoxicity of 4a, 4b, and 4c was evaluated in HeLa cells at a light dose of 16 J x cm(-2) with lambda > 500 nm and increased in the order of 4a < 4b < 4c at the concentration of 0.5 microM. The photocytotoxicity of 4b and 4c was significantly inhibited by addition of sodium azide, but not D-mannitol, suggesting that (1)O(2) is the major species causing cell death. Our results clearly indicate that 4b and 4c act as efficient (1)O(2) generators due to the heavy-atom effect in a cellular microenvironment as well as in nonphysiological media.
Dependence of light outcoupling in organic light-emitting devices on ITO thickness and roughness (2015)

The efficiency of organic light-emitting devices (OLEDs) is shown to significantly depend on both the thickness and roughness of the indium tin oxide (ITO) anode. The effects of changing the ITO thickness from 45 nm to 130 nm are found to be able to vary the current efficiency by 40%. The underlying mechanism is studied and revealed to be related to microcavity effects. The transmittance of the ITO substrate changes significantly with the ITO thickness, resulting in variations in microcavity, and thus light outcoupling efficiency. On the other hand, the effects of increasing the ITO roughness (rms) from 3.3 nm to 8.5 nm are found to increase light scattering at the ITO/organic interface, thus improving extraction of light trapped in the organic/ITO wave-guided mode. In addition to the enhancement in current efficiency, the device fabricated on rough ITO shows similar driving voltage to that made on smooth ITO, indicating that charge balance is not altered by ITO roughness. Contrary to common belief in the community, the lifetime of the OLED is not affected when using rough ITO. The results demonstrate the significant efficiency benefits of using ITO with optimal thicknesses and higher roughness in OLEDs.