gebhart/patrepeval huggingface dataset:
Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component (2015)

The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.
Categorical performance characteristics of method ISO 7899-2 and indicator value of intestinal enterococci for bathing water quality monitoring (2018)

Intestinal enterococci indicate the fecal contamination of bathing waters. This study defines the performance characteristics of the reference method ISO 7899-2:2000 with water samples collected from inland and coastal bathing areas in Finland. From a total of 341 bacterial isolates grown on Slanetz and Bartley medium, 63.6% were confirmed as intestinal enterococci on bile aesculin agar. The partial 16S rRNA gene sequences showed that Enterococcus faecium and Enterococcus faecalis clades accounted for 93.1% of the confirmed isolates. The range of the false positive and false negative rate of the ISO 7899-2 was 0.0-18.5% and 5.6-57.1%, respectively, being affected by the presumptive colony count on the membrane. The analysis of multiple sample volumes is proposed to reach 10-100 colonies per membrane when 47 mm diameter membranes are used to prevent overestimation of low counts and underestimation of the high counts.
Total Ankle Arthroplasty Survival and Risk Factors for Failure (2019)

Level III, retrospective cohort study using prospectively collected data.
Coresets for Vector Summarization with Applications to Network Graphs (2017)

We provide a deterministic data summarization algorithm that approximates the mean $\bar{p}=\frac{1}{n}\sum_{p\in P} p$ of a set $P$ of $n$ vectors in $\REAL^d$, by a weighted mean $\tilde{p}$ of a \emph{subset} of $O(1/\eps)$ vectors, i.e., independent of both $n$ and $d$. We prove that the squared Euclidean distance between $\bar{p}$ and $\tilde{p}$ is at most $\eps$ multiplied by the variance of $P$. We use this algorithm to maintain an approximated sum of vectors from an unbounded stream, using memory that is independent of $d$, and logarithmic in the $n$ vectors seen so far. Our main application is to extract and represent in a compact way friend groups and activity summaries of users from underlying data exchanges. For example, in the case of mobile networks, we can use GPS traces to identify meetings, in the case of social networks, we can use information exchange to identify friend groups. Our algorithm provably identifies the {\it Heavy Hitter} entries in a proximity (adjacency) matrix. The Heavy Hitters can be used to extract and represent in a compact way friend groups and activity summaries of users from underlying data exchanges. We evaluate the algorithm on several large data sets.
Study on Wind Consumption in Regenerative Electric Heating Considering Thermal Comfort of Users (2019)

In order to solve the problem of inadequate wind power consumption in northern China during winter heating period, this paper considers the thermal comfort of users, and establishes a multi-objective function based on the minimum coal consumption of the system and the optimum heating comfort of users. Then, based on the constraints of system operation, unit operation, thermal comfort of users and power balance, an optimal model of regenerative electric heating considering user thermal comfort is established. The results show that the wind power consumption considering the thermal comfort of users is stronger than that without considering the thermal comfort of users. The abandoned wind power decreases by 35.29%, due to the power of thermal power units decreases, the cost of coal consumption decreases by 2.75%. The economic effect is remarkable.
Preparation of high porosity xerogels by chemical surface modification. (2023)

This invention provides an extremely porous xerogel dried at vacuum-to-below supercritical pressures but having the properties of aerogels which are typically dried at supercritical pressures. This is done by reacting the internal pore surface of the wet gel with organic substances in order to change the contact angle of the fluid meniscus in the pores during drying. Shrinkage of the gel (which is normally prevented by use of high autoclave pressures, such that the pore fluid is at temperature and pressure above its critical values) is avoided even at vacuum or ambient pressures.
Assessment of Turbulence Models for Predicting Coaxial Jets relevant to Turbofan Engines (2012)

A numerical study is carried out for analyzing the compressible, non-isothermal flow associated with a separate-flow exhaust nozzle system with conic plug. Within the steady-state Reynolds Averaged Navier-Stokes (RANS) framework, several two-equation turbulence models among which the standard k-epsilon, the standard k-omega, and two different Shear Stress Transport (SST) k-omega formulations are evaluated. In addition, Large Eddy Simulation (LES) approach is employed for capturing the flow dynamics associated with the coaxial jet. The computational results are compared against available experimental Particle Imaging Velocimetry (PIV) flow data, in terms of time-averaged axial velocity and turbulent kinetic energy levels. As compared with the experimental data the standard k-omega turbulence model performed worst, overpredicting the length of the potential core region of the jet. The same model predicted significantly lower turbulent kinetic energy levels in the shear layer between the secondary (fan) stream and the ambient air, corresponding to a slower mixing rate. No significant differences were observed between the data obtained with the two different SST k-omega turbulence models with the mention that the Transition-SST k-omega solves two additional transport equations as compared with the classical k-omega SST model. A fair agreement was found between the experimental PIV data and the predictions obtained with the standard k-epsilon and k-omega SST turbulence models.
Low-Temperature, Mercury-Mediated Synthesis of Aluminum Intermetallics (2000)

The preparative-scale synthesis of intermetallic phases in the Al−Au and Al−Pd systems can be achieved at the relatively low temperature of boiling Hg (∼350 °C at 1 atm). In particular, Al2Au, AlAu, AlAu2, Al3Pd2, and AlPd can be made in high yield either as single products or as multiple products by dissolution of the elements in liquid Hg, followed by distillation of the solvent. The reaction products were determined by X-ray diffraction and electron microprobe analysis. A systematic study reveals that the products of these reactions depend strongly on initial mole ratios. A thermodynamic phase stability analysis was conducted using estimated free energies for the intermetallic phases. From these calculations and from the observed products and their sequence of formation, some of the reactions are shown to be kinetically controlled. Direct synthesis reactions tend to be favored for concentration ratios that correspond to intermetallic phases that exhibit a coexistence tie line with the Hg solution.
Coupled Macroscopic Modelling of Electric Vehicle Traffic and Energy Flows for Electromobility Control (2022)

The simultaneous proliferation of electric vehicles and intermittent renewable energy sources promises to expedite decarbonization of two sectors with highest emissions. However, both these developments threaten to endanger power system stability, which may hinder their widespread adoption. To tackle these challenges, there is a need for joint modelling of electric vehicle traffic flows, together with their battery dynamics. We propose a macroscopic electromobility model, augmenting the LWR model, describing the traffic dynamics, with an inhomogeneous advection equation, describing the evolution of vehicles’ State of Charge (SoC). The Riemann problem for the joint model is solved for the case of triangular fundamental diagram, and the solutions are used to formulate a Godunov-like scheme for model discretization. Additionally, we propose an advection-based charging station model, discretize it, and link it with the rest of the traffic and SoC model. We demonstrate the capabilities and use of the full coupled model by proposing a pedagogic example where a simple control law regulates the average SoC of all vehicles on a ring road by controlling the traffic flow entering the charging station.
In Vitro Model of Mycobacterial Growth Arrest Using Nitric Oxide with Limited Air (2008)

An in vitro model of mycobacterial growth arrest was developed using Mycobacterium bovis BCG. When an exponentially growing culture was transferred to an evacuated tube, growth continued; treatment with a source of nitric oxide (diethylenetriamine-nitric oxide adduct [DETA-NO] at 50 microM) halted growth immediately, and aeration restored growth. When the period of growth arrest exceeded 4 h, a time lag occurred before aeration could restore growth. The lag time was maximal (24 h) after 16 h of growth arrest. These time lags indicated that one transition period was required for cells to achieve full arrest of growth and another for them to recover fully from growth arrest. DETA-NO-induced growth arrest failed to protect from the lethal effects of anaerobic shock, which caused rapid lysis of both growing and growth-arrested cells. While growth arrest had little effect on the lethal action of rifampin, it eliminated isoniazid lethality. Growth arrest reduced but did not eliminate fluoroquinolone lethality. Two fluoroquinolones, moxifloxacin and gatifloxacin, were equally lethal to exponentially growing cells, but moxifloxacin was more active during growth arrest. This difference is attributed to the fluoroquinolone C-7 ring structure, the only difference between the compounds. Collectively these data characterize a new system for halting mycobacterial growth that may be useful for evaluating new antituberculosis agents.
Size-Dependent Knockdown Potential of siRNA-Loaded Cationic Nanohydrogel Particles (2014)

To overcome the poor pharmacokinetic conditions of short double-stranded RNA molecules in RNA interference therapies, cationic nanohydrogel particles can be considered as alternative safe and stable carriers for oligonucleotide delivery. For understanding key parameters during this process, two different types of well-defined cationic nanohydrogel particles were synthesized, which provided nearly identical physicochemical properties with regards to their material composition and resulting siRNA loading characteristics. Yet, according to the manufacturing process using amphiphilic reactive ester block copolymers of pentafluorophenyl methacrylate (PFPMA) and tri(ethylene glycol)methyl ether methacrylate (MEO3MA) with similar compositions but different molecular weights, the resulting nanohydrogel particles differed in size after cross-linking with spermine (average diameter 40 vs 100 nm). This affected their knockdown potential significantly. Only the 40 nm sized cationic nanogel particles were able to generate moderate gene knockdown levels, which lasted, however, up to 3 days. Interestingly, primary cell uptake and colocalization studies with lysosomal compartments revealed that only these small sized nanogels were able to avoid acidic compartments of endolysosomal uptake pathways, which may contribute to their knockdown ability exclusively. To that respect, this size-dependent intracellular distribution behavior may be considered as an essential key parameter for tuning the knockdown potential of siRNA nanohydrogel particles, which may further contribute to the development of advanced siRNA carrier systems with improved knockdown potential.
Direct Adaptive NN Control of Nonlinear Systems in Strict-Feedback Form Using Dynamic Surface Control (2007)

In this paper, direct adaptive neural control is investigated for a class of strict-feedback nonlinear systems with both unknown system functions and virtual control gain functions. The explosion of complexity in traditional backstepping design is avoided by utilizing dynamic surface control (DSC) and introducing integral-type Lyapunov function. It is proved that the proposed design method is able to guarantee semi-global uniform ultimate boundedness of all signals in the closed-loop system, with arbitrary small tracking error by appropriately choosing design constants.
Study on Flexural Behavior of Steel-Concrete Composite Members (1992)

There is a method called “generalized superpose flexural strength method” which is widely used to calculate ultimate flexural bearing capacity of Steel Reinforced Concrete Structures in Japan. This method is easier and more practical than a method calculate ultimate strength of structural members based on equilibrium of stresses and compatibility of strains. On the other hand, this method overestimates flexural bearing capacity in a certain case that concrete reaches ultimate strain yielding of steels. The author proposes a modified method which solves problem of overestimation. The modified method evaluates the yielding condition of steels properly in and case, and estimates flexural bending capacity and deformation of Steel-Concrete composite members preisely.
Power system dynamic model reduction by means of an iterative SVD-Krylov model reduction method (2016)

This paper introduces the application of an iterative SVD-Krylov algorithm for dynamic model reduction of power systems. The method is a two-sided projection combining advantages of the singular value decomposition based and the Krylov-based model reduction methods. The significance and accuracy of the method are numerically investigated. The full linearized dynamic model of the original nonlinear power system is determined and used as the input of dynamic reduction technique. The capability of this technique in keeping dominant oscillation modes after reduction is utilized as the comparison criteria. Physical relationship between the reduced and the original system is also discussed by mean of coherency in power systems.
212 Adoptively transferred Th17 cells cooperate with host B cells to mediate robust immunity to tumors (2022)

<h3>Background</h3> Adoptive T cell transfer therapy mediates potent immunity in some patients with aggressive malignancies, but many individuals do not respond, or may relapse. One reason for therapy failure is due to lack of T cell persistence. To overcome this problem, we aimed to generate a cell product that will lead to long term antitumor immunity in aggressive models. Accordingly, our team reported that a subset of CD4<sup>+</sup> T cells termed Th17 cells, persist long term and can eradicate solid tumors when infused into mice. However, how Th17 cells mediate tumor immunity is unclear. <h3>Methods</h3> To model Th17 cell adoptive T cell transfer therapy, we use a transgenic mouse model in which CD4<sup>+</sup> cells express a T cell receptor (TCR) that recognizes tyrosinase-related protein 1 (TRP-1) expressed on melanoma, and polarized naïve CD4<sup>+</sup> T cell to Th17 cells. These cells are infused into mice bearing B16F10 melanoma tumors that received non-myeloablative lymphodepleting total body irradiation. Tumor growth is measured over time or tumors, spleen, and lymph nodes are analyzed 12 days post cell transfer. <h3>Results</h3> To understand how Th17 cells elicit robust antitumor activity, we performed an unbiased analysis of RNA transcripts on tumor-draining lymph nodes of mice treated with Th17 cells. Surprisingly, we found that mice infused with anti-tumor Th17 cells have increased transcripts associated with B cells, and factors that trigger B cell maturation, antibody-secretion, and enhanced antigen presentation. Furthermore, host B cells, but not CD8<sup>+</sup> T cells, were surprisingly critical in sustaining long-term immunity, as their depletion significantly impaired survival. B cells enhance Th17 cell persistence and promote their differentiation into IFN-g producers and away from regulatory IL-10 production. Th17 cells induce B cell activation and maturation in an IL-21-dependent manner, causing the production of class switched antibodies which can alone partially protect against tumor challenge. Finally, we found that IL-21, ICOS, and IFN-g are required for this antitumor response as inhibition of any of these three abrogates durable tumor immunity. <h3>Conclusions</h3> Altogether, this suggests a cooperative relationship between transferred Th17 cells and host B cells in mediating long term tumor immunity. Our novel findings highlight Th17 cell therapy as a way to harness both T and B cell responses against cancer. Ongoing experiments will further determine the mechanism of how B cells collaborate with Th17 cells to mediate superior antitumor activity. <h3>Acknowledgements</h3> We would like to acknowledge Emory University, The Winship Cancer Institute, and the Pediatrics/Winship Flow Cytometry Core. <h3>Ethics Approval</h3> All animal procedures were approved by the Institutional Animal Care and Use Committee of Emory University, protocol number 201900225.
10 kHz inductively coupled power transfer - concept and control (1994)

Electric vehicles are used throughout the materials handling industry because they are low cost, reliable, inoffensive, and simple to control compared to alternative forms of motive power. But conventional methods of power transfer to the vehicle such as electrified tracks and batteries have remained less than ideal; that is until the recent development of a novel inductively coupled power transmission (IPT) system that is clean and spark-free, is robust to dust and water, and has very low maintenance. Load power in an IPT system is sourced at 10 kHz from tuned pick-up coils mounted adjacent to, but not touching, a sealed track conductor driven by a resonant power electronic converter. Power transfer of several kilowatts is possible from a single pick-up coil, and multiple pick-ups can be powered from the same track. The paper describes the IPT concept and presents practical control solutions to some important problems.
Low-dose fractionated radiotherapy and concomitant chemotherapy in glioblastoma multiforme with poor prognosis: a feasibility study (2011)

We explored the feasibility of concurrent palliative chemotherapy and low-dose fractionated radiotherapy (LD-FRT) in glioblastoma multiforme (GBM). Patients with recurrent/progressive GBM at least 3 months after the end of primary radiotherapy received 0.3 Gy twice daily with cisplatin and fotemustine if progressing on temozolomide, or 0.4 Gy twice daily with temozolomide if recurrent 4-6 months later (retreatment group). Newly diagnosed GBM with gross residual mass received 30 Gy with concomitant and adjuvant temozolomide and 0.4 Gy twice daily from the second adjuvant cycle (naive group) for 2-4 cycles. Twenty-six patients were enrolled. In the retreatment group (n = 17; median LD-FRT total dose 7.2 Gy [range 2.4-11.6]), grade 3 or 4 hematological toxicity was observed in 5.9% of patients. Median follow-up time was 20 months (range 4-35). Median progression-free survival (PFS) and overall survival (OS) from the time of recurrence or progression were 4 and 8 months, respectively (OS at 6 months, 69%; at 12 months, 16.7%). In the naive group (n = 9; median LD-FRT total dose 8 Gy [range 3.2-16]), grade 3 or 4 hematological toxicity was observed in 11.1% of patients. Median follow-up time was 17 months (range 8-20)-median PFS was 9 months, with PFS at 6 months and at 1 year of 66.7% and 26.7%, respectively; and median OS was 12 months, with OS at 6 months and at 1 year of 77.8% and 34.6%, respectively. LD-FRT with concurrent chemotherapy was well tolerated.
EWS-FLI-1-Targeted Cytotoxic T-cell Killing of Multiple Tumor Types Belonging to the Ewing Sarcoma Family of Tumors (2012)

These data show that YLNPSVDSV peptide is a promising antigen for ESFT immunotherapy and warrants further clinical development.
Current researches in ornamental plant breeding (2018)

Human beings are instinctively drawn to beauty, as it gives joy, eases our minds, and makes us happy.A representative of beauty in nature is ornamental plants.We can live without ornamental plants, but when we are surrounded by flowers and greenery, it makes for a better, more joyful life.Ornamental plants are also important in the agricultural industry.In Japan, 3.8 billion cut flowers and 226 million potted flowers were produced in 2016.Breeding new and attractive cultivars is necessary for further growth of the flower industry.Consumers are always seeking new varieties of ornamental plants.Breeders are asked to create new flower colors, attractive shapes, improved longevity, better fragrance, etc., and basic research on physiological and genetic mechanisms on such target characteristics is very important for breeding new cultivars.Development and adaptation of new breeding methods such as genetic transformation and mutation using ion beams are also useful for efficiently creating epoch-making unique cultivars.A large number of plant species are used as ornamentals, and these plants harbor a wide range of breeding targets.The current special issue presents fourteen recent works selected from the numerous research subjects related to ornamental plant breeding.It is our pleasure to introduce these research studies to everyone who is interested in ornamental horticulture.Ornamental plants provide comfort and peace in our everyday lives.Progress in ornamental plant breeding research will lead to the creation of more ornamentals, thus contributing to the development of the flower industry while making human lives more pleasant.
Binarized Neural Machine Translation (2023)

The rapid scaling of language models is motivating research using low-bitwidth quantization. In this work, we propose a novel binarization technique for Transformers applied to machine translation (BMT), the first of its kind. We identify and address the problem of inflated dot-product variance when using one-bit weights and activations. Specifically, BMT leverages additional LayerNorms and residual connections to improve binarization quality. Experiments on the WMT dataset show that a one-bit weight-only Transformer can achieve the same quality as a float one, while being 16x smaller in size. One-bit activations incur varying degrees of quality drop, but mitigated by the proposed architectural changes. We further conduct a scaling law study using production-scale translation datasets, which shows that one-bit weight Transformers scale and generalize well in both in-domain and out-of-domain settings. Implementation in JAX/Flax will be open sourced.