gebhart/patrepeval huggingface dataset:
Ion Homeostasis Response to Nutrient-Deficiency Stress in Plants (2020)

A crucial feature of plant performance is its strong dependence on the availability of essential mineral nutrients, affecting multiple vital functions. Indeed, mineral-nutrient deficiency is one of the major stress factors affecting plant growth and development. Thereby, nitrogen and potassium represent the most abundant mineral contributors, critical for plant survival. While studying plant responses to nutrient deficiency, one should keep in mind that mineral nutrients, along with their specific metabolic roles, are directly involved in maintaining cell ion homeostasis, which relies on a finely tuned equilibrium between cytosolic and vacuolar ion pools. Therefore, in this chapter we briefly summarize the role of the ion homeostasis system in cell responses to environmental deficiency of nitrate and potassium ions. Special attention is paid to the implementation of plant responses via NO3− and K+ root transport and regulation of ion distribution in cell compartments. These responses are strongly dependent on plant species, as well as severity and duration of nutrient deficiency.
Consent and Internet-Enabled Human Genomics (2010)

This month, PLoS Genetics is publishing an article from the company 23andMe reporting the first genome-wide association studies (GWAS) on multiple traits ascertained by self-reported information provided through the Internet from over 10,000 participants who pay the company for providing whole genome genotypes [1]. The paper passed through scientific review by a panel of three experts relatively quickly and is sure to attract the attention of anyone with freckles, curly hair, or an aversion to asparagus. Novel associations are described for four intrinsically interesting traits (out of 22 considered), while known associations with hair and eye color are replicated in a dynamic data-gathering context. Additionally, intriguing observations on the interaction between genetic self-knowledge and self-report of phenotypes are described. The implications of the successful application of this Internet-enabled approach to GWAS research were considered to be more than sufficient to warrant publication in the journal.

However, publication was delayed for six months while the editors sought a variety of opinions on three issues: ethical review, consent, and data access. Anyone who has read Rebecca Skloot's The Immortal Life of Henrietta Lacks [2] will be sensitive to the ongoing ethical and moral concerns surrounding consent and research with human samples. The editors of PLoS Genetics decided to proceed after satisfying ourselves on two major points, namely that the participants were not coerced to participate in the study in any way, and they were clearly aware that their samples would be used for genetic research. Recognizing that institutional review is an imperfect process and that the complexities raised by GWAS are not readily resolved, we call for a concerted effort on the part of granting agencies, scientists, review boards, and the public communities they serve to standardize processes and procedures of consent and review of human genomic research. It also needs to be stated that the Editor-in-Chief, Professor Greg Barsh, is a potential consultant to 23andMe, and so recused himself from all dealings with this paper prior to acceptance.
Theory of quantized Hall effect at low temperatures (1983)

At millikelvin temperatures the quantized Hall effect (QHE) is characterized by sharp steps connecting the quantized Hall resistance plateaus. We explain this behavior on the basis of the single-electron approximation and continuum percolation theory. It is shown that even when the magnetic field corresponds to partially filled Landau level on average, locally the sample breaks into patches having the occupation numbers 0 or 1. This represents a peculiar type of the metal-insulator transition, driven by disorder. Extended (global) electron states may not exist at equilibrium or arbitrarily small applied voltage $V$. Global states begin to appear at a certain critical voltage ${V}_{\mathrm{cr}}$, which is of the order of characteristic magnitude of potential fluctuations on the scale of the sample size. For small $V&gt;{V}_{\mathrm{cr}}$ the fraction of global states is still small owing to the smallness of the average electric field compared with the fluctuating field in the inversion layer. Because of this, transitions between the QHE plateaus require only a minor change in the density of states and at $T=0$ they occur in small intervals of the magnetic field. Owing to the tail of the Fermi-Dirac distribution at nonzero $T$ the deviation of the Hall conductivity from its nearest quantized value, $(\frac{{e}^{2}}{h})\ifmmode\times\else\texttimes\fi{}\mathrm{integer}$, is activated. This explains the plateau flatness and the high precision of the QHE measurements of the fine-structure constant.
Multiwatt high-efficiency CW single-mode visible lasers for ultrahigh-resolution displays (2009)

An ultrahigh-resolution display (~ 33 megapixels) employs high-power CW visible lasers which are generated through three-wave external mixing of infrared fiber lasers. The lasers provide &gt; 6 W at red, green and blue wavelengths.
2452 (2017)

OBJECTIVES/SPECIFIC AIMS: Stress urinary incontinence (SUI) significantly affects quality of life and occurs in 60% of men after radical prostatectomy, with 5% requiring surgical treatment. The artificial urinary sphincter (AUS) offers these patients excellent control of their post-prostatectomy SUI. The device contains 3 parts: the pump, urethral cuff, and pressure regulating balloon. Despite the effectiveness of AUS, up to 50% of patients require surgical revision after initial placement due to recurring SUI. Thus far, literature is heterogeneous regarding the causes of mechanical AUS failure and appropriate surgical management. Our study aims to characterize the most common reasons of AUS failure requiring surgical revision and the survival of each AUS component. METHODS/STUDY POPULATION: We report a series of 48 patients who received AUS placement and/or revision by 1 surgeon from 2010 to 2013. Upon presenting for revision, intraoperatively, the surgeon systematically evaluated the device for failure of the balloon, cuff and pump as well as urethral erosion and atrophy. In patients not requiring revision all device components were presumed functional. We conducted retrospective chart review to collect baseline characteristics, intraoperative findings, and postoperative outcomes. Using Kaplan-Meier estimates, we calculated incidence rates of component failure for the cuff, pump, and balloon. To identify risk factors for AUS failure, Cox regression was performed for univariate and multivariable testing. Multivariable modeling included those variables considered biologically plausible and significant in univariate testing. RESULTS/ANTICIPATED RESULTS: In total, 48 patients were studied with median follow up of 4.25 years. All patients received an AMS 800 device with a 61–70 mL balloon filled with 27 cc of isotonic contrast. Cuff sizes ranged from 3.5 to 5.5 cm, with 4.5 cm selected in 33/48 cases (68.8%); 19 of the patients required AUS correction (41.7%). Balloon leak constituted 57.9% (11/19) of failures, followed by cuff failure/urethral atrophy (21.1%), urethral erosion (10.5%), and individual cases of infection and pump failure. Median time to mechanical failure due to balloon leak was 3.67 years (IQR 2.17, 5.33); median time to failure for nonballoon causes was 0.54 years (IQR 0.25, 1.83). Survival of the balloon, cuff, and pump was 100%, 95.7%, and 97.9% at 1 year and 76.9%, 91.0%, and 97.9% at 5 years, respectively. DISCUSSION/SIGNIFICANCE OF IMPACT: Our study identifies fluid leakage from the balloon as the most common cause of AUS failure, particularly in patients presenting between 1 and 5 years after initial placement. For such patients, interrogating the balloon first can decrease infection risk and surgical morbidity as it can avoid manipulation of the urethral cuff. Furthermore, simply replacing lost fluid saves cost and allows for immediate reactivation of the AUS device.
Os<scp>ARID</scp>3, an <scp>AT</scp>‐rich Interaction Domain‐containing protein, is required for shoot meristem development in rice (2015)

Summary The shoot apical meristem ( SAM ) produces all of the plant's aerial organs. The SAM is established either during embryogenesis or experimentally in in vitro tissue culture. Although several factors including the Class I KNOTTED 1‐ LIKE HOMEOBOX ( KNOXI ) proteins, auxin, and cytokinin are known to play essential roles in SAM development, the underlying mechanisms of SAM formation and maintenance are still largely not understood. Herein we demonstrate that Os ARID 3, a member of the rice ( Oryza sativa ) AT ‐rich Interaction Domain ( ARID ) family, is required for SAM development. Disruption of Os ARID 3 leads to a defective SAM , early seedling lethality, and impaired capacity of in vitro shoot regeneration. We show that the expression levels of several KNOXI genes and the biosynthetic genes for auxin and cytokinin are significantly altered in the Osarid 3 mutant calli. Moreover, we determine that auxin concentrations are increased, whereas cytokinin levels are decreased, in Osarid3 calli. Furthermore, chromatin immunoprecipitation results demonstrate that Os ARID 3 binds directly to the KNOXI gene OSH 71 , the auxin biosynthetic genes Os YUC 1 and Os YUC 6 , and the cytokinin biosynthetic genes Os IPT 2 and Os IPT 7 . We also show through electrophoretic mobility shift assays that Os ARID 3 specifically binds to the AT ‐rich DNA sequences of the identified target genes. We conclude that Os ARID 3 is an AT ‐rich specific DNA ‐binding protein and that it plays a major role in SAM development in rice.
Breakthroughs in Photonics 2013: Advances in Nanoantennas (2014)

The field of nanoantennas overlaps several areas of scientific interest, from fundamental physics to commercial technologies. Advances in the understanding of such complex devices hold the promises to novel applications in sensing, telecommunications, optical processing, and security, among others. Here, we review the main advances in the field of nanoantennas in 2013, from single metallic and dielectric devices to nanostructured metasurfaces and phased arrays.
Definition of Species in the &lt;I&gt;Culex sitiens&lt;/I&gt; Subgroup (Diptera: Culicidae) from Papua New Guinea and Australia (2000)

Japanese encephalitis is a disease of major importance in Asia, which from 1995 has extended its range into the north of Australia. Culex annulirostris Skuse of the Culex sitiens subgroup of Culex was incriminated as the most likely mosquito vector. Because misidentifications previously have occurred within this subgroup, our paper defines electrophoretic methods to identify Culex specimens from Queensland and the Northern Territory in Australia and from Western Province in Papua New Guinea. In collections from 1996 to 1998 Culex sitiens Wiedemann, Cx. palpalis Taylor, and Cx. annulirostris comprised 93.1% of the total banded proboscis Culex mosquitoes collected; 6.9% remained unidentified to species by morphological or electrophoretic examination. The prevalence of Cx. palpalis was variable and appeared to be associated with below average rainfall during 1997. In Papua New Guinea, this species comprised up to 97.4% of banded proboscis Culex, with smaller numbers collected from the Torres Strait Islands and Cape York; none was collected from other Queensland localities. Cx. annulirostris was more prevalent during years of average or above average rainfall and was predominant in most localities, especially in the Torres Strait and Queensland. These data confirmed the problems in separating Cx. sitiens from Cx. palpalis and Cx. annulirostris using morphological characters.
Generation of terahertz transients from <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>Co</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi>Fe</mml:mi><mml:mrow><mml:mn>0.4</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi>Mn</mml:mi><mml:mrow><mml:mn>0.6</mml:mn></mml:mrow></mml:msub><mml:mi>Si</mml:mi></mml:mrow></mml:math>-Heusler-alloy/normal-metal nanobilayers excited by femtosecond optical pulses (2021)

We generated pulses of electromagnetic radiation in the terahertz (THz) frequency range by optical excitation of ${\mathrm{Co}}_{2}{\mathrm{Fe}}_{0.4}{\mathrm{Mn}}_{0.6}\mathrm{Si}$ (CFMS)/normal-metal (NM) bilayer structures. The CFMS is a Heusler alloy showing a band gap in one spin channel and is therefore a half metal. We compared the THz emission efficiency in a systematic manner for four different CFMS/NM bilayers, where NM was either Pt, Ta, Cr, or Al. Our measurements show that the THz intensity is highest for a Pt capping. We also demonstrate the tunability of the THz amplitude by varying the magnetic field for all four bilayers. We attribute the THz generation to the inverse spin Hall effect. In order to investigate the role of the interface in THz generation, we measured the spin mixing conductance for each CFMS/NM bilayer using a ferromagnetic resonance method. We found that the spin-orbit coupling cannot completely describe the THz generation in the bilayers and that the spin transmission efficiency of the CFMS/NM interface and the spin diffusion length, as well as the oxidation of the NM layer, play crucial roles in the THz emission process.
Supplementary Data from The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy (2023)

&lt;p&gt;Table S4&lt;/p&gt;
Adaptive bilateral matching for decoder-side motion vector refinement in video coding (2022)

This paper presents an adaptive bilateral matching technique for decoder-side motion vector refinement in video coding. It allows encoder to choose not only the conventional bilateral matching mode with symmetric motion vector difference but also the asymmetric alternatives. To study the efficiency of the proposed technique, the proposed method is integrated in the Versatile Video Coding Test Model 11.0. The experimental result reports an overall of &#x2212;2.78&#x0025; luma Bjontegaard Delta rate for the random-access configurations. The compression efficiency on top of the Enhanced Compression Model that beyond the VVC capability are also reported.
Safety and immunogenicity of an HIV-1 gp120-CD4 chimeric subunit vaccine in a phase 1a randomized controlled trial (2021)

A major challenge for HIV vaccine development is to raise anti-envelope antibodies capable of recognizing and neutralizing diverse strains of HIV-1. Accordingly, a full length single chain (FLSC) of gp120-CD4 chimeric vaccine construct was designed to present a highly conserved CD4-induced (CD4i) HIV-1 envelope structure that elicits cross-reactive anti-envelope humoral responses and protective immunity in animal models of HIV infection. IHV01 is the FLSC formulated in aluminum phosphate adjuvant. We enrolled 65 healthy adult volunteers in this first-in-human phase 1a randomized, double-blind, placebo-controlled study with three dose-escalating cohorts (75 µg, 150 µg, and 300 µg doses). Intramuscular injections were given on weeks 0, 4, 8, and 24. Participants were followed for an additional 24 weeks after the last immunization. The overall incidence of adverse events (AEs) was not significantly different between vaccinees and controls. The majority (89%) of vaccine-related AE were mild. The most common vaccine-related adverse event was injection site pain. There were no vaccine-related serious AE, discontinuation due to AE, intercurrent HIV infection, or significant decreases in CD4 count. By the final vaccination, all vaccine recipients developed antibodies against IHV01 and demonstrated anti-CD4i epitope antibodies. The elicited antibodies reacted with CD4 non-liganded Env antigens from diverse HIV-1 strains. Antibody-dependent cell-mediated cytotoxicity against heterologous infected cells or gp120 bound to CD4+ cells was evident in all cohorts as were anti-gp120 T-cell responses. IHV01 vaccine was safe, well tolerated, and immunogenic at all doses tested. The vaccine raised broadly reactive humoral responses against conserved CD4i epitopes on gp120 that mediates antiviral functions.
Zero-field edge plasmons in a magnetic topological insulator (2017)

Incorporating ferromagnetic dopants into three-dimensional topological insulator thin films has recently led to the realisation of the quantum anomalous Hall effect. These materials are of great interest since they may support electrical currents that flow without resistance, even at zero magnetic field. To date, the quantum anomalous Hall effect has been investigated using low-frequency transport measurements. However, transport results can be difficult to interpret due to the presence of parallel conductive paths, or because additional non-chiral edge channels may exist. Here we move beyond transport measurements by probing the microwave response of a magnetised disk of Cr-(Bi,Sb)<sub>2</sub>Te<sub>3</sub>. We identify features associated with chiral edge plasmons, a signature that robust edge channels are intrinsic to this material system. Our results provide a measure of the velocity of edge excitations without contacting the sample, and pave the way for an on-chip circuit element of practical importance: the zero-field microwave circulator.
Phytochemical and pharmacological progress on (2015)

Genus Syringa, belonging to the Oleaceae family, consists of more than 40 plant species worldwide, of which 22 species, including 18 endemic species, are found in China. Most Syringa plants are used in making ornaments and traditional medicines, whereas some are employed for construction or economic use. Previous studies have shown that extracts of Syringa plants mainly contain iridoids, lignans, and phenylethanoids that have antitumor, antihypertensive, anti-oxidant, and anti-inflammatory activities. This study reviews phytochemical and pharmacological progress on Syringa in the recent 20 years and discusses the future research prospects to provide a reference in further promotion and application of the genus.
Artificial Antigen Presenting Cell Can Be Used To Propagate Genetically Modified CD19-Specific T Cells through Chimeric Antigen Receptor. (2005)

Abstract The safety and feasibility of adoptive immunotherapy, using CD19-specific T cells that have been genetically modified to express a chimeric antigen receptor (CAR) and numerically expanded ex vivo, need to be addressed. Second-generation trials are being developed incorporating improvements into the design of the CAR as well as the manufacturing processes. Here we describe a platform for propagating CD19-specific T cells through an artificial antigen presenting cell (aAPC) which co-expresses CD19 and T-cell co-stimulatory molecules to provide a fully-competent T-cell activation signal leading to T-cell proliferation. K562 cells were selected as the platform for the aAPCs since (i) they have previously been used in compliance with current good manufacturing practice (cGMP), (ii) they express the desired endogenous T-cell adhesion molecules, and (iii) they fail to express classical HLA class I/II molecules and thus are not targets for a T-cell mediated allogeneic immune response. Therefore, K562 cells were genetically modified to co-express CD19 and both of the T-cell co-stimulatory molecules 4-1BBL (CD137L) and MICA. We then tested the ability of these K562 aAPCs to expand T cells expressing a new CD19-specific CAR designated CD19RCD28. This CAR utilizes a CD19-specific scFv to bind to CD19 independent of MHC and confers an activation signal to genetically modified T cells through both CD28 and CD3-ζ. The CD19RCD28+ T cells could be rapidly expanded (50-fold in 14 days) when cultured in the presence of recombinant human IL-2 and irradiated K562 aAPCs (1:50 ratio, T cell to aAPC). The use of freshly thawed aAPCs improved the practicality of using this antigen-driven expansion method in compliance with cGMP. The numerical expansion of the genetically modified T cells was associated with an increased CAR cell-surface expression, from 17 ± 11% (mean ± SD) before co-culture compared with 44 ± 8% (mean ± SD) after co-culture with the aAPCs, which is consistent with T-cell activation through the CAR. A 3H-thymidine incorporation assay was used to demonstrate that CD19 on the K562 aAPC was necessary, but not sufficient, to proliferate CD19RCD28+ T cells. Furthermore, this proliferation assay demonstrated that co-expression of both 4-1BBL (CD137L) and MICA along with CD19 resulted in the most efficient proliferation of the genetically modified T cells. The propagation of CAR+ T cells on antigen+ aAPCs may thus (i) avoid the need for allogeneic peripheral blood mononuclear feeder cells, which are expensive and time-consuming to prepare in compliance with cGMP, (ii) select in vitro for genetically modified T cells with proven CAR-dependent replicative capacity, and (iii) provide conditions for the outgrowth of subpopulations of T cells within a bulk culture that have increased transgene expression. The feasibility of this new T-cell propagation method using aAPC will be tested in the upcoming clinical trials.
Symbolic Semantic Segmentation and Interpretation of COVID-19 Lung Infections in Chest CT volumes based on Emergent Languages (2020)

The coronavirus disease (COVID-19) has resulted in a pandemic crippling the a breadth of services critical to daily life. Segmentation of lung infections in computerized tomography (CT) slices could be be used to improve diagnosis and understanding of COVID-19 in patients. Deep learning systems lack interpretability because of their black box nature. Inspired by human communication of complex ideas through language, we propose a symbolic framework based on emergent languages for the segmentation of COVID-19 infections in CT scans of lungs. We model the cooperation between two artificial agents - a Sender and a Receiver. These agents synergistically cooperate using emergent symbolic language to solve the task of semantic segmentation. Our game theoretic approach is to model the cooperation between agents unlike Generative Adversarial Networks (GANs). The Sender retrieves information from one of the higher layers of the deep network and generates a symbolic sentence sampled from a categorical distribution of vocabularies. The Receiver ingests the stream of symbols and cogenerates the segmentation mask. A private emergent language is developed that forms the communication channel used to describe the task of segmentation of COVID infections. We augment existing state of the art semantic segmentation architectures with our symbolic generator to form symbolic segmentation models. Our symbolic segmentation framework achieves state of the art performance for segmentation of lung infections caused by COVID-19. Our results show direct interpretation of symbolic sentences to discriminate between normal and infected regions, infection morphology and image characteristics. We show state of the art results for segmentation of COVID-19 lung infections in CT.