gebhart/patrepeval huggingface dataset:
Mechanism of Triplet Energy Transfer in Photosynthetic Bacterial Reaction Centers (2017)

In purple bacterial reaction centers, triplet excitation energy transfer occurs from the primary donor P, a bacteriochlorophyll dimer, to a neighboring carotenoid to prevent photodamage from the generation of reactive oxygen species. The B<sub>B</sub> bacteriochlorophyll molecule that lies between P and the carotenoid on the inactive electron transfer branch is involved in triplet energy transfer between P and the carotenoid. To expand the high-resolution spectral and kinetic information available for describing the mechanism, we investigated the triplet excited state formation and energy transfer pathways in the reaction center of Rhodobacter sphaeroides using pump-probe transient absorption spectroscopy over a broad spectral region on the nanosecond to microsecond time scale at both room temperature and at 77 K. Wild-type reaction centers were compared with a reaction center mutant (M182HL) in which B<sub>B</sub> is replaced by a bacteriopheophytin (Φ), as well as to reaction centers that lack the carotenoid. In wild-type reaction centers, the triplet energy transfer efficiency from P to the carotenoid was essentially unity at room temperature and at 77 K. However, in the M182HL mutant reaction centers, both the rate and efficiency of triplet energy transfer were decreased at room temperature, and at 77 K, no triplet energy transfer was observed, attributable to a higher triplet state energy of the bacteriopheophytin that replaces bacteriochlorophyll in this mutant. Finally, detailed time-resolved spectral analysis of P, carotenoid, and B<sub>B</sub> (Φ in the M182HL mutant) reveals that the triplet state of the carotenoid is coupled fairly strongly to the bridging intermediate B<sub>B</sub> in wild-type and Φ in the M182HL mutant, a fact that is probably responsible for the lack of any obvious intermediate <sup>3</sup>B<sub>B</sub>/<sup>3</sup>Φ transient formation during triplet energy transfer.
Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity (2018)

Zika virus (ZIKV) has reemerged in the population and caused unprecedented global outbreaks. Here, the transcriptomic consequences of ZIKV infection were studied systematically first in human peripheral blood CD14<sup>+</sup> monocytes and monocyte-derived macrophages with high-density RNA sequencing. Analyses of the ZIKV genome revealed that the virus underwent genetic diversification, and differential mRNA abundance was found in host cells during infection. Notably, there was a significant change in the cellular response, with cross talk between monocytes and natural killer (NK) cells as one of the highly identified pathways. Immunophenotyping of peripheral blood from ZIKV-infected patients further confirmed the activation of NK cells during acute infection. ZIKV infection in peripheral blood cells isolated from healthy donors led to the induction of gamma interferon (IFN-γ) and CD107a-two key markers of NK cell function. Depletion of CD14<sup>+</sup> monocytes from peripheral blood resulted in a reduction of these markers and reduced priming of NK cells during infection. This was complemented by the immunoproteomic changes observed. Mechanistically, ZIKV infection preferentially counterbalances monocyte and/or NK cell activity, with implications for targeted cytokine immunotherapies. <b>IMPORTANCE</b> ZIKV reemerged in recent years, causing outbreaks in many parts of the world. Alarmingly, ZIKV infection has been associated with neurological complications such as Guillain-Barré syndrome (GBS) in adults and congenital fetal growth-associated anomalies in newborns. Host peripheral immune cells are one of the first to interact with the virus upon successful transmission from an infected female <i>Aedes</i> mosquito. However, little is known about the role of these immune cells during infection. In this work, the immune responses of monocytes, known target cells of ZIKV infection, were investigated by high-density transcriptomics. The analysis saw a robust immune response being elicited. Importantly, it also divulged that monocytes prime NK cell activities during virus infection. Removal of monocytes during the infection changed the immune milieu, which in turn reduced NK cell stimulation. This study provides valuable insights into the pathobiology of the virus and allows for the possibility of designing novel targeted therapeutics.
Prevention of Graft-versus-Host Disease by Adoptive T Regulatory Therapy Is Associated with Active Repression of Peripheral Blood Toll-Like Receptor 5 mRNA Expression (2013)

Acute graft-versus-host disease (GVHD) occurs in 40% to 60% of recipients of partially matched umbilical cord blood transplantation (UCBT). In a phase I study, adoptive transfer of expanded CD4(+)CD25(+)Foxp3(+) natural regulatory T cells (nTregs) resulted in a reduced incidence of grade II-IV acute GVHD. To investigate potential mechanisms responsible for the reduced GVHD risk, we analyzed peripheral blood mononuclear cell mRNA expression of a tolerance gene set previously identified in operation- tolerant kidney transplant recipients, comparing healthy controls and patients who received nTregs and those who did not receive nTregs with and without experiencing GVHD. Samples from patients receiving nTregs regardless of GVHD status showed increased expression of Foxp3 expression, as well as B cell-related tolerance marker. This was correlated with early B cell recovery, predominately of naïve B cells, and nearly normal T cell reconstitution. CD8(+) T cells showed reduced signs of activation (HLA-DR(+) expression) compared with conventionally treated patients developing GVHD. In contrast, patients with GVHD had significantly increased TLR5 mRNA expression, whereas nTreg-treated patients without GVHD had reduced TLR5 mRNA expression. We identified Lin(-)HLADR(-)CD33(+)CD16(+) cells and CD14(++)CD16(-) monocytes as the main TLR5 producers, especially in samples of conventionally treated patients developing GVHD. Taken together, these data reveal interesting similarities and differences between tolerant organ and nTreg-treated hematopoietic stem cell transplantation recipients.
The influence of the package environment on the functioning and reliability of RF-MEMS switches (2005)

This paper discusses the influence of pressure and gas inside a package on the functioning and lifetime of capacitive RF-MEMS switches. It is shown that decreasing the pressure strongly influences the switching speed of a switch, but if it becomes too low it causes anomalous vibration effects. When testing at the same pressure, it is shown that the lifetime of the capacitive switches is higher in a nitrogen environment than in ambient air (lab) environment. These effects are attributed to the humidity of the air and its influence on charge trapping in the insulator, resulting in stiction of the switch bridge. It is also shown that this charge is not stable and that the switch recovers when it is not actuated.
Supplementary Figure S5 from Tankyrase-Binding Protein TNKS1BP1 Regulates Actin Cytoskeleton Rearrangement and Cancer Cell Invasion (2023)

&lt;p&gt;TNKS1BP1 is poly(ADP-ribosyl)ated by tankyrase but does not affect the telomeric function of tankyrase.&lt;/p&gt;
Robust vibration control of flexible structures using smart materials with uncertainties (2012)

International audience
Differential gain and damping factor in strained inGaAs/GaAs quantum well lasers (1992)

The differential gain, modulation response, and damping rate of strained-layer Ino•3Ga(J•7As multiple quantum well (MQW) short cavity graded-index separate confmement heterostrucutre (GRINSCH) and SCH lasers fabricated by chemically-assisted ion beam etching (CAIBE) are analyzed. Calculated differential gains vary from 0.7 to. 1 .6 x 1015 cm2, with only relatively long lasers of 400 p.m demonstrating very high differential gain. For the GRINSCH lasers, a CW 3-dB bandwidth of 22 GHz has been measured that is limited primarily by heating and a low frequency rolloff. The latter is improved dramatically using an SCH design resulting in an improvement of the 3-dB bandwidth to 28 GHz. Cather transport theory (also known as well-barrier hole burning) is shown to model the damping behavior of quantum well lasers from low to moderate photon densities.
&lt;title&gt;Total internal reflection mirrors fabricated in polymeric optical waveguides via excimer laser ablation&lt;/title&gt; (1991)

Excimer laser (248 rim) ablation has been used for rapid large area defmition of total internal reflection (TIR) mirrors in thick (50 tim) polymeric optical waveguides. The mitrors are capable of reflecting light into or out of the waveguide plane with a loss of less than 1 dB
Sample Tracking and Use in Published Genome-wide Association Studies (2010)

JAMA Genome-wide Analysis of Genetic Loci Associated With Alzheimer Disease Sudha Seshadri, MD; Annette L. Fitzpatrick, PhD; M. Arfan Ikram, MD, PhD; Anita L. DeStefano, PhD; Vilmundur Gudnason, MD, PhD; Merce Boada, MD, PhD; Joshua C. Bis, PhD; Albert V. Smith, PhD; Minerva M. Carrasquillo, PhD; Jean Charles Lambert, PhD; Denise Harold, PhD; Elisabeth M. C. Schrijvers, MD; Reposo Ramirez-Lorca, PhD; Stephanie Debette, MD, PhD; W. T. Longstreth Jr, MD; A. Cecile J. W. Janssens, PhD; V. Shane Pankratz, PhD; Jean Francois Dartigues, PhD; Paul Hollingworth, PhD; Thor Aspelund, PhD; Isabel Hernandez, MD; Alexa Beiser, PhD; Lewis H. Kuller, MD; Peter J. Koudstaal, MD, PhD; Dennis W. Dickson, MD; Christophe Tzourio, MD; Richard Abraham, PhD; Carmen Antunez, MD; Yangchun Du, PhD; Jerome I. Rotter, MD; Yurii S. Aulchenko, PhD; Tamara B. Harris, MD; Ronald C. Petersen, MD; Claudine Berr, MD, PhD; Michael J. Owen, MbChB, PhD; Jesus Lopez-Arrieta, MD; Badri N. Vardarajan, MS; James T. Becker, PhD; Fernando Rivadeneira, MD, PhD; Michael A. Nalls, PhD; Neill R. Graff-Radford, MD; Dominique Campion, MD, PhD; Sanford Auerbach, MD; Kenneth Rice, PhD; Albert Hofman, MD, PhD; Palmi V. Jonsson, MD; Helena Schmidt, MD, PhD; Mark Lathrop, PhD; Thomas H. Mosley, PhD; Rhoda Au, PhD; Bruce M. Psaty, MD, PhD; Andre G. Uitterlinden, PhD; Lindsay A. Farrer, PhD; Thomas Lumley, PhD; Agustin Ruiz, MD, PhD; Julie Williams, PhD; Philippe Amouyel, MD, PhD; Steve G. Younkin, PhD; Philip A. Wolf, MD; Lenore J. Launer, PhD; Oscar L. Lopez, MD; Cornelia M. van Duijn, PhD; Monique M. B. Breteler, MD, PhD; for the CHARGE, GERAD1, and EADI1 Consortia Context: Genome-wide association studies (GWAS) have recently identifiedCLU,PICALM, andCR1as novel genes for late-onset Alzheimer disease (AD). Objectives: To identify and strengthen additional loci associated with AD and confirm these in an independent sample and to examine the contribution of recently identified genes to AD risk prediction in a 3-stage analysis of new and previously published GWAS on more than 35 000 persons (8371 AD cases). Design, Setting, and Participants: In stage 1, we identified strong genetic associations (P Main Outcome Measure: Presence of Alzheimer disease. Results: Two loci were identified to have genome-wide significance for the first time: rs744373 nearBIN1(odds ratio [OR], 1.13; 95% confidence interval [CI], 1.06-1.21 per copy of the minor allele;P = 1.59 × 10−11) and rs597668 nearEXOC3L2/BLOC1S3/MARK4(OR, 1.18; 95% CI, 1.07-1.29;P = 6.45 × 10−9). Associations of these 2 loci plus the previously identified lociCLUandPICALMwith AD were confirmed in the Spanish sample (P Conclusions: Two genetic loci for AD were found for the first time to reach genome-wide statistical significance. These findings were replicated in an independent population. Two recently reported associations were also confirmed. These loci did not improve AD risk prediction. While not clinically useful, they may implicate biological pathways useful for future research. JAMA. 2010;303(18):1832-1840.
RASAL1 is a potent regulator of hepatic stellate cell activity and liver fibrosis (2017)

Liver fibrosis, leading to cirrhosis and liver failure, can occur after chronic liver injury. The transition of hepatic stellate cells (HSCs) from quiescent cells into proliferative and fibrogenic cells is a central event in liver fibrosis. Here, we show that RAS protein activator like-1 (RASAL1), a RAS-GTPase-activating protein, which switches off RAS activity, is significantly decreased during HSC activation, and that HSC activation can be antagonized by forced expression of the RASAL1 protein. We demonstrate that RASAL1 suppresses HSC proliferation by regulating the Ras-MAPK pathway, and that RASAL1 suppresses HSC fibrogenic activity by regulating the PKA-LKB1-AMPK-SRF pathway by interacting with angiotensin II receptor, type 1. We also show that RASAL1-deficient mice are more susceptible to liver fibrosis. These data demonstrate that deregulated RASAL1 expression levels and the affected downstream intracellular signaling are central mediators of perpetuated HSC activation and fibrogenesis in the liver.
Motion Generation Using Bilateral Control-Based Imitation Learning With Autoregressive Learning (2021)

Imitation learning has been studied as an efficient and high-performance method to generate robot motion. Specifically, bilateral control-based imitation learning has been proposed as a method of realizing fast motion. However, the learning approach of this method leads to the accumulation of prediction errors during the prediction process and may not generate desirable long-term behavior. Therefore, in this paper, we propose a method of autoregressive learning for bilateral control-based imitation learning to reduce the accumulation of prediction errors. A new neural network model for implementing autoregressive learning is also proposed. Three types of experiments are conducted to verify the effectiveness of the proposed method, where the method is shown to have improved performance over those of conventional approaches. Due to the structure and method of autoregressive learning employed by the developed model, the proposed method can generate desirable long-term motion for successful tasks and has a high generalization ability for environmental changes based on the human demonstrations of tasks.
Fabrication of a Porous TiO<sub>2</sub>-Coated Silica Glass Tube and Its Application for a Handy Water Purification Unit (2014)

A simple, handy, reusable, and inexpensive water purification unit including a one-end sealed porous amorphous-silica (a-silica) tube coated with 2 μ m of porous TiO 2 photocatalyst layers has been developed. Both TiO 2 and a-silica layers were formed through outside vapor deposition (OVD). Raman spectrum of the porous TiO 2 -coated a-silica glass tube indicated that the anatase content of the TiO 2 layers of the tube was estimated to be approximately 60 wt%. Developed porous TiO 2 -coated a-silica glass tube has been assayed for the tube filtering feature against Escherichia coli ( E. coli ) solution used as one of the typical bacteria size species or Q<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi>β</mml:mi></mml:mrow></mml:math>phage also used as typical virus size species and compared with the feature of porous a-silica tubes alone. The tubes removed E. coli completely from the aqueous suspension which contained 10 6 CFU/mL of E. coli without UV irradiation. The porous TiO 2 -coated a-silica glass tube with UV-C lamps successfully reduced the Q<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:mi>β</mml:mi></mml:mrow></mml:math>phage amount in the suspension from 10 9 to 10 3 PFU/mL.
Bioelectronic Skin Based on Nociceptive Ion Channel for Human‐Like Perception of Cold Pains (2020)

A bioelectronic skin device based on nociceptive ion channels in nanovesicles is developed for the detection of chemical cold-pain stimuli and cold environments just like human somesthetic sensory systems. The human transient receptor potential ankyrin 1 (hTRPA1) is involved in transmission and modulation of cold-pain sensations. In the bioelectronic skin, the nanovesicles containing the hTRPA1 nociceptive ion channel protein reacts to cold-pain stimuli, and it is electrically monitored through carbon nanotube transistor devices based on floating electrodes. The bioelectronic skin devices sensitively detect chemical cold-pain stimuli like cinnamaldehyde at 10 fm, and selectively discriminate cinnamaldehyde among other chemical stimuli. Further, the bioelectronic skin is used to evaluate the effect of cold environments on the response of the hTRPA1, finding that the nociceptive ion channel responds more sensitively to cinnamaldehyde at lower temperatures than at higher temperatures. The bioelectronic skin device could be useful for a basic study on somesthetic systems such as cold-pain sensation, and should be used for versatile applications such as screening of foods and drugs.
Chalcogenide Glass-on-Graphene Photonics (2017)

Photonic integration with 2-D materials conventionally relied on transfer processes. We developed an approach to monolithically fabricate photonic devices on 2-D materials including graphene and demonstrated its significant potential for high-performance photonic integration.
Clinical sensitivity of antibodies against cyclic citrulinated peptide in patients with rheumatoid arthritis (2001)

We discuss the presence of anti-keratin antibodies (AKA) of the IgG class in patients with defined juvenile idiopathic arthritis (JIA). An indirect immunofluorescence test and rat oesophagus substrate was used for the detection and quantification of AKA antibodies in patients sera. Overall 33/60 patients with JIA had sera positive for AKA (55 %, P = 0,0001) ranging from 1:10 to 1:160 dilutions. Following idiopathic arthritis of childhood classification criteria AKA occurred in 2/7 patients with systemic disease (28,6 %), in 13/30 patients with RF negative polyarthritis (43,3 %, P = 0,008) and in 15/18 RF positive polyarthritis (83,3 %, P = 0,000002). AKA were also found in a small cohort of patients with oligoarthritis (1/3) and psoriatic arthritis (2/2). AKA positivity occurred in 3/26 healthy controls at a 1:20 dilution. The presence of AKA was correlated as well as with the severity of the disease. Our study revealed that AKA was present overall in 18/29 patients (62%) with severe JIA and in 12/26 patients (46,2 %) with non-severe disease, however this did not reach statistical significance (P = 0,18). We also observed that AKA remained positive regardless of disease activity. AKA were detectable in 55,6 % patients with active JIA and in 48,6 % patients in the complete or near remission.
Autologous Vein Transplantation for Correction of Dermal Atrophic Changes (2002)

Autologous vein collagen transplantation can correct dermal defects with long-lasting and perhaps permanent results.
Multiple Myeloma-Associated Amyloidoma of the Sacrum: Case Report and Review of the Literature (2013)

Study Design Case report. Objectives With only two previously reported cases, localized amyloidosis of the sacrum is extremely rare. Here we report a 64-year-old woman with a large osteolytic lesion accompanied by weakness and paresthesia of the right leg and difficulties in bladder control. Methods Fine needle biopsy and standard staging procedures revealed a primary solitary amyloidoma that was treated with intralesional resection, lumbopelvic stabilization, and consolidation radiotherapy. Results Clinical follow-up revealed the diagnosis of multiple myeloma 9 months after initial treatment. At 12 months, no local recurrence has occurred, the neurologic symptoms have resolved, and the systemic disease is in remission. Conclusions Intralesional resection with adjuvant radiotherapy of the amyloidoma achieved good local tumor control with limited morbidity.
A Hyperspectral Survey of New York City Lighting Technology (2016)

Using side-facing observations of the New York City (NYC) skyline, we identify lighting technologies via spectral signatures measured with Visible and Near Infrared (VNIR) hyperspectral imaging. The instrument is a scanning, single slit spectrograph with 872 spectral channels from 0.4-1.0 μ m. With a single scan, we are able to clearly match the detected spectral signatures of 13 templates of known lighting types. However, many of the observed lighting spectra do not match those that have been measured in the laboratory. We identify unknown spectra by segmenting our observations and using Template-Activated Partition (TAP) clustering with a variety of underlying unsupervised clustering methods to generate the first empirically-determined spectral catalog of roughly 40 urban lighting types. We show that, given our vantage point, we are able to determine lighting technology use for both interior and exterior lighting. Finally, we find that the total brightness of our scene shows strong peaks at the 570 nm Na - II , 595 nm Na - II and 818 nm Na - I lines that are common in high pressure sodium lamps, which dominate our observations.
CD8<sup>+</sup>T Cell Exhaustion During Persistent Viral Infection is Regulated Independently of the Virus-Specific T Cell Receptor (2013)

During chronic viral infections, responses by virus-specific CD8(+) T cells become marginalized by the acquisition of functional defects and reduced cell numbers in a process defined as T cell exhaustion. Similarly, T cell tolerance to self-antigen is also characterized by impaired effector function and eventual deletion of self-reactive T cells. Induction of both tolerance and exhaustion involve many shared inhibitory mechanisms, thus similar therapeutic approaches have proven effective in these distinct environments. We previously demonstrated that tolerant self-reactive CD8(+) T cells expressing dual-T cell receptors (i.e., dual-TCR) could be rescued by immunization through a second TCR specific for a foreign antigen. These data revealed that T cell tolerance was regulated at the level of the self-reactive TCR. Here, dual-TCR CD8(+) T cells were used to examine if exhaustion during persistent viral infection could be rescued by an analogous strategy of immunization through a second TCR not involved in recognition of virus. In direct contrast to the rescue achievable in tolerant CD8(+) T cells, exhausted T cells were equally impaired through both TCR. These findings suggest that exhaustion is maintained by defects downstream of the virus-specific TCR, and establish that exhaustion and tolerance are distinctly regulated states of T cell dysfunction.
Non-obstructive azoospermia and maturation arrest with complex translocation 46,XY t(9;13;14)(p22;q21.2;p13) is consistent with the Luciani-Guo hypothesis of latent aberrant autosomal regions and infertility (2005)

Although genes mapped to the Y-chromosome have been established as critical to normal testicular development and spermatogenesis, certain autosomal genes are now also recognized as important in these processes. Here we present clinical evidence to support the Luciani-Guo hypothesis (first advanced in 1984 and refined in 2002), which predicts severe spermatogenic impairment with aberrations involving chromosomes 9, 13, and/or 14, independent of Y-chromosome status. Additional study including fluorescent in situ hybridization and molecular analysis of specific chromosomal regions is needed to characterize more fully the contribution(s) of these autosomes to male testicular development and spermatogenesis.