gebhart/patrepeval huggingface dataset:
Chondrogenesis, joint formation, and articular cartilage regeneration (2009)

The repair of joint surface defects remains a clinical challenge, as articular cartilage has a limited healing response. Despite this, articular cartilage does have the capacity to grow and remodel extensively during pre- and post-natal development. As such, the elucidation of developmental mechanisms, particularly those in post-natal animals, may shed valuable light on processes that could be harnessed to develop novel approaches for articular cartilage tissue engineering and/or regeneration to treat injuries or degeneration in adult joints. Much has been learned through mouse genetics regarding the embryonic development of joints. This knowledge, as well as the less extensive available information regarding post-natal joint development is reviewed here and discussed in relation to their possible relevance to future directions in cartilage tissue repair and regeneration.
Inhibition of Haspin Kinase Promotes Cell-Intrinsic and Extrinsic Antitumor Activity (2019)

Patients with melanoma resistant to RAF/MEK inhibitors (RMi) are frequently resistant to other therapies, such as immune checkpoint inhibitors (ICI), and individuals succumb to their disease. New drugs that control tumor growth and favorably modulate the immune environment are therefore needed. We report that the small-molecule CX-6258 has potent activity against both RMi-sensitive (RMS) and -resistant (RMR) melanoma cell lines. Haspin kinase (HASPIN) was identified as a target of CX-6258. HASPIN inhibition resulted in reduced proliferation, frequent formation of micronuclei, recruitment of cGAS, and activation of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. In murine models, CX-6258 induced a potent cGAS-dependent type-I IFN response in tumor cells, increased IFNγ-producing CD8<sup>+</sup> T cells, and reduced Treg frequency <i>in vivo</i>. HASPIN was more strongly expressed in malignant compared with healthy tissue and its inhibition by CX-6258 had minimal toxicity in <i>ex vivo</i>-expanded human tumor-infiltrating lymphocytes (TIL), proliferating TILs, and <i>in vitro</i> differentiated neurons, suggesting a potential therapeutic index for anticancer therapy. Furthermore, the activity of CX-6258 was validated in several Ewing sarcoma and multiple myeloma cell lines. Thus, HASPIN inhibition may overcome drug resistance in melanoma, modulate the immune environment, and target a vulnerability in different cancer lineages. SIGNIFICANCE: HASPIN inhibition by CX-6258 is a novel and potent strategy for RAF/MEK inhibitor-resistant melanoma and potentially other tumor types. HASPIN inhibition has direct antitumor activity and induces a favorable immune microenvironment.
Analytical model for superconducting generators for wave energy systems (2016)

The objective of the research is to obtain a better understanding of the feasibility of superconducting machine concepts for wave energy systems. These topologies were previously investigated by Keysan with regards to wind energy. An optimization design tool is developed in Matlab for the electrical design of the machine types. Two case studies, namely the Archimedes Wave Swing and the Oyster wave energy converter for the double-claw pole design are applied and presented in this work. The main advantage of the configurations is the significantly less superconducting tape requirement compared to conventional configurations. Both designs apply less than 10 km of superconducting tape.
Complete Genome Sequence of Mycobacterium intracellulare Strain ATCC 13950T (2012)

Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC 13950(T), a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of the disparity between MAC members.
Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology (2021)

Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.
Anti-dsDNA antibody assay: high specificity and sensitivity with a filtration radioassay in comparison to low specificity with the standard ELISA. (2007)

The fluid-phase filtration radioassay demonstrated high sensitivity and specificity for the detection of anti-dsDNA antibodies in SLE, with the standard ELISA exhibiting lower specificity. We suggest that testing for anti-dsDNA antibodies can be improved using a fluid-phase filtration radioassay in comparison to commercial assays.
Ventilatory responses to inspiratory threshold loading and role of muscle fatigue in task failure (1994)

To examine respiratory muscle recruitment pattern during inspiratory loading and role of fatigue in limiting endurance, we studied seven normal subjects on 17 +/- 6 days during breathing against progressive inspiratory threshold load. Threshold pressure (Pth) was progressively increased 14 +/- 5 cmH2O every 2 min until voluntary cessation (task failure). Subjects could adopt any breathing pattern. Tidal volume (VT), chest wall motion, end-tidal PCO2, and arterial O2 saturation were measured. At moderate loads [50-75% of maximum Pth (Pthmax)], inspiratory time (TI) decreased and VT/TI and expiratory time increased, increasing time for recovery of muscles between inspirations. At high loads (> 75% Pthmax), VT/TI decreased, which, with progressive decrease in end-expiratory lung volume (EELV) throughout, increased potential for inspiratory force development. Progressive hypoxia and hypercapnia occurred at higher work loads. Immediately after task failure all subjects could recover at high loads and still reachieve initial Pthmax on reimposition of progressive loading. Respiratory pressures were measured in subgroup of three subjects: transdiaphragmatic pressure response to 0.1-ms bilateral supramaximal phrenic nerve stimulation at end expiration initially increased with increasing load/decreasing EELV, consistent with increasing mechanical advantage of diaphragm, but decreased at highest loads, suggesting diaphragm fatigue. Full recovery had not occurred at 30 min after task failure. We demonstrated that progressive threshold loading is associated with systematic changes in breathing pattern that act to optimize muscle strength and increase endurance. Task failure occurred when these compensatory mechanisms were maximal. Inspiratory muscles appeared relatively resistant to fatigue, which was late but persistent.
Discharge Variability of Motor Units in an Intrinsic Muscle of Transplanted Hand (2008)

The study analyzed the discharge characteristics of the motor units in an intrinsic muscle of a transplanted hand. Multichannel electromyographic (EMG) recordings were obtained in 11 experimental sessions over 16 mo starting from day 205 after a hand was transplanted in a 35-yr-old man who had lost his right hand 22 yr earlier. The action potentials discharged by single motor units were identified from the surface EMG signals of the abductor digiti minimi muscle in the transplanted hand as the individual performed 60-s maximal and linearly increasing (ramp) contractions. Discharge rate decreased from 27.1 +/- 8.4 pulses per second (pps) at the start of the maximal contractions to 17.2 +/- 2.9 pps at the end (P < 0.001) and increased from 17.4 +/- 4.3 to 22.1 +/- 5.0 pps during the ramp contractions (P < 0.05). The SD of the interspike interval (ISI) nearly related to the mean ISI with a similar regression slope for the maximal (0.49 +/- 0.09) and ramp contractions (0.43 +/- 0.10). The coefficient of variation for ISI was higher than values in able-bodied persons and did not change during either the maximal (36.8 +/- 10.8%) or the ramp contractions (35.9 +/- 7.4%). High-frequency bursts of activity with <20 ms between two and six action potentials occurred during both maximal and ramp contractions. In conclusion, motor neurons that reinnervated a muscle in a transplanted hand discharged action potentials with a high degree of variability that suggested greater synaptic noise during the voluntary contractions.
Box of Lies: Multimodal Deception Detection in Dialogues (2019)

Felix Soldner, Verónica Pérez-Rosas, Rada Mihalcea. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers). 2019.
Coverage enhancement through two-hop relaying in cellular radio systems (2003)

Digital relaying is a technique that uses certain mobile terminals that have good communication links with the base station to act as relay nodes for those that do not have. With this technique, the signal quality at the destination is expected to improve since the signal only goes through favorable links and, at each intermediate node, the signal is decoded and re-encoded (so that no noise is propagated) before forwarding. One of the major costs of relaying is that additional channels are needed. We investigated the effect of using different schemes for selecting channels - among those already used in the adjacent cells - for relaying on performance improvement. Our simulation results show that not only can relaying improve the performance; but also, with power control this improvement is quite insensitive to the channel selection scheme. Furthermore, with small cell radii where there is a potential for high interference level, only a low relay node transmit power is sufficient to improve the system performance significantly.
Functionalization of Alginate with Extracellular Matrix Peptides Enhances Viability and Function of Encapsulated Porcine Islets (2020)

Translation of transplanted alginate-encapsulated pancreatic islets to treat type 1 diabetes has been hindered by inconsistent long-term efficacy. This loss of graft function can be partially attributed to islet dysfunction associated with the destruction of extracellular matrix (ECM) interactions during the islet isolation process as well as immunosuppression-associated side effects. This study aims at recapitulating islet-ECM interactions by the direct functionalization of alginate with the ECM-derived peptides RGD, LRE, YIGSR, PDGEA, and PDSGR. Peptide functionalization is controlled in a concentration-dependent manner and its presentation is found to be homogeneous across the microcapsule environment. Preweaned porcine islets are encapsulated in peptide-functionalized alginate microcapsules, and those encapsulated in RGD-functionalized alginate displays enhanced viability and glucose-stimulated insulin release. Effects are RGD-specific and not observed with its scrambled control RDG nor with LRE, YIGSR, PDGEA, and PDSGR. This study supports the sustained presentation of ECM-derived peptides in helping to maintain health of encapsulated pancreatic islets and may aid in prolonging longevity of encapsulated islet grafts.
The Hsp90 Inhibitor, Monorden, Is a Promising Lead Compound for the Development of Novel Fungicides (2020)

Endophytic fungi are great resources for the identification of useful natural products such as antimicrobial agents. In this study, we performed the antifungal screening of various plant endophytic fungi against the dollar spot pathogen <i>Sclerotinia homoeocarpa</i> and finally selected <i>Humicola</i> sp. JS-0112 as a potential biocontrol agent. The bioactive compound produced by the strain JS-0112 was identified as monorden known as an inhibitor of heat shock protein 90 (Hsp90). Monorden exhibited strong antagonistic activity against most tested plant pathogenic fungi particularly against tree pathogens and oomycetes with the minimum inhibitory concentration values less than 2.5 μg mL<sup>-1</sup>. Extensive <i>in planta</i> assays revealed that monorden effectively suppressed the development of several important plant diseases such as rice blast, rice sheath blight, wheat leaf rust, creeping bentgrass dollar spot, and cucumber damping-off. Especially, it showed much stronger disease control efficacy against cucumber damping-off than a synthetic fungicide chlorothalonil. Subsequent molecular genetic analysis of fission yeast and <i>Fusarium graminearum</i> suggested that Hsp90 is a major inhibitory target of monorden, and sequence variation among fungal Hsp90 is a determinant for the dissimilar monorden sensitivity of fungi. This is the first report dealing with the disease control efficacy and antifungal mechanism of monorden against fungal plant diseases and we believe that monorden can be used as a lead molecule for developing novel fungicides with new action mechanism for the control of plant diseases caused by fungi and oomycetes.
Rate of Contrast Material Extravasations and Allergic-like Reactions: Effect of Extrinsic Warming of Low-Osmolality Iodinated CT Contrast Material to 37°C (2011)

Extrinsic warming (to 37°C) does not appear to affect adverse event rates for intravenous injections of iopamidol 300 of less than 6 mL/sec but is associated with a significant reduction in extravasation and overall adverse event rates for the more viscous iopamidol 370.
Modification of Energy Level Alignment for Boosting Carbon‐Based CsPbI<sub>2</sub>Br Solar Cells with 14% Certified Efficiency (2021)

Abstract Hole transfer material (HTM)‐free, carbon‐based all‐inorganic perovskite solar cells (C‐PSCs) are promising alternatives to conventional organic–inorganic hybrid PSCs in addressing thermal and moisture instability issues. However, the energy level mismatch between the inorganic perovskite and carbon electrode coupled, together with the incapability of the carbon electrode to reflect incident light for reabsorption, limits the power conversion efficiency (PCE) of C‐PSCs. To address these issues, herein, a new strategy of a hexyltrimethylammonium bromide (HTAB)‐modified CsPbI 2 Br perovskite surface is devised to reduce this energy offset from 0.70 to 0.32 eV and increase the built‐in potential by 70 mV for the final devices. Additionally, a CsPbI 2 Br perovskite film with a thickness of up to 800 nm is realized via a hot‐flow‐assisted spin coating approach in an ambient atmosphere with humidity of less than 80%. Reduced energy offset coupled with suppressed charge recombination and thick perovskite layer boosts the champion PCE of CsPbI 2 Br C‐PSCs to 14.3% ( J sc = 14.1 mA cm −2 , V oc = 1.26 V, and fill factor = 0.806), and the average PCE to 13.9% under one sun illumination. A new certified efficiency record of 14.0% is obtained for HTM‐free inorganic C‐PSCs. Meanwhile, the moisture‐resistant barrier from the alkyl chain in HTAB improves the stability of the final devices.
PS-04-004 Transcriptome-wide Analysis of Peyronie's Disease Plaques using RNA Sequencing Uncovers Targetable Signaling Pathways for Medical Therapy (2019)

[Milenkovic, U.] Katholieke Univ Leuven, Dept Dev & Regenerat, Leuven, Belgium. [Janky, R.; De Ridder, D.; Albersen, M.] Katholieke Univ Leuven, Leuven, Belgium. [Hatzichristodoulou, G.] Julius Maximilians Univ, Wurzburg, Germany. [van Renterghem, K.] Univ Hasselt, Hasselt, Belgium. [Cellek, S.] Anglia Ruskin Univ, Chelmsford, Essex, England. [Bivalacqua, T.] Johns Hopkins Univ, Baltimore, MD USA.
Sex Pheromone of the Queen Butterfly: Biology (1969)

Males of the queen butterfly Danaus gilippus berenice, deprived of the two extrusible brushlike "hairpencils" at the rear of their abdomen, are capable of courting females but incapable of seducing them. In normal courtship, an aphrodisiac secretion associated with the hairpencils is transferred by way of tiny cuticular "dust" particles to the antennae of the females. Of the two substances identified from the secretion, one (the ketone) acts as the chemical messenger that induces the females to mate. The only known function of the other compound (the diol) is to serve as a glue that sticks the dust to the female. Males were reared under conditions in which they produced subnormal amounts of ketone and showed reduced seductive capacity. Under certain experimental circumstances, the competence of these males was restored by addition of synthetic ketone.
Mouthpiece Use Reduces Post Exercise Serum Cortisol Levels (2012)

Recent work has shown that a lower jaw mouthpiece (MP) can decrease lactate, improve airway dynamics and decrease salivary cortisol following exercise. This study aimed to determine if wearing a lower jaw MP (ArmourBite Technology) altered serum cortisol in 13 collegiate‐aged males during or after physical work. At least 7 days following one repetition maximum (1RM) testing, subjects completed 2 trials, separated by 7 days, of 6 sets x 10 repetitions of back squats with 2 min rest between sets. Load was set at 80% of each subject's 1RM and resistance was adjusted during testing so subjects completed 10 repetitions during each set. Treatment order was randomized and blood was sampled: pre exercise, after 3 sets (mid), post exercise, 30, 60 and 120 min post exercise. Each sample was labeled and frozen for determination of cortisol (ìg/dL) via ELISA (ALPCO Diagnostics, Salem, NH). There was no difference in pre exercise cortisol between groups (MP: 21.55±9.82 vs 25.58±10.88). The MP group had lower (P&lt;.05) cortisol levels at mid (MP: 19.39±6.90 vs 27.84±14.55) and post 30 (MP: 22.91±8.47 vs 31.81±10.79), while no differences existed immediately post exercise, post 60, or post 120. These results confirm in serum that the use of lower jaw MPs attenuates the cortisol response following strenuous physical exercise. This suggests that the use of a MP may aid in post exercise recovery and may diminish the stress of physical exercise.
Evaluation of stress stabilities in amorphous In–Ga–Zn–O thin-film transistors: Effect of passivation with Si-based resin (2017)

Fabrication process conditions of a passivation (PV) layer correlated with stress stabilities of amorphous In–Ga–Zn–O (a-IGZO) thin-film transistors (TFTs). In etch-stop layer (ESL)-TFTs, by inserting a Si-based resin between SiNx and SiOx PV layers, the peak intensity in the photoinduced transient spectroscopy (PITS) spectrum was notably reduced. This suggested the suppression of hydrogen incorporation into a-IGZO, which led to the improvement of stability under negative bias thermal illumination stress (NBTIS). In contrast, the hydrogen-related defects in the a-IGZO were easily formed by the back-channel etch (BCE) process. Furthermore, it was found that, under NBTIS, the transfer curves of the BCE-TFTs shifted in parallel owing to the positive fixed charge located in the back channel of the a-IGZO TFTs. The hump-shaped shift increased with stress time. This is because hydrogen atoms located at the back-channel surfaces of the a-IGZO and/or PV layers were incorporated into the channel region of the BCE-TFTs and induced the hydrogen-related defects.
Inactivation decoding analysis for LT codes (2015)

We provide two analytical tools to model the inactivation decoding process of LT codes. First, a model is presented which derives the expected number of inactivations occurring in the decoding process of an LT code. This analysis is then extended allowing the derivation of the distribution of the number of inactivations. The accuracy of the method is verified by Monte Carlo simulations. The proposed analysis opens the door to the design of LT codes optimized for inactivation decoding.
Upgrade of the Photon Factory Control System (2007)

The Photon Factory control system was originally developed more than 20 years ago and has been upgraded several times. As a part of the straight‐sections upgrade, which started in March, 2005, we renewed the control system incorporating modern technologies in both low‐level and high‐level control layers. In the low‐level layer, a PLC (Programmable Logic Controller) is now intensively used for title safety control system, for RF klystron control boards and for the vacuum control system. In the middle‐level and high‐level layers, the EPICS (Experimental Physics and Industrial Control System) software toolkit was adopted. We also replaced VME‐board computers with HP‐RT operating system by Linux‐based computers, which are now used as input/output controllers (IOCs) for the EPICS. The new system has been running without any serious problems since its commissioning in September, 2005.
Elucidating the oncogene-driven regulatory T cell responses during melanoma tumorigenesis. (2016)

Abstract Regulatory T cells (Tregs) are critical mediators of tumor immune suppression. While Tregs are found in established tumors, little is known about the kinetics and dynamics of Treg accumulation and the factors promoting it during oncogene-driven tumorigenesis. The present studies characterize Treg response kinetics and conversion dynamics during early tumor development in a model of autochthonous, tamoxifen-inducible BrafV600E Pten−/− melanoma. While microscopic skin dysplasia appeared 16 days following tumor induction, FoxP3+ Treg frequency and absolute numbers accumulated by day 26, coinciding with locally-invasive neoplasm development. BrafV600E inhibition with PLX4720 prevented Treg accumulation, suggesting that oncogenic Braf controls this process. Following adoptive transfer of CD4+ T cells specific to TRP-1, antigen-specific FoxP3+ Tregs preferentially accumulated in tumor-induced skin and draining lymph nodes (dLNs), as compared to tumor-free counterparts. In contrast, depleting Tregs prior to transfer abrogated the TRP-1-specific Treg response, suggesting a predominant role for natural Tregs. Furthermore, we observed an increase in chemokine (C-C motif) ligand 17 (Ccl17) and Ccl2 prior to Treg influx to tumor-induced skin. Oncogenic Braf regulated expression of Ccl17 and Ccl2, both of which mediated Treg migration in vitro. We are currently investigating the putative role of Ccl17/2-Ccr4 chemotactic axis in Treg recruitment to sites of Braf-driven tumorigenesis in vivo.
Chemical Interaction among Termite-Associated Microbes (2017)

Bacteria and fungi in shared environments compete with one another for common substrates, and this competition typically involves microbially-produced small molecules. An investigation of one shared environmental niche, the carton material of the Formosan subterranean termite Coptotermes formosanus, identified the participants on one of these molecular exchanges. Molecular characterization of several termite-associated actinobacteria strains identified eleven known antimicrobial metabolites that may aid in protecting the C. formosanus colony from pathogenic fungal infections. One particular actinobacterial-derived small molecule, bafilomycin C1, elicited a strong chemical response from Trichoderma harzianum, a common soil saprophyte. Upon purification and structure elucidation, three major fungal metabolites were identified, t22-azaphilone, cryptenol, and homodimericin A. Both t22-azaphilone and homodimericin A are strongly upregulated, 123- and 38-fold, respectively, when exposed to bafilomycin C1, suggesting each play a role in defending T. harzianum from the toxic effect of bafilomycin C1.