gebhart/patrepeval huggingface dataset:
Cortico-muscular coherence increases with tremor improvement after deep brain stimulation in Parkinson's disease (2009)

Deep brain stimulation on the subthalamic nucleus has been used to relieve Parkinsonian motor symptoms. However, the underlying physiological mechanism has not been fully understood. Beta-band cortico-muscular coherence increases when healthy humans perform isometric contraction. We hypothesized that this might be a measure of symptomatic improvement in motor performance after subthalamic nucleus deep brain stimulation. Here, we measured the beta-band cortico-muscular coherence with magnetoencephalography from three Parkinson's disease patients. We then compared the coherence values for stimulator on-state and off-state. We found that when the stimulator is on, the beta cortico-muscular coherence elevates significantly for the tremorous hand compared with that when the stimulator is off. This suggests that deep brain stimulation resulted in better cortico-muscular coordination.
Subchronic Exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin Modulates the Pathophysiology of Endometriosis in the Cynomolgus Monkey (2000)

An increase in the incidence and severity of endometriosis following treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) was a serendipitous finding in a reproductive toxicology study in rhesus monkeys. The purpose of this study was to investigate the effects of subchronic exposure to TCDD on the survival and growth of surgically implanted endometrial fragments. Endometrial fragments of equal size (4 x 1 mm(2)) were auto-transplanted to the pelvic cavity of nulliparous cynomolgus monkeys (Macaca fascicularis, n = 23), who were divided into 4 treatment groups and dosed 5 days a week with gelatin capsules containing 0, 1, 5, or 25 ng/kg body weight of TCDD mixed with glucose. Endometrial implant survival was monitored by laparoscopy at intervals of 1, 3, and 6 months. Animals were euthanized at 12 months of treatment in the early to mid luteal phase and the maximal and minimal endometrial implant diameter was measured. Both the maximal and minimal diameters were significantly reduced in the 0.71-ng/kg/day-TCDD dose group, compared to controls, whereas the survival rate was unaffected (20 vs. 16%, respectively). In contrast, exposure to 3.57 and 17.86 ng/kg/day TCDD for 1 year resulted in a significantly higher survival rate of implants (26.7% and 33.3% respectively vs. 16.0%) and significantly larger diameter implants in the 17.86-ng/kg/day dose group only, compared to the control group. Treatment had no effect on circulating gonadal steroid levels or menstrual cycle characteristics. It is concluded that TCDD facilitates the survival of endometrial implants and exerts a bimodal effect on endometrial implant growth.
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data (2013)

The novel high-throughput technology of protein-binding microarrays (PBMs) measures binding intensity of a transcription factor to thousands of DNA probe sequences. Several algorithms have been developed to extract binding-site motifs from these data. Such motifs are commonly represented by positional weight matrices. Previous studies have shown that the motifs produced by these algorithms are either accurate in predicting in vitro binding or similar to previously published motifs, but not both. In this work, we present a new simple algorithm to infer binding-site motifs from PBM data. It outperforms prior art both in predicting in vitro binding and in producing motifs similar to literature motifs. Our results challenge previous claims that motifs with lower information content are better models for transcription-factor binding specificity. Moreover, we tested the effect of motif length and side positions flanking the “core” motif in the binding site. We show that side positions have a significant effect and should not be removed, as commonly done. A large drop in the results quality of all methods is observed between in vitro and in vivo binding prediction. The software is available on acgt.cs.tau.ac.il/rap.
CCDC 639875: Experimental Crystal Structure Determination (2016)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Bcl-2 and Bcl-XL Can Differentially Block Chemotherapy-Induced Cell Death (1997)

Bcl-2 and its homologue Bcl-XL are expressed in a variety of tumors and their expression modulates the sensitivity of tumor cells to a wide spectrum of chemotherapeutic agents and γ-irradiation. In the present report, we generated clones of FL5.12 lymphoid cells with similar levels of Bcl-2 and Bcl-XL using the Flag epitope to determine if these survival proteins could provide equivalent protection when challenged with chemotherapy or γ-irradiation. Using four M-phase specific chemotherapeutic agents, Bcl-XL and Bcl-2 provided similar protection against vincristine and vinblastine whereas Bcl-XL afforded as much as 50% greater cell viability than Bcl-2 against etoposide and teniposide-induced cell death. In addition, Bcl-XL provided significantly greater cell viability than Bcl-2 against methotrexate, fluorouracil, and hydroxyurea, three S-phase specific agents. In apoptosis induced by γ-irradiation and cisplatin, two antitumor treatments that are cell-cycle phase-nonspecific agents, both Bcl-XL and Bcl-2 conferred similar protection against γ-irradiation, but Bcl-XL provided better protection than Bcl-2 against cisplatin. These results indicate that Bcl-XL and Bcl-2 confer a differential ability to protect against chemotherapy-induced cell death, which appears to be dependent on the molecular mechanism targeted by the drug rather than its cell-cycle phase specificity.
Novel Specific Pyruvate Kinase M2 Inhibitor, Compound 3h, Induces Apoptosis and Autophagy through Suppressing Akt/mTOR Signaling Pathway in LNCaP Cells (2022)

Pyruvate kinase M2 (PKM2) is a key enzyme involved in the regulation of glycolysis. Although PKM2 is overexpressed in various tumor tissues, its functional role in cancer chemotherapy remains unexplored. In this study, we investigated the anticancer activity of a new PKM2 inhibitor, compound <b>3h</b>, through the cell metabolism and associated signaling pathways in prostate cancer cells. To evaluate the molecular basis of specific PKM2 inhibitors, the interactions of compounds <b>3h</b> and <b>3K</b> with the PKM2 protein were assessed via molecular docking. We found that, compared to compound <b>3K</b>, compound <b>3h</b> exhibited a higher binding affinity for PKM2. Moreover, compound <b>3h</b> significantly inhibited the pyruvate kinase activity and PKM2 expression. Cytotoxicity and colony formation assays revealed the potent anticancer activity of compound <b>3h</b> against LNCaP cells. Compound <b>3h</b> significantly increased the apoptotic and autophagic cell death in LNCaP cells. In addition, compound <b>3h</b> induced AMPK activation along with the inhibition of the mTOR/p70S6K pathway. Furthermore, compound <b>3h</b> significantly inhibited glycolysis and mitochondrial respiration, as determined by analyzing the extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) production. Our results revealed that compound <b>3h</b> caused apoptotic and autophagic cell death in LNCaP cells by inhibiting cancer cell metabolism. Therefore, blocking glycolytic pathways using specific PKM2 inhibitors can target cancer cell metabolism in PKM2-overexpressed prostate cancer cells.
Artificial Birefringence with Moving Metasurfaces (2021)

We theoretically characterize a compact optical polarizer consisting of two cascaded metasurfaces. The relative movement of the metasurfaces is tailored to create an artificial birefringence effect which is utilized to design optical waveplates.
&lt;title&gt;Use of collateral text in understanding photos in documents&lt;/title&gt; (1994)

This research explores the interaction of textural and photographic information in document understanding. Specifically, it presents a computational model whereby textural captions are used as collateral information in the interpretation of the corresponding photographs. The final understanding of the picture and caption reflects a consolidation of the information obtained from each of the two sources and can thus be used in intelligent information retrieval tasks. The problem of performing general-purpose vision without a-priori knowledge is very difficult at best. The concept of using collateral information in scene understanding has been explored in systems that use general scene context in the task of object identification. The work described here extends this notion by incorporating picture specific information. A multistage system PICTION, which uses captions to identify humans in an accompanying photograph, is described. This provides a computationally less expensive alternative to traditional methods of face recognition. It does not require a prestored database of face models for all people to be identified. A key component of the system is the utilization of spatial and characteristic constraints (derived from the caption) in labeling face candidates (generated by a face locator).
Neurobiología de la adicción a opiáceos. (2005)

"Los opiáceos poseen una gran capacidad adictiva y su administración incontrolada produce una serie de cambios adaptativos a nivel celular y molecular en diversos sistemas neuroquímicos que origina la aparición de un cuadro de dependencia. Los fenómenos adictivos inducidos por los opioides y otras drogas de abuso están relacionados tanto con los efectos reforzantes de estas drogas como con la necesidad que se genera en el adicto para paliar las consecuenciasnegativas de la ausencia de las mismas. Estudios bioquímicos, farmacológicos, electrofisiológicos y moleculares han identificado diversos sistemas neuroquímicos que constituyen un sustrato común para los efectos reforzantes inducidos por diferentes drogas de abuso incluídos los opioides. Este sustrato integra al sistema mesolímbico y en particular a dos sistemas neuroquímicos, el dopaminérgico y el opioide. El sistema dopaminérgico mesolímbico junto con los circuitos cerebrales que controlan las respuestas al estrés representan el principal sustrato neurobiológico para las manifestaciones motivacionales de la abstinencia de opioides. Finalmente, los opiáceos inducen algunas modificaciones persistentes a nivel de determinados factores de transcripción que podrían participar en la mayor vulnerabilidad para la recaída incluso después de un periodo prolongado de ausencia de consumo de droga."
Implementation of large-scale routine diagnostics using whole slide imaging in Sweden: Digital pathology experiences 2006-2013 (2014)

Recent technological advances have improved the whole slide imaging (WSI) scanner quality and reduced the cost of storage, thereby enabling the deployment of digital pathology for routine diagnostics. In this paper we present the experiences from two Swedish sites having deployed routine large-scale WSI for primary review. At Kalmar County Hospital, the digitization process started in 2006 to reduce the time spent at the microscope in order to improve the ergonomics. Since 2008, more than 500,000 glass slides have been scanned in the routine operations of Kalmar and the neighboring Linköping University Hospital. All glass slides are digitally scanned yet they are also physically delivered to the consulting pathologist who can choose to review the slides on screen, in the microscope, or both. The digital operations include regular remote case reporting by a few hospital pathologists, as well as around 150 cases per week where primary review is outsourced to a private clinic. To investigate how the pathologists choose to use the digital slides, a web-based questionnaire was designed and sent out to the pathologists in Kalmar and Linköping. The responses showed that almost all pathologists think that ergonomics have improved and that image quality was sufficient for most histopathologic diagnostic work. 38 ± 28% of the cases were diagnosed digitally, but the survey also revealed that the pathologists commonly switch back and forth between digital and conventional microscopy within the same case. The fact that two full-scale digital systems have been implemented and that a large portion of the primary reporting is voluntarily performed digitally shows that large-scale digitization is possible today.
Highly Linear Broadband Photonic-Assisted Q-Band ADC (2015)

A highly linear broadband photonic-assisted analog-to-digital converter (ADC) based on high-frequency optical sampling utilizing a dual output Mach-Zehnder modulator operating with signal frequencies up to 50 GHz is presented. The pulses employed in the optical sampling were generated by a cavity-less pulse source operated at 10 GHz in preference to conventional mode-locked lasers. The optical sampling front-end greatly extends the operational frequency range of the Nyquist limited electronic digitization back-end. The performance of the sampling system is characterized with 7.1 effective number of bits (ENOBs) at 40 with 5 GHz fully accessible bandwidth, and greater than 99 dB·Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sup> spurious free dynamic range for the 30-40 GHz frequency range. Furthermore, more than 8 ENOB was achieved by reducing the effective bandwidth to 1 GHz with a digital filter, demonstrating the additional advantage of using a higher sampling rate compared to previous demonstrations. A new figure of merit of photonic-assisted sub-sampled ADCs is also presented accompanied with a comparison to previous implementations.
Isosorbide and dimethyl carbonate: a green match (2016)

In this review the reactivity of the bio-based platform compounds D-sorbitol and isosorbide with green reagents and solvent dimethyl carbonate (DMC) is reported. Dehydration of D-sorbitol via DMC in the presence of catalytic amounts of base is an efficient and viable process for the preparation of the industrially relevant anhydro sugar isosorbide. This procedure is "chlorine-free", one-pot, environmental friendly and high yielding. The reactivity of isosorbide with DMC is equally interesting as it can lead to the formation of dicarboxymethyl isosorbide, a potential monomer for isosorbide-based polycarbonate, and dimethyl isosorbide, a high boiling green solvent. The peculiar reactivity of isosorbide and the non-toxic properties of DMC represent indeed a green match leading to several industrial appealing potential applications.
Motor block in regional anaesthesia (2001)

A device based on a load cell was constructed to measure the strength of foot dorsiflexion and plantarflexion. Performance of the device was evaluated for both movements. The influence of foot position within the device, its use over a 30‐min period at 30‐s intervals and the effect of the removal and reapplication of the device on measured force of dorsiflexion and plantarflexion was studied in six volunteers. Both dorsiflexion and plantarflexion are suitable movements on which to base a device to quantify the density of motor block during the onset and offset of neuraxial block. Dorsiflexion has a number of advantages: muscle strength is independent of knee position, and therefore a below‐knee device can be constructed; strength of dorsiflexion is less affected by the foot position; we found the device easier to apply using dorsiflexion as the heel tended to self‐locate; innervation of the muscles responsible for dorsiflexion involves fewer spinal segments.
Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives (2005)

Pyridoxal kinase (PDXK) catalyzes the phosphorylation of pyridoxal, pyridoxamine, and pyridoxine in the presence of ATP and Zn2+. This constitutes an essential step in the synthesis of pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, a cofactor for over 140 enzymes. (R)-Roscovitine (CYC202, Seliciclib) is a relatively selective inhibitor of cyclin-dependent kinases (CDKs), currently evaluated for the treatment of cancers, neurodegenerative disorders, renal diseases, and several viral infections. Affinity chromatography investigations have shown that (R)-roscovitine also interacts with PDXK. To understand this interaction, we determined the crystal structure of PDXK in complex with (R)-roscovitine, N6-methyl-(R)-roscovitine, and O6-(R)-roscovitine, the two latter derivatives being designed to bind to PDXK but not to CDKs. Structural analysis revealed that these three roscovitines bind similarly in the pyridoxal-binding site of PDXK rather than in the anticipated ATP-binding site. The pyridoxal pocket has thus an unexpected ability to accommodate molecules different from and larger than pyridoxal. This work provides detailed structural information on the interactions between PDXK and roscovitine and analogs. It could also aid in the design of roscovitine derivatives displaying strict selectivity for either PDXK or CDKs.
Electron beam irradiated silver nanowires for a highly transparent heater (2015)

Transparent heaters have attracted increasing attention for their usefulness in vehicle windows, outdoor displays, and periscopes. We present high performance transparent heaters based on Ag nanowires with electron beam irradiation. We obtained an Ag-nanowire thin film with 48 ohm/sq of sheet resistance and 88.8% (substrate included) transmittance at 550 nm after electron beam irradiation for 120 sec. We demonstrate that the electron beam creates nano-soldering at the junctions of the Ag nanowires, which produces lower sheet resistance and improved adhesion of the Ag nanowires. We fabricated a transparent heater with Ag nanowires after electron beam irradiation, and obtained a temperature of 51 °C within 1 min at an applied voltage of 7 V. The presented technique will be useful in a wide range of applications for transparent heaters.
Airflow Dynamics of Human Jets: Sneezing and Breathing - Potential Sources of Infectious Aerosols (2013)

Natural human exhalation flows such as coughing, sneezing and breathing can be considered as 'jet-like' airflows in the sense that they are produced from a single source in a single exhalation effort, with a relatively symmetrical, conical geometry. Although coughing and sneezing have garnered much attention as potential, explosive sources of infectious aerosols, these are relatively rare events during daily life, whereas breathing is necessary for life and is performed continuously. Real-time shadowgraph imaging was used to visualise and capture high-speed images of healthy volunteers sneezing and breathing (through the nose - nasally, and through the mouth - orally). Six volunteers, who were able to respond to the pepper sneeze stimulus, were recruited for the sneezing experiments (2 women: 27.5±6.36 years; 4 men: 29.25±10.53 years). The maximum visible distance over which the sneeze plumes (or puffs) travelled was 0.6 m, the maximum sneeze velocity derived from these measured distances was 4.5 m/s. The maximum 2-dimensional (2-D) area of dissemination of these sneezes was 0.2 m(2). The corresponding derived parameter, the maximum 2-D area expansion rate of these sneezes was 2 m(2)/s. For nasal breathing, the maximum propagation distance and derived velocity were 0.6 m and 1.4 m/s, respectively. The maximum 2-D area of dissemination and derived expansion rate were 0.11 m(2) and 0.16 m(2)/s, respectively. Similarly, for mouth breathing, the maximum propagation distance and derived velocity were 0.8 m and 1.3 m/s, respectively. The maximum 2-D area of dissemination and derived expansion rate were 0.18 m(2) and 0.17 m(2)/s, respectively. Surprisingly, a comparison of the maximum exit velocities of sneezing reported here with those obtained from coughing (published previously) demonstrated that they are relatively similar, and not extremely high. This is in contrast with some earlier estimates of sneeze velocities, and some reasons for this difference are discussed.
Complement activation and inflammation triggered by model biomaterial surfaces (1998)

Biomaterial-mediated complement activation repeatedly has been invoked as a trigger of phagocyte reactions and inflammation. However, a direct correlation between complement activation and inflammatory responses to biomaterial surfaces has yet to be established. Using an animal implantation model and gold surfaces bearing various thiol-linked functionalities, we investigated the potency of different surface groups in prompting complement activation in vitro and surface-mediated accumulation of inflammatory cells in vivo. Among the surfaces tested, mercaptoglycerol- and mercaptoethanol-bearing surfaces engendered the strongest inflammatory responses, as reflected by the accumulation of large numbers of adherent neutrophils and monocytes/macrophages. In contrast, L-cysteine-coated surfaces caused only minor inflammatory responses, and both glutathione-modified and untreated gold implants attracted minimal numbers of inflammatory cells. The accumulation of inflammatory cells on mercaptoglycerol surfaces appears to arise from surface-mediated complement activation because complement-depleted animals failed to exhibit inflammatory responses to mercaptoglycerol-modified implants. Furthermore, there is a close relationship between surface-mediated complement activation (as measured by in vitro iC3b/C5b-9 generation and C3 deposition) and in vivo inflammatory responses. At least in this animal model and with these model surfaces, our results indicate that surface-mediated complement activation can be responsible for the subsequent accumulation of inflammatory cells on implant surfaces.
Photoemission from<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">C</mml:mi></mml:mrow><mml:mrow><mml:mn>8</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Rb and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">C</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">RbTl</mml:mi></mml:mrow><mml:mrow><mml:mn>1.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>: Effects of ternarization in donor graphite intercalates (1987)

The electronic structure of the ternary donor graphite intercalation compound (DGIC) ${\mathrm{C}}_{4}$${\mathrm{RbTl}}_{1.5}$ has been studied with various techniques of photoemission. Ultraviolet photoelectron spectroscopy, x-ray photoelectron spectroscopy, and Auger electron spectroscopy were used to study the electronic effects of the cointercalation of thallium into the first-stage binary precursor intercalation compound ${\mathrm{C}}_{8}$Rb. In the ternary DGIC a significant Rb-Tl interaction modifies the charge transfer from the donor alloy to the graphite host. The results indicate a substantial charge transfer from the alkali metal to graphite-derived \ensuremath{\pi} states which is reduced upon ternarization. The reactivities of clean surfaces of elemental thallium and of the ternary intercalation compound towards oxidation have been investigated. Different reaction products and pathways of oxidation were found. The experimental data presented suggest that the mechanism of charge transfer is better described in the hybridization model rather than in the approximation of complete ionicity.