gebhart/patrepeval huggingface dataset:
Von Willebrand Factor-Dependent Inflammatory Responses in Mouse Septic Model By Cecal Ligation and Puncture (2014)

Abstract Sepsis is a serious inflammatory response syndrome, in which systemic activation of both inflammatory and coagulation pathways are provoked by severe microbial infection. In addition to the known hemostatic functions, von Willebrand factor (VWF) is recently assumed to participate in a cross-talk between inflammation and thrombosis. Indeed, recent mouse model studies demonstrated that proper functional regulation of VWF-dependent inflammatory responses by ADAMTS13 considerably improved the disease progression of brain stroke or myocardial infarction. However, little is known about the detailed mechanisms or relevant role of VWF functions in inflammation. We therefore studied the physiologic relevance of VWF-dependent inflammatory responses in a mouse model of experimental sepsis by cecal ligation and puncture (CLP). The mouse CLP was performed according to the established standard protocol (Rittirsch D, et al., Nat Protoc, 2009). Briefly, mouse cecum was ligated distal to the ileocecal valve under laparotomy, punctured with 18 gauge needle and gently pressed until a small drop of stool appeared. The cecum was returned to the peritoneal cavity and 200 μL of saline was injected into the cavity to avoid dehydration before body wall and skin incision were closed with a 4-0 Sofsilk. We compared 17 wild-type (WT) and 17 VWF-gene deleted (knock-out; KO) mice (from The Jackson Laboratory, Bar Harbor, ME), all of which were 10-12 weeks of age, healthy and fertile. Excess blood loss was not observed in all (WT or KO) mice during the CLP operation. Kaplan-Meier analysis revealed the significantly (p &lt; 0.05) lower survival rate of KO mice than that of WT (KO; 23.5% vs. WT; 58.8% at the Day 7 of CLP). The impaired survival rate of KO mice was restored by the bolus administration of human VWF (n=21, 2.5 U/mouse) to an extent comparable to that of WT. Peripheral blood analysis of KO mice at 24 hours after CLP showed the severe leukocytopenia with sharp decrease of neutrophils in blood, as compared to WT. In addition, formation of walled-off abscess was confirmed at the peri-cecal space in all the WT and KO mice alive even at the Day 7 of CLP, while such focal abscess formation was not found in mice died before the Day 3 of CLP. Thus, our results altogether indicate that VWF could play a role on the recruitment or accumulation of neutrophils for microbial killing at the local inflammatory focus. VWF-mediated platelet aggregate formation in peripheral capillary vessels then could shut down the local microcirculation, thereby blocking systemic microbial expansion as a crucial biological defense mechanism. Disclosures Shima: Chugai Pharmaceutical Co., Ltd.: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.
Structural insight into the calcium ion modulated interdomain electron transfer in cellobiose dehydrogenase (2015)

Cellobiose dehydrogenase (CDH) from wood degrading fungi represents a subclass of oxidoreductases with unique properties. Consisting of two domains exhibiting interdomain electron transfer, this is the only known flavocytochrome involved in wood degradation. High resolution structures of the separated domains were solved, but the overall architecture of the intact protein and the exact interface of the two domains is unknown. Recently, it was shown that divalent cations modulate the activity of CDH and its pH optimum and a possible mechanism involving bridging of negative charges by calcium ions was proposed. Here we provide a structural explanation of this phenomenon confirming the interaction between negatively charged surface patches and calcium ions at the domain interface.
Enhanced Carbon Dioxide Reduction Activity on Indium-Based Nanoparticles (2016)

Nanoparticles of indium, indium hydroxide, and indium oxide were synthesized and evaluated for their electrocatalytic abilities in the reduction of CO2 to formate. These nanoparticles were characterized with several microscopic and spectroscopic techniques in order to investigate their structure and surface features. Their electrochemical behavior was also probed through voltammetry and bulk electrolysis. faradaic efficiencies approaching 100% were achieved on these particles at potentials as positive as −1.3 V vs. Ag/AgCl, which represents a significant decrease in the overpotential compared to that observed using bulk indium electrodes. The nanostructuring of the particles and the partial surface oxidation of the indium nanoparticles to yield catalytic surface indium hydroxide species are implicated in the high efficiencies at low overpotentials.
ROMP from ROMP: A New Approach to Graft Copolymer Synthesis (2009)

A new strategy is presented for the synthesis of graft copolymers using only the ring-opening metathesis polymerization (ROMP). From a ROMP-derived main chain, pendant maleimide functional groups are converted into norbornene moieties via a Diels-Alder reaction with cyclopentadiene. The norbornene groups serve as sites of initiation, and subsequent ROMP from the main chain yields graft copolymers with both main and side chains derived from ROMP. This strategy offers ready access to defined graft copolymers.
Supplementary Table 1 from Targeting CD4<sup>+</sup> T-Helper Cells Improves the Induction of Antitumor Responses in Dendritic Cell–Based Vaccination (2023)

&lt;p&gt;PDF file - 52K, Characteristics matched controls&lt;/p&gt;
Mechanistic and functional differentiation of tapentadol and tramadol (2012)

The distinct properties of tapentadol and tramadol generate different CNS functional activities, making each drug the prototype of different classes of opioid/nonopioid analgesics. Tramadol's analgesia derives from relatively weak µ-opioid receptor (MOR) agonism, plus norepinephrine and serotonin reuptake inhibition, provided collectively by the enantiomers of the parent drug and a metabolite that is a stronger MOR agonist, but has lower CNS penetration. Tapentadol's MOR agonist activity is several-fold greater than tramadol's, with prominent norepinephrine reuptake inhibition and minimal serotonin effect. Accordingly, tramadol is well-suited for pain conditions for which a strong opioid component is not needed-and it has the benefit of a low abuse potential; whereas tapentadol, a schedule-II controlled substance, is well-suited for pain conditions requiring a strong opioid component-and it has the benefit of greater gastrointestinal tolerability compared to classical strong opioids. Both drugs offer distinct and complementary clinical options.
Gli strumenti per governare (2009)

Più che a fattori geografici e commerciali, lo sviluppo economico di uno stato è legato alla qualità delle sue istituzioni. Puntare a questo sviluppo significa assicurarsi delle istituzioni che funzionino. Le istituzioni sono le regole fondamentali del gioco, gli strumenti necessari per governare. E questi strumenti non sono affatto neutrali: essi veicolano valori, creano abitudini e schemi di pensiero.\nRecuperando la grande tradizione di studi inaugurata da Max Weber e Michel Foucault, gli autori si interrogano sui complessi rapporti fra società politica e società civile, individuando in questi strumenti una chiave fondamentale per comprendere le cause dell’inerzia e dei grandi cambiamenti della nostra società. Dopo il grande dibattito sollevato in Francia e nel mondo anglosassone, l’edizione italiana curata da Tommaso Vitale presenta delle versioni aggiornate dei saggi originali, che tengono maggiormente conto delle specificità del caso italiano, in prospettiva comparata. (Résumé éditeur)
Folding Lennard-Jones proteins by a contact potential (1999)

We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native) conformations were then identified by Molecular Dynamics. Then we turned to investigate whether one can find a pairwise contact potential, whose ground states are the contact maps associated with these native conformations. We show that such a requirement cannot be satisfied exactly - i.e. no such contact parameters exist. Nevertheless, we found that one can find contact energy parameters for which an energy minimization procedure, acting in the space of contact maps, yields maps whose corresponding structures are close to the native ones. Finally we show that when these structures are used as the initial point of a Molecular Dynamics energy minimization process, the correct native folds are recovered with high probability.
Entirely VPE-grown 1-5μm DFB lasers with low threshold currents (1987)

Entirely hydride VPE-grown 1.5μm DFB lasers have been obtained by means of high controllability in film thickness and alloy composition for the GalnAsP/InP system. A low threshold current of 13 mA was achieved by improving the growth method for the layer burying the grating. High uniformity in threshold current and lasing wavelength (Ith = 27.3 ± 9.7 mA, λ = 15571 ± 12Å) was obtained.
. Microbial Genomics and Global Health (2012)

Abstract Over the past two decades, microbiology and infectious disease research have undergone the most profound revolution since the times of Pasteur. Genomic sequencing has revealed the much-awaited blueprint of most pathogens. Screening blood for the nucleic acids of infectious agents has blunted the spread of pathogens by transfusion, the field of antiviral therapeutics has exploded, and technologies for the development of novel and safer vaccines have become available. The quantum jump in our ability to detect, prevent, and treat infectious diseases resulting from improved technologies and genomics was moderated during this period by the greatest emergence of new infectious agents ever recorded, and a worrisome increase in resistance to existing therapies. Dozens of new infectious diseases are expected to emerge in the coming decades. Controlling these diseases will require a better understanding of the worldwide threat and economic burden of infectious diseases, and a global agenda. This chapter focuses on the major changes in infectious diseases and the scientific progress in the field during the last two decades, and how this may impact on global health.
Practicing the top antireflector process (1992)

Thickness variations in photoresist caused by substrate topography, and normal variations in deposited thin films, arc unavoidable sources of linewidth variation in optical lithography. Thin film interference effects cause exposure to vary by large amounts. A new approach to controlling these effects is the use of a top antircficctor (TAR) film on top of the photoresist. In this paper, the performance of a process using a water soluble TAR material is described. Simulation and experimental results arc given which show the effectiveness in controlling wafer reflectivity, and exposure dose in the presence of varying insulator and resist films. The effect of the TAR process on focus and exposure latitude is examined and initial results from device manufacturing are presented.
Aqueous-Phase Methane Oxidation over Fe-MFI Zeolites; Promotion through Isomorphous Framework Substitution (2013)

Fe- and Cu-containing zeolites have recently been shown to be efficient catalysts for the one-step selective transformation of methane into methanol in an aqueous medium at only 50 °C, using H2O2 as green oxidant. Previously, we have observed that Fe species alone are capable of catalyzing this highly selective transformation. However, further catalytic testing and spectroscopic investigations demonstrate that although these extra-framework Fe species are the active component of the catalyst, significant promotion is observed upon the incorporation of other trivalent cations, e.g., Al3+ or Ga3+, into the MFI-framework. While these additional framework species do not constitute active catalytic centers, promotion is observed upon their incorporation as they (1) facilitate the extraction of Fe from the zeolite framework and hence increase the formation of the active Fe species and (2) provide an associated negatively charged framework, which is capable of stabilizing and maintaining the dispersion of the cationic extra-framework Fe species responsible for catalytic activity. By understanding these phenomena and subsequently controlling the overall composition of the catalyst (Fe and Al), we have subsequently been able to prepare a catalyst of equal intrinsic activity (i.e., TOF) but five-times higher productivity (i.e., space-time-yield) compared with the best catalysts reported for this reaction to date.
A Chemical Genetics Analysis of the Roles of Bypass Polymerase DinB and DNA Repair Protein AlkB in Processing N2-Alkylguanine Lesions In Vivo (2014)

DinB, the E. coli translesion synthesis polymerase, has been shown to bypass several N2-alkylguanine adducts in vitro, including N2-furfurylguanine, the structural analog of the DNA adduct formed by the antibacterial agent nitrofurazone. Recently, it was demonstrated that the Fe(II)- and α-ketoglutarate-dependent dioxygenase AlkB, a DNA repair enzyme, can dealkylate in vitro a series of N2-alkyguanines, including N2-furfurylguanine. The present study explored, head to head, the in vivo relative contributions of these two DNA maintenance pathways (replicative bypass vs. repair) as they processed a series of structurally varied, biologically relevant N2-alkylguanine lesions: N2-furfurylguanine (FF), 2-tetrahydrofuran-2-yl-methylguanine (HF), 2-methylguanine, and 2-ethylguanine. Each lesion was chemically synthesized and incorporated site-specifically into an M13 bacteriophage genome, which was then replicated in E. coli cells deficient or proficient for DinB and AlkB (4 strains in total). Biochemical tools were employed to analyze the relative replication efficiencies of the phage (a measure of the bypass efficiency of each lesion) and the base composition at the lesion site after replication (a measure of the mutagenesis profile of each lesion). The main findings were: 1) Among the lesions studied, the bulky FF and HF lesions proved to be strong replication blocks when introduced site-specifically on a single-stranded vector in DinB deficient cells. This toxic effect disappeared in the strains expressing physiological levels of DinB. 2) AlkB is known to repair N2-alkylguanine lesions in vitro; however, the presence of AlkB showed no relief from the replication blocks induced by FF and HF in vivo. 3) The mutagenic properties of the entire series of N2-alkyguanines adducts were investigated in vivo for the first time. None of the adducts were mutagenic under the conditions evaluated, regardless of the DinB or AlkB cellular status. Taken together, the data indicated that the cellular pathway to combat bulky N2-alkylguanine DNA adducts was DinB-dependent lesion bypass.
Mapping of contactless photoelectrochemical etched GaN Schottky contacts using scanning internal photoemission microscopy—difference in electrolytes (2022)

Abstract We present the experimental results on the mapping characterization of n-type GaN Schottky contacts with selective contactless photoelectrochemical (CL-PEC) etching by using scanning internal photoemission microscopy (SIPM). The CL-PEC etching was performed in four kinds of aqueous solutions (KOH mixed with K 2 S 2 O 8 (oxidant), phosphoric acid mixed with oxidant, only oxidant, and ammonia). The Schottky barrier height ( qϕ B ) values decreased by less than 0.1 eV in the etching with the KOH and oxidant solutions. On the other hand, the opposite trend was observed for the samples etched with the phosphoric acid solution. Whereas the samples etched with the ammonia solution had a scattered qϕ B value, they were not affected by the etching. However, the photoyield increased by 2.5–3.5 times in all kinds of etching. SIPM was found to be sensitive in visualizing the effect of the CL-PEC etching as an image.
Supplementary Figure Legends from Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6 (2023)

&lt;p&gt;Legend for Supplemental Figures S1-S6.&lt;/p&gt;
COMPRESSING BEHAVIOR AND TEXTURE EVALUATION FOR POTATOES PRETREATED BY PULSED ELECTRIC FIELD (2009)

ABSTRACT The objective of this study was to investigate the effects of pulsed electric field (PEF) treatment on compressing behavior and texture of potatoes. Textural data reveal that PEF treatment can cause enlargement of pressure for the same level of deformation. The fracture pressures P c were approximately the same for both untreated and PEF‐treated specimens, P c ≈ 4.5 ± 0.4 MPa. The maximal pressure P m , at which the time of the pressure‐induced rupture of intact cells should be of the same order of magnitude as the time of fluid expression from damaged cells, was estimated as P m ≈ 6 MPa. For a small pressure ( P = 1 MPa) to obtain a similar deformation ( ε = 0.15) requires pressing time t ≈ 3.5 h for untreated tissue and t ≈ 70 s for PEF‐treated tissue. Measured electrical conductivity was practically constant and exhibited no noticeable time dependence during constant pressure stage in untreated samples, while the conductivity of PEF‐treated specimens decreases in the course of pressing. PRACTICAL APPLICATIONS Solid–liquid expression is widely used in the food industry for the extraction of fruit and vegetables. Efficiency of this process can be increased by different pretreatment methods. Pulsed electric field (PEF) has been shown to be good for juice yield intensification and for improving the product quality in juice production. It is of great interest for process purposes to study texture proprieties of PEF‐treated and untreated tissues, because texture is one of the most important quality attributes of food products. This work also gives new information about the mechanism of the PEF‐induced damage and expression from tissues. The obtained results may be helpful for development of new engineering concepts based on PEF‐enhanced extraction at comparatively low pressures and moderate time of processing.
Cross-reactivity between avian influenza A (H7N9) virus and divergent H7 subtypic- and heterosubtypic influenza A viruses (2016)

The number of human avian H7N9 influenza infections has been increasing in China. Understanding their antigenic and serologic relationships is crucial for developing diagnostic tools and vaccines. Here, we evaluated the cross-reactivities and neutralizing activities among H7 subtype influenza viruses and between H7N9 and heterosubtype influenza A viruses. We found strong cross-reactivities between H7N9 and divergent H7 subtypic viruses, including H7N2, H7N3, and H7N7. Antisera against H7N2, H7N3, and H7N7 could also effectively neutralize two distinct H7N9 strains. Two-way cross-reactivities exist within group 2, including H3 and H4, whereas one-way cross-reactivities were found across other groups, including H1, H10, H9, and H13. Our data indicate that the hemaglutinins from divergent H7 subtypes may facilitate the development of vaccines for distinct H7N9 infections. Moreover, serologic diagnoses for H7N9 infections need to consider possible interference from the cross-reactivity of H7N9 with other subtype influenza viruses.
Multi‐wavelength channel 1.5 μm and 10 Gb/s EMBH DFB‐LD array module using SAG technology (2015)

A multi‐wavelength channel distributed feedback laser diode array (DFB‐LDA) for the low‐cost and low‐power consumption applications of WDM‐based datacentre networks is reported. The gain spectrum and lasing wavelength of each channel are controlled by using selective area growth and E‐beam lithography techniques, respectively. To reduce the operation current and parasitic capacitance of the proposed array, an etched mesa buried hetero‐structure (EMBH) is introduced. From this study, it was found that an eight‐channel 300 μm long λ /4‐shifted DFB‐LDA has a threshold current of 10 ± 1.5 mA and a side mode suppression ratio of over 50 dB at a current of 50 mA for all channels. A transmission test for this LDA showed a clear eye opening with a dynamic extinction ratio of over 4.5 dB at 10 Gb/s after a 2 km transmission.
VITREOUS DYNAMICS (2008)

The vitrectomy systems each illustrate different performances of vitreous removal. The physical characteristics of vitreous resulted in nonuniform flow in all vitreous cutters.
A holistic view on hyper-dense heterogeneous and small cell networks (2013)

The wireless industry has been experiencing an explosion of data traffic usage in recent years and is now facing an even bigger challenge, an astounding 1000-fold data traffic increase in a decade. The required traffic increase is in bits per second per square kilometer, which is equivalent to bits per second per Hertz per cell × Hertz × cell per square kilometer. The innovations through higher utilization of the spectrum (bits per second per Hertz per cell) and utilization of more bandwidth (Hertz) are quite limited: spectral efficiency of a point-to-point link is very close to the theoretical limits, and utilization of more bandwidth is a very costly solution in general. Hyper-dense deployment of heterogeneous and small cell networks (HetSNets) that increase cells per square kilometer by deploying more cells in a given area is a very promising technique as it would provide a huge capacity gain by bringing small base stations closer to mobile devices. This article presents a holistic view on hyperdense HetSNets, which include fundamental preference in future wireless systems, and technical challenges and recent technological breakthroughs made in such networks. Advancements in modeling and analysis tools for hyper-dense HetSNets are also introduced with some additional interference mitigation and higher spectrum utilization techniques. This article ends with a promising view on the hyper-dense HetSNets to meet the upcoming 1000× data challenge.
MmpL Genes Are Associated with Mycolic Acid Metabolism in Mycobacteria and Corynebacteria (2012)

Mycolic acids are vital components of the cell wall of the tubercle bacillus Mycobacterium tuberculosis and are required for viability and virulence. While mycolic acid biosynthesis is studied extensively, components involved in mycolate transport remain unidentified. We investigated the role of large membrane proteins encoded by mmpL genes in mycolic acid transport in mycobacteria and the related corynebacteria. MmpL3 was found to be essential in mycobacteria and conditional depletion of MmpL3 in Mycobacterium smegmatis resulted in loss of cell wall mycolylation, and of the cell wall-associated glycolipid, trehalose dimycolate. In parallel, an accumulation of trehalose monomycolate (TMM) was observed, suggesting that mycolic acids were transported as TMM. In contrast to mycobacteria, we found redundancy in the role of two mmpL genes, in Corynebacterium glutamicum; a complete loss of trehalose-associated and cell wall bound corynomycolates was observed in an NCgl0228-NCgl2769 double mutant, but not in individual single mutants. Our studies highlight the role of mmpL genes in mycolic acid metabolism and identify potential new targets for anti-TB drug development.