gebhart/patrepeval huggingface dataset:
Degradation and recovery of In/sub 0.53/Ga/sub 0.47/As photodiodes by 1-MeV fast neutrons (1996)

Irradiation damage in In/sub 0.53/Ga/sub 0.47/As p-i-n photodiodes by 1-MeV fast neutrons is studied as a function of fluence for the first time. The degradation of the electrical and optical performance of diodes increases with increasing fluence. The induced lattice defects in the In/sub 0.53/Ga/sub 0.47/As epitaxial layers and the InP substrate are studied by DLTS methods. In the In/sub 0.53/Ga/sub 0.47/As epitaxial layers, hole and electron capture levels are induced by irradiation. The influence of radiation source on device degradation is then discussed by comparison to 1-MeV electrons with respect to the numbers of knock-on atoms and the nonionizing energy loss (NIEL). In order to examine the recovery behavior, isochronal thermal annealing is carried out for temperatures ranging from 75 to 300/spl deg/C. After 300/spl deg/C thermal annealing, the light current only recovers to 20% of pre-irradiation for a fluence of 1/spl times/10/sup 13/ n/cm/sup 2/, while it recovers to 53% for a fluence of 1/spl times/10/sup 15/ e/cm/sup 2/. The different of recovery behavior is thought to be due a different type of radiation damage.
In situ measurement of intracellular thermal conductivity using heater-thermometer hybrid diamond nanosensor (2020)

Abstract Understanding heat dissipation processes at nanoscale during cellular thermogenesis is essential to clarify the relationships between the heat and biological processes in cells and organisms. A key parameter determining the heat flux inside a cell is the local thermal conductivity, a factor poorly investigated both experimentally and theoretically. Here, using a nanoheater/nanothermometer hybrid based on a polydopamine shell encapsulating a fluorescent diamond nanocrystal, we measured the intracellular thermal conductivity of HeLa cell with a spatial resolution of about 200 nm. Its mean value of 0.11 Wm -1 K -1 determined for the first time is significantly smaller than that of water. Bayesian analysis of the data strongly supports the existence of variation of the intracellular thermal conductivity of about 40%. These results present a major milestone towards understanding the intracellular heat transfer phenomena at nanoscale.
Exposure to a Cutinase-like Serine Esterase Triggers Rapid Lysis of Multiple Mycobacterial Species (2012)

Mycobacteria are shaped by a thick envelope made of an array of uniquely structured lipids and polysaccharides. However, the spatial organization of these molecules remains unclear. Here, we show that exposure to an esterase from Mycobacterium smegmatis (Msmeg_1529), hydrolyzing the ester linkage of trehalose dimycolate in vitro, triggers rapid and efficient lysis of Mycobacterium tuberculosis, Mycobacterium bovis BCG, and Mycobacterium marinum. Exposure to the esterase immediately releases free mycolic acids, while concomitantly depleting trehalose mycolates. Moreover, lysis could be competitively inhibited by an excess of purified trehalose dimycolate and was abolished by a S124A mutation affecting the catalytic activity of the esterase. These findings are consistent with an indispensable structural role of trehalose mycolates in the architectural design of the exposed surface of the mycobacterial envelope. Importantly, we also demonstrate that the esterase-mediated rapid lysis of M. tuberculosis significantly improves its detection in paucibacillary samples.
Numerical simulation of the flow behind a rotary oscillating circular cylinder (1998)

A numerical study was made of flow behind a circular cylinder in a uniform flow, where the cylinder was rotationally oscillated in time. The temporal behavior of vortex formation was scrutinized over broad ranges of the two externally specified parameters, i.e., the dimensionless rotary oscillating frequency (0.110⩽Sf⩽0.220) and the maximum angular amplitude of rotation (θmax=15°, 30°, and 60°). The Reynolds number (Re=U∞D/ν) was fixed at Re=110. A fractional-step method was utilized to solve the Navier–Stokes equations with a generalized coordinate system. The main emphasis was placed on the initial vortex formations by varying Sf and θmax. Instantaneous streamlines and pressure distributions were displayed to show the vortex formation patterns. The oscillatory forcing was in the vicinity of the lock-on range, which can be applied to flow feedback control afterwards. The vortex formation modes and relevant phase changes were characterized by measuring the lift coefficient (CL) and the time of negative maximum CL (t−CLmax) with variable forcing conditions.
Retraction: Immunoisolating Pancreatic Islets by Encapsulation with Selective Withdrawal (2010)

The article, “Immunoisolating Pancreatic Islets by Encapsulation with Selective Withdrawal” by J. L. Wyman, S. Kizilel, R. Skarbek, X. Zhao, M. Connors, W. S. Dillmore, W. L. Murphy, M. Mrksich,* S. R. Nagel,* and M. R. Garfinkel,* published online on March 6, 2007 (DOI:10.1002/smll.200600231) on Wiley Online Library (onlinelibrary.wiley.com), and in print Small, 2007, 3, 683–690 has been retracted by agreement between the authors, the journal Editor-in-Chief, José Oliveira, and Wiley-VCH Verlag GmbH & Co. KGaA Weinheim. After the publication of this article, the corresponding authors discovered that the results of Figure 6 could not be reproduced. Upon bringing this matter to the attention of the University of Chicago Academic Fraud Committee, the Committee came to the conclusion that Matthew Connors fabricated these data. The Committee determined that there was no evidence that the rest of the authors engaged in unethical behavior or were aware of the data being fabricated. No questions were raised with respect to the results describing the design of the apparatus for the selective withdrawal method and the photochemical cross-linking of a polymeric shell around the islets. The corresponding authors and the rest of the authors (other than Matthew Connors) have requested and agreed to this retraction.
An automatic speech translation system for travel conversation (2002)

We present a speech-to-speech translation system for notebook PC's that helps oral communication between Japanese and English speakers in the various situations in the travel abroad. Due to the high accuracy of the compact continuous speech recognition engine and our lexicalized grammar approach to machine translation that utilizes corpus but is oriented to model general linguistic phenomena as well as word-specific ones, a versatile speech-to-speech translation system for travel abroad is achieved, which is with much larger vocabulary (50,000 Japanese words and 10,000 English words) and capable of translating spoken conversations in more situations compared to previous work [1].
Oligonucleotide Probe for Transcriptome in Vivo Analysis (TIVA) of Single Neurons with Minimal Background (2020)

Messenger RNA (mRNA) isolated from single cells can generate powerful biological insights, including the discovery of new cell types with unique functions as well as markers potentially predicting a cell's response to various therapeutic agents. We previously introduced an oligonucleotide-based technique for site-selective, photoinduced biotinylation and capture of mRNA within a living cell called transcriptome <i>in vivo</i> analysis (TIVA). Successful application of the TIVA technique hinges upon its oligonucleotide probe remaining completely inert (or "caged") to mRNA unless photoactivated. To improve the reliability of TIVA probe caging in diverse and challenging biological conditions, we applied a rational design process involving iterative modifications to the oligonucleotide construct. In this work, we discuss these design motivations and present an optimized probe with minimal background binding to mRNA prior to photolysis. We assess its caging performance through multiple <i>in vitro</i> assays including FRET analysis, native gel comigration, and pull down with model mRNA transcripts. Finally, we demonstrate that this improved probe can also isolate mRNA from single living neurons in brain tissue slices with excellent caging control.
Immunogenicity of Golimumab and its Clinical Relevance in Patients With Ulcerative Colitis (2019)

A more sensitive DT-EIA identified higher proportions of ADA-positive patients. A trend of decreasing drug concentrations with increasing ADA titers was observed. Pharmacokinetic impact was better elucidated with DT-EIA. Although development of ADA did not preclude efficacy, a trend toward decreased efficacy in ADA-positive vs ADA-negative patients was observed during maintenance treatment. Antidrug antibody status did not impact safety.
Abstract 3070: Discovery of novel potent allele-selective KRAS-G12C covalent inhibitors stemming from DNA-encoded library (2019)

From a screening of 27 106 covalent DNA-encoded compound library, a novel KRAS G12C chemical series has been identified. Original hit series compound displayed low µM covalent binding activity to KRAS G12C under GDP form associated with a k(inact)/Ki of 1,03 M-1.s-1, a stable electrophilic covalent warhead (T1/2 in 5mM GSH > 24h), +12°C stabilization Delta Tm in DSF assay and 3 µM IC50 value in GEF assay, while no detectable covalent binding to KRAS G12C under GTP form and to KRAS WT or KRAS G12D under GDP form. From 3 µM, it also induced significant pERK inhibition in H358 KRAS-G12C but not in A549 KRAS G12S NSCLC cell lines. Unique binding mode to SII pocket was demonstrated by Xray crystallography. Multi-parametric and structural biology guided chemical optimization yielded potent KRAS G12C lead compounds which combine k(inact)/Ki > 500 M-1.s-1, Delta Tm=20°C, 10 nM range pERK IC50 values with correlated direct KRAS G12C selective covalent modification. They also exhibited 100 nM range KRAS G12C allele-specific anti-proliferative activity and triggered significant apoptosis induction. In vivo treatment of mice bearing H358 tumour xenografts through oral route with optimized candidates showed a marked and prolonged inhibition of both pERK and DUSP6 mRNA as well as consistent direct KRAS-G12C covalent modification as evidenced by LC-MS in tumor samples. Altogether, these data demonstrate the power of DNA-encoded library approach to deliver potential drug candidates with selective cysteine-targeted irreversible mechanism of action on challenging oncology targets such as KRAS.Citation Format: Gary McCort, Rosalia Arrebola, Loreley Calvet, Baptiste Ronan, Fabrice Vergne, Francis Duffieux, Alexey Rak, Isabelle Meaux, David Papin, Florence Fassy, Cecile Delorme, Magali Matthieu, Jean-Paul Nicolas, Christophe Marcireau, Valerie Steier, Pierre-Yves Abecassis, Valerie Czepczor, Heather A. Thomson, Christopher D. Hupp, J.P. Guilinger, Ying Zhang, Anthony D. Keefe, John W. Cuozzo, Julie Liu, Laurent Debussche. Discovery of novel potent allele-selective KRAS-G12C covalent inhibitors stemming from DNA-encoded library [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3070.
Long Term Weight Cycling Affects Fecal Microbiota of Mice (2022)

Compared to continuous HF or LF diets, cyclic diet specifically alters the composition and function of the mouse fecal microbiota, suggesting that fight against weight gain should be considered on a long-term basis.
Rehabilitation and outcomes after complicated vs uncomplicated mild TBI: results from the CENTER-TBI study (2022)

ClinicalTrials.gov NCT02210221.
Genetic control of the immune response to myoglobins. Both low and high responder T cells tolerant to the other major histocompatibility complex help high but not low responder B cells (1982)

We sought to examine the role of immune response (Ir) genes in helper T cells. To eliminate allogeneic effects, we used neonatally tolerized mice. The results bear not only on the mechanism of Ir genes, but also on the development of the T cell repertoire. B 10.BR (H-2(k)) or C57BL/10 (H-2(b)) mice, which were low responders to myoglobin (Mb), were neonatally tolerized to high responder H-2(d) alloantigens, and B10.D2 mice, which were high responders to Mb, were neonatally tolerized to low responder H-2(k) or H-2(b) alloantigens. Spleen cells from these tolerized mice did not show any reactivity in mixed-lymphocyte reaction or cell-mediated lympholysis against alloantigens used in tolerization. Mb-immune F(1) B cells were helped comparably by Mb-immune tolerized low or high responder T cells. Thus, low responder T cells functioned equivalently to high responder T cells. The failure of nonimmune T cells from tolerized low responder mice to help F(1) B cells and antigen-presenting cells (APC) indicated that collaboration between B10.BR or C57BL/10 T cells and F(1) B cells was not caused by a positive allogeneic effect. Spleen cells from tolerized mice were contaminated with 2-4 percent chimeric F(1) cells, as judged by fluorescence-activated cell sorter analysis, and no F(1) alloantigens were detectable in the thymus. However, removal of chimeric F(1) T cells from the tolerized cell population by treatment with anti-H-2 and complement did not change the helper activity of tolerized low responder T cells. These data indicated that helper activity in the T cell population from low responder mice was not due to F(1) cells. Also, the level of contamination was not sufficient to quantitatively account for the help. In examining the genetic restriction of these tolerized T cells, we found that T cells from tolerized low responder B10.BR or C57BL/10 mice helped F(1) or high responder B10.D2 B cells and APC but not syngeneic B10.BR or C57BL/10 B cells and APC, which were immunized with Mb-coupled fowl gamma globulin instead of Mb to prime low responder B cells with Mb. On the other hand, high responder B 10.D2 tolerized T cells helped syngeneic B 10.D2 B cells but not allogeneic low responder B10.BR B cells. These data indicated that clones of helper T cells specific for Mb exist in low responder mice, and these are not phenotypically different from those in high responder mice, in that both help high responder and F(1) but not low responder B cells and APC. These data are discussed in terms of the mechanism for Ir gene control, and the mechanism of T cell repertoire development- whether intra- or extrathymically-in neonatally tolerized mice.
Phosphoramidite Quinaphos‐Type Ligands for Highly Selective Ni‐Catalyzed Asymmetric C—C Bond Forming Reactions. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Human prostate cancer metastases target the hematopoietic stem cell niche to establish footholds in mouse bone marrow (2011)

HSC homing, quiescence, and self-renewal depend on the bone marrow HSC niche. A large proportion of solid tumor metastases are bone metastases, known to usurp HSC homing pathways to establish footholds in the bone marrow. However, it is not clear whether tumors target the HSC niche during metastasis. Here we have shown in a mouse model of metastasis that human prostate cancer (PCa) cells directly compete with HSCs for occupancy of the mouse HSC niche. Importantly, increasing the niche size promoted metastasis, whereas decreasing the niche size compromised dissemination. Furthermore, disseminated PCa cells could be mobilized out of the niche and back into the circulation using HSC mobilization protocols. Finally, once in the niche, tumor cells reduced HSC numbers by driving their terminal differentiation. These data provide what we believe to be the first evidence that the HSC niche serves as a direct target for PCa during dissemination and plays a central role in bone metastases. Our work may lead to better understanding of the molecular events involved in bone metastases and new therapeutic avenues for an incurable disease.
Novel roles for two-component regulatory systems in cytotoxicity and virulence-related <em>properties in Pseudomonas aeruginosa</em> (2018)

The rapid adaptation of the opportunistic bacterial pathogen <i>Pseudomonas aeruginosa</i> to various growth modes and environmental conditions is controlled in part through diverse two-component regulatory systems. Some of these systems are well studied, but the majority are poorly characterized, even though it is likely that several of these systems contribute to virulence. Here, we screened all available strain PA14 mutants in 50 sensor kinases, 50 response regulators and 5 hybrid sensor/regulators, for contributions to cytotoxicity against cultured human bronchial epithelial cells, as assessed by the release of cytosolic lactate dehydrogenase. This enabled the identification of 8 response regulators and 3 sensor kinases that caused substantial decreases in cytotoxicity, and 5 response regulators and 8 sensor kinases that significantly increased cytotoxicity by 15-58% or more. These regulators were additionally involved in motility, adherence, type 3 secretion, production of cytotoxins, and the development of biofilms. Here we investigated in more detail the roles of FleSR, PilSR and WspR. Not all cognate pairs contributed to cytotoxicity (e.g. PhoPQ, PilSR) in the same way and some differences could be detected between the same mutants in PAO1 and PA14 strain backgrounds (e.g. FleSR, PhoPQ). This study highlights the potential importance of these regulators and their downstream targets on pathogenesis and demonstrates that cytotoxicity can be regulated by several systems and that their contributions are partly dependent on strain background.
Cost-Effective Multimode Polymer Waveguides for High-Speed On-Board Optical Interconnects (2009)

Cost-effective multimode polymer waveguides, suitable for use in high-speed on-board optical interconnections, are presented. The fundamental light transmission properties of the fabricated waveguides are studied under different launch conditions and in the presence of input misalignments. Low loss (~0.04 dB/cm at 850 nm) and low crosstalk (<-30 dB) performance, relaxed alignment tolerances (plusmn20 mum) and high-speed operation at a 10-Gb/s data rate are achieved. No degradation in the high-speed link performance is observed when offset input launches are employed. Moreover, a range of useful waveguide components that add functionality and enable complex on-board topologies are presented. The optical transmission characteristics of the fabricated components are investigated and it is shown that excellent performance is achieved. Excess losses as low as 0.01 dB per waveguide crossing, the lowest reported value for such components, and bending losses below 1 dB for 90-degree and S-shaped bends are obtained even with multimode fiber launches. Moreover, high-uniformity power splitting and low-loss signal combining are achieved with Y-shaped splitter/combiners while a variable splitting ratio between 30%-75% is demonstrated with the use of multimode couplers. Overall, the devices presented are attractive potential candidates for use in on-board optical links.
Comparative mapping and marker-assisted selection in Rosaceae fruit crops (2004)

The development of saturated linkage maps using transferable markers, restriction fragment length polymorphisms, and micro-satellites has provided a foundation for fruit tree genetics and breeding. A Prunus reference map with 562 such markers is available, and a further set of 13 maps constructed with a subset of these markers has allowed genome comparison among seven Prunus diploid (x = 8) species (almond, peach, apricot, cherry, Prunus ferganensis, Prunus davidiana, and Prunus cerasifera); marker colinearity was the rule with all of them. Preliminary results of the comparison between apple and Prunus maps suggest a high level of synteny between these two genera. Conserved genomic regions have also been detected between Prunus and Arabidopsis. By using the data from different linkage maps anchored with the reference Prunus map, it has been possible to establish, in a general map, the position of 28 major genes affecting agronomic characters found in different species. Markers tightly linked to the major genes responsible for the expression of important traits (disease/pest resistances, fruit/nut quality, self-incompatibility, etc.) have been developed in apple and Prunus and are currently in use for marker-assisted selection in breeding programs. Quantitative character dissection using linkage maps and candidate gene approaches has already started. Genomic tools such as the Prunus physical map, large EST collections in both Prunus and Malus, and the establishment of the map position of high numbers of ESTs are required for a better understanding of the Rosaceae genome and to foster additional research and applications on fruit tree genetics.
Microwave sintering of sol-gel derived abrasive grain (2023)

A method is provided for making microwave-sintered, free flowing alpha alumina-based ceramic abrasive grain, under conditions effective to couple microwaves with calcined alpha alumina-based abrasive gain precursor and sinter it at a temperature of at least about 1150.degree. C.
Coagulation at the Blood–Electrode Interface: The Role of Electrochemical Desorption and Degradation of Fibrinogen (2014)

The influence of electrochemistry on the coagulation of blood on metal surfaces was demonstrated several decades ago. In particular, the application of cathodic currents resulted in reduced surface thrombogenicity, but no molecular mechanism has been so far proposed to explain this observation. In this article we used for the first time the quartz crystal microbalance with dissipation monitoring technique coupled with an electrochemical setup (EQCM-D) to study thrombosis at the blood-electrode interface. We confirmed the reduced thrombus deposition at the cathode, and we subsequently studied the effect of cathodic currents on adsorbed fibrinogen (Fg). Using EQCM and mass spectrometry, we found that upon applying currents Fg desorbed from the electrode and was electrochemically degraded. In particular, we show that the flexible N-terminus of the α-chain, containing an important polymerization site, was cleaved from the protein, thus affecting its clottability. Our work proposes a molecular mechanism that at least partially explains how cathodic currents reduce thrombosis at the blood-electrode interface and is a relevant contribution to the rational development of medical devices with reduced thrombus formation on their surface.
Virus-driven Inflammation Is Associated With the Development of bNAbs in Spontaneous Controllers of HIV (2017)

These results suggest that low antigenic diversity in the setting of a unique inflammatory profile associated with antigen persistence may be linked to the evolution of neutralizing antibody breadth.
Providing connection-oriented network services to mobile hosts (1993)

Mobile computers using wireless networks, along with multimedia applications, are two emerging trends in computer systems. This new mobile multimedia computing environment presents many challenges, due to the requirements of multimedia applications and the mobile nature of hosts. We present several alternative schemes for maintaining network connections used to provide multimedia service, as hosts move through a nano-cellular radio network. These algorithms modify existing connections by partially reestablishing them to perform handoffs. Using a simple analytical model, we compare the schemes on the basis of the service disruption caused by handoffs, required buffering, and excess resources required to perform the handoffs. Two technological trends of the 1990s are the emerging use of wireless computers and network support for multimedia services. The products of these trends hold forth the promise of being combined in innovative ways to provide applications such as mobile digital video and audio conferencing. The new computing environment presented by wireless multimedia personal communication systems such as discussed in