gebhart/patrepeval huggingface dataset:
Rapid molecular assays for microbial contaminant monitoring in the bioprocess industry. (2016)

Adventitious contaminations with bacterial, viral, or fungal infectious agents represent a major risk associated with the manufacture and release of pharmaceutical products for human use, including vaccines, protein-based therapeutics, and antibodies. Early detection of contaminants in the biologicals production process might allow immediate action to correct such events without a significant interruption in the rate of production. Among the methods currently used for testing are cell culture, animal inoculation, electron microscopy, and in vitro molecular and antibody assays. Bacteria such as mycoplasma and mycobacterial species and most of the viral and fungal agents can take several days to weeks or even months to grow in culture. We have developed a broad-range microbial detection assay that uses the innovative Ibis biosensor platform, a rapid and high-throughput biosensor that is based on polymerase chain reaction (PCR) and electrospray ionization mass spectrometry to identify and quantify microbial contaminants. By combining the sensitivity of PCR with the accuracy of mass spectrometric detection, this technology generates a fingerprint that uniquely identifies an organism without a priori assumptions of the sample identity. This approach is capable of detecting known and unknown pathogens, as well as providing high-resolution genotyping and strain typing, and drug resistance and virulence information. Representative case studies are discussed here showing detection of minute virus of mice, mycoplasma, and an unknown virus that was identified as bluetongue virus.
(Invited) Composition and Interfacial Engineering of Lithium Iron Orthosilicate Cathodes with Superior Intercalation Properties (2020)

The quest for Li-ion batteries (LIBs) delivering higher energy density while being safer and sustainable has intensified recently. This work presents our advances towards improving the intercalation properties of an important cathode material, Li 2 FeSiO 4 (LFS), in order to take advantage of its attractive properties in terms of sustainability and safety. LFS theoretically has 330 mAh g -1 capacity (2 Li + per formula unit), however, inherently it exhibits relatively poor Li-ion intercalation kinetics, interfacial reactivity and complex phase transitions resulting in lower than one Li + storage and poor capacity retention.In this work, we apply a multi-prong strategy to overcome these obstacles making use of compositional engineering to tune the electronic and crystal structures of LFS in concert withmechanochemical processing and polymer coating to provide a stabilizing interphase. We take advantage of the versatility of hydrothermal synthesis [1a] and mechanochemical activation and synthesize various cation-substituted and non-stoichiometric LFS nanomaterials with annealed orthorhombic Pmn 2 1 structure. Firstly, mechanochemical annealing leads to activation of Li-ion diffusion (D Li ) by one order of magnitude enhancement [2a,b]. Secondly, partial substituting Co for Fe is found to allow faster phase transformation from pristine Pmn 2 1 to inverse Pmn 2 1 with important positive ramifications in its cycling performance [1b]. Thirdly, we boost the capacity of LFS, bydesigning Fe-rich (and not Li-rich!) LFS materials that deliver higher capacity within a reasonable voltage window [1c]. Lastly, PEDOT coating and near the surface composition alteration allows for stable cycling performance with &gt;1.2 Li capacity [2c]. Acknowledgments:This research was supported by a NSERC grant and the McGill Sustainability Systems Initiative (MSSI). References: [1] Yan Zeng et al., (a) Hydrothermal Crystallization of Pmn 2 1 Li 2 FeSiO 4 Hollow Mesocrystals for Li-Ion Cathode Application, Chem. Eng. J., 359 (2019), 1592-1602; (b) Unveiling the mechanism of improved capacity retention in Pmn 2 1 Li 2 FeSiO 4 cathode by cobalt substitution, J. Materials Chem. A 2019, 7 , 25399 – 25414; (c) Defect Engineering of Fe-Rich Orthosilicate Cathode Materials with Enhanced Li-Ion Intercalation Capacity and Kinetics, ACS Applied Energy Materials, 2020, 3, 675−686 [2] Majid Rasool et al., (a) Mechanochemically-tuned structural annealing: a new pathway to enhancing Li-ion intercalation activity in nanosized β II Li 2 FeSiO 4 , J Mater. Chem. A 2019, 7 , 13705 – 13713; (b) Unusual Li-ion intercalation activation with stepwise capacity increase in orthosilicates, J. Phys. Chem. C ;DOI: 10.1021/acs.jpcc.9b11896; (c) PEDOT encapsulated and mechanochemically engineered silicate nanocrystals for high energy density cathodes, Advanced Materials Interfaces , 2020, 2000226; DOI: 10.1002/admi.202000226
Table S4 from Intratumoral Plasmid IL12 Expands CD8<sup>+</sup> T Cells and Induces a CXCR3 Gene Signature in Triple-negative Breast Tumors that Sensitizes Patients to Anti–PD-1 Therapy (2023)

&lt;p&gt;Table S4&lt;/p&gt;
The Existence of Myocardial Repair (2013)

The lack of myocardial repair after myocardial infarction and the heart failure that eventually ensues was thought of as proof that myocardial cell regeneration and myocardial repair mechanisms do not exist. Recently, growing experimental and clinical evidence has proven this concept wrong. Cardiac stem cells and endogenous myocardial repair mechanisms do exist; however, they do not produce significant myocardial repair. Similarly, the preliminary results of stem cell therapy for myocardial repair have shown early promise but modest results. Preclinical studies are the key to understanding stem cell senescence and lack of cellular contact and vasculature in the infarcted region. Additional laboratory studies are sure to unlock the therapeutic mechanisms that will be required for significant myocardial repair.
An assessment of the RIFLE criteria for acute renal failure in hospitalized patients* (2006)

The RIFLE criteria for acute renal failure classified close to 20% of our study patients as having some degrees of acute impairment in renal function and were useful in predicting their hospital mortality.
ChemInform Abstract: An Efficient Copper‐Catalyzed Coupling of Aryl Halides with Imidazoles. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Plasma Monocyte Chemoattractant Protein-1 and Pulmonary Vascular Resistance in Chronic Thromboembolic Pulmonary Hypertension (2001)

The pathogenesis of severe pulmonary hypertension seems to be related to inflammatory response in diseased sites. Monocyte chemoattractant protein-1 (MCP-1) has been reported to play a role in the development of congestive heart failure. In this immunological response, activation and migration of leukocytes including macrophages to the inflammatory region are important factors. We hypothesized that the severity of pulmonary hypertension may be related to MCP-1, which is thought to be upregulated by blood pressure or shear stress in pulmonary vasculature as well as by immunological and inflammatory reactions in chronic thromboembolic pulmonary hypertension (CTEPH). Circulating levels of MCP-1, interleukin-1beta (IL-1beta), and tumor necrosis factor-alpha (TNF-alpha) were measured by sandwich ELISA in 14 patients with CTEPH. The plasma level of MCP-1 was significantly correlated with pulmonary vascular resistance. In IL-1beta and TNF-alpha, on the other hand, there was no correlation between cytokines and pulmonary hemodynamics. Pathological specimens obtained from the patients with CTEPH undergoing thromboendarterectomy demonstrated immunoreactivity of MCP-1 in endothelium, smooth muscle cells, and macrophages within neointima in the hypertensive large elastic pulmonary artery. We conclude that MCP-1 is upregulated in the remodeling of pulmonary arteries in close association with increased pulmonary vascular resistance in CTEPH.
Improving taxi traffic flow by real-time runway sequence optimization using dynamic taxi route planning (2011)

Traffic control on the airport surface is tactical rather than strategic, preventing the optimal use of the available taxiway and runway infrastructure. In the current taxi process the controller has to estimate a number of time windows while optimizing the traffic flow. To compensate for the uncertainties in these time windows and to prevent the runway from not being utilized efficiently, the controllers create buffers by planning a queue of aircraft at the runway. As a result aircraft have to wait while the engines are running which may lead to unnecessary fuel consumption. One of the goals of the described research is to reduce the amount of unnecessary taxi time while engines are running, by reducing the taxi process uncertainties and thus reducing the need of aircraft queuing at the runway. At the same time reducing taxi time uncertainties enables runway sequence planning when the aircraft is still at the gate improving the optimal use of the available runway infrastructure. Our proposed approach is to develop a planning function that will optimize the traffic flow by real-time sequencing the departure traffic at the gate and provide the controller and pilots with timing information. This paper describes a proposed taxi operation and real-time planning function to compensate for taxi operation uncertainties. Part of the planning function was implemented and evaluated using scenarios based on actual data from Amsterdam airport.
Exploratory search over social-medical data (2011)

In this demo we shall present the IBM Patient Empowerment System (PES), and more specifically, its social-medical discovery sub-system. Social and medical data are represented using entities and relationships and are explored using a combination of expressive, yet intuitive, query language, faceted search, and ER graph navigation. While this demonstration focuses on the healthcare domain, the underlining search technology is generic and can be utilized in many other domains. Therefore, this demo has two main contributions. First, we present a novel entity-relationship indexing and retrieval solution, and discuss its implementation challenges. Second, the demonstration depicts a practical entity-relationship discovery technology in a real domain setting within a real IBM system.
GaSb/InGaAs quantum dot-well solar cells (2013)

GaSb/InGaAs quantum dot-well (QDW) hybrid active regions with type-II band alignment are explored for increasing infrared absorption in GaAs solar cells. GaAs p-i-n structures studied in this work comprise five layers of either GaSb quantum dots (QD), InGaAs quantum wells (QW) or GaSb/InGaAs QDWs in the i-region. The QDW solar cells exhibited superior performance beyond the GaAs band edge compared to the QW and QD solar cells. In QDW solar cells improved efficiency is observed over QD solar cells due to additional QW absorption. An analysis of bulk response degradation in a QDW solar cell is also presented. Improved photo response in QDW solar cells over QW and QD solar cells proves the potential of QDW hybrid structures for realizing high efficiency intermediate band solar cells.
Catalytic Z‐Selective Cross‐Metathesis with Secondary Silyl‐ and Benzyl‐Protected Allylic Ethers: Mechanistic Aspects and Applications to Natural Product Synthesis (2013)

Gib mir ein­ Z(-Olefin): Effiziente katalytische Kreuzmetathesen ergeben Z-disubstituierte allylische Silyl- oder Benzylether (siehe Schema, MAP=Monoalkoxidpyrrolid). In Kombination mit einer katalytischen Kreuzkupplung dient der Ansatz als eine allgemeine Synthesemethode für ansonsten schwer zugängliche Z-Olefine mit Alkingruppen.
Acetyl-L-Carnitine Modulates TP53 and IL10 Gene Expression Induced by 3-NPA Evoked Toxicity in PC12 Cells (2011)

The neurotoxicity induced by the mitochondrial inhibitor 3-nitropropionic acid (3-NPA) is associated with a decrease of ATP synthesis and an increase of free radical production which can lead to apoptosis or necrosis. We have used the PC12, neuron-like rat pheochromocytoma cell line, to study further the mechanism of 3-NPA-evoked neurotoxicity and the effects of acetyl-L-carnitine (ALC) which has neuroprotective actions against various types of mitochondrial inhibitors.Cultured PC 12 cells were exposed to a low dose of 3-NPA 50 (microM) in the presence or absence of 5 mM ALC. The dose of 3-NPA was sub toxic and no changes in pro-apoptotic Bax or anti-apoptotic Bcl-2 gene expression were observed. We followed specific genetic markers to look for changes evoked by 3-NPA toxicity and also changes associated with neuroprotection exerted by the ALC treatment, using RT-PCR arrays (delta-delta method). 3-NPA exposure evoked a decrease in expression of the Tp53 gene. This down regulation was prevented by pretreatment of the cells with ALC. The Tp53 gene responds to cellular stresses and the effects seen here are possibly associated with the 3-NPA evoked changes in mitochondrial metabolism. Other genes associated with stress and apoptosis, Parp-1, Bcl-2, and Bax were not affected by 3-NPA or ALC. The decrease of inflammatory response Il-10 gene expression due to 3-NPA was further lowered by presence of ALC. Other inflammation related genes, Il1rn, Nr3c1 and Cxcr4 were not affected. Interestingly, the glutamate transporter slc17a7, carnitine-acylcarnitine translocase Slc25a20 and heat shock proteins genes, Hsp27, Hmox1 (Hsp32, HO1) as well as Hspa 1a (Hsp 70) increased only when both ALC and small dose of 3-NPA were present. The alterations in gene expression detected in this study suggest role of several intracellular pathways in the neurotoxicity of 3-NPA and the neuroprotection against 3-NPA-induced neurotoxicity by ALC.
Very high-gain two-wave mixing in photorefractive BaTiO 3 with a self-bended pump beam (1995)

In most photorefractive materials with a large diffusion-type non-linearity, it is often observed that light beams follow curved paths [1], [2]. This phenomenon is known as the self-bending effect. We propose a two-wave mixing (2WM) interaction in BaTiO3 between such a self-bended pump beam and a weak signal beam that permits to achieve very high-gain 2WM. In our new 2WM configuration (Fig. 1), the extraordinary-polarized pump beam Pin, incident on the (010) face of the crystal, rapidly undergoes a bended trajectory in the direction of the c-axis. The output self-bended pump beam P out ′ then emerges from the (001) face perpendicularly to the entrance face. The input signal beam Sin, incident on the (001) face, is arranged to interact with the bended beam. In the steady state, the intensity into P out ′ represents about 45 % of the total output intensity. Thus, an interesting feature of such configuration is that an important amount of the incident pump energy is guided into the self-bended beam. More energy is thus available for the 2WM coupling while in a conventional 2WM geometry where the pump and the signal beams enter the crystal at the same (001) face [3],[4], the pump beam Pout is almost completly depleted (~ 95 %) into the fanning, corrupting the 2WM gain.
Plasma-aided manufacturing (1990)

Plasma-aided manufacturing is used for producing new materials with unusual and superior properties, for developing new chemical compounds and processes, for machining, and for altering and refining materials and surfaces. Plasma-aided manufacturing has direct applications to semiconductor fabrication, materials synthesis, welding, lighting, polymers, anticorrosion coatings, machine tools, metallurgy, electrical and electronics devices, hazardous waste removal, high-performance ceramics, and many other items in both the high-technology and the more traditional industries.
Sub-Nanomolar Detection of Limonin Using Cnps Integrated Silk Fibroin As Transducer on Organic Electrochemical Transistor (2018)

Limonin is a biomolecule which is responsible for the bitter element in many citrus fruits and vegetables. It has proven to be antioxidants which are biologically active and exhibit anticarcinogenic activity. It is formed from a tasteless precursor called limonite β ring lactone, which is found in the juice sacs. During juice extraction from the fruit, the precursor encounters the acidic compound of the juice and is gradually lactonized to form bitter limonin. This bitterness is generally not desired, therefore quantification and detection of limonin is very crucial for improving fruit quality in the citrus industry. The current techniques available for detecting limonin in fruits are time consuming, expensive and not fit for active monitoring of limonin levels. In this study, we have shown the applicability of ceria nanoparticles (CNPs) to be used as a transducer integrated in silk fibroins that is coupled with an organic electrochemical transistor to detect limonin. CNPs possess antioxidant properties which is attributed to the redox nature of dual oxidations states, Ce3+ and Ce4+, switching on the surface. This constant switching of oxidation states on the surface produce oxygen vacancies that act like hot spots for targeting electroactive entities like limonin. Therefore, in the present work, the electrochemical interaction between CNPs and limonin has been exploited to detect limonin using a transistor platform. Multiple characterization techniques were done to confirm the presence of CNPs in silk fibroins. The SOD and the catalase mimetic activity was assessed using SOD assay kit and Amplex red kit which showed the preservation of CNPs antioxidant properties in silk. Immobilizing and embedding CNPs in silk fibroins was studied to provide the most sensitive and efficient transducer for the OECT. In order to find the limit of detection of the OECT, limonin concentrations were varied and tested at different gate voltage (V G ). The limonin OECT prepared in this study showed a detection limit of 10nM with a constant increase in the I D current with limonin concentration. A range of interfering species which are commonly available in citrus fruits, were also tested to investigate the selectivity of the sensor. It was observed that none of the analytes, other than the limonin, produced a noticeable change in current. Thus, the CNPs-OECT limonin sensor has potential applications in sensing limonin on field applications. Future field and research application of the CNPs-OECT sensor could include real time monitoring of the amount of limonin in fruit juices or to study and reduce the amount of limonin in citrus fruits and to quantify the dosage of limonin as a potential antioxidant material.
Blood natural killer cell deficiency reveals an immunotherapy strategy for atopic dermatitis (2020)

Atopic dermatitis (AD) is a widespread, chronic skin disease associated with aberrant allergic inflammation. Current treatments involve either broad or targeted immunosuppression strategies. However, enhancing the immune system to control disease remains untested. We demonstrate that patients with AD harbor a blood natural killer (NK) cell deficiency that both has diagnostic value and improves with therapy. Multidimensional protein and RNA profiling revealed subset-level changes associated with enhanced NK cell death. Murine NK cell deficiency was associated with enhanced type 2 inflammation in the skin, suggesting that NK cells play a critical immunoregulatory role in this context. On the basis of these findings, we used an NK cell-boosting interleukin-15 (IL-15) superagonist and observed marked improvement in AD-like disease in mice. These findings reveal a previously unrecognized application of IL-15 superagonism, currently in development for cancer immunotherapy, as an immunotherapeutic strategy for AD.
The Temperature and Depth Accuracy of Sippican T-5 XBTs (1993)

Thirty-four near-simultaneous pairs of CTD and Sippican model T-5 XBT profiles were obtained during an experiment in the Sargasso Sea during the summer of 1991. The data were analyzed to assess the temperature and fall-rate accuracies of the T-5 probes. The XBT temperatures averaged 0.07°C warmer than CTD temperatures, with some suggestion that the offset might be different for different acquisition acquisition systems and that it might be slightly temperature or pressure dependent. When the offset was removed, the differences between CTD and XBT temperatures had a standard deviation of about 0.08°C over a temperature range of 3°–29°C. An improved elapsed fall-time-to-depth conversion equation for Sippican T-5's in the Sargasso Sea was found to be z=6.705t−0.001619t2, with z the depth in meters and t the elapsed fall time of the probe in seconds. The standard deviation of depth was about 8 m over a depth range of 0 to approximately 1800 m. A cubic fit to the data was equally good or slightly better. Whether a geographically universal fall-rate equation can he devised for each model XBT is still unclear. In addition, now that a number of different manufacturers are introducing their versions of XBTs and XBT acquisition systems onto the market, unresolved questions exist regrading the differences in data taken with these different models.
A measurement based architecture for adaptive network environments (2005)

The Internet constitutes a heterogeneous mesh of networks with highly varying characteristics. One of the features of this environment is that there normally are a number of possible paths for data to travel between two end-hosts. These different paths exhibit highly different properties in terms of bandwidth, delay, reliability etc. One of the challenges in this environment is to map the properties of a path to application specific requirements. To this end, the concept of adaptive network architectures has been introduced. These architectures can perform the mapping of path characteristics to application requirements but one of the remaining problems with these architectures is how to discover the available paths and their properties. We present a novel architecture that overcomes this problem. The architecture consists of two parts, a hybrid network-monitoring tool and a path discovery algorithm.
Monoalkoxy BODIPYs—A Fluorophore Class for Bioimaging (2014)

Small molecule fluorophores are indispensable tools for modern biomedical imaging techniques. In this report, we present the development of a new class of BODIPY dyes based on an alkoxy-fluoro-boron-dipyrromethene core. These novel fluorescent dyes, which we term MayaFluors, are characterized by good aqueous solubility and favorable in vitro physicochemical properties. MayaFluors are readily accessible in good yields in a one-pot, two-step approach starting from well-established BODIPY dyes, and allow for facile modification with functional groups of relevance to bioconjugate chemistry and bioorthogonal labeling. Biological profiling in living cells demonstrates excellent membrane permeability, low nonspecific binding, and lack of cytotoxicity.