gebhart/patrepeval huggingface dataset:
Bulk Droplet Vitrification for Primary Hepatocyte Preservation (2019)

Vitrification is a promising ice-free alternative for classic slow-freezing (at approximately 1 °C/min) cryopreservation of biological samples. Vitrification requires extremely fast cooling rates to achieve transition of water into the glass phase while avoiding injurious ice formation. Although pre-incubation with cryoprotective agents (CPA) can reduce the critical cooling rate of biological samples, high concentrations are generally needed to enable ice-free cryopreservation by vitrification. As a result, vitrification is hampered by CPA toxicity and restricted to small samples that can be cooled fast. It was recently demonstrated that these inherent limitations can be overcome by bulk droplet vitrification. Using this novel method, cells are first pre-incubated with a low intracellular CPA concentration. Leveraging rapid osmotic dehydration, the intracellular CPA is concentrated directly ahead of vitrification, without the need to fully equilibrate toxic CPA concentrations. The cellular dehydration is performed in a fluidic device and integrated with continuous high throughput generation of large sized droplets that are vitrified in liquid nitrogen. This ice-free cryopreservation method with minimal CPA toxicity is suitable for large cell quantities and results in increased hepatocyte viability and metabolic function as compared to classical slow-freezing cryopreservation. This manuscript describes the methods for successful bulk droplet vitrification in detail.
Abstract B005: FPT155, a novel therapeutic CD80-Fc fusion protein with potent antitumor activity in preclinical models (2018)

Abstract Optimal activation of T cells requires both antigen-specific signaling and induction of costimulatory pathways. Costimulatory pathways are upregulated by foreign antigenic challenge but are not active in the normal immune state, thus maintaining peripheral tolerance to self-antigens. The absence of costimulatory signaling may likewise play a role in tolerance to cancer cells. Five Prime has developed a CD80 (B7.1) extracellular domain (ECD)-Fc fusion protein (FPT155) as a costimulatory molecule that can stimulate T-cell activation and break tumor immune tolerance. In vitro studies show that FPT155 induces T-cell activation and cytokine production via CD28. FPT155 activity requires T-cell receptor engagement, which indicates that FPT155 is not a CD28 “superagonist” that can drive T-cell activation independently of antigenic stimulation. To investigate the impact of CD80-Fc in preclinical models, we generated murine FPT155 (mFPT155), a surrogate fusion protein, composed of the mouse CD80 ECD fused with the murine Fc region of IgG2a. mFPT155 is well tolerated in mice and has potent efficacy in syngeneic tumor models, including the induction of complete tumor regression in the CT26 model. mFPT155 promotes the infiltration of T cells into the tumor core and increases the effector T:Treg ratio, thus inducing a favorable microenvironment for an effective antitumor immune response. Furthermore, combination of mFPT155 and anti-PD1 therapy leads to stronger antitumor efficacy compared to either therapy alone. Together these results indicate that mFPT155 is a potent T-cell costimulator with strong antitumor activity in mouse tumor models. We are currently performing IND-enabling studies and plan to initiate a clinical study with FPT155 in 2018. Citation Format: Susannah D. Barbee, Barbara Sennino, Jacqueline De La Torre, Monica Macal, Quinn Walker, Marc R. Jabon, Amanda Chen, David A. Busha, Margaret Best, Kristen L. Pierce, Luis Borges, Kevin P. Baker, Thomas Brennan. FPT155, a novel therapeutic CD80-Fc fusion protein with potent antitumor activity in preclinical models [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B005.
Enterprise content management: an overview (2003)

As Web sites move from simple presentation mediums to dynamic content providers, content issues are moving to the forefront of many enterprise Web site owners. The author gives an overview of enterprise content management, what it means, how to implement it and how to measure the benefits. The basic concept is to get organized and find a logical, consistent and easy way to place content on the Web. Employees will use an enterprise Intranet if it has timely material that is well organized and searchable. The best way to ensure that your Web content is timely is to implement a distributed authorship program, where the original content creators place the material on the Web and keep it updated. In order to ensure a well-organized site, you must start with an information model that is based on research of your enterprise and publish a site policy. To ensure the Web site is searchable, all content must be tagged and held in a consistent manner. These steps will produce a site with a high return on investment (ROI) that will become a valuable asset of the enterprise.
Improving microseismic imaging: Role of acquisition, velocity model, and imaging condition (2013)

Surface microseismic data is being increasingly used in monitoring hydraulic-fracturing. Here, we suggest changes in the acquisition as well as processing stages to improve microseismic imaging and source characterization. Improved microseismic hypocenter imaging and reliable source mechanism estimation can be achieved by illuminating the hypocenter evenly from all directions. We introduce methodologies for designing optimized surface arrays for 2D and 3D acquisitions. Accurate microseismic imaging also requires the exact Green's function between the image point and the receivers. An inaccurate Green’s function leads to poor focusing and numerous spurious microseismic hypocenters. We also introduce imaging conditions that can yield accurate source signatures even if they are extended in space and time. Such source signatures can yield the time history of fracture propagation in space and might be used to infer the time-varying slip along pre-existing fractures. These imaging conditions also reduce spurious events in the image. All conclusions are supported with numerical examples.
Solution-Processed Zinc Oxide Transistors for Low-Cost Electronics Applications (2009)

Transparent conductive oxides are promising candidates for realization of transparent electronics for display applications. The use of solution-processing techniques allows for a dramatic reduction in cost per unit area of electronic functionality. As a result, there is tremendous interest in the use of solution-processed transparent conductive oxides for realization of low-cost transparent electronic systems. Zinc oxide is processable out of solution using a variety of routes, including the use of nanoparticles, nanowires, and chemical bath deposition. By optimizing the deposition processes, it is possible to realize solution-processed transparent semiconductor films offering performance that is comparable to or better than amorphous silicon, while offering the advantages of transparency. Here, techniques for fabrication of solution-processed ZnO-based transistors are reviewed, and the outlook for such technologies is discussed.
Pseudomonas aeruginosa:Role in the Pathogenesis of the CF Lung Lesion (2003)

Lung disease is the leading cause of morbidity and mortality in individuals with cystic fibrosis (CF), with P. aeruginosa the main pulmonary infectious agent. Although CF patients can become infected with other microorganisms (such as Burkholderia cepacia complex, Staphylococcus aureus, Haemophilus influenzae, and atypical mycobacteria), P. aeruginosa predominates, eventually infecting approximately 80% of patients. Once established, P. aeruginosa infection usually persists until death. The interaction between the CF host and this opportunistic pathogen is unique and most likely directly contributes to the classical end-stage pathology of CF lung disease. However, the extent to which this constitutes success by the pathogen or failure by the host, or both, is yet to be determined. Many important questions remain regarding host susceptibility, the role of both innate and adaptive immune defenses, bacterial infectivity and transmission, and pathogen virulence factors. Here, we discuss some recent advances toward understanding this complex interaction between host and pathogen and how the interplay influences the CF lung lesion.
Near-surface Velocity Model Building and Statics in Permafrost Regions (2011)

Summary Near-surface velocity model building represents a major problem in processing of reflection data from permafrost regions because of the strong lateral velocity variations and negative velocity gradients present in these regions. The negative gradients prevent the application of conventional refraction methods in nearsurface velocity determination, and the strong lateral variations introduce severe statics anomalies. We show in this study that first-arrival tomography can be used to invert the near-surface structures so long as there are observed turning waves that transverse the low-velocity zones formed by the negative velocity gradients. In the cases where no turning waves are observed, the near-surface structures can be determined by combining first-arrival tomography with reflection tomography.
Integrated Reasoning Systems - A Knowledge-Level Perspective with a Case Based Bias (2009)

An increasing amount of work in AI in general, and case-based reasoning in particular, is addressing means of integrating different types of reasoning methods for building and maintaining AI systems. This paper first takes a step back in an attempt to identify a descriptive and comparative framework for the corresponding methods. It is argued that the knowledge level is the appropriate level for describing the behaviour of an intended system, and for identifying its methods and knowledge components. Main research activities in the author’s research group in Trondheim over the last twenty years are summarized with reference to the framework. 1.
Aerosol Penetration through Filtering Facepieces and Respirator Cartridges (1992)

Air-purifying respirators must be certified following the National Institute for Occupational Safety and Health (NIOSH) filter test criteria (30 CFR 11). The criteria specify a range for the mean particle size and the measure of spread permissible for the test aerosol. The authors' experiments have shown that aerosol penetration as a function of particle size differs considerably among certified respirators of the same type. Filtering facepieces (disposable respirators) and cartridges of the dust-mist, dust-mist-fume, and high-efficiency particulate air type were tested. The respirators were sealed to mannequins in a test chamber. The aerosol concentrations inside and outside the respirator were measured by an aerodynamic particle sizer and a laser aerosol spectrometer over a particle size range of 0.1 to 15 µm. Five flow rates ranging from 5 to 100 L/min were used to study flow dependency. The aerosol penetration through the filters is presented as a function of particle size. Aerosol penetration and pressure drop are combined to express the performance of each filter in terms of “ quality factor.” Under the same test conditions, the quality factor of one respirator may be as much as 6.6 times more than that of another respirator of the same type. The filter quality factor has a greater aerosol size dependency as airflow and aerosol size increase. In general, cartridges have a larger surface area than filtering facepieces but not necessarily lower filter penetration or higher filter quality. An analysis of the data shows that the best dust-mist respirator tested may provide five times more protection than the worst dust-mist respirator tested when exposed to the aerosol size distribution specified by the NIOSH filter test criteria.
Application of Lexicographic Goal Programming with Convex Optimization in Control Systems (2013)

Goal Programming (GP) is a multi-objective optimization technique that is used when there are multiple conflicting goals in the cost function of an optimization problem. Lexicographic Goal Programming (LGP) is most commonly used form of GP when there are clear priorities in the goals that leads to a lexicographic order, i.e., priroritization. We can solve LGP problems by solving a sequence of optimization problems, where the optimal cost of an optimization problem in the sequence becomes a constraint for all optimization problems that are solved afterwards. In this paper, we present the basic LGP framework where each problem in the sequence is a convex optimization problem. We provide examples from control systems where LGP is a natural choice due to the clear priorities of objectives. LGP formulation leads to a sequence of convex optimization problems, which enables us to use polynomial time Interior Point Method (IPM) algorithms to solve these problems efficiently and potentially in real-time. In some cases, we also show that this prioritization provides convexification of the problem at hand, which would have otherwise required the solution of a non-convex optimization problem. Our primary objective in writing this paper is to illustrate the usefulness LGP formulation of control problems that can be encountered in aerospace engineering.
Combined High-Resolution Solid-State 1H/13C NMR Spectroscopy and 1H NMR Relaxometry for the Characterization of Kerogen Thermal Maturation (2020)

A key factor for the petroleum potential of source rock is the degree of chemical and physical structure evolution of its kerogen fraction through a range of maturation processes. In this study, various high-field, solid-state NMR methods have been applied to a series of kerogen isolates (type I) over a defined maturity range (vitrinite reflectance R0 from 0.98 to 1.86%). Results obtained from 13C MAS NMR show that the sp2/sp3-hybridized carbon ratio of kerogen, here defined as the aromatic/aliphatic ratio, increases with increasing maturity. 1H MAS NMR spectra contain partly overlapping aliphatic and aromatic resonances with distinct transverse relaxation behavior. In Hahn-echo experiments, the aromatic signal decays more slowly than the aliphatic signal, indicating that for these systems, transverse 1H relaxation is rather controlled by local distances between hydrogen atoms than by molecular mobility. Similar relaxation differences are also found in static (nonspinning) 1H Hahn-echo NMR experiments, here used to discriminate between phases with different proton mobilities and/or densities in the kerogen samples and, ultimately, between aromatic and aliphatic fractions. The distributions of the static transverse relaxation time (T2), extracted from the Hahn-echo decays, are characterized by a short-T2 peak (∼10 μs) and a long-T2 peak (∼100 μs). The ratio between these two peaks correlates well with the aliphatic-to-aromatic signal intensity ratios in MAS NMR spectra of the corresponding kerogen samples, suggesting that a net decrease in kerogen proton density—occurring during maturation—is also reflected by 1H NMR relaxation. For the investigated kerogen isolates, the long-T2 peak in the T2 distribution can be considered an indicator of aromatic content, which can be directly detected by measuring 1H T2 relaxation.
Synthesis of Silicone‐Methacrylate Copolymers by ATRP Using a Nickel‐Based Supported Catalyst (2006)

Abstract Summary: A nickel (II) bromide catalyst immobilized onto crosslinked diphenylphosphinopolystyrene (PS‐PPh 3 /NiBr 2 ) was used for the synthesis of silicone‐methacrylate copolymers by atom transfer radical polymerization (ATRP) of various methacrylate monomers using ω ‐bromide silicone chains as macroinitiator. The polymerization proved to be very well‐controlled when a sufficient amount of soluble ligand, i.e., triphenylphosphine (PPh 3 ), was added to the polymerization medium. Under these conditions, this technique efficiently led to the production of different copolymers with controlled compositions and molecular weights as well as narrow polydispersity indices ( $\overline M _{\rm w} /\overline M _{\rm n}$ &lt; 1.5). The recovered copolymers proved to be almost free of catalyst residues. Indeed, inductively coupled plasma (ICP) analysis revealed a metal content lower than 100 ppm, representing only a few percent of the initial metal content in the polymerization medium. Synthesis of PDMS block copolymer in toluene catalyzed by PS‐PPh 3 /NiBr 2 in the presence of soluble PPh 3 at 90 °C. image Synthesis of PDMS block copolymer in toluene catalyzed by PS‐PPh 3 /NiBr 2 in the presence of soluble PPh 3 at 90 °C.
Data from Molecular Epidemiology of <i>EGFR</i> and <i>KRAS</i> Mutations in 3,026 Lung Adenocarcinomas: Higher Susceptibility of Women to Smoking-Related <i>KRAS</i>-Mutant Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The molecular epidemiology of most &lt;i&gt;EGFR&lt;/i&gt; and &lt;i&gt;KRAS&lt;/i&gt; mutations in lung cancer remains unclear.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We genotyped 3,026 lung adenocarcinomas for the major &lt;i&gt;EGFR&lt;/i&gt; (exon 19 deletions and L858R) and &lt;i&gt;KRAS&lt;/i&gt; (G12, G13) mutations and examined correlations with demographic, clinical, and smoking history data.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt;&lt;i&gt;EGFR&lt;/i&gt; mutations were found in 43% of never smokers and in 11% of smokers. &lt;i&gt;KRAS&lt;/i&gt; mutations occurred in 34% of smokers and in 6% of never smokers. In patients with smoking histories up to 10 pack-years, &lt;i&gt;EGFR&lt;/i&gt; predominated over &lt;i&gt;KRAS&lt;/i&gt;. Among former smokers with lung cancer, multivariate analysis showed that, independent of pack-years, increasing smoking-free years raise the likelihood of &lt;i&gt;EGFR&lt;/i&gt; mutation. Never smokers were more likely than smokers to have &lt;i&gt;KRAS&lt;/i&gt; G &gt; A transition mutation (mostly G12D; 58% vs. 20%, &lt;i&gt;P&lt;/i&gt; = 0.0001). &lt;i&gt;KRAS&lt;/i&gt; G12C, the most common G &gt; T transversion mutation in smokers, was more frequent in women (&lt;i&gt;P&lt;/i&gt; = 0.007) and these women were younger than men with the same mutation (median 65 vs. 69, &lt;i&gt;P&lt;/i&gt; = 0.0008) and had smoked less.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The distinct types of &lt;i&gt;KRAS&lt;/i&gt; mutations in smokers versus never smokers suggest that most &lt;i&gt;KRAS&lt;/i&gt;-mutant lung cancers in never smokers are not due to second-hand smoke exposure. The higher frequency of &lt;i&gt;KRAS&lt;/i&gt; G12C in women, their younger age, and lesser smoking history together support a heightened susceptibility to tobacco carcinogens. &lt;i&gt;Clin Cancer Res; 18(22); 6169–77. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
VIRAL DELIVERY OF GDNF PROMOTES FUNCTIONAL INTEGRATION OF HUMAN STEM CELL GRAFTS IN PARKINSON’S DISEASE (2019)

Abstract The derivation of neurotransmitter and region-specific neuronal populations from human pluripotent stem cells (PSC) provides impetus for advancing cell therapies into the clinic. At the forefront is our ability to generate ventral midbrain (VM) dopaminergic (DA) progenitors, suitable for transplantation in Parkinson’s disease (PD). Pre-clinical studies, however, have highlighted the low proportion of DA neurons within these grafts and their inferior plasticity by comparison to human fetal donor transplants. Here we sought to examine whether modification of the host environment, through viral delivery of a developmentally critical molecule, glial cell line-derived neurotrophic factor (GDNF), could improve graft survival, integration and function in Parkinsonian rodents. Utilising LMX1A- and PITX3-GFP hPSC reporter lines, we tracked the response of DA progenitors implanted into either a GDNF-rich environment, or in a second group, after a 3-week delay in onset of exposure. We found that early exposure of the graft to GDNF promoted survival of DA and non-DA cells, leading to enhanced motor recovery in PD rats. Delayed overexpression of intrastriatal GDNF also promoted motor recovery in transplanted rats, through alternate selective mechanisms including enhanced A9/A10 specification, increased DA graft plasticity, greater activation of striatal neurons and elevated DA metabolism. Lastly, transcriptional profiling of the grafts highlighted novel genes underpinning these changes. Collectively these results demonstrate the potential of targeted neurotrophic gene therapy strategies to improve human PSC graft outcomes.
Healthcare utilization and cost of cancer-related care prior to allogeneic hematopoietic cell transplantation for hematologic malignancies in the US: a retrospective real-world analysis (2021)

This study demonstrates that overall patients with hematologic malignancies requiring HCT have considerable cancer-related healthcare resource utilization and costs leading up to HCT compared to the period of time prior to developing cancer.
Clinical application of HE4 and CA125 in qualitative distinctions of pelvic mass (2014)

Objective To study the clinical application value of HE4 and CA125 in qualitative distinctions of pelvic mass. Methods 100 cases of ovarian cancer and 100 cases of benign ovarian tumor from March 2012 to March 2014 in Women and Children's Medical Center of Guangzhou City(our for short) were enrolled, and they were divided into ovarian cancer group and benign tumor group respectively, healthy subjects received physical examination in the same period in our hospital were enrolled as healthy control group. Then serum HE4 and CA125 content were compared, and the sensitivity, specificity, positive predictive value, negative predictive value were analyzed. Results There were no statistically difference of serum HE4 and CA125 between benign ovarian cancer group and healthy control group(P 0.05); the serum HE4 and CA125 levels of ovarian cancer group [(154.56±20.41) μmol/L,(251.52±39.52) U/m L]were significantly higher than benign ovarian tumor group [(35.52±5.62) μmol/L,(48.52±1.94) U/m L] and the healthy control group [(33.48 ±4.95) μmol/L,(42.48 ±5.62) U/m L], the differences were statistically significant(t =57.662, 56.241;50.97, 52.368; all P 0.01); HE4 combined with CA125 detection sensitivity, specificity, positive predictive value,negative predictive value(94%, 98%, 97.92%, 94.23%) were significantly higher than separate detection HE4(69%, 64%,65.71, 67.37%), CA125(59%, 68%, 65.84, 62.39%), the differences were statistically significant(χ2=20.726, 34.070;37.557, 31.893; 33.920, 34.368; 23.669, 31.685; all P 0.01); serum CA125 and HE4 content of different TNM stage patients were different, as TNM stage increasing, CA125 and HE4 content were higher. Conclusion HE4 and CA125 are helpful to identity property of pelvic mass and diagnose ovarian cancer and benign ovarian tumor and have ideal sensitivity and specificity.
Mining frequent sequential patterns under regular expressions: a highly adaptative strategy for pushing constraints (2003)

This paper introduces a new framework for the extraction of frequent sequences satisfying a given regular expression (RE) constraint. Contrary to previous work (SPIRIT algorithms), we represent REs by tree structures and our algorithm can choose dynamically an extraction method according to the local selectivity of the sub-REs. Interestingly, pruning can rely not only on the anti-monotonic minimal frequency constraint but also to the RE constraint that is generally not anti-monotonic. Preliminary experiments on synthetic data have shown that our algorithm takes the shape of the best algorithm from the SPIRIT family and even surpasses it.