gebhart/patrepeval huggingface dataset:
Observations of elevated formaldehyde over a forest canopy suggest missing sources from rapid oxidation of arboreal hydrocarbons (2010)

Abstract. To better understand the processing of biogenic VOCs (BVOCs) in the pine forests of the US Sierra Nevada, we measured HCHO at Blodgett Research Station using Quantum Cascade Laser Spectroscopy (QCLS) during the Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX) of late summer 2007. Four days of the experiment exhibited particularly copious HCHO, with midday peaks between 15–20 ppbv, while the other days developed delayed maxima between 8–14 ppbv in the early evening. From the expansive photochemical data set, we attempt to explain the observed HCHO concentrations by quantifying the various known photochemical production and loss terms in its chemical budget. Overall, known chemistry predicts a factor of 3–5 times less HCHO than observed. By examining diurnal patterns of the various budget terms we conclude that, during the high HCHO period, local, highly reactive oxidation chemistry produces an abundance of formaldehyde at the site. The results support the hypothesis of previous work at Blodgett Forest suggesting that large quantities of oxidation products, observed directly above the ponderosa pine canopy, are evidence of profuse emissions of very reactive volatile organic compounds (VR-VOCs) from the forest. However, on the majority of days, under generally cooler and more moist conditions, lower levels of HCHO develop primarily influenced by the influx of precursors transported into the region along with the Sacramento plume.
Testing plasmid stability of Escherichia coli using the Continuously Operated Shaken BIOreactor System (2016)

Plasmids are common vectors to genetically manipulate Escherichia coli or other microorganisms. They are easy to use and considerable experience has accumulated on their application in heterologous protein production. However, plasmids can be lost during cell growth, if no selection pressure like, e.g., antibiotics is used, hampering the production of the desired protein and endangering the economic success of a biotechnological production process. Thus, in this study the Continuously Operated Shaken BIOreactor System (COSBIOS) is applied as a tool for fast parallel testing of strain stability and operation conditions and to evaluate measures to counter such plasmid loss. In specific, by applying various ampicillin concentrations, the lowest effective ampicillin dosage is investigated to secure plasmid stability while lowering adverse ecological effects. A significant difference was found in the growth rates of plasmid-bearing and plasmid-free cells. The undesired plasmid-free cells grew 30% faster than the desired plasmid-bearing cells. During the testing of plasmid stability without antibiotics, the population fraction of plasmid-bearing cells rapidly decreased in continuous culture to zero within the first 48 h. An initial single dosage of ampicillin did not prevent plasmid loss. By contrast, a continuous application of a low dosage of 10 µg/mL ampicillin in the feed medium maintained plasmid stability in the culture. Consequently, the COSBIOS is an apt reactor system for measuring plasmid stability and evaluating methods to enhance this stability. Hence, decreased production of heterologous protein can be prevented. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1418-1425, 2016.
IL11 is prognostic of survival in lung adenocarcinoma (2011)

Mounting evidence suggests that the chronic presence and activation of immune cells exerts a promoting role during cancer development. The inflammatory cytokine IL11 has been linked to tumorigenesis in a variety of solid organ tumors, however, there are no reports of its role in lung cancer. This study assessed the significance of IL11 in lung adenocarcinoma including bronchioloalveolar carcinoma.
Enhancement of La0.6Sr0.4Co0.2Fe0.8O3-δSurface Exchange through Ion Implantation (2015)

La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) has been demonstrated to be one of the best performing mixed ionic-electronic conductors (MIEC) for SOFC cathode materials. Surface exchange on LSCF, however, limits oxygen transport and performance. We investigated surface modified LSCF, by Mn ion implantation, for an enhanced surface oxygen exchange rate while maintaining LSCFs oxygen ion conductivity through the bulk. Various implantation energies and ion concentrations were used to create samples with different Mn-ion depth profiles. The oxygen transport properties, chemical diffusion coefficient (Dchem) and effective chemical surface exchange coefficient (kchem), were characterized by electrical conductivity relaxation (ECR), using DC four-point probe measurements during the oxygen re-equilibration process. The changes of kchem for different Mn doping levels and ion acceleration energies determined with ECR are compared with surface configurations obtained using X-ray photoelectron spectroscopy. The Mn ion implanted LSCF samples show an enhanced kchem, improving the overall oxygen reduction reaction for the LSCF cathode material. Possible factors for the increase in surface exchange for the Mn implanted LSCF samples are discussed.
Selective immortalization of a phenotypically distinct epithelial cell type by microinjection of SV40 DNA into cultured human milk cells (1990)

An immortal cell line, MMSV-1, has been developed which exhibits many features of the common luminal epithelial cell of the human mammary gland. The cell line was developed by microinjection of SV40 DNA into individual cells in selected colonies in cultures of human milk epithelial cells. Immunohistochemical staining shows that the MMSV-1 cells express keratins 7, 8, 18 and 19 homogeneously in organized filaments which lead into well-developed desmosomes. They do not express vimentin or keratins found in stratified epithelia or keratin 14 found in basal cells in the mammary gland. The PEM mucin, recognized by the antibody HMFG-I, is also expressed and appears to be processed normally. Fibronectin is detected but shows the punctate pattern typical of cultured normal milk epithelial cells. MMSV-1 cells show a reduced requirement for added growth factors, including cyclic AMP-elevating agents, but do not grow in agar or form tumours in nude mice. Since the transfected cells could be selected on the basis of an extended in vitro life span, antibiotic resistance markers were not introduced and the cells remain sensitive to hygromycin and neomycin.
AlphaB-crystallin (aBC) expression in breast cancer brain metastases (BM) and primary breast cancer (pBC) with eventual BM and association with outcome. (2011)

2041 Background: aBC, a small heat shock protein, is commonly expressed in basal BC and predicts poor survival in BC patients (pts). aBC has been associated with the development of BM within basal BC. We evaluated the expression of aBC in BM and pBC with eventual BM and its association with survival. Methods: Under IRB approval (UNC/Duke), we established a clinically-annotated biobank from 78 pts: 51 BM and 38 pBC with eventual BM (11 were matched BC and BM pairs); 59 pts had complete treatment (tx) data. IHC subtype was assigned for BM and pBC: HR+ (hormone receptor)/HER2-, triple-negative (TN; ER-/PR-/HER2-), and HR+or-/HER2+. aBC expression was based on % of positively stained tumor cells: negative (0%), weak (<30%) and strong positive (≥30%). Overall survival (OS) and survival after BM were evaluated by the Kaplan-Meier method (log-rank test). Results: Median age was 50 yrs (26-84). 67% were Caucasian, 32% African American. 90% received systemic tx for metastatic BC, of which 67% followed BM. 90% received local tx (resection and/or radiation) for BM. There was no difference in receipt of local or systemic tx by aBC. Subtype for pBC (n=36) was 31% (HR+/HER2-), 42% (TN), and 28% (HR+or-/HER2+); for BM (n=42) 33%, 43% and 24%, respectively. aBC was expressed in 37% (14/38) of pBC and 47% (24/51) of BM. Concordance of aBC expression between pBC and BM was 55% (6/11). Gain of aBC expression (4/11) was more common in BM than loss (1/11). aBC was more commonly expressed in TNBC (pBC 73%; BM 67%) compared to HR+/HER2- (pBC 9%; 29% BM) or HR+or-/HER2+ (pBC 0%; 30% BM). OS and survival after BM differed by subtype (all p<0.02); pts with TNBC experienced the poorest outcome. OS and survival after BM was inferior for all pts (n=38) and those with TNBC (n=15) whose pBC expressed aBC (Table). aBC expression within BM was not prognostic (p>0.05). Conclusions: aBC expression in BM and pBC with eventual BM is frequent and associated with TNBC. Among pts with BM, expression of aBC in the pBC predicts for inferior OS and survival after BM even among poor prognosis pts with TNBC BM. pBC aBC+ aBC- P value TNBC aBC+ TNBC aBC- P value OS (yrs) 1.4 4.7 0.0002 1.4 4.7 0.01 Survival after BCBM (yrs) 0.13 0.91 0.001 0.14 1.5 0.02
Novel Geometric Operations for Linear Programming (2020)

This report summarizes the work performed under the project "Linear Programming in Strongly Polynomial Time." Linear programming (LP) is a classic combinatorial optimization problem heavily used directly and as an enabling subroutine in integer programming (IP). Specifically IP is the same as LP except that some solution variables must take integer values (e.g. to represent yes/no decisions). Together LP and IP have many applications in resource allocation including general logistics, and infrastructure design and vulnerability analysis. The project was motivated by the PI's recent success developing methods to efficiently sample Voronoi vertices (essentially finding nearest neighbors in high-dimensional point sets) in arbitrary dimension. His method seems applicable to exploring the high-dimensional convex feasible space of an LP problem. Although the project did not provably find a strongly-polynomial algorithm, it explored multiple algorithm classes. The new medial simplex algorithms may still lead to solvers with improved provable complexity. We describe medial simplex algorithms and some relevant structural/complexity results. We also designed a novel parallel LP algorithm based on our geometric insights and implemented it in the Spoke-LP code. A major part of the computational step is many independent vector dot products. Our parallel algorithm distributes the problem constraints across processors. Current commercial and high-quality free LP solvers require all problem details to fit onto a single processor or multicore. Our new algorithm might enable the solution of problems too large for any current LP solvers. We describe our new algorithm, give preliminary proof-of-concept experiments, and describe a new generator for arbitrarily large LP instances.
Improving Collection Dynamics by Monotonic Filtering (2020)

A key coordination problems in distributed open systems is distributed sensing, as achieved by cooperation and interaction among individual devices. An archetypal operation of distributed sensing is data summarization over a region of space, by which many higher level problems can be addressed, including counting items, measuring space, averaging environmental values, etc. A typical coordination strategy to perform data summarization in a peer-to-peer scenario, where devices can communicate only with a neighborhood, is to progressively accumulate information towards one or more collector devices, though this typically exhibits problems of reactivity and fragility. In this paper, we present a monotonic filtering strategy for improving the dynamics of single path collection algorithms. The strategy consists of inhibiting communication across devices whose distance towards the collector device is not decreasing. We prove that single path collection in a line graph results in quadratic overestimates after a source change and that these overestimates disappear with the application of monotonic filtering. These preliminary results suggest that monotonic filtering is likely to improve the dynamics of singlepath collection algorithms, by preventing excessive overestimates.
Reply by Authors (2019)

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Identification of the Progenitors of Indonesian and Vietnamese Avian Influenza A (H5N1) Viruses from Southern China (2008)

The transmission of highly pathogenic avian influenza H5N1 virus to Southeast Asian countries triggered the first major outbreak and transmission wave in late 2003, accelerating the pandemic threat to the world. Due to the lack of influenza surveillance prior to these outbreaks, the genetic diversity and the transmission pathways of H5N1 viruses from this period remain undefined. To determine the possible source of the wave 1 H5N1 viruses, we recently conducted further sequencing and analysis of samples collected in live-poultry markets from Guangdong, Hunan, and Yunnan in southern China from 2001 to 2004. Phylogenetic analysis of the hemagglutinin and neuraminidase genes of 73 H5N1 isolates from this period revealed a greater genetic diversity in southern China than previously reported. Moreover, results show that eight viruses isolated from Yunnan in 2002 and 2003 were most closely related to the clade 1 virus sublineage from Vietnam, Thailand, and Malaysia, while two viruses from Hunan in 2002 and 2003 were most closely related to viruses from Indonesia (clade 2.1). Further phylogenetic analyses of the six internal genes showed that all 10 of those viruses maintained similar phylogenetic relationships as the surface genes. The 10 progenitor viruses were genotype Z and shared high similarity (>/=99%) with their corresponding descendant viruses in most gene segments. These results suggest a direct transmission link for H5N1 viruses between Yunnan and Vietnam and also between Hunan and Indonesia during 2002 and 2003. Poultry trade may be responsible for virus introduction to Vietnam, while the transmission route from Hunan to Indonesia remains unclear.
Does Pandemic A/H1N1 Virus Have the Potential To Become More Pathogenic? (2010)

Epidemiologic observations that have been made in the context of the current pandemic influenza virus include a stable virulence phenotype and a lack of propensity to reassort with seasonal strains. In an attempt to determine whether either of these observations could change in the future, we coinfected differentiated human airway cells with seasonal oseltamivir-resistant A/New Jersey/15/07 and pandemic A/Tennessee/1-560/09 (H1N1) viruses in three ratios (10:90, 50:50, and 90:10) and examined the resulting progeny viruses after 10 sequential passages. When the pandemic virus was initially present at multiplicities of infection equal to or greater than those for the seasonal virus, only pandemic virus genotypes were detected. These adapted pandemic strains did, however, contain two nonsynonymous mutations (hemagglutinin K154Q and polymerase acidic protein L295P) that conferred a more virulent phenotype, both in cell cultures and in ferrets, than their parental strains. The polymerase acidic protein mutation increased polymerase activity at 37°C, and the hemagglutinin change affected binding of the virus to α2,6-sialyl receptors. When the seasonal A/H1N1 virus was initially present in excess, the dominant progeny virus was a reassortant containing the hemagglutinin gene from the seasonal strain and the remaining genes from the pandemic virus. Our study demonstrates that the emergence of an A/H1N1 pandemic strain of higher virulence is possible and that, despite their lack of detection thus far in humans, viable seasonal/pandemic virus reassortants can be generated.
Application of 3-D Δ Check Graphs to HbA1cQuality Control and HbA1cUtilization (2008)

Delta checking is a laboratory information system (LIS)-based tool that detects patient and laboratory quality control errors. By using hemoglobin A1c (HbA1c) data, we developed a novel approach to summarizing and presenting patient Delta values to address limitations of current Delta check algorithms. Delta values were calculated from intrapatient pairs of HbA1c (n = 55,327) measured during 2 years in a single referral or a university hospital laboratory. Three-dimensional Delta-time (DeltaT) and percentile limit graphs were constructed. Cumulative distribution function analysis was used to explore clinical utilization. The DeltaT graphs showed that HbA1c Delta values increase asymmetrically over time. Although the 2.5 to 97.5 and 5.0 to 95.0 percentile Delta check limits were similar for both sites, the referral laboratory's 0.5 to 99.5 percentile limits were wider. For acute patient care environments, we recommend limits of -3.5% and 1.8% for measurements between 0 and 60 days and -4.0% and 2.0% for measurements between 60 and 120 days. For the outpatient environment, we recommend limits of -4.2% and 2.1% and 5.0% and 2.5% for measurements between 0 and 60 days and 60 and 120 days, respectively.Delta checking can be significantly improved with customization of limits set by population and interobservation period. Because LIS systems are incapable of these customizations, customers must become advocates for these modifications.
Study of in vitro mitral valve filling flow. (2004)

Diastolic function is a good indicator of overall cardiac health. This study is in support of a non-invasive technique to measure diastolic function. Interpretation of mitral flow, and early diagnosis of normality or dysfunction, can be enhanced by improved understanding of the fluid dynamics. A simple in-vitro model of mitral flow is being used to illustrate vortex dynamics associated with diastolic inflow. A range of tailored mitral flow waveforms are being developed to mimic normal velocity profiles. Laser Doppler velocimetry (LDV) is being used to measure the flow speed. By combining flow visualization, particle image velocimetry and LDV, vortex ring signatures including size, circulation, and propagation speed are being examined as possible metrics for diastolic dysfunction. The detection of these signatures in the downstream flow will be compared to clinical waveforms derived from Doppler ultrasound.
Conference Report: from Challenges to Solutions (2011)

The European Bioanalysis Forum is a bioanalytical nonprofit organization comprised of European pharmaceutical companies (27 members to date) and currently expanding to include CROs as well. The European Bioanalysis Forum provides a broad European bioanalytical network for the discussion of scientific, technological and regulatory topics of bioanalytical interest. The 3rd Annual Open Symposium was again much anticipated after the two previous successful meetings. The symposium included sessions on thinking outside the 'commodity' box, bioanalytical challenges with blood, global harmonization, assay platforms, dried blood spots, immunogenicity, matrix effects, anomalous results, biomarkers and two plenary technology sessions hosted by the Platinum sponsors. Experts and key opinion leaders were invited as guest speakers. A total of 424 delegates registered from 113 companies representing a large percentage of the European bioanalytical community. In addition to 48 oral presentations, 88 posters were presented and there was a vendor exposition of 40 companies.
The pSC101 par locus alters protein-DNA interactions in vivo at the plasmid replication origin (1993)

We report here direct evidence that mutations in the par locus affect protein-DNA interactions in vivo at the replication origin of plasmid pSC101. Concomitant with par-mediated plasmid stabilization, two sites in the origin region show an altered methylation pattern as detected by in vivo footprinting with dimethyl sulfate. One site is located near an integration host factor-binding sequence adjacent to the first of three direct repeats known to be involved in the initiation of pSC101 replication; the second site is within the third direct repeat.
Bacterial species selective toxicity of two isomeric α/β-peptides: Role of membrane lipids (2005)

We have studied how membrane interactions of two synthetic cationic antimicrobial peptides with alternating alpha- and beta-amino acid residues ("alpha/beta-peptides") impact toxicity to different prokaryotes. Electron microscopic examination of thin sections of Escherichia coli and of Bacillus subtilis exposed to these two alpha/beta-peptides reveals different structural changes in the membranes of these bacteria. These two peptides also have very different effects on the morphology of liposomes composed of phosphatidylethanolamine and phosphatidylglycerol in a 2:1 molar ratio. Freeze fracture electron microscopy indicates that with this lipid mixture, alpha/beta-peptide I induces the formation of a sponge phase. 31P NMR and X-ray diffraction are consistent with this conclusion. In contrast, with alpha/beta-peptide II and this same lipid mixture, a lamellar phase is maintained, but with a drastically reduced d-spacing. alpha/beta-Peptide II is more lytic to liposomes composed of these lipids than is I. These findings are consistent with the greater toxicity of alpha/beta-peptide II, relative to alpha/beta-peptide I, to E. coli, a bacterium having a high content of phosphatidylethanolamine. In contrast, both alpha/beta-peptides display similar toxicity toward B. subtilis, in accord with the greater anionic lipid composition in its membrane. This work shows that variations in the selectivity of these peptidic antimicrobial peptides toward different strains of bacteria can be partly determined by the lipid composition of the bacterial cell membrane.
Obstructive Sleep Apnea–Induced Neurogenic Nocturnal Hypertension (2021)

There is a bidirectional, causal relationship between obstructive sleep apnea (OSA) and hypertension. OSA-related hypertension is characterized by high rates of masked hypertension, elevated nighttime blood pressure, a nondipper pattern of nocturnal hypertension, and abnormal blood pressure variability. Hypoxia/hypercapnia-related sympathetic activation is a key pathophysiological mechanism linking the 2 conditions. Intermittent hypoxia also stimulates the renin-angiotensin-aldosterone system to promote hypertension development. The negative and additive cardiovascular effects of OSA and hypertension highlight the importance of effectively managing these conditions, especially when they coexist in the same patient. Continuous positive airway pressure is the gold standard therapy for OSA but its effects on blood pressure are relatively modest. Furthermore, this treatment did not reduce the cardiovascular event rate in nonsleepy patients with OSA in randomized controlled trials. Antihypertensive agents targeting sympathetic pathways or the renin-angiotensin-aldosterone system have theoretical potential in comorbid hypertension and OSA, but current evidence is limited and combination strategies are often required in drug resistant or refractory patients. The key role of sympathetic nervous system activation in the development of hypertension in OSA suggests potential for catheter-based renal sympathetic denervation. Although long-term, randomized controlled trials are needed, available data indicate sustained and relevant reductions in blood pressure in patients with hypertension and OSA after renal denervation, with the potential to also improve respiratory parameters. The combination of lifestyle interventions, optimal pharmacological therapy, continuous positive airway pressure therapy, and perhaps also renal denervation might improve cardiovascular risk in patients with OSA.