gebhart/patrepeval huggingface dataset:
Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6 (2018)

Our results are consistent with a model of intermittent de novo integration of HHV-6B into host germline cells during active infection with a large contribution of founder effect in iciHHV-6B. Our data provide a significant advance in the genomic annotation of HHV-6B, which will contribute to the detection, diversity, and control of this virus.
pTAC10, a Key Subunit of Plastid-Encoded RNA Polymerase, Promotes Chloroplast Development (2017)

Regulation of photosynthetic gene expression by plastid-encoded RNA polymerase (PEP) is essential for chloroplast development. The activity of PEP largely relies on at least 12 PEP-associated proteins (PAPs) encoded in the nuclear genome of plant cells. A recent model proposed that these PAPs regulate the establishment of the PEP complex through broad PAP-PEP or PAP-PAP interactions. In this study, we identified the Arabidopsis (<i>Arabidopsis thaliana</i>) seedling-lethal mutant <i>ptac10-1</i>, which has defects in chloroplast development, and found that the mutant phenotype is caused by the suppression of <i>PLASTID S1 RNA-BINDING DOMAIN PROTEIN</i> (<i>pTAC10/PAP3</i>). Analysis of the heterozygous mutant and <i>pTAC10</i>-overexpressing transgenic plants indicated that the expression level of <i>pTAC10</i> is tightly linked to chloroplast development. Characterization of the interaction of pTAC10 with PAPs revealed that pTAC10 interacts with other PAPs, such as FSD2, FSD3, TrxZ, pTAC7, and pTAC14, but it does not interact with PEP core enzymes, such as rpoA and rpoB. Analysis of pTAC10 interactions using truncated pTAC10 proteins showed that the pTAC10 carboxyl-terminal region downstream of the S1 domain is involved in the pTAC10-PAP interaction. Furthermore, overexpression of truncated <i>pTAC10s</i> lacking the C-terminal regions downstream of the S1 domain could not rescue the <i>ptac10-1</i> mutant phenotype and induced an abnormal whitening phenotype in Columbia-0 plants. Our observations suggested that these pTAC10-PAP interactions are essential for the formation of the PEP complex and chloroplast development.
Harnessing Single Cell Sorting to Identify Cell Division Genes and Regulators in Bacteria (2013)

Cell division is an essential cellular process that requires an array of known and unknown proteins for its spatial and temporal regulation. Here we develop a novel, high-throughput screening method for the identification of bacterial cell division genes and regulators. The method combines the over-expression of a shotgun genomic expression library to perturb the cell division process with high-throughput flow cytometry sorting to screen many thousands of clones. Using this approach, we recovered clones with a filamentous morphology for the model bacterium, Escherichia coli. Genetic analysis revealed that our screen identified both known cell division genes, and genes that have not previously been identified to be involved in cell division. This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development.
Integrating High-Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities (2011)

New high-throughput technologies continue to emerge for studying complex microbial communities. In particular, massively parallel pyrosequencing enables very high numbers of sequences, providing a more complete view of community structures and a more accurate inference of the functions than has been possible just a few years ago. In parallel, quantitative real-time PCR (QPCR) allows quantitative monitoring of specific community members over time, space, or different environmental conditions. In this review, we discuss the principles of these two methods and their complementary applications in studying microbial ecology in bioenvironmental systems. We explain parallel sequencing of amplicon libraries and using bar codes to differentiate multiple samples in a pyrosequencing run. We also describe best procedures and chemistries for QPCR amplifications and address advantages of applying automation to increase accuracy. We provide three examples in which we used pyrosequencing and QPCR together to define and quantify members of microbial communities: in the human large intestine, in a methanogenic digester whose sludge was made more bioavailable by a high-voltage pretreatment, and on the biofilm anode of a microbial electrolytic cell. We highlight our key findings in these systems and how both methods were used in concert to achieve those findings. Finally, we supply detailed methods for generating PCR amplicon libraries for pyrosequencing, pyrosequencing data analysis, QPCR methodology, instrumentation, and automation.
Patient-reported financial toxicity following management of localized prostate cancer. (2021)

e17053 Background: Cancer patients’ potential for severe financial toxicity (FT) is well-established, however there is limited data on the magnitude of this challenge associated with treatment of localized prostate cancer (PC). The extent to which men consider potential financial implications prior to selection of a treatment strategy remains poorly understood. Methods: Between 5/2020-10/2020, 1233 insured PC patients treated at a comprehensive cancer center completed a one-time FT survey which included the COmprehensive Score for financial Toxicity (COST) instrument, impressions of PC costs and financial coping strategies. Inclusion criteria was localized disease and treatment with either radical prostatectomy (RP) or definitive radiotherapy (RT) in the previous 4-26 months (mo) or at least 6mo of active surveillance (AS) prior to survey. To assess possible temporal differences in FT, responses were grouped into 6, 12, 18 and 24 months after treatment start, and we plotted COST against time, using generalized additive models to allow for non-linearity. Results: Overall, 988 men were eligible for analysis: 347 (35%) underwent RP, 384 (39%) underwent RT, and 257 (26%) were on AS. The median age at survey completion was 67 years (quartiles 62, 72). Men were predominantly white (89%), English-speakers (99%) and married (84%). The median (quartiles) COST score for all patients was 33 (26, 38) with possible range of 0-44 with lower scores indicating greater FT; median values were identical with similar quartiles (+/- 1 point) when stratified by treatment type. There were no significant changes in median COST between men surveyed at the four time points for any treatment subgroup. In total, 66 men (7.1%) reported spending &gt; 20% of annual income on treatment and 10% felt that PC has created at least somewhat of a financial hardship for their family. Top drivers of burdensome cost included medical bills (37%) and transportation costs (21%). Most (83%) reported giving little or no consideration to possible costs prior to making a PC treatment decision, yet the majority (77%) felt that out of pocket costs should be communicated to a patient prior to decision making. Most believed patients should definitely (46%) or possibly (33%) have the opportunity to discuss financial concerns with the radiation oncologist or urologist. Conclusions: Our study is the first reported use of the COST instrument to assess subjective financial distress in localized PC patients. Our results demonstrate that the overall degree of FT in this cohort of insured patients treated at a specialized cancer center is low. While potential financial burden does not strongly influence treatment decision making in this cohort, most want this information and an opportunity to discuss financial concerns with their oncologist. Next steps include identification of predictors for high FT risk and extension of our survey to hospital systems with differing demographic profiles.
The Uncertain Scope of Malicious Prosecution: Insights from Canada (2016)

In the last fifteen years, courts throughout the commonwealth have been struggling to redefine the scope of malicious prosecution. The vexing question is whether the cause of action may lie for wrongful administrative and civil proceedings, or whether it is restricted to criminal ones. This is exemplified by a number of divergent judgments in the United Kingdom and Australia, which are very difficult to reconcile on principled grounds. This paper brings the Canadian experience to bear on this issue through an empirical analysis of cases from Ontario, which extended malicious prosecution to administrative proceedings 25 years ago and thus offers a natural experiment of the implications of broadening the tort. This analysis shows that fears about opening the floodgates of litigation are unsubstantiated. Most claims in the sample did not make it to trial and three-quarters of them were dismissed. Furthermore, defendants usually prevailed on pre-trial motions to dismiss, which suggests that baseless claims may be disposed of quickly. Not surprisingly, the most common ground for dismissal was absence of malice, which indicates that the tort is sufficiently onerous to keep it in check. In addition to this empirical analysis, the article examines both the early and more recent case law, concluding that defining the scope of the tort based on the nature of the underlying proceeding is unsupportable. Specifically, such a categorical approach produces inconsistent and arbitrary outcomes that have little to do with the tort’s policy rationale. And malicious prosecution fills a real gap in the law because other torts do not apply, meaning that without it victims of wrongful administrative or civil proceedings would be left uncompensated.
Arachidonic acid release from NIH 3T3 cells by group‐I phospholipase A2: Involvement of a receptor‐mediated mechanism (1995)

Group I pancreatic phospholipase A2 (PLA2 I) is primarily a digestive enzyme. Recently, however, in addition to its catalytic activity a receptor-mediated function has been described for this enzyme. PLA2 I binding to its receptor induces cellular chemokinesis, proliferation, and smooth muscle contraction. This enzyme also induces the production of prostaglandin E2 in certain cells and may have a proinflammatory role. However, despite its ability to hydrolyze phospholipids in in vitro assays, PLA2-I does not efficiently catalyze release of AA from intact cells. Here, we demonstrate that while short-term exposure of NIH 3T3 cells to PLA2-I is ineffective, exposure of 6 h or longer significantly increases the basal release of AA. Dose-response curve of PLA2-I-induced AA release was saturable with an EC50 of 14.01 +/- 1.36 nM (n = 3). [3H]-AA was preferentially released over [3H]-oleic acid by PLA2-I. PLA2-I, inactivated with 4-bromophenacyl bromide, was fully capable of mediating AA release. These data suggest that a non-catalytic, receptor-mediated mechanism is involved in PLA2-I-induced AA release in NIH-3T3 cells. This release of AA is not dependent on protein kinase C or Ca2+ concentration. Comparison of the effect of PLA2-I with those of ATP and platelet-derived growth factor indicates that each of these agonists regulates AA release via independent pathways. Neither the basal enzymatic activity of the 85-kDa cytosolic PLA2 nor the protein level of this enzyme was affected by treatment of cells with PLA2-I. However, the increase in basal enzymatic activity of 85 kDa PLA2 due to protein kinase C activation was further enhanced by pretreatment of cells with PLA2-I. We conclude that: (1) short-term exposure of cells to PLA2 I does not cause measurable AA release; (2) release of AA from intact cells by this enzyme requires long-term exposure; (3) AA release is not mediated by a direct catalytic effect of PLA2 I; and (4) AA release by PLA2 I is accomplished via a receptor-mediated process. Taken together, these results raise the possibility that PLA2 I, in addition to its digestive function, may also contribute to aggravate preexisting inflammatory processes and/or to initiate new ones when chronic exposure of cells to this enzyme occurs.
Case Study of Transportation Benefits Using GIS in Distributed Preprocessing of Corn Stover into Crude Biobutanol (2021)

Highlights Total transportation costs were reduced by 32% to 63% with distributed biobutanol depots. An 8 km distance to the depot manifested the most desirable transportation costs. Across regions, biomass transport costs from field to depot were similar at equivalent distances. Abstract . The transportation efficiencies of centralized biomass processing facilities were compared to a proposed distributed preprocessing network with centralized refining facilities. Centralized biomass processing was defined as transport of baled corn stover directly from the field to the refinery. Distributed preprocessing with centralized refining was defined as transport of baled corn stover from the field to a biobutanol preprocessing depot and transport of completely dewatered crude biobutanol solution from the depot to a centralized refinery. For both systems, the locations of the corn fields, as identified through the cropland data layer, and of the refinery were fixed. For the distributed system, the biobutanol depot locations were variable and depended on different maximum transport distances (8 to 80 km) from the field to the depot. In this case study, site-specific transportation costs and biobutanol production capacities were developed for different agricultural regions in Kentucky. The distributed system produced a 32% to 63% reduction in total transportation cost with decreased (50% to 90%) fuel use as compared to the centralized system. The GIS transportation model demonstrated that on-farm biofuel production could be an effective means of producing biofuel and reducing transportation costs. Keywords: Biomass transport, Depot, Distributed biomass collection, GIS location-allocation, Minimize facilities, Satellite facilities.
4′-Methoxyphenacyl-Assisted Synthesis of β-Kdo Glycosides (2016)

3-Deoxy-β-d-manno-oct-2-ulosonic acid (β-Kdo) glycosides are mainly found in capsular polysaccharides and extracellular exopolysaccharides from Gram-negative bacteria. These compounds have profound biological implications in immune response and act as virulence factors. We have developed a novel methodology for the stereoselective synthesis of β-Kdo glycosides via the use of a 4'-methoxyphenacyl (Phen) auxiliary group at the C1 position of a peracetylated β-Kdo thioglycoside. Under the promotion of NIS/AgOTf in acetonitrile, a series of Kdo glycosides was synthesized in good yield and β-selectivity while minimizing the formation of undesirable glycals. Stereoselectivity of the glycosylation was shown to be modulated by various factors such as promotor, solvent, anomeric ratio of donor, nature of acceptor, and Phen substitution. Chemoselective cleavage of the Phen group was performed under the action of Zn/HOAc. DFT calculations together with experimental results suggested that α-triflate and a six-membered α-spiroPhen are plausible intermediates of the reaction, accounting for the enhanced formation of β-Kdo glycosides. The developed methodology could be applied to the synthesis of β-Kdo-containing glycans from pathogenic bacteria.
Identification of a prostanoid FP receptor population producing endothelium‐dependent vasorelaxation in the rabbit jugular vein (1995)

1. Prostaglandin F2 alpha (PGF2 alpha) and its synthetic analogue, fluprostenol, potently relaxed the precontracted isolated jugular vein of the rabbit (RJuV). The vasorelaxant activity of PGF2 alpha and fluprostenol was dependent upon an intact vascular endothelium. Although removal of the vascular endothelium abolished activity associated with PGF2 alpha-like agonists, it did not significantly alter the relaxant effects of prostaglandin E2 (PGE2). 2. The nitric oxide synthase inhibitor, NG-nitro-L-arginine methyl ester (L-NAME), at 100 microM significantly inhibited the endothelium-dependent relaxations induced by PGF2 alpha. Lower doses (1 microM, 10 microM) of L-NAME had little or no effect. The relaxant effects of PGE2 were not affected by L-NAME (1-100 microM). D-NAME at 100 microM was without effect on the vasorelaxant responses to either PGF2 alpha or PGE2. 3. The potassium (K)-channel blockers tetraethylammonium (TEA, 1 mM), barium (1 mM) and quinine (100 microM), each tested in the presence of the inactive enantiomer D-NAME (100 microM) did not significantly affect the response to PGF2 alpha. Unexpectedly, both TEA and barium significantly and partially reversed the inhibitory effects of 100 microM L-NAME, whereas quinine had no effect. In similar studies, none of the three potassium channel blockers had any effect on relaxations elicited by PGE2 when given with D-NAME or L-NAME. 4. These results indicate that the PGF2 alpha-sensitive prostanoid receptors found in the vascular endothelium of the rabbit jugular vein are of the FP-receptor subtype. Nitric oxide (NO) appears to be the predominant messenger involved in PGF2 alpha-induced relaxation of the rabbit jugular vein. Potassium channels may have a minor role in mediating the vasorelaxation response to PGF2 alpha. When both NO synthesis and K-channels are simultaneously blocked, inhibition of PGF2 alpha-induced vasorelaxation by L-NAME is opposed by K-channel blockers. This diminution of the inhibitory effect of L-NAME by TEA and barium suggests that K-channels may possibly serve a compensatory role via the NO pathway.
The Assessment of Carrier Status of Canine Hemophilia A in a Hemophilic Colony. (2002)

Hemophilic dogs have an identical inheritance pattern and bleeding symptoms to human hemophilia A and therefore are a most suitable animal model of the human disease. The probability based on the pedigree data and the measurement of factor VIII coagulant activity (FVIII : C) have been used for carrier detection of canine hemophilia A. In order to improve the precision of carrier diagnosis, a ratio of FVIII : C to von Willebrand factor antigen (VWF : Ag) was used for the assessment of carrier status of canine hemophilia A. Two beagle dogs suspected to be hemophilic carriers by the reduction of FVIII : C to around 50 U/dl were tested for the ratio of FVIII : C/VWF : Ag. They were mated with a normal male beagle, and newborn puppies were tested for coagulation assays. One dog strongly suspected of being a carrier by the ratio was confirmed as a definite carrier by the production of a hemophilic puppy, which may be the first hemophilic dog in Japan resulting from a planned mating. The other dog suspected not to be a carrier by the ratio has never produced any hemophilic puppies. These findings suggest that the FVIII : C/VWF : Ag assessment is more reliable than FVIII : C alone for carrier detection of canine hemophilia A and is useful in the establishment of a canine hemophilic colony.
Multiple scan chain design technique for power reduction during test application in BIST (2004)

The multiple scan chain has been used in DFT (design for test) architectures primarily to reduce test application time. Since power is an emerging problem, in this paper, we present a design technique for multiple scan chains in BIST (built-in self test) to reduce average power dissipation and test application time, while maintaining the fault coverage. First, we partition the scan chain into a set of smaller chains of similar lengths in such a way that the total number of scan transitions in the scan chain is minimized. Then, we use a novel scan re-ordering algorithm in each smaller chain to further reduce the transitions. Experiments on ISCAS'89 benchmarks show up to 46.2% (average 24.4%) power reduction using the proposed technique, compared to the scan partitions given in the RTL description. Unlike previous approaches, our solution is computationally efficient and test-set independent and thus, can be effectively applied to large BIST circuitry.
Bioimpedance spectroscopy for fluid status assessment in patients with decompensated liver cirrhosis: Implications for peritoneal dialysis (2020)

Bioimpedance spectroscopy (BIS) is routinely used in peritoneal dialysis patients and might aid fluid status assessment in patients with liver cirrhosis, but the effect of ascites volume removal on BIS-readings is unknown. Here we determined changes in BIS-derived parameters and clinical signs of fluid overload from before to after abdominal paracentesis. Per our pre-specified sample size calculation, we studied 31 cirrhotic patients, analyzing demographics, labs and clinical parameters along with BIS results. Mean volume of the abdominal paracentesis was 7.8 ± 2.6 L. From pre-to post-paracentesis, extracellular volume (ECV) decreased (20.2 ± 5.2 L to 19.0 ± 4.8 L), total body volume decreased (39.8 ± 9.8 L to 37.8 ± 8.5 L) and adipose tissue mass decreased (38.4 ± 16.0 kg to 29.9 ± 12.9 kg; all p < 0.002). Correlation of BIS-derived parameters from pre to post-paracentesis ranged from R² = 0.26 for body cell mass to R² = 0.99 for ECV. Edema did not correlate with BIS-derived fluid overload (FO ≥ 15% ECV), which occurred in 16 patients (51.6%). In conclusion, BIS-derived information on fluid status did not coincide with clinical judgement. The changes in adipose tissue mass support the BIS-model assumption that fluid in the peritoneal cavity is not detectable, suggesting that ascites (or peritoneal dialysis fluid) mass should be subtracted from adipose tissue if BIS is used in patients with a full peritoneal cavity.
Hydrodynamique induite par un oxygénateur de surface : influence du design des agitateurs sur la qualité de la dispersion (2002)

Le turboxal TM est un nouveau systeme d'agitation flottant concu pour oxygener et brasser les bassins d'epuration biologique des eaux. Il comprend trois agitateurs entoures d'une volute fixe comportant six chicanes. L'objectif est d'ameliorer les performances c'est a dire augmenter le debit de gaz injecte tout en maintenant un transfert de matiere correct. L'analys, a la fois experimentale et numerique, du fonctionnement a fait ressortir que les performances ne pouvaient etre accrues par de simples modifications geometriques. Le deuxieme point de ce travail a alors porte sur la recherche par simulation numerique d'une nouvelle geometrie de la turbine remplacant a la fois la turbine existante et l'helice a refoulement vers le haut. 3 turbines modifiees ont ete selectionnees et testees experimentalement au sein du Turboxal TM. Finalement un Turboxal TM de 2eme generation permettant de satisfaire notre objectif a ete propose.