gebhart/patrepeval huggingface dataset:
YALI0E32769g (DGA1) and YALI0E16797g (LRO1) encode major triacylglycerol synthases of the oleaginous yeast Yarrowia lipolytica (2011)

The oleaginous yeast Yarrowia lipolytica has an outstanding capacity to produce and store triacylglycerols resembling adipocytes of higher eukaryotes. Here, the identification of two genes YALI0E32769g (DGA1) and YALI0E16797g (LRO1) encoding major triacylglycerol synthases of Yarrowia lipolytica is reported. Heterologous expression of either DGA1 or LRO1 in a mutant of the budding yeast Saccharomyces cerevisiae defective in triacylglycerol synthesis restores the formation of this neutral lipid. Whereas Dga1p requires acyl-CoA as a substrate for acylation of diacylglycerol, Lro1p is an acyl-CoA independent triacylglycerol synthase using phospholipids as acyl-donor. Growth of Yarrowia lipolytica strains deleted of DGA1 and/or LRO1 on glucose containing medium significantly decreases triacylglycerol accumulation. Most interestingly, when oleic acid serves as the carbon source the ratio of triacylglycerol accumulation in mutants to wild-type is significantly increased in strains defective in DGA1 but not in lro1Δ. In vitro experiments revealed that under these conditions an additional acyl-CoA dependent triacylglycerol synthase contributes to triacylglycerol synthesis in the respective mutants. Taken together, evidence is provided that Yarrowia lipolytica contains at least four triacylglycerol synthases, namely Lro1p, Dga1p and two additional triacylglycerol synthases whereof one is acyl-CoA dependent and specifically induced upon growth on oleic acid.
What makes vessels grow with exercise training? (2004)

Exercise and muscle contractions create a powerful stimulus for structural remodeling of the vasculature. An increase in flow velocity through a vessel increases shear stress, a major stimulus for enlargement of conduit vessels. This leads to an endothelial-dependent, nitric oxide-dependent enlargement of the vessel. Increased flow within muscle, in the absence of contractions, leads to an enhanced capillarity by intussusceptive angiogenesis, a process of capillary splitting by intraluminal longitudinal divide. In contrast, sprouting angiogenesis requires extensive endothelial cell proliferation, with degradation of the extracellular matrix to permit migration and tube formation. This occurs during muscle adaptations to chronic contractions and/or muscle overload. The angiogenic growth factor VEGF appears to be an important element in angiogenesis. Recent advances in research have identified hemodynamic and mechanical stimuli that upregulate angiogenic processes, demonstrated a complexity of potent growth factors and interactions with their corresponding receptors, detected an interaction of cellular signaling events, and identified important tissue reorganization processes that must be coordinated to effect vascular remodeling. It is likely that much of this information is applicable to the vascular remodeling that occurs in response to exercise and/or muscle contractions.
Sources and Magnitude of Intralaboratory Variability in a Sequence-Based Genotypic Assay for Human Immunodeficiency Virus Type 1 Drug Resistance (2003)

We assessed the intralaboratory reproducibility of a system for sequencing human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) by using replicate subanalyses of 46 plasma samples collected from HIV-1-infected, antiretroviral-experienced patients in order to determine the relative contributions of the different procedural steps to final sequence variability. Complete sequence concordance between duplicates of each sample was 99.4%. Complete and partial mismatches occurred scattered throughout the PR-RT genome segment at >300 positions. Approximately 75% of the discordances involved mixtures, some of which appeared at key resistance sites. Most differences were the result of the first-round RT-PCR procedure. Inter-rater concordance for sequence analysis and assembly was >99.9%. There was no observed correlation between the number or frequency of mismatches and plasma viral loads. A separate longitudinal analysis of a single routine control sample sequenced 103 times over 9 months consistently gave highly reproducible sequences (median percentage of nucleotide discordances, 0.04%; range, 0 to 0.2%). Finally, sequence data from 168 sequential samples collected from 22 patients with long-term, predominantly wild type HIV showed that intrapatient nucleotide concordance with individual index sequences ranged from 96.5 to 100%. Together, these results confirm that sequence-based genotyping can be a precise and reliable tool for monitoring HIV drug resistance, and they suggest that efforts to reduce variability should focus on the first RT-PCR step. Consequently, the data suggest that the composition of external quality assessment panels should be based on clinical HIV isolates rather than DNA clones.
Humanization of a mouse antibody against human alpha-4 integrin: A potential therapeutic for the treatment of multiple sclerosis (1997)

alpha 4 beta 1 integrin (VLA-4) is crucial for the adhesion of leukocytes to human vascular cell adhesion molecule-1 (VCAM-1) on inflamed endothelium. This cell adhesion event is the first step in leukocyte extravasation across the blood-brain barrier in inflammatory diseases of the central nervous system (CNS) such as experimental autoimmune encephalomyelitis (EAE). Prevention of leukocyte infiltration by antibodies against the alpha 4 integrin, which block the alpha 4 beta 1 integrin/VCAM-1 interaction, have been shown to suppress clinical and pathological features of EAE. In this study, two mouse monoclonal antibodies (MAb) directed against human alpha 4 integrin were analyzed in vitro for their ability to block the interaction of leukocytes with VCAM-1 under different assay conditions. The best blocking MAb, AN100226m, was humanized by complementarily-determining region grafting, associated with human C regions and expressed. We found that modification of two structural determinants (H27 and H29) for the heavy chain CDR1 loop in one hand, and modification of framework amino acid H38, H40 and H44 in the other hand, had no effect on antigen binding. In contrast, modification of a structural determinant (H71) for the heavy chain CDR2 loop resulted in loss of binding. The humanized antibody. AN100226, was equivalent to the murine antibody. AN100226m, in binding to alpha 4 beta 1 integrin and in blocking cell adhesion. More importantly, AN100226 was as effective as AN100226m in the reversal of active EAE in guinea pigs and thus may be useful in the treatment of autoimmune diseases such as multiple sclerosis. AN100226 is currently in phase II clinical trials in the UK for the treatment of multiple sclerosis exacerbations.
Induction of anti-double stranded DNA antibodies in normal mice by immunization with bacterial DNA. (1989)

Because of recent observations suggesting that bacterial DNA is immunogenic, the induction in normal mice of antibodies to Escherichia coli (EC) dsDNA was investigated. BALB/c and C57BL/6 mice were immunized with dsEC or ds calf thymus (CT) DNA complexed to methylated BSA in adjuvant; antibody responses were measured by ELISA. In both strains, dsEC DNA immunization induced a much higher anti-dsDNA response to dsEC DNA than did dsCT DNA immunization. Neither immunized group showed an appreciable antibody response when tested on dsCT DNA. Anti-dsDNA antibodies were also demonstrated by ELISA using synthetic DNA duplexes as well as a filter binding assay using 3H-labeled dsEC DNA as Ag. These results suggest that bacterial dsDNA is immunogenic and that at least some anti-dsDNA specificities can arise by immunization.
Polymorphisms Associated with Cholesterol and Risk of Cardiovascular Events (2008)

A genotype score of nine validated SNPs that are associated with modulation in levels of LDL or HDL cholesterol was an independent risk factor for incident cardiovascular disease. The score did not improve risk discrimination but did modestly improve clinical risk reclassification for individual subjects beyond standard clinical factors.
Chronic effects of β2 agonists on body composition and protein synthesis in the rat (1984)

Chronic treatment of rats with the beta 2-adrenergic agonists clenbuterol and fenoterol over 16-19 d raised energy intake, expenditure, and body weight gain but did not affect fat or energy deposition, and body protein gain was increased by 50 and 18%, respectively. Both drugs increased the protein content and mitochondrial GDP-binding capacity of brown adipose tissue. Clenbuterol did not affect plasma insulin, growth hormone, or triiodothyronine levels, although insulin levels were reduced by fenoterol. Both drugs caused hypertrophy of skeletal muscle (gastrocnemius), and muscle protein synthesis in vivo (fractional rate) was elevated by 34 and 26% in clenbuterol and fenoterol-treated rats, respectively.
Photochromic fulgides. Spectroscopy and mechanism of photoreactions (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochromic fulgides. Spectroscopy and mechanism of photoreactionsAzucena Santiago and Ralph S. BeckerCite this: J. Am. Chem. Soc. 1968, 90, 14, 3654–3658Publication Date (Print):July 1, 1968Publication History Published online1 May 2002Published inissue 1 July 1968https://pubs.acs.org/doi/10.1021/ja01016a009https://doi.org/10.1021/ja01016a009research-articleACS PublicationsRequest reuse permissionsArticle Views519Altmetric-Citations70LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Complications after uterine artery embolization for leiomyomas (2002)

The short-term complication rate was low in women undergoing uterine embolization.
Selective CD4+ Lymphopenia in Melanoma Patients Treated With Temozolomide: A Toxicity With Therapeutic Implications (2004)

TMZ at this dose and schedule results in CD4(+) lymphopenia in a majority of patients that can result in OIs. Pneumocystis pneumonia prophylaxis should be considered for patients who develop sustained lymphopenia on TMZ.
Phosphorylation Events During Müllerian Duct Regression (1984)

Regression of the fetal rat Müllerian duct in vitro was stimulated by sodium fluoride in the absence of Müllerian inhibiting substance. The action of Müllerian inhibiting substance was inhibited by sodium vanadate, adenosine 5'-triphosphate, and several related nucleotides in the presence of manganese ions. Epidermal growth factor specifically inhibited the substance, but only with manganese ions present. Insulin, platelet-derived growth factor, and nerve growth factor had no effect. These results suggest that dephosphorylation of membrane proteins mediates the action of Müllerian inhibiting substance.
ace , Which Encodes an Adhesin in Enterococcus faecalis , Is Regulated by Ers and Is Involved in Virulence (2009)

Enterococcus faecalis is an opportunistic pathogen that causes numerous infectious diseases in humans and is a major agent of nosocomial infections. In this work, we showed that the recently identified transcriptional regulator Ers (PrfA like), known to be involved in the cellular metabolism and the virulence of E. faecalis, acts as a repressor of ace, which encodes a collagen-binding protein. We characterized the promoter region of ace, and transcriptional analysis by reverse transcription-quantitative PCR and mobility shift protein-DNA binding assays revealed that Ers directly regulates the expression of ace. Transcription of ace appeared to be induced by the presence of bile salts, probably via the deregulation of ers. Moreover, with an ace deletion mutant and the complemented strain and by using an insect (Galleria mellonella) virulence model, as well as in vivo-in vitro murine macrophage models, we demonstrated for the first time that Ace can be considered a virulence factor for E. faecalis. Furthermore, animal experiments revealed that Ace is also involved in urinary tract infection by E. faecalis.
Large-Scale Domain Adaptation via Teacher-Student Learning (2017)

High accuracy speech recognition requires a large amount of transcribed data for supervised training. In the absence of such data, domain adaptation of a well-trained acoustic model can be performed, but even here, high accuracy usually requires significant labeled data from the target domain. In this work, we propose an approach to domain adaptation that does not require transcriptions but instead uses a corpus of unlabeled parallel data, consisting of pairs of samples from the source domain of the well-trained model and the desired target domain. To perform adaptation, we employ teacher/student (T/S) learning, in which the posterior probabilities generated by the source-domain model can be used in lieu of labels to train the target-domain model. We evaluate the proposed approach in two scenarios, adapting a clean acoustic model to noisy speech and adapting an adults speech acoustic model to children speech. Significant improvements in accuracy are obtained, with reductions in word error rate of up to 44% over the original source model without the need for transcribed data in the target domain. Moreover, we show that increasing the amount of unlabeled data results in additional model robustness, which is particularly beneficial when using simulated training data in the target-domain.
Multiple-rate low-density parity-check codes with constant blocklength (2009)

This paper describes and analyzes low-density parity-check code families that support variety of different rates while maintaining the same fundamental decoder architecture. Such families facilitate the decoding hardware design and implementation for applications that require communication at different rates, for example to adapt to changing channel conditions. Combining rows of the lowest-rate parity-check matrix produces the parity-check matrices for higher rates. An important advantage of this approach is that all effective code rates have the same blocklength. This approach is compatible with well known techniques that allow low-complexity encoding and parallel decoding of these LDPC codes. This technique also allows the design of programmable analog LDPC decoders. The proposed design method maintains good graphical properties and hence low error floors for all rates.
Toward a commercial gas field ion source (1995)

Focused ion beam systems have traditionally used liquid gallium as the ion source material. It may now be possible to have high current density focused beams of gas ions like hydrogen, helium, neon, and oxygen. This paper discusses the progress recently made toward the commercialization of an alternative to gallium, the gas field ion source, or GFIS.
Creation of sub-20-nm contact using diblock copolymer on a 300mm wafer for complementary metal oxide semiconductor applications (2007)

The authors have demonstrated a method to form 20nm contact features of uniform size over a large area by integrating a self-assembling diblock copolymer with optical lithography. The diblock copolymer contacts are formed in topographical placers which are patterned with using optical lithography. A diblock copolymer pattern can only be formed in a placer and not in the narrower trenches that connect to the placer. This concept can be applied to form local interconnects using a single mask dual damascene process, where vias are self-aligned to the line. Some design rule restrictions must be applied to certain structures to enable patterning with diblock copolymer. They also observed that diblock copolymer contact formation was strongly influenced by the shape of the placer and the size of the cylindrical contact hole could be varied by the molecular weight of the block copolymer.
Greater Gains in Spine and Hip Strength for Romosozumab Compared With Teriparatide in Postmenopausal Women With Low Bone Mass (2017)

Romosozumab is a monoclonal antibody that inhibits sclerostin and has been shown to reduce the risk of fractures within 12 months. In a phase II, randomized, placebo-controlled clinical trial of treatment-naïve postmenopausal women with low bone mass, romosozumab increased bone mineral density (BMD) at the hip and spine by the dual effect of increasing bone formation and decreasing bone resorption. In a substudy of that trial, which included placebo and teriparatide arms, here we investigated whether those observed increases in BMD also resulted in improvements in estimated strength, as assessed by finite element analysis. Participants received blinded romosozumab s.c. (210 mg monthly) or placebo, or open-label teriparatide (20 μg daily) for 12 months. CT scans, obtained at the lumbar spine (n = 82) and proximal femur (n = 46) at baseline and month 12, were analyzed with finite element software (VirtuOst, O.N. Diagnostics) to estimate strength for a simulated compression overload for the spine (L<sub>1</sub> vertebral body) and a sideways fall for the proximal femur, all blinded to treatment assignment. We found that, at month 12, vertebral strength increased more for romosozumab compared with both teriparatide (27.3% versus 18.5%; p = 0.005) and placebo (27.3% versus -3.9%; p < 0.0001); changes in femoral strength for romosozumab showed similar but smaller changes, increasing more with romosozumab versus teriparatide (3.6% versus -0.7%; p = 0.027), and trending higher versus placebo (3.6% versus -0.1%; p = 0.059). Compartmental analysis revealed that the bone-strengthening effects for romosozumab were associated with positive contributions from both the cortical and trabecular bone compartments at both the lumbar spine and hip. Taken together, these findings suggest that romosozumab may offer patients with osteoporosis a new bone-forming therapeutic option that increases both vertebral and femoral strength within 12 months. © 2017 American Society for Bone and Mineral Research.
The Origin of the Differences in (R)‐ and (S)‐Desmethyldesferrithiocin: Iron‐Clearing Propertiesa (1998)

The iron clearance properties, toxicity, and pharmacokinetics of (R)- and (S)-desmethyldesferrithiocin (DMDFT) are described. The studies were performed in rodent and primate models. While both enantiomers were found to be effective iron chelators with minimal toxicity in the rodents, only (S)-DMDFT was able to induce the clearance of any iron in the primates. In addition, two out of nine of the monkeys given (R)-DMDFT died within 24 h of drug administration. The reason for the differences in iron clearance properties and the apparent toxicity of the (R)-enantiomer in the primates is likely related to the disparities in the pharmacokinetics of the two analogues. The pharmacokinetic data suggest enantioselectivity in renal clearance of the desferrithiocins and their iron complexes with (S)-DMDFT clearance 3.5 times greater than that of (R)-DMDFT, and FeIII [(S)-DMDFT]2 clearance 6.8 times greater than that of FeIII [R-DMDFT]2. In all primates studied FeIII [(R)-DMDFT]2 in the plasma exceeded 25 mg/L (50 microM) for several hours and remained above 10 mg/L (20 microM) at 8 h while levels of FeIII [(S)-DMDFT]2 never exceeded 50 microM and were at or below the limits of detection 8 h post-injection.
RNA Helicase Signaling Is Critical for Type I Interferon Production and Protection against Rift Valley Fever Virus during Mucosal Challenge (2013)

Rift Valley fever virus (RVFV) is an emerging RNA virus with devastating economic and social consequences. Clinically, RVFV induces a gamut of symptoms ranging from febrile illness to retinitis, hepatic necrosis, hemorrhagic fever, and death. It is known that type I interferon (IFN) responses can be protective against severe pathology; however, it is unknown which innate immune receptor pathways are crucial for mounting this response. Using both in vitro assays and in vivo mucosal mouse challenge, we demonstrate here that RNA helicases are critical for IFN production by immune cells and that signaling through the helicase adaptor molecule MAVS (mitochondrial antiviral signaling) is protective against mortality and more subtle pathology during RVFV infection. In addition, we demonstrate that Toll-like-receptor-mediated signaling is not involved in IFN production, further emphasizing the importance of the RNA cellular helicases in type I IFN responses to RVFV.
Identification of the Last Unknown Genes in the Fermentation Pathway of Lysine (2006)

Although the proteins of the lysine fermentation pathway were biochemically characterized more than thirty years ago, the genes encoding the proteins that catalyze three steps of this pathway are still unknown. We combined gene context, similarity of enzymatic mechanisms, and molecular weight comparisons with known proteins to select candidate genes for these three orphan proteins. We used a wastewater metagenomic collection of sequences to find and characterize the missing genes of the lysine fermentation pathway. After recombinant protein production and purification following cloning in Escherichia coli, we demonstrated that these genes (named kdd, kce, and kal) encode a l-erythro-3,5-diaminohexanoate dehydrogenase, a 3-keto-5-aminohexanoate cleavage enzyme, and a 3-aminobutyryl-CoA ammonia lyase, respectively. Because all of the genes of the pathway are now identified, we used this breakthrough to detect lysine-fermenting bacteria in sequenced genomes. We identified twelve bacteria that possess these genes and thus are expected to ferment lysine, and their gene organization is discussed.
Sorting hierarchical data in external memory for archiving (2008)

Sorting hierarchical data in external memory is necessary for a wide variety of applications including archiving scientific data and dealing with large XML datasets. The topic of sorting hierarchical data, however, has received little attention from the research community so far. In this paper we focus on sorting arbitrary hierarchical data that far exceed the size of physical memory. We propose HErMeS, an algorithm that generalizes the most widely-used techniques for sorting flat data in external memory. HErMeS efficiently exploits the hierarchical structure to minimize the number of disk accesses and optimize the use of available memory. We extract the theoretical bounds of the algorithm with respect to the structure of the hierarchical dataset. We then show how the algorithm can be used to support efficient archiving. We have conducted an experimental study using several workloads and comparing HErMeS to the state-of-the-art approaches. Our results show that our algorithm ( a ) meets its theoretical expectations, ( b ) allows for scalable database archiving, and ( c ) outperforms the competition by a significant factor. These results, we believe, prove our technique to be a viable and scalable solution to the problem of sorting hierarchical data in external memory.