gebhart/patrepeval huggingface dataset:
Induction of 1-Aminocyclopropane-1-Carboxylate Synthase mRNA by Auxin in Mung Bean Hypocotyls and Cultured Apple Shoots (1992)

Auxin is known to promote ethylene production in vegetative tissues by increasing the activity of 1-aminocyclopropane-1-carboxylate (ACC) synthase; therefore, we have studied the effect of auxins on ACC synthase mRNA expression. Total RNA was isolated from auxin-incubated cultured apple (Malus sylvestris Mill.) shoots or mung bean (Vigna radiata L.) hypocotyls. These RNAs and a set of oligonucleotide primers corresponding to two conserved amino acid sequences (SNPLGTT and MSSFGLV) found in ACC synthases isolated from other species were used for polymerase chain reaction-based amplification of DNA fragments encoding the ACC synthase-active site domain. We obtained and sequenced a 290-base pair cDNA fragment (pAA1) from cultured apple shoots and a 328-base pair cDNA clone (pMBA1) from mung bean hypocotyls. Comparisons of their deduced amino acid sequences with those of previously characterized ACC synthase cDNAs indicate that both fragments are, indeed, closely related to ACC synthase cDNA. Northern blot analyses further showed that the expression of these transcripts is regulated by auxin treatment. These data indicate that auxin induces ethylene production transcriptionally by increasing the ACC synthase transcripts. The pAA1 shares 46% amino acid sequence homology with ripening-regulated apple fruit ACC synthase, indicating that ripening-regulated and auxin-regulated ACC synthases are encoded by different genes. In mung bean hypocotyls, aminooxyacetic acid, a potent inhibitor of ACC synthase activity, promoted the expression of auxin-induced ACC synthase mRNA, but cycloheximide inhibited this induction.
Phospholamban deficiency alters inactivation kinetics of L-type Ca2+ channels in mouse ventricular myocytes (1997)

Entry of Ca2+ through voltage-dependent L-type Ca2+ channels is critical for contraction in cardiac cells. In recent studies, cells from phospholamban (PLB) knockout (PLB-KO) mouse hearts showed significantly increased basal contractility with enhanced sarcoplasmic reticulum (SR) Ca2+ uptake. To test whether these effects of PLB ablation were associated with alterations of L-type Ca2+ channel function, we compared the properties of Ca2+ channel currents (I(Ca)) in ventricular myocytes isolated from wild-type (WT) and PLB-KO mouse hearts. L-type Ca2+ channels from mouse myocytes exhibited voltage-dependent gating and sensitivity to dihydropyridine drugs, similar to other mammalian species, and these properties were not altered by PLB ablation. I(Ca) from both WT and PLB-KO cells revealed two (fast and slow) components of inactivation kinetics. However, the proportion of the faster component was significantly larger in PLB-KO cells. Ryanodine (10 microM) reduced the rate of inactivation of I(Ca) for both WT and PLB-KO cells, but the reduction was more prominent in PLB-KO cells compared with WT cells. In contrast, the inactivation in a Ba2+ solution could be fitted by a single exponential similar to the slower component in Ca2+, and this was not altered in PLB-KO cells. The increase in the fast Ca2+-dependent inactivation component in PLB-KO cells supports the hypothesis that Ca2+ released from the SR regulates Ca2+ channel inactivation by affecting the levels of Ca2+ near the channel and suggests that this may be an important compensatory mechanism in the hyperdynamic PLB-KO heart.
Smoothly varying affine stitching (2011)

Traditional image stitching using parametric transforms such as homography, only produces perceptually correct composites for planar scenes or parallax free camera motion between source frames. This limits mosaicing to source images taken from the same physical location. In this paper, we introduce a smoothly varying affine stitching field which is flexible enough to handle parallax while retaining the good extrapolation and occlusion handling properties of parametric transforms. Our algorithm which jointly estimates both the stitching field and correspondence, permits the stitching of general motion source images, provided the scenes do not contain abrupt protrusions.
Location of progenitor cells in periodontal ligament of mouse molar stimulated by wounding (1977)

Abstract Wounds were made in the alveolar process overlying the mesial root of the mandibular first molar of 35‐g mice to expose periodontal ligament. Dividing cells were arrested in metaphase by injection of vinblastine sulphate three hours before death three, five and seven days after wounding. Serial 1‐m̈m plastic sections of the wound were stained with hematoxylin and eosin. The distance between the mitotic figures and the nearest blood vessel, bone and cementum was measured in every fourth section. No mitotic figure was measured twice. The distances of at least 500 interphase cells from the closest blood vessel were measured in each wound. At all time periods the distribution of mitotic cells was significantly closer to blood vessels than that of interphase cells (p &lt; 0.01). From three days to seven days after wounding there was a significant shift of mitotic activity away from the bone side of the ligament, but not away from blood vessels (p &lt; 0.05). Approximately 10% of all mitotic cells lay close to cementum, but not close to blood vessels. The majority of the dividing cells were confirmed to be paravascular, and appeared to belong to two populations, one adjacent to bone, the other in the body of the ligament. A third population, not paravascular, lay adjacent to cementum.
A phase Ib/II study of olutasidenib in patients with relapsed/refractory IDH1 mutant solid tumors: Safety and efficacy as single agent. (2020)

e16643 Background: Isocitrate dehydrogenase 1 mutations (mIDH1) are present in a variety of solid tumors resulting in production and accumulation of (R)-2-hydroxyglutarate causing DNA hypermethylation and promoting tumorigenesis. Olutasidenib is an oral, potent and selective inhibitor of mutated IDH1 protein. We report preliminary results from the ongoing, first-in-human, Phase 1, open-label, single-arm study of olutasidenib in non-CNS solid tumors. Methods: Patients with advanced relapsed/refractory (R/R) mIDH1 solid tumors received olutasidenib 150 mg BID, orally. Following a dose confirmation cohort (Phase 1b), patients with intrahepatic cholangiocarcinoma (IHCC), chondrosarcoma (CS), or unspecified mIDH1 solid tumors (Other) were enrolled in a Phase 2 efficacy evaluation (NCT: 03684811). Results: As of 31-Oct-2019, 44 patients with relapsed or refractory mIDH1 solid tumors were treated with olutasidenib. Diagnosis included: IHCC (n = 26), CS (n = 13), and Other (n = 5). The median age was 58 years (range: 29-81) and 43% were male. Median number of prior treatments was 2 (1-10). mIDH1 status was locally determined (IHC, NGS or PCR): R132C (61%), R132G (7%), R132S (7%), R132H (2%), R132L (2%), Others (2%) &amp; unspecified (18%). Fourteen patients discontinued treatment (disease progression [n = 6; 3 IHCC, 2 CS, 1 Other], AE [n = 4; 3 IHCC, 1 CS], PI decision [n = 3; IHCC] &amp; withdraw consent [n = 1; IHCC]). Treatment emergent adverse events (all grades, regardless of attribution) that occurred in &gt; 15% of pts were: nausea (43%), fatigue (25%), decreased appetite (22%), AST increase (18%), ALT increase (16%), and constipation (16%). No protocol-defined DLTs occurred. Best responses by tumor type are shown in the table. Conclusions: Single agent olutasidenib at 150 mg BID demonstrates acceptable safety and tolerability with preliminary clinical activity in patients with R/R mIDH1 solid tumors. Updated safety and clinical activity, as well as exploratory evaluations of PK/PD will be provided. Clinical trial information: 03684811 . [Table: see text]
Unified approach to the temporal evolution of surface profiles in solid etch and deposition processes (1989)

The differential equation describing the temporal evolution of solid surfaces subject to etching or depositon is derived. Its general properties are discussed and solutions to particular problems are obtained. The differential equation explicitly shows the evolution of the shape of the surface to be the product of a geometric factor which is common to all etch/deposition processes and a rate factor which depends on the physics of the process considered. The rate factor must in general be derived from first principles. Here we limit consideration to rate factors that describe isotropic and unidirectional processes, as well as linear combinations of these two processes. The properties of the evolution of surface profiles are studied in detail for each case. A unidirectional etch with a rate factor dependent on the local surface curvature is shown to produce good agreement with the observed shapes of deep isolation trenches in silicon. Finally, the surface evolution equation is used to expore the ability of certain processes to smooth and polish initially rough surfaces.
Articulation Rules For Automatic Music Performance (2001)

Rules for legato, staccato, and repeated notes articulation in automatic piano performance are presented. These rules were obtained applying the analysis-by-measurement method to performances of Mozart piano sonatas on MIDIfied acoustic grand pianos. The effects produced by the rules vary with tempo indications, with expressive intentions and with musical context. The articulation rules are part of the Director Musices system for automatic music performance. It has been demonstrated that proper setting of the articulation rules enables more realistic automatic performances that can also differ in emotional expression. These rules are also being applied in control models for sound synthesis algorithms. 1
Simultaneous measurement of strain (to 2000 /spl mu//spl epsiv/) and temperature (to 600/spl deg/C) using a combined Sb-Er-Ge-codoped fiber-fluorescence and grating-based technique (2005)

An optical fiber-based sensing scheme for the simultaneous measurement of strain and temperature over a wider range has been demonstrated by writing a grating with very high reflectivity in a 10-cm-long specially fabricated antimony-erbium-germanium (Sb-Er-Ge)-doped silica fiber. The scheme exploits the grating sensitivity to both strain and temperature in association with the temperature-dependent peak power ratio of the two fluorescence peaks around 1535 and 1552 nm of the amplified spontaneous emission due to /sup 4/I/sub 13/2//spl rarr//sup 4/I/sub 15/2/ transition arising from the presence of erbium ions in the fiber core, using a 980-nm laser diode as a pumping source. The sensor created using this fiber can be used for the simultaneous measurement of strain and temperature over the wide ranges of 0-2000 /spl mu//spl epsiv/ and 20/spl deg/C-600/spl deg/C, with root-mean-square errors of 36 /spl mu//spl epsiv/ and 2.8/spl deg/C, respectively.
Interleukin-1α enhances the aggressive behavior of pancreatic cancer cells by regulating the α6β1-integrin and urokinase plasminogen activator receptor expression (2006)

Based on these findings, we conclude that IL-1alpha can induce selective upregulation of alpha6beta1-integrin and uPA/uPAR in pancreatic cancer cells and these changes may modulate the aggressive functions of pancreatic cancer.
Replicative Capacity of MERS Coronavirus in Livestock Cell Lines (2013)

Replicative capacity of Middle East respiratory syndrome coronavirus (MERS-CoV) was assessed in cell lines derived from livestock and peridomestic small mammals on the Arabian Peninsula. Only cell lines originating from goats and camels showed efficient replication of MERS-CoV. These results provide direction in the search for the intermediate host of MERS-CoV.
New Amide-Bearing Benzolactam-Based Protein Kinase C Modulators Induce Enhanced Secretion of the Amyloid Precursor Protein Metabolite sAPPα (2002)

Protein kinase C (PKC) is known to participate in the processing of the amyloid precursor protein (APP). Abnormal processing of APP through the action of the beta- and gamma-secretases leads to the production of the 39-43 amino acid Abeta fragment, which is neurotoxic and which is believed to play an important role in the etiology of Alzheimer's disease. PKC activation enhances alpha-secretase activity, which results in a decrease of the amyloidogenic products of beta-secretase. In this article, we describe the synthesis of 10 new benzolactam V8 based PKC activators having side chains of varied saturation and lipophilicity linked to the aromatic ring through an amide group. The K(i) values measured for the inhibition of phorbol ester binding to PKCalpha are in the nanomolar range and show some correlation with their lipophilicity. Compounds 5g and 5h show the best binding affinity among the 10 benzolactams that were synthesized. By use of a cell line derived from an AD patient, significant enhancement of sAPPalpha secretion was achieved at 1 microM concentration for most of the compounds studied and at 0.1 microM for compounds 5e and 5f. At 1 microM the enhancement of sAPPalpha secretion for compounds 5c-h is higher than that observed for the control compound 8-(1-decynyl)benzolactam (BL). Of interest is the absence of activity found for the highly lipophilic ligand 5i, which has a K(i) of 11 nM. On the other hand, its saturated counterpart 5j, which possesses a comparable K(i) and ClogP, retains activity in the secretase assay. In the hyperplasia studies, 5f showed a modest response at 100 microg and 5e at 300 microg, suggesting that 5f was approximately 30-fold less potent than the PKC activator mezerein and 100-fold less potent than TPA. 5e was approximately 3-fold less active than 5f. On the basis of the effect of unsaturation for other potent PKC ligands, we would predict that 5e would retain biological activity in most assays but would show a marked loss of tumor-promoting activity. Compound 5e thus becomes a viable candidate compound in the search for Alzheimer's therapeutics capable of modulating amyloid processing.
ATP drives direct photosynthetic production of 1-butanol in cyanobacteria (2012)

While conservation of ATP is often a desirable trait for microbial production of chemicals, we demonstrate that additional consumption of ATP may be beneficial to drive product formation in a nonnatural pathway. Although production of 1-butanol by the fermentative coenzyme A (CoA)-dependent pathway using the reversal of β-oxidation exists in nature and has been demonstrated in various organisms, the first step of the pathway, condensation of two molecules of acetyl-CoA to acetoacetyl-CoA, is thermodynamically unfavorable. Here, we show that artificially engineered ATP consumption through a pathway modification can drive this reaction forward and enables for the first time the direct photosynthetic production of 1-butanol from cyanobacteria Synechococcus elongatus PCC 7942. We further demonstrated that substitution of bifunctional aldehyde/alcohol dehydrogenase (AdhE2) with separate butyraldehyde dehydrogenase (Bldh) and NADPH-dependent alcohol dehydrogenase (YqhD) increased 1-butanol production by 4-fold. These results demonstrated the importance of ATP and cofactor driving forces as a design principle to alter metabolic flux.
Anti-antibody enhancement of iodine-131 anti-CEA radioimmunodetection in experimental and clinical studies. (1987)

Imaging of tumors with radiolabeled antibodies, especially when located in the blood-rich visceral organs, may be improved through administration of a second antibody directed against the primary tumor-associated antibody. In hamsters bearing a human colonic carcinoma xenograft producing carcinoembryonic antigen (CEA), we injected donkey anti-goat IgG 24 hr after administration of 131I-labeled goat anti-CEA IgG and achieved enhanced tumor imaging 24-48 hr later, with a significant relative decrease of radioactivity in blood and all major organs except the spleen. In seven of nine patients, this method of anti-antibody clearance of nontargeted radioactive murine monoclonal antibodies revealed sites of cancer, including liver metastases. Characterization of radioactivity in the plasma before and after administration of the second antibody confirmed that complexes were quickly formed between primary and secondary antibodies, and imaging of the patients revealed a rapid uptake of radioactivity in the liver at 2 hr that dissipated within 24 hr. Radioactivity in the spleen gradually increased over time. The method of anti-antibody immunological enhancement of cancer imaging is feasible and may reveal tumor sites missed by conventional imaging.
The NLRP3 Inflammasome and IL-1β Accelerate Immunologically Mediated Pathology in Experimental Viral Fulminant Hepatitis (2015)

Viral fulminant hepatitis (FH) is a severe disease with high mortality resulting from excessive inflammation in the infected liver. Clinical interventions have been inefficient due to the lack of knowledge for inflammatory pathogenesis in the virus-infected liver. We show that wild-type mice infected with murine hepatitis virus strain-3 (MHV-3), a model for viral FH, manifest with severe disease and high mortality in association with a significant elevation in IL-1β expression in the serum and liver. Whereas, the viral infection in IL-1β receptor-I deficient (IL-1R1-/-) or IL-1R antagonist (IL-1Ra) treated mice, show reductions in virus replication, disease progress and mortality. IL-1R1 deficiency appears to debilitate the virus-induced fibrinogen-like protein-2 (FGL2) production in macrophages and CD45+Gr-1high neutrophil infiltration in the liver. The quick release of reactive oxygen species (ROS) by the infected macrophages suggests a plausible viral initiation of NLRP3 inflammasome activation. Further experiments show that mice deficient of p47phox, a nicotinamide adenine dinucleotide phosphate (NADPH) oxidase subunit that controls acute ROS production, present with reductions in NLRP3 inflammasome activation and subsequent IL-1β secretion during viral infection, which appears to be responsible for acquiring resilience to viral FH. Moreover, viral infected animals in deficiencies of NLRP3 and Caspase-1, two essential components of the inflammasome complex, also have reduced IL-1β induction along with ameliorated hepatitis. Our results demonstrate that the ROS/NLRP3/IL-1β axis institutes an essential signaling pathway, which is over activated and directly causes the severe liver disease during viral infection, which sheds light on development of efficient treatments for human viral FH and other severe inflammatory diseases.
A Dissociation Insertion Causes a Semidominant Mutation That Increases Expression of TINY, an Arabidopsis Gene Related to APETALA2 (1996)

Kate Wilson, Deborah Long, June Swinburne, George Coupland, A Dissociation Insertion Causes a Semidominant Mutation That Increases Expression of TINY, an Arabidopsis Gene Related to APETALA2, The Plant Cell, Vol. 8, No. 4 (Apr., 1996), pp. 659-671
Joint optimization of segmentation and appearance models (2009)

Many interactive image segmentation approaches use an objective function which includes appearance models as an unknown variable. Since the resulting optimization problem is NP-hard the segmentation and appearance are typically optimized separately, in an EM-style fashion. One contribution of this paper is to express the objective function purely in terms of the unknown segmentation, using higher-order cliques. This formulation reveals an interesting bias of the model towards balanced segmentations. Furthermore, it enables us to develop a new dual decomposition optimization procedure, which provides additionally a lower bound. Hence, we are able to improve on existing optimizers, and verify that for a considerable number of real world examples we even achieve global optimality. This is important since we are able, for the first time, to analyze the deficiencies of the model. Another contribution is to establish a property of a particular dual decomposition approach which involves convex functions depending on foreground area. As a consequence, we show that the optimal decomposition for our problem can be computed efficiently via a parametric maxflow algorithm.
Quantification of Contrast Recognizability during Brilliant Blue G– and Indocyanine Green–Assisted Chromovitrectomy (2011)

To evaluate the potential of brilliant blue G (BBG) and indocyanine green (ICG) for intraoperative staining of the internal limiting membrane (ILM) with respect to perceivable contrast.In a retrospective clinical case series the authors analyzed 26 consecutive chromovitrectomy interventions in 26 patients with macular holes, epiretinal fibrosis, vitreoretinal traction syndromes, or persistent macular edema. Fourteen subjects underwent ICG and 12 subjects, BBG chromovitrectomy. The main outcome measure was the difference in chromaticity between the stained ILM and the unstained underlying retina, measured by means of a novel objective and quantitative video-based analysis method to describe color contrast strengths as they are perceived by the human eye.Objective chromaticity measurements of the intraoperative videos of all 26 interventions showed a significantly inferior contrast for BBG compared with that of ICG (BBG = 6.1, ICG = 14.9; P = 3.885 × 10⁻¹⁵).As an adjunct to chromovitrectomy to stain the ILM, BBG yields a significantly less well discernible contrast to the human eye than that of ICG under the premises of this study.
Flat XOR-based erasure codes in storage systems: Constructions, efficient recovery, and tradeoffs (2010)

Large scale storage systems require multi-disk fault tolerant erasure codes. Replication and RAID extensions that protect against two- and three-disk failures offer a stark tradeoff between how much data must be stored, and how much data must be read to recover a failed disk. Flat XOR-codes-erasure codes in which parity disks are calculated as the XOR of some subset of data disks-offer a tradeoff between these extremes. In this paper, we describe constructions of two novel flat XOR-code, Stepped Combination and HD-Combination codes. We describe an algorithm for flat XOR-codes that enumerates recovery equations, i.e., sets of disks that can recover a failed disk. We also describe two algorithms for flat XOR-codes that generate recovery schedules, i.e., sets of recovery equations that can be used in concert to achieve efficient recovery. Finally, we analyze the key storage properties of many flat XOR-codes and of MDS codes such as replication and RAID 6 to show the cost-benefit tradeoff gap that flat XOR-codes can fill.
Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae (2009)

The cofactor preference of P. stipitis XR was altered by site-directed mutagenesis. When the K270R XR was combined with a metabolic engineering strategy that ensures high xylose utilization capabilities, a recombinant S. cerevisiae strain was created that provides a unique combination of high xylose consumption rate, high ethanol yield and low xylitol yield during ethanolic xylose fermentation.