gebhart/patrepeval huggingface dataset:
The maize lipoxygenase, ZmLOX10, mediates green leaf volatile, jasmonate and herbivore‐induced plant volatile production for defense against insect attack (2012)

Fatty acid derivatives are of central importance for plant immunity against insect herbivores; however, major regulatory genes and the signals that modulate these defense metabolites are vastly understudied, especially in important agro-economic monocot species. Here we show that products and signals derived from a single Zea mays (maize) lipoxygenase (LOX), ZmLOX10, are critical for both direct and indirect defenses to herbivory. We provide genetic evidence that two 13-LOXs, ZmLOX10 and ZmLOX8, specialize in providing substrate for the green leaf volatile (GLV) and jasmonate (JA) biosynthesis pathways, respectively. Supporting the specialization of these LOX isoforms, LOX8 and LOX10 are localized to two distinct cellular compartments, indicating that the JA and GLV biosynthesis pathways are physically separated in maize. Reduced expression of JA biosynthesis genes and diminished levels of JA in lox10 mutants indicate that LOX10-derived signaling is required for LOX8-mediated JA. The possible role of GLVs in JA signaling is supported by their ability to partially restore wound-induced JA levels in lox10 mutants. The impaired ability of lox10 mutants to produce GLVs and JA led to dramatic reductions in herbivore-induced plant volatiles (HIPVs) and attractiveness to parasitoid wasps. Because LOX10 is under circadian rhythm regulation, this study provides a mechanistic link to the diurnal regulation of GLVs and HIPVs. GLV-, JA- and HIPV-deficient lox10 mutants display compromised resistance to insect feeding, both under laboratory and field conditions, which is strong evidence that LOX10-dependent metabolites confer immunity against insect attack. Hence, this comprehensive gene to agro-ecosystem study reveals the broad implications of a single LOX isoform in herbivore defense.
Template Recognition and Ribonucleotide Specificity of the DNA Primase of Bacteriophage T7 (1997)

The 63-kDa gene 4 DNA primase of phage T7 catalyzes the synthesis of oligoribonucleotides on single-stranded DNA templates. At the sequence, 5'-GTC-3', the primase synthesizes the dinucleotide pppAC; the cytidine residue of the recognition sequence is cryptic. Only tetraribonucleotides function as primers, but the specificity for the third and fourth position is not as stringent with a preference of CMP > AMP >> UMP > GMP. The predominant recognition sites on M13 DNA are 5'-(G/T)GGTC-3' and 5'-GTGTC-3'. Synthesis is usually limited to tetranucleotides, but T7 primase can synthesize longer oligoribonucleotides on templates containing long stretches of guanosine residues 5' to the recognition sequence. The specificity beyond the first two positions of the primer increases as the length of the template on the 3'-side of 5'-GTC-3' increases. On an oligonucleotide having 20 3'-flanking cytidine residues GMP is incorporated at the third position; incorporation is reduced 4-fold when the flanking sequence reaches 65 residues, and little is incorporated on M13 templates. The presence of the 56-kDa gene 4 helicase decreases the incorporation of GMP on long templates. We propose that pausing is required for the incorporation of less preferred nucleotides and that pausing is decreased by the ability of the primase to translocate 5' to 3' on templates having long 3'-flanking sequences.
Micron-Scale Friction and Sliding Wear of Polycrystalline Silicon Thin Structural Films in Ambient Air (2008)

Micron-scale static friction and wear coefficients, surface roughness, and resulting wear debris have been studied for sliding wear in polycrystalline silicon in ambient air at micro- Newton normal loads using on-chip sidewall test specimens, fabricated with the Sandia SUMMiT V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> process. With increasing number of wear cycles friction coefficients increased by a factor of two up to a steady-state regime, concomitant with a decay (after an initial sharp increase) in the wear coefficients and roughness. Wear coefficients were orders of magnitude smaller than reported macroscale values, suggesting that the wear resistance is higher at micrometer dimensions. Based on our observations, a sequence of micron-scale wear mechanisms is proposed involving: 1) a short adhesive wear regime (< 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> cycles), where the oxide is worn away and the first silicon debris particles form and 2) a regime dominated by abrasive wear, where silicon particles (50-100 nm) are created by fracture through the grains (~500 nm). These particles subsequently oxidize and agglomerate into larger debris clusters, while "ploughing" by this debris leads to abrasive grooves associated with local cracking events rather than plastic deformation.
Joint biomarker response to mechanical stimuli in osteoarthritis – A scoping review (2023)

The literature is dominated by small, simplistic studies, but suggests that mechanical stimulation can induce acute changes in joint biomarkers. In order to diminish the existing bias in future studies, it is important to recognize methodological considerations e.g. patient and biomarker selection as well as peri-interventional control. Common potential sources of bias include the acute shift in plasma volume due to cardiovascular stress and postural changes.
A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification (2018)

Despite recent clinical successes for irreversible drugs, potential toxicities mediated by unpredictable modification of off-target cysteines represents a major hurdle for expansion of covalent drug programs. Understanding the proteome-wide binding profile of covalent inhibitors can significantly accelerate their development; however, current mass spectrometry strategies typically do not provide a direct, amino acid level readout of covalent activity for complex, selective inhibitors. Here we report the development of CITe-Id, a novel chemoproteomic approach that employs covalent pharmacologic inhibitors as enrichment reagents in combination with an optimized proteomic platform to directly quantify dose-dependent binding at cysteine-thiols across the proteome. CITe-Id analysis of our irreversible CDK inhibitor THZ1 identified dose-dependent covalent modification of several unexpected kinases, including a previously unannotated cysteine (C840) on the understudied kinase PKN3. These data streamlined our development of JZ128 as a new selective covalent inhibitor of PKN3. Using JZ128 as a probe compound, we identified novel potential PKN3 substrates, thus offering an initial molecular view of PKN3 cellular activity. CITe-Id provides a powerful complement to current chemoproteomic platforms to characterize the selectivity of covalent inhibitors, identify new, pharmacologically addressable cysteine-thiols, and inform structure-based drug design programs.
Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis (2018)

Both host race/ethnicity and pathogen strain influence the innate immune response. Such variation may have implications for the development of new tools across TB therapeutics, immunodiagnostics and vaccines.
Risk Profiles of Alzheimer Disease (2011)

Alzheimer disease (AD) is a dementing, neurodegenerative disorder that affects approximately 500,000 Canadians and its prevalence is expected to double over the next 30 years. Although several medications may temporarily augment cognitive abilities in AD, there presently exists no proven method to avoid the inevitable clinical deterioration in this devastating condition. The delineation of risk factors for the development of AD offers hope for the advent of effective prevention or interventions that might retard the onset of symptoms. In this article, we provide a comprehensive review of midlife risk factors implicated in the etiopathogenesis of sporadic AD. Although some risk factors are heritable and largely beyond our control, others are determined by lifestyle or environment and are potentially modifiable. In a companion paper, we introduce the concept of an Alzheimer Risk Assessment Clinic for ascertainment and mitigation of these and other putative dementia risk factors in middle-aged adults.
Review—The Physics of Recombinations in III-Nitride Emitters (2019)

The physics of carrier recombinations in III-nitride light emitters are reviewed, with an emphasis on experimental investigations. After a discussion of various methods of measuring recombination dynamics, important results on recombination physics are examined. The radiative rate displays a complex behavior, influenced by Coulomb interaction and carrier screening. Non-radiative recombinations at low and high current are shown to scale with the overlap of electron-hole wavefunctions, similarly to the radiative rate, leading to a compensation effect which explains the high efficiency of III-nitride emitters. Finally, the droop current is decomposed into two contributions: the well-known Auger scattering, and a defect-assisted droop process, which is shown to play an important role in the green gap.
COVID-19 Outbreak Prediction and Analysis using Self Reported Symptoms (2020)

It is crucial for policymakers to understand the community prevalence of COVID-19 so combative resources can be effectively allocated and prioritized during the COVID-19 pandemic. Traditionally, community prevalence has been assessed through diagnostic and antibody testing data. However, despite the increasing availability of COVID-19 testing, the required level has not been met in most parts of the globe, introducing a need for an alternative method for communities to determine disease prevalence. This is further complicated by the observation that COVID-19 prevalence and spread varies across different spatial, temporal, and demographics. In this study, we understand trends in the spread of COVID-19 by utilizing the results of self-reported COVID-19 symptoms surveys as an alternative to COVID-19 testing reports. This allows us to assess community disease prevalence, even in areas with low COVID-19 testing ability. Using individually reported symptom data from various populations, our method predicts the likely percentage of the population that tested positive for COVID-19. We do so with a Mean Absolute Error (MAE) of 1.14 and Mean Relative Error (MRE) of 60.40\% with 95\% confidence interval as (60.12, 60.67). This implies that our model predicts +/- 1140 cases than the original in a population of 1 million. In addition, we forecast the location-wise percentage of the population testing positive for the next 30 days using self-reported symptoms data from previous days. The MAE for this method is as low as 0.15 (MRE of 23.61\% with 95\% confidence interval as (23.6, 13.7)) for New York. We present an analysis of these results, exposing various clinical attributes of interest across different demographics. Lastly, we qualitatively analyze how various policy enactments (testing, curfew) affect the prevalence of COVID-19 in a community.
miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton (2013)

In this study, we characterized the miR482 family in cotton using existing small RNA datasets and the recently released draft genome sequence of Gossypium raimondii, a diploid cotton species whose progenitor is the putative contributor of the Dt (representing the D genome of tetraploid) genome of the cultivated tetraploid cotton species G. hirsutum and G. barbadense. Of the three ghr-miR482 members reported in G. hirsutum, ghr-miR482a has no homolog in G. raimondii, ghr-miR482b and ghr-miR482c each has a single homolog in G. raimondii. Gra-miR482d has five homologous loci (gra-miR482d, f-i) in G. raimondii and also exists in G. hirsutum (ghr-miR482d). A variant, miR482.2 that is a homolog of miR2118 in other species, is produced from several GHR-MIR482 loci in G. hirsutum. Approximately 12% of the G. raimondii NBS-LRR genes were predicted targets of various members of the gra-miR482 family. Based on the rationale that the regulatory relationship between miR482 and NBS-LRR genes will be conserved in G. raimondii and G. hirsutum, we investigated this relationship using G. hirsutum miR482 and G. raimondii NBS-LRR genes, which are not currently available in G. hirsutum. Ghr-miR482/miR482.2-mediated cleavage was confirmed for three of the four NBS-LRR genes analysed. As in tomato, miR482-mediated cleavage of NBS-LRR genes triggered production of phased secondary small RNAs in cotton. In seedlings of the susceptible cultivar Sicot71 (G. hirsutum) infected with the fungal pathogen Verticillium dahliae, the expression levels of ghr-miR482b/miR482b.2, ghr-miR482c and ghr-miR482d.2 were down-regulated, and several NBS-LRR targets of ghr-miR482c and ghr-miR482d were up-regulated. These results imply that, like tomato plants infected with viruses or bacteria, cotton plants are able to induce expression of NBS-LRR defence genes by suppression of the miRNA-mediated gene silencing pathway upon fungal pathogen attack.
Reducing the crystallinity of PCL chains by copolymerization with substituted δ/ε-lactones and its impact on the phase separation of PCL-based block copolymers (2022)

Different self-segregation behavior of ABA triblock copolymers with central PBD or PBD H blocks and semi-crystalline or amorphous PCL-like external blocks.
Regio‐ and Stereoselective Intermolecular Hydroalkoxylation of Alkynes Catalysed by Cationic Gold(I) Complexes (2010)

Abstract Vinyl ethers and ketals are obtained from the reaction of phenylacetylene derivatives and dimethyl acetylenedicarboxylate (DMAD) with alcohols in good yields and levels of stereoselectivity by using cationic gold(I)‐phosphine complexes as catalysts. By choosing the appropriate phosphine, the selective formation of the Z or the E isomer of the vinyl ether can be tuned, and the undesired formation of the ketal can be controlled. The isomerisation of fumarates ( Z ‐isomer) to maleates ( E ‐isomer) is a gold‐catalysed process that can be conducted in one‐pot. When using polyols, 5‐membered cyclic ketals are easily isolated by extraction with hexane and the gold complex can be reused.
Ex vivo expansion of autologous pericardial patch structures (2008)

Pericardial patch structures play an important role in the reconstruction of congenital heart failures, e.g. correction of a univentricular heart (Fontan procedure). The difficulty associated with Fontan tunnel reconstruction is the limited availability and size of of autologous pericardium due to adhesion after the preliminary surgical procedure. The aim of the current project is to realise ex vivo cultivation and expansion of autologous pericardium. The cultivation technique is based on a combination of a surgical mesh graft technique and principles of tissue engineering. By applying parallel incisions and uni-directional stretching, pores generated within the pericardial tissue are subsequently sealed with a fibrin gel/cell suspension. In order to stimulate cell growth into the pores, a customised bioreactor system was developed to generate cyclic stress conditions. After production of a mechanically stable patch structure, the procedure of incision, sealing and cultivation is repeated until the tissue has reached the desired dimensions.
S‐Adenosyl‐L‐Methionine Hydrolase (Adenosine‐Forming), a Conserved Bacterial and Archeal Protein Related to SAM‐Dependent Halogenases (2008)

Halogenase versus hydrolase: The newly discovered SAM-dependent halogenases belong to a family of over 100 proteins from bacteria and archaea. Biochemical and in silico analyses reported here suggest, however, that most of these relatives act as previously unknown SAM adenosylhydrolases rather than halogenases.
Consideration of number of via holes for high efficiency GaN based VI-LED design (2015)

This study examined the electrical and optical characteristics of GaN-based vertical-injection light-emitting diodes (VI-LEDs) with various numbers of via holes.
Chemical design and magnetic ordering in thin layers of 2D MOFs (2021)

Through rational chemical design, and thanks to the hybrid nature of metal-organic frameworks (MOFs), it is possible to prepare molecule-based 2D magnetic materials stable at ambient conditions. Here, we illustrate the versatility of this approach by changing both the metallic nodes and the ligands in a family of layered MOFs that allows the tuning of their magnetic properties. Specifically, the reaction of benzimidazole-type ligands with different metal centres (MII = Fe, Co, Mn, Zn) in a solvent-free synthesis produces a family of crystalline materials, denoted as MUV-1(M), which order antiferromagnetically with critical temperatures that depend on M. Furthermore, the incorporation of additional substituents in the ligand results in a novel system, denoted as MUV-8, formed by covalently bound magnetic double-layers interconnected by van der Waals interactions, a topology that is very rare in the field of 2D materials and unprecedented for 2D magnets. These layered materials are robust enough to be mechanically exfoliated down to a few layers with large lateral dimensions. Finally, the robustness and crystallinity of these layered MOFs allow the fabrication of nanomechanical resonators that can be used to detect -- through laser interferometry -- the magnetic order in thin layers of these 2D molecule-based antiferromagnets.
Cell Surface Organization of Stress-inducible Proteins ULBP and MICA That Stimulate Human NK Cells and T Cells via NKG2D (2004)

Cell surface proteins major histocompatibility complex (MHC) class I-related chain A (MICA) and UL16-binding proteins (ULBP) 1, 2, and 3 are up-regulated upon infection or tumor transformation and can activate human natural killer (NK) cells. Patches of cross-linked raft resident ganglioside GM1 colocalized with ULBP1, 2, 3, or MICA, but not CD45. Thus, ULBPs and MICA are expressed in lipid rafts at the cell surface. Western blotting revealed that glycosylphosphatidylinositol (GPI)-anchored ULBP3 but not transmembrane MICA, MHC class I protein, or transferrin receptor, accumulated in detergent-resistant membranes containing GM1. Thus, MICA may have a weaker association with lipid rafts than ULBP3, yet both proteins accumulate at an activating human NK cell immune synapse. Target cell lipid rafts marked by green fluorescent protein-tagged GPI also accumulate with ULBP3 at some synapses. Electron microscopy reveals constitutive clusters of ULBP at the cell surface. Regarding a specific molecular basis for the organization of these proteins, ULBP1, 2, and 3 and MICA are lipid modified. ULBP1, 2, and 3 are GPI anchored, and we demonstrate here that MICA is S-acylated. Finally, expression of a truncated form of MICA that lacks the putative site for S-acylation and the cytoplasmic tail can be expressed at the cell surface, but is unable to activate NK cells.
Multiple object identification using grid voting of object center estimated from keypoint matches (2013)

This paper proposes a method to detect and identify multiple objects in an image using grid voting of object center positions estimated from local descriptor keypoint matches. For each keypoint match, the proposed method estimates the object center position using scale and orientation associated with the keypoints. Then, it casts a vote for an image grid where the estimated object center is located. For the grids with high number of votes, geometric verification of the keypoint matches is carried out to accurately localize multiple objects in the image. Since the computational complexity of the grid voting is O(n), where n is the number of estimated object centers, the proposed method runs faster than a conventional method using mean shift clustering with O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) complexity. Experimental results using images with 52 objects show that the proposed method reduces the computational time by approximately 60% compared to the conventional method, while identification accuracy is comparable. With the reduced computational complexity, industrial applications such as an efficient inventory management in retail using images are enabled in practical computational time.
Expression of Genes for Metabolism of Cyclic Adenosine 3′:5′-Monophosphate in Somatic Cells (1973)

Abstract The effects of catecholamines (norepinephrine and isoproterenol) on the intracellular accumulation of cyclic adenosine 3':5'-monophosphate (cyclic AMP) were determined for clonal cell lines cultured in vitro. Catecholamine responsive (β+) and unresponsive (β-) clones were found. β+ responses were inhibited selectively by propranolol (1 µm) but not by practolol (10 µm), indicating that the response should be classified as β2+. These cell lines then were used as parents in somatic cell hybridization to study the genetic control of the β2+ response. In general, β2+ x β2+ matings yielded β2+ hybrid cells, while β2+ x β- matings yielded β- hybrid cells (less than 2% of the β2+ parental response). However, β2+ parental cells with large responses (300-fold stimulation) to catecholamine, when fused to β2+ parents with smaller (15-fold stimulation) responses, yielded hybrids with definite but minimal (average of 3-fold) stimulation. Chromosome analysis of all hybrid cells revealed no evidence for preferential loss of marker chromosomes of the β2+ parent. These data represent evidence for a heritable negative control mechanism regulating catecholamine responsiveness. In addition, the hybrid cell lines represent new biologic material for biochemical study of the macromolecular events between β-adrenergic stimulation and the accumulation of intracellular cyclic AMP.
Glycoengineering Human Neural and Adipose Stem Cells with Novel Thiol-Modified N-Acetylmannosamine (ManNAc) Analogs (2021)

This report describes novel thiol-modified <i>N</i>-acetylmannosamine (ManNAc) analogs that extend metabolic glycoengineering (MGE) applications of Ac<sub>5</sub>ManNTGc, a non-natural monosaccharide that metabolically installs the thio-glycolyl of sialic acid into human glycoconjugates. We previously found that Ac<sub>5</sub>ManNTGc elicited non-canonical activation of Wnt signaling in human embryoid body derived (hEBD) cells but only in the presence of a high affinity, chemically compatible scaffold. Our new analogs Ac<sub>5</sub>ManNTProp and Ac<sub>5</sub>ManNTBut overcome the requirement for a complementary scaffold by displaying thiol groups on longer, <i>N</i>-acyl linker arms, thereby presumably increasing their ability to interact and crosslink with surrounding thiols. These new analogs showed increased potency in human neural stem cells (hNSCs) and human adipose stem cells (hASCs). In the hNSCs, Ac<sub>5</sub>ManNTProp upregulated biochemical endpoints consistent with Wnt signaling in the absence of a thiol-reactive scaffold. In the hASCs, both Ac<sub>5</sub>ManNTProp and Ac<sub>5</sub>ManNTBut suppressed adipogenic differentiation, with Ac<sub>5</sub>ManNTBut providing a more potent response, and they did not interfere with differentiation to a glial lineage (Schwann cells). These results expand the horizon for using MGE in regenerative medicine by providing new tools (Ac<sub>5</sub>ManNTProp and Ac<sub>5</sub>ManNTBut) for manipulating human stem cells.