gebhart/patrepeval huggingface dataset:
Phylogenetic relationships of eight new Dacrymycetes collected from new Zealand (2017)

<i>Dacrymycetes</i>, sister to <i>Agaricomycetes</i>, is a noteworthy lineage for studying the evolution of wood-decaying basidiomycetes; however, its species diversity and phylogeny are largely unknown. Species of <i>Dacrymycetes</i> previously used in molecular phylogenetic analyses are mainly derived from the Northern Hemisphere, thus insufficient knowledge exists concerning the Southern Hemisphere lineages. In this study, we investigated the species diversity of <i>Dacrymycetes</i> in New Zealand. We found 11 previously described species, and eight new species which were described here: <i>Calocera pedicellata</i>, <i>Dacrymyces longistipitatus</i>, <i>D. pachysporus</i>, <i>D. stenosporus</i>, <i>D. parastenosporus</i>, <i>D. cylindricus</i>, <i>D. citrinus</i>, and <i>D. cyrtosporus</i>. These eight newly described species and seven of the known ones, namely, <i>Calocera fusca</i>, <i>C.</i> cf. <i>guepinioides</i>, <i>C. lutea</i>, <i>Dacrymyces flabelliformis</i>, <i>D. intermedius</i>, <i>D. subantarcticensis</i>, and <i>Heterotextus miltinus</i>, have rarely or never been recorded from the Northern Hemisphere. In a molecular-based phylogeny, these New Zealand strains were scattered throughout the <i>Dacrymycetaceae</i> clade. Sequences obtained from specimens morphologically matching <i>C. guepinioides</i> were separated into three distant clades. Because no obvious morphological differences could be discerned between the specimens in each clade and no sequence exists from the type specimen, a <i>C. guepinioides</i> s.str. clade could not be determined. This survey of dacrymycetous species in the Southern Hemisphere has increased taxon sampling for phylogenetic analyses that can serve as a basis for the construction of a stable classification of <i>Dacrymycetes</i>.
Fabrication of a biodegradable scaffold with localized response to bacterial infections (2018)

Implant-associated infections remain a significant source of morbidity in the clinic. Systemic administration of antibiotics is often ineffective, due in part to limited vascularization of the implant site. Here, we describe a physical method of incorporating antibiotics into biodegradable scaffolds. Antibiotics gentamicin sulfate (GS) and metronidazole (MZ) were cryomilled with polycaprolactone (PCL) and subsequently heat-melded. Antibiotic-loaded films were evaluated for mechanical properties, drug release characteristics, anti-microbial efficacy and cytotoxicity. Our results suggest this process to be feasible for the generation of thin film coatings with varying drug concentrations. Release profiles indicated an initial burst release for both antibiotics with a sustained release of 3 and 8 days for GS and MZ films respectively. The films inhibited bacterial growth, while viability assays suggest low mammalian cytotoxicity. Taken together, these findings establish this method as a chemical-free means to form biodegradable drug scaffolds for the tailored local delivery of antibiotics.
Nathanson Young Engineer of the Year (2015)

The Nathanson Young Engineer of the Year is an annual award, in honor of the late Fred Nathanson, sponsored by the IEEE/AES Radar Systems Panel of the Aerospace and Electronic Systems Society. The purpose of this award is to grant international recognition for outstatanding contributions to the radar art by young IEEE/AESS members. The goals of the Radar Systems Panel in granting this award are to encourage individual effort and to fostor increased participation by developing radar engineers.
SEM observations of the sliding behavior of A12O3 and CBN against steel (1989)

Abstract Both aluminum oxide (A1 2 O 3 ) and cubic boron nitride (CBN) are being used as the abrasive medium in grinding wheels. To compare the effectiveness of these abrasives, a study was made, using the scanning electron microscope (SEM), to observe the sliding behavior and surface damage resulting from single particles of polycrystalline A1 2 O 3 and CBN sliding dry against hardened M‐50 tool steel. These experiments were run in the chamber of the SEM, which permitted direct observation of the contact areas at high magnifications. Friction force was monitored and videotape recordings were made continuously during these tests. Significantly lower friction and smoother wear tracks were obtained with the CBN. The A1 2 O 3 grit produced much sharper ridges and considerable microcracking on the ridges. These microcracks were formed perpendicular to the wear track. The wear tracks obtained in the SEM were compared with the surfaces produced by surface grinding hardened steel with both CBN and A1 2 O 3 wheels. At high magnifications, marked similarities between the ground surfaces and the surfaces produced by the basic sliding tests were noted. It is suggested that because of the large number of microcracks formed during the grinding process with the A1 2 O 3 , the fatigue life of parts ground with an A1 2 O 3 wheel would be shorter than those ground with CBN. Practical experience indicates that this is true.
28nm Metal Hard Mask etch process development (2015)

Metal Hard Mask (MHM)-All In One (AIO) technology has been widely used in the process flow of copper inter-connect since 28 nm technology node and below. This is because AF immersion exposure technology reaches its limitation for line edge roughness control, photoresist (PR) thickness and profile control. In this paper, we described the issues and the solutions in the development of 28 nm node MHM etch process, including selectivity improvement for photoresist, optimization of line edge roughness (LER), and optimization of TiN profile & CD uniformity. Base on fundamental etch theory, several experiments were conducted, and we successfully achieved TiN with desired profile and CD with good uniformity for 28nm MHM process.
RTK Inhibitors in Melanoma: From Bench to Bedside (2021)

MAPK (mitogen activated protein kinase) and PI3K/AKT (Phosphatidylinositol-3-Kinase and Protein Kinase B) pathways play a key role in melanoma progression and metastasis that are regulated by receptor tyrosine kinases (RTKs). Although RTKs are mutated in a small percentage of melanomas, several receptors were found up regulated/altered in various stages of melanoma initiation, progression, or metastasis. Targeting RTKs remains a significant challenge in melanoma, due to their variable expression across different melanoma stages of progression and among melanoma subtypes that consequently affect response to treatment and disease progression. In this review, we discuss in details the activation mechanism of several key RTKs: type III: c-KIT (mast/stem cell growth factor receptor); type I: EGFR (Epidermal growth factor receptor); type VIII: HGFR (hepatocyte growth factor receptor); type V: VEGFR (Vascular endothelial growth factor), structure variants, the function of their structural domains, and their alteration and its association with melanoma initiation and progression. Furthermore, several RTK inhibitors targeting the same receptor were tested alone or in combination with other therapies, yielding variable responses among different melanoma groups. Here, we classified RTK inhibitors by families and summarized all tested drugs in melanoma indicating the rationale behind the use of these drugs in each melanoma subgroups from preclinical studies to clinical trials with a specific focus on their purpose of treatment, resulted effect, and outcomes.
Long-term Safety and Efficacy of Etrasimod for Ulcerative Colitis: Results from the Open-label Extension of the OASIS Study (2021)

In this long-term extension study, etrasimod 2 mg demonstrated a favourable safety profile. Most patients with clinical response, clinical remission, or endoscopic improvement at Week 12 maintained that status to end of treatment.
Southampton Recommendations to 2004 UK Parliamentary Select Committee on Science and Technology: Open Access Policy (2004)

The 2004 UK Parliamentary Select Committee on Science and Technology essentially adopted the Southampton recommendations in full, recommending that Open-Access Provision through institutional self-archiving should be made mandatory for all journal articles resulting from UK-funded research.
Unexpected Phase Behavior of Amylose in a High Solids Environment (2010)

The purpose of this paper is to present and rationalize data concerning the structural behavior of amylose in the presence of glucose syrup. Observations were obtained by the experimental methods of small-deformation dynamic oscillation on shear, modulated differential scanning calorimetry, and scanning electron microscopy. In contrast to industrial polysaccharides that undergo readily a coil-to-helix transition (e.g., agarose, deacylated gellan, and kappa-carrageenan), amylose holds its structural characteristics unaltered at low and intermediate levels of glucose syrup. This is followed by an early phase inversion from a polysaccharide to cosolute dominated system at levels of solids above 70.0%, as compared to industrial polysaccharides that can dictate kinetics of vitrification at a solid content as high as 90.0% in the formulation. Additional viscoelastic "anomalies" include a clear breakdown of thermorheological simplicity with data exhibiting two tan delta peaks in the passage from the softening dispersion to the glassy state. Besides phenomenological evidence, mechanistic modeling using the combined framework of the free volume/reaction rate theories argue for two distinct glass transition temperatures in the mixture. It is proposed that the amylose/glucose syrup/water system does not reach a state of molecular mixing, with the morphological features being those of a micro phase-separated material.
Laminin α1 chain mediated reduction of laminin α2 chain deficient muscular dystrophy involves integrin α7β1 and dystroglycan (2006)

Transgenically introduced laminin (LN) alpha1 chain prevents muscular dystrophy in LNalpha2 chain deficient mice. We now report increased integrin alpha7Bbeta1D synthesis in dystrophic LNalpha2 chain deficient muscle. Yet, immunofluorescence demonstrated a reduced expression of integrin alpha7B subunit at the sarcolemma. Transgenic expression of LNalpha1 chain reconstituted integrin alpha7B at the sarcolemma. Expression of alpha- and beta-dystroglycan is enhanced in LNalpha2 chain deficient muscle and normalized by transgenic expression of LNalpha1 chain. We suggest that LNalpha1 chain in part ameliorates the development of LNalpha2 chain deficient muscular dystrophy by retaining the binding sites for integrin alpha7Bbeta1D and alpha-dystroglycan, respectively.
Minimal Generators for Symmetric Ideals (2006)

Let $K$ be a field, and let $R = K[X]$ be the polynomial ring in an infinite collection $X$ of indeterminates over $K$. Let ${\mathfrak S}_{X}$ be the symmetric group of $X$. The group ${\mathfrak S}_{X}$ acts naturally on $R$, and this in turn gives $R$ the structure of a left module over the (left) group ring $R[{\mathfrak S}_{X}]$. A recent theorem of Aschenbrenner and Hillar states that the module $R$ is Noetherian. We prove that submodules of $R$ can have any number of minimal generators.
Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism (2000)

The Y chromosome provides a unique opportunity to study mutational processes within the human genome, decoupled from the confounding effects of interchromosomal recombination. It has been suggested that the increased density of certain dispersed repeats on the Y could account for the high frequency of causative microdeletions relative to single nucleotide mutations in infertile males. Previously we localised breakpoints of an AZFa microdeletion close to two highly homologous complete human endogenous retroviral sequences (HERV), separated by 700 kb. Here we show, by sequencing across the breakpoint, that the microdeletion occurs in register within a highly homologous segment between the HERVs. Furthermore, we show that recurrent double crossovers have occurred between the HERVs, resulting in the loss of a 1.5 kb insertion from one HERV, an event underlying the first ever Y chromosomal polymorphism described, the 12f2 deletion. This event produces a substantially longer segment of absolute homology and as such may result in increased predisposition to further intrachromosomal recombination. Intrachromosomal crosstalk between these two HERV sequences can thus result in either homogenising sequence conversion or a microdeletion causing male infertility. This represents a major subclass of AZFa deletions.
Design compromise between the efficiency and spectral re-growth of power amplifiers using second harmonic source/load impedance (2003)

This paper investigates the effect of second harmonic impedance on power added efficiency (PAE) and spectral re-growth for use in GaAs MESFET class A power amplifier at 1.9 GHz. By choosing the proper source and load second harmonic impedance, a compromise between high efficiency and low spectral re-growth can be obtained.
Diallel analysis of root‐knot nematode resistance based on galling index in upland cotton (2007)

Abstract The southern root‐knot nematode (RKN) [ Meloidogyne incognita (Kofoid and White) Chitwood) RKN] is one of the most destructive pests in the Cotton Belt of the U.S. Developing and employing resistant cultivars is the most economical and efficient method for RKN management. This greenhouse investigation was conducted to understand the quantitative genetic basis of RKN resistance in the major RKN resistance sources using a nine‐parent diallel analysis based on improved RKN evaluation techniques. The selected genotypes consisted of three ‘Aubrun 623 RNR’ (here RNR = R oot‐knot N ematode R esistance)‐derived resistant lines, one moderately resistant cultivar ‘Acala Nem‐X’, and five susceptible cultivars. Comparison between F 1 and their parents in galling index revealed that the RKN resistance is partially dominant. The general combining ability was more important than the specific combining ability for RKN resistance. The estimates for broad‐sense and narrow‐sense heritabilities on galling index were 0.82 and 0.65, respectively, indicating that RKN resistance in the Auburn and Nem‐X resistance sources is largely controlled by genetic and additive effects. The minimum number of genes for RKN resistance was estimated to be two. Therefore, under reliable and uniform RKN inoculation and infestation conditions, single plant selection should be efficient in transferring Auburn RKN resistance into elite genetic backgrounds.
An update on the acclimatization issue (1999)

Ruth Bentler, PhD, is Associate Professor and Christopher Turner, PhD, is Professor, both in the Department of Speech Pathology and Audiology, The University of Iowa. Lenore Holte, PhD, is Director of Speech, Language, and Hearing Services at The University of Iowa. Direct all correspondence to Dr. Bentler at Department of Speech Pathology & Audiology, The University of Iowa, Iowa City, Iowa 52242; e-mail: [email protected].
Design and analysis of PKM robots for ultra fast blanking (2013)

This paper presents the methodology and results of a feasibility study for design and analysis of PKM robots suitable for high speed blanking applications in a press shop. A concept of a robotic blanking line is used to extract requirements on the robots. The scalability of PKM robots are investigated using model-based design methods. CAD models of the PKM robots are prepared to extract parameters for the models that are implemented in Dymola for dynamic simulation and visualization/animation. Robot movements for blanking are simulated and various design quantities are extracted, which give input for drive train design, and thus give good indications of the feasibility of the design solution, considering known drive train components that are available. Evaluations and comparisons of designs for different PKM configurations are made as well as a benchmark against a serial robot. The results show the great potential of the PKM concept for high speed blanking application.
Transport and Metabolism of Adenosine and its Metabolites in Capillary Endothelial Cells of Guinea Pig Hearts (2018)

Adenosine (Ado) plays an important role in cardioprotection during ischemia by enhancing coronary flow through binding to purinoceptors on smooth muscle cells (SMC), and by preserving nucleotide pools through purine salvage in cardiomyocytes (MC). However, two questions impede our understanding of the mechanism by which Ado acts on MCs or SMCs: (1) how much Ado reaches cardiomyoctyes or SMC when EC avidly take‐up Ado from blood stream and interstitium? and (2) how much Ado degrades to uric acid (UA), or is salvaged back into cellular pools, mainly ATP? Our goal here is to quantify the fluxes of Ado and its metabolites in ECs. The multiple‐indicator‐dilution technique (MID) was used to measure the capillary transport and metabolism of Ado and metabolites in isolated, Krebs‐Ringer perfusated guinea pig hearts. Radiolabeled [ 14 C]‐ adenosine, or inosine, or hypoxanthine, or xanthine was injected with [ 131 I]‐albumin (intravascular reference solute) and [ 3 H] AraH or L‐[ 3 H] glucose (extracellular references) as a bolus into the coronary flow; venous outflow dilution curves of the injectate and its metabolites were quantified with HPLC and LS counting. The permeabilities of each solute (via interendothelial clefts, PSg, trans‐endothelial membrane, PSecl, trans‐cardiomyocytes PSpc) and the metabolism in ECs and MCs were estimated by fitting the MID curves with a general convection‐diffusion‐exchange‐reaction model, Gentex. Results are: Intracellular sequestration of injected Ado is high compared to its metabolites (~60% of Ado vs. ~50% of Ino). Similarly, PSecl is higher for Ado than metabolites, INo&gt;Hx&gt;Xa&gt; UA (Ado:1.9±0.7 vs. Ino:1.7±0.5 vs. Hx: 0.5±0.1 ml·min −1 ·g −1 ). The low permeabilities help to retain purine in the cells. Plasma injectate Ado that enters ECs is estimated to be ~50% oxidized to UA, ~50% retained; Hx is ~67% oxidized, ~23% retained, both presumably incorporated into nucleotide pools. Thus ECs actively participate in purine salvage via both Ado and Hx. Uncertainty for EC parameters is much smaller than for MC. Having well‐defined parameters for permeabilities and metabolism for Ado and its metabolites in ECs is an essential step toward understanding the fate of endogenous Ado generated from cardiomyocytes during ischemia and reperfusion. Support or Funding Information Our study was supported by NIH research grant U01HL122199. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
The debut of anti-TNF therapy of rheumatoid arthritis in the clinic (2000)

Tumour necrosis factor a (TNFα) was cloned and expressed as a recombinant protein in the middle 1980s and shown to be identical to “cachectin” [1, 2]. Shortly afterwards nucleic acid and monoclonal antibody probes became available that permitted analysis of the expression of TNF and its receptors in human tissue from patients and controls. The demonstration in in vitro systems that both TNF and IL-1, individually and in combination, stimulated cartilage degradation [3], bone loss [4] and production of prostaglandin E2 and collagenase [5], promoted interest in the role that these cytokines might play in rheumatoid arthritis (RA). In 1988 and 1989 experiments by Buchan et al. [6] and Brennan et al. [7] demonstrated the expression of TNFα at messenger RNA and production of TNFα protein by disaggregated cells obtained from rheumatoid synovial membranes in tissue culture. Specific antibodies were then applied to microscopic sections of synovial membrane from rheumatoid joints and showed that TNFα was present in cells in the lining layer as well as in the deeper parts of the synovium, predominantly in CD68+ cells (macrophage phenotype) but also in a minority of CD3+ T cells in perivascular areas [8]. More interestingly, it was possible to demonstrate the presence of TNFα in cells at the cartilage/pannus junction, the site of the destructive and invasive tissue that leads to the loss of cartilage and bone in rheumatoid joints [8, 9].
Luminometric measurement of population activity of genetically modifiedPseudomonas fluorescensin the soil (1992)

Genetically modified cells of Pseudomonas fluorescens, chromosomally marked with genes for bioluminescence, were inoculated into sterile soil microcosms. During incubation for 90 days, viable cell concentration did not change significantly but light output, measured by luminometry, decreased, indicating reduced metabolic activity due to lack of substrates. Amendment with nutrients resulted in parallel increases in both luminescence and dehydrogenase activity. Luminometry therefore enables rapid monitoring of the activity of populations of luminescence-marked microbial inocula in the soil, with greater sensitivity and selectivity than traditional techniques.
Silodosin versus tamsulosin for medical expulsive treatment of ureteral stones: A systematic review and meta-analysis (2018)

Silodosin, a recently introduced selective α-blocker, has a much higher selectivity for the α-1A receptor. The efficacy and safety of silodosin compared to tamsulosin in medical expulsive therapy (MET) are controversial. The objective of this study was to assess the efficacy and safety of silodosin compared to tamsulosin for treating ureteral stones <10 mm in diameter. We systematically searched the PubMed, EMBASE, Cochrane library, and Scopus databases from their inception to May 2018. We included randomized controlled studies (RCTs) and observational studies, which investigated stone expulsion rates using silodosin compared to tamsulosin. Data were synthesized using a random-effects model. Sixteen studies with 1824 patients were eligible for inclusion. Silodosin achieved significantly higher expulsion rates than tamsulosin (pooled risk difference (RD): 0.13, 95% confidence interval (CI): 0.09 to 0.18, GRADE: high). A subgroup analyses showed that silodosin has a significantly higher expulsion rate on stone sizes of 5-10 mm than tamsulosin (pooled RD: 0.14, 95% CI: 0.06 to 0.22, I2 = 0%). The superior effect was not observed on stone sizes <5 mm. A multivariate regression showed that the RD was negatively associated with the control expulsion rate after adjusting for age and gender (coefficient -0.658, p = 0.01). A sensitivity analysis showed that our findings were robust. Patients receiving silodosin also probably had a significantly shorter expulsion time (pooled mean difference (MD): -2.55 days, 95% CI: -4.06 to -1.04, I2 = 85%, GRADE: moderate) and may have fewer pain episodes (pooled MD: -0.3, 95% CI: -0.51 to -0.09, GRADE: low) but a higher incidence of retrograde ejaculation by 5% compared to those receiving tamsulosin. In conclusion, compared to tamsulosin, silodosin provided significantly better stone passage for patients with ureteral stones (particularly for sizes of 5~10 mm), shorter expulsion times, and fewer pain episodes but caused a higher incidence of retrograde ejaculation.
Enhancement of coherent Smith-Purcell radiation at THz frequency (2015)

This paper explores several mechanisms to enhance the coherent Smith-Purcell radiation (SPR) at THz frequencies. A simple analytical dispersion relation is derived to predict the operating frequency for both open grating and Orotron-like devices. The analytical predictions are in excellent agreement with particle-in-cell simulations. It is found that the start current for a continuous electron beam to excite coherent SPR can be reduced by orders of magnitude, by merely varying the groove width and height of the grating, with grating period and beam energy being held constant. Other mechanisms, such as prebunched beams and open cavity configurations are also investigated for the enhancement of coherent SPR.