gebhart/patrepeval huggingface dataset:
Leaf palatability and decomposability increase during a 200-year-old post-cultural woody succession in New Zealand (2010)

Question: How do aggregate trait values and functional diversity of leaf traits linked to palatability and decomposability change during a woody post-cultural succession spanning 200 years? Location: Coastal Marlborough, South Island, New Zealand. Methods: The biomass of all woody species was determined in 32 20-m × 20-m plots ranging from 10 to 200 years in time since last disturbance. Species abundances were combined with data on leaf nutrient, secondary metabolite and structural carbohydrate content to calculate biomass-weighted trait means (i.e. aggregate trait values) and functional diversity index values for each plot. Aggregate trait values and functional diversity were regressed on successional age and total live above-ground carbon content to examine functional shifts with succession and one consequence of succession – increasing above-ground carbon. Results: Almost all significant regressions between aggregate trait values and both successional age and above-ground carbon indicated a shift toward increased leaf palatability and decomposability during succession. The relationships were all non-linear, with aggregate trait value shifts occurring relatively early in the successional sequence. There was weak evidence for an increase in functional richness with succession, but this was a secondary effect relative to the shifts in aggregate trait values. Conclusions: These results are in direct contrast with studies of the early stages of herbaceous post-cultural successions from grasslands to shrublands, which have found a shift towards communities of decreasing palatability and decomposability, suggesting that functional shifts in woody succession may be fundamentally different.
Porous silicon mirrors with enlarged omnidirectional band gap (2005)

Multilayers consisting of the periodic repetition of two layers with different refractive indices (nH and nL) may have an omnidirectional band gap, the width of which depends on the incidence medium and on the refractive index ratio nH∕nL. In porous silicon, this ratio is limited by the material and fabrication characteristics. This article makes a theoretical study of two multilayer structures in order to enlarge the omnidirectional band gap with the same refractive index ratio by varying only the thickness of the period. These structures are named balanced and unbalanced mirrors and consist of a few periodic multilayers stacked together. Porous silicon balanced and unbalanced mirrors with enlarged omnidirectional band gap for 1.55-μm applications are proposed. The results obtained with these mirror structures are compared with the results obtained with a chirped structure with the same characteristics.
Site-specific gene expression analysis using an automated tissue micro-dissection punching system (2017)

Site-specific gene expression analyses are important for understanding tissue functions. Despite rapid developments in DNA-related technologies, the site-specific analysis of whole genome expression for a tissue remains challenging. Thus, a new tool is required for capturing multiple tissue micro-dissections or single cells while retaining the positional information. Here, we describe the development of such a system, which can pick up micro-dissections by punching a tissue repeatedly in a very short period, e.g., 5 s/sampling cycle. A photo of the punched tissue provides information on the dissected positions, allowing site-specific gene expression analysis. We demonstrate the site-specific analysis of a frozen tissue slice of mouse brain by analyzing many micro-dissections produced from the tissue at a 300-μm pitch. The site-specific analysis provided new insights into the gene expression profiles in a tissue and on tissue functions. The analysis of site-specific whole genome expression may therefore, open new avenues in life science.
The role of dissolved carbon dioxide in both the decline in rumen pH and nutritional diseases in ruminants (2016)

Rumen pH has been central to theories of nutritional disease and nutrient digestion in ruminants for decades. In particular, rumen pH is the measurement of a physical phenomenon that describes the balance between bases and acids in a solution. Here, I take a closer look at rumen pH and suggest that its decline during acidosis is a sign of an increased concentration of dissolved carbon dioxide (dCO2), which is the acid in the main buffer system. Rumen dCO2 concentrations are thought to be constant and low, but modern feeding practices can lead to carbon dioxide (CO2) holdup, which is defined as a decline in CO2 fugacity due to changes in the physicochemical properties of the rumen liquor. Gas holdup might thus be responsible for increasing rumen dCO2 concentrations, with a concomitant pH decline. Dissolved CO2 is a biologically active molecule that directly influences bacterial metabolism and that, if found at high concentrations, might enhance rumen CO2 diffusion into the blood, leading to hypercapnia or high blood CO2 concentrations. Hypercapnia has known cellular and physiological effects that are closely associated with rumen acidosis. In this review, I discuss the implication of a high rumen dCO2 concentration for the onset of nutritional diseases and highlight the need to explore rumen acidosis from a physicochemical point of view and beyond pH decline.
PREFATORY NOTE (2010)

THE fragmentary Introduction which was begun by Dr Hort in 1872, and continued at two later dates, gives in part the history and scope of the present volume; but the revision indicated in the opening paragraph was not completely carried into effect. The first two Lectures were set up in slip in 1872, and after careful revision were passed for press at the close of 1874. The first four sheets were printed off (pp. 1—80), the remainder of Lecture II. remained in slip, and pencillings on the copy suggest that some enlargement of the conclusion was in contemplation. The third Lecture has been printed partly from the original MS. (pp. 95—107; 146—8), and partly (pp. 108–146) from a MS of later date. The fourth Lecture has been printed as it was originally written. The MS. has not received any later additions, but something appears to be wanting on p. 166. The ‘Notes and Illustrations’ were taken from collections made for the Lectures and for the revision of them, and will serve in some measure to illustrate the wider range which was designed for Lectures III., IV. (p. xxvii.).
Phase III Trial of Vinflunine Plus Best Supportive Care Compared With Best Supportive Care Alone After a Platinum-Containing Regimen in Patients With Advanced Transitional Cell Carcinoma of the Urothelial Tract (2009)

VFL demonstrates a survival advantage in second-line treatment for advanced TCCU. Consistency of results exists with significant and meaningful benefit over all efficacy parameters. Safety profile is acceptable, and therefore, VFL seems to be a reasonable option for TCCU progressing after first-line platinum-based therapy.
Improved Syntheses of [3,2-b]- and [2,3-b]-fused Selenolo- and Thienopyrroles, and of Furo[3,2-b]pyrrole (1999)

Article Improved Syntheses of [3,2-b]- and [2,3-b]-fused Selenolo- and Thienopyrroles, and of Furo[3,2-b]pyrrole was published on August 1, 1999 in the journal Heterocyclic Communications (volume 5, issue 4).
Large arterioles in the control of blood flow: role of endothelium‐dependent dilation (2000)

Although it is generally assumed that small arterioles form the major site of vascular resistance, microcirculatory studies revealed that 40-55% of the total network resistance can reside in large arterioles and small arteries. Thus, the mechanisms that control smooth muscle tone in these vessels have a major impact on the overall conductance of the vascular network. These control mechanisms are different from those in small arterioles: Aside from an apparently reduced sensitivity to metabolites, the large resistance vessels are normally too far away from the capillary areas which they feed to be reached by diffusing metabolites from dependent cells within a reasonable period of time. Rather, recent intravital microscopic studies suggest that large resistance vessels are under tight control of endothelial factors such as nitric oxide and endothelium-derived hyperpolarising factor (EDHF). Nitric oxide opposes myogenic constrictions of large arterioles that potentially would impair tissue perfusion and oxygenation. Moreover, nitric oxide and EDHF play an important role in the co-ordination of large and small resistance vessel behaviour that is pivotal for the adaptation of blood flow to altered tissue oxygen demands.
Artificial GeSi substrates for heteroepitaxy: Achievements and problems (2003)

It is desirable to have a set of substrates which are based on Si and ensure growth of heterostructures with various lattice parameters in order to develop electronic devices composed of semiconductor materials whose epitaxial growth is reasonably well developed. Such substrates are typically referred to as artificial. In this paper, a comparative analysis of various methods for the fabrication of artificial substrates (heterostructures), in which the relaxation of stresses is based on the introduction of misfit dislocations, is performed. Based on published and new experimental data, the mechanisms for attaining a low density of threading dislocations in plastically relaxed films represented by heterostructures composed of GeSi and an Si buffer layer grown at low temperatures are analyzed. The problems and results of another group of methods for obtaining artificial substrates which gained favor recently and become known as “compliant” or “soft” substrates are discussed. The most important electrical parameters of Si and GeSi films grown on artificial substrates are considered.
Transplantation of mesenchymal stem cells from young donors delays aging in mice (2011)

Increasing evidence suggests that the loss of functional stem cells may be important in the aging process. Our experiments were originally aimed at testing the idea that, in the specific case of age-related osteoporosis, declining function of osteogenic precursor cells might be at least partially responsible. To test this, aging female mice were transplanted with mesenchymal stem cells from aged or young male donors. We find that transplantation of young mesenchymal stem cells significantly slows the loss of bone density and, surprisingly, prolongs the life span of old mice. These observations lend further support to the idea that age-related diminution of stem cell number or function may play a critical role in age-related loss of bone density in aging animals and may be one determinant of overall longevity.
Z-selective olefin metathesis processes and Cis/syndioselective ROMP with high oxidation state molybdenum alkylidenes (2012)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012.
Silicon optical Fiber (2008)

Described herein are initial experimental details and properties of a silicon core, silica glass-clad optical fiber fabricated using conventional optical fiber draw methods. Such semiconductor core fibers have potential to greatly influence the fields of nonlinear fiber optics, infrared and THz power delivery. More specifically, x-ray diffraction and Raman spectroscopy showed the core to be highly crystalline silicon. The measured propagation losses were 4.3 dB/m at 2.936 microm, which likely are caused by either microcracks in the core arising from the large thermal expansion mismatch with the cladding or to SiO(2) precipitates formed from oxygen dissolved in the silicon melt. Suggestions for enhancing the performance of these semiconductor core fibers are provided. Here we show that lengths of an optical fiber containing a highly crystalline semiconducting core can be produced using scalable fiber fabrication techniques.
Synergy between cationic lipid and co-lipid determines the macroscopic structure and transfection activity of lipoplexes (2002)

The large number of cytofectin and co-lipid combinations currently used for lipoplex-mediated gene delivery reflects the fact that the optimal cytofectin/co-lipid combination varies with the application. The effects of structural changes in both cytofectin and co-lipid were systematically examined to identify structure-activity relationships. Specifically, alkyl chain length, degree of unsaturation and the head group to which the alkyl side chain was attached were examined to determine their effect on lipoplex structure and biological activity. The macroscopic lipoplex structure was assessed using a dye-binding assay and the biological activity was examined using in vitro transfection in three diverse cell lines. Lipoplexes were formulated in three different vehicles currently in use for in vivo delivery of naked plasmid DNA (pDNA) and lipoplex formulations. The changes in dye accessibility were consistent with structural changes in the lipoplex, which correlated with alterations in the formulation. In contrast, transfection activity of different lipoplexes was cell type and vehicle dependent and did not correlate with dye accessibility. Overall, the results show a correlation between transfection and enhanced membrane fluidity in both the lipoplex and cellular membranes.
Loss and recovery ofArabidopsis–type telomere repeat sequences 5′–(TTTAGGG)n–3′ in the evolution of a major radiation of flowering plants (2001)

Fluorescent in situ hybridization and Southern blotting were used for showing the predominant absence of the Arabidopsis-type telomere repeat sequence (TRS) 5'-(TTTAGGG)(n)-3' (the 'typical' telomere) in a monocot clade which comprises up to 6300 species within Asparagales. Initially, two apparently disparate genera that lacked the typical telomere were identified. Here, we used the new angiosperm phylogenetic classification for predicting in which other related families such telomeres might have been lost. Our data revealed that 16 species in 12 families of Asparagales lacked typical telomeres. Phylogenetically, these were clustered in a derived clade, thereby enabling us to predict that the typical telomere was lost, probably as a single evolutionary event, following the divergence of Doryanthaceae ca. 80--90 million years ago. This result illustrates the predictive value of the new phylogeny, as the pattern of species lacking the typical telomere would be considered randomly placed against many previous angiosperm taxonomies. Possible mechanisms by which chromosome end maintenance could have evolved in this group of plants are discussed. Surprisingly, one genus, Ornithogalum (Hyacinthaceae), which is central to the group of plants that have lost the typical telomere, appears to have regained the sequences. The mechanism(s) by which such recovery may have occurred is unknown, but possibilities include horizontal gene transfer and sequence reamplification.
Inhibitory activity of IL-1 receptor antagonist depends on the balance between binding capacity for IL-1 receptor type 1 and IL-1 receptor type II (1997)

A series of mutants of human IL-1 receptor antagonist (IL-1ra) has been designed by comparison of IL-1ra and IL-1beta structures in order to increase receptor antagonist capacity. Upon in vitro and in vivo assay of IL-1 antagonism, the IL-1ra mutants DoB 0039 (N91-->R), DoB 0040 (T109-->A) and DoB 0041 (N91/T109-->R/A) could inhibit IL-1beta effects more efficiently than wild-type IL-1ra, with DoB 0041 being the most active. Analysis of the receptor-binding capacity of the IL-1ra mutants showed that all three mutants could inhibit binding of IL-1alpha or IL-1beta to IL-1RI-bearing cells more efficiently than wild-type IL-1ra. Conversely, binding of IL-1beta to IL-1RII-bearing cells could be inhibited by DoB 0041 much less efficiently than by wild-type IL-1ra. It is known that the two types of IL-1 receptors (IL-1RI and IL-1RII) play different roles in the regulation of IL-1 activity, with IL-1RI being solely responsible for cell triggering upon IL-1 binding, whereas IL-1RII acts as a scavenger of IL-1 and can thus be considered as a natural IL-1 inhibitor. Thus, the enhanced inhibitory capacity of DoB 0041 as compared with wild-type IL-1ra is explained in terms of better binding to the activating receptor IL-1RI and poorer interaction with the inhibitory receptor IL-1RII.
Involvement of Adenosine A2a Receptor in Intraocular Pressure Decrease Induced by 2-(1-Octyn-1-yl)adenosine or 2-(6-Cyano-1-hexyn-1-yl)adenosine (2005)

The aim of the present study is to clarify the mechanism for the decrease in intraocular pressure by 2-alkynyladenosine derivatives in rabbits. The receptor binding analysis revealed that 2-(1-octyn-1-yl)adenosine (2-O-Ado) and 2-(6-cyano-1-hexyn-1-yl)adenosine (2-CN-Ado) selectively bound to the A(2a) receptor with a high affinity. Ocular hypotensive responses to 2-O-Ado and 2-CN-Ado were inhibited by the adenosine A(2a)-receptor antagonist 1,3,7-trimethyl-8-(3-chlorostyryl)xanthine (CSC), but not by the adenosine A(1)-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (DPCPX) or the adenosine A(2b)-receptor antagonist alloxazine. In addition, 2-O-Ado and 2-CN-Ado caused an increase in outflow facility, which was inhibited by CSC, but not by DPCPX or alloxazine. Moreover, 2-O-Ado and 2-CN-Ado increased cAMP in the aqueous humor, and the 2-O-Ado-induced an increase in cAMP was inhibited by CSC. These results suggest that 2-O-Ado and 2-CN-Ado reduced intraocular pressure via an increase in outflow facility. The ocular hypotension may be mainly mediated through the activation of adenosine A(2a) receptor, although a possible involvement of adenosine A(1) receptor cannot be completely ruled out. 2-O-Ado and 2-CN-Ado are useful lead compounds for the treatment of glaucoma.
Quantitative characterization of the corticospinal tract at 3T. (2007)

The results constitute a normative dataset for the following imaging parameters of the CST: T1, T2, MTR, fractional anisotropy, mean diffusivity, transverse diffusivity, and the 3 diffusion tensor eigenvalues. These data can be used to identify, characterize, and establish the significance of changes in diseases that affect the CST.
Purification and characterization of glycerol‐3‐phosphate dehydrogenase ofSaccharomyces cerevisiae (1992)

The NAD-dependent glycerol-3-phosphate dehydrogenase (glycerol-3-phosphate:NAD+ oxidoreductase; EC 1.1.1.8; G3P DHG) was purified 178-fold to homogeneity from Saccharomyces cerevisiae strain H44-3D by affinity- and ion-exchange chromatography. SDS-PAGE indicated that the enzyme had a molecular mass of approximately 42,000 (+/- 1,000) whereas a molecular mass of 68,000 was observed using gel filtration, implying that the enzyme may exist as a dimer. The pH optimum for the reduction of dihydroxyacetone phosphate (DHAP) was 7.6 and the enzyme had a pI of 7.4. NADPH will not substitute for NADH as coenzyme in the reduction of DHAP. The oxidation of glycerol-3-phosphate (G3P) occurs at 3% of the rate of DHAP reduction at pH 7.0. Apparent Km values obtained were 0.023 and 0.54 mM for NADH and DHAP, respectively. NAD, fructose-1,6-bisphosphate (FBP), ATP and ADP inhibited G3P DHG activity. Ki values obtained for NAD with NADH as variable substrate and FBP with DHAP as variable substrate were 0.93 and 4.8 mM, respectively.
Design and synthesis of amphipathic 3(10)-helical peptides and their interactions with phospholipid bilayers and ion channel formation. (1994)

It has been reported that a peptide corresponding to the S4 segment in sodium channel protein is able to form voltage-dependent cation-selective ion channels (Tosteson, M. T., Auld, D. S., and Tosteson, D. C. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 707-710). However, biological and other physical properties remain unexamined. In the present study, three peptides, H-(Ala-Arg-Leu)8-OH (ARL8), H-(Val-Arg-Leu)8-OH (VRL8), and H-(Leu-Arg-Leu)8-OH (LRL8) which were designed on the basis of the S4 segment and expected to form 3(10)-helix, were synthesized and examined with regard to conformational change by the interaction with membranes, membrane perturbation ability, ion channel formation, and antimicrobial activity. According to CD spectra, these peptides were found to form a 3(10)-helical structure in the presence of dipalmitoyl-DL-alpha-phosphatidylcholine/dipalmitoyl-DL-alpha- phosphatidylglycerol (3:1) liposomes. The experiment of the peptide-induced leakage of carboxyfluorescein from liposomes showed that all the peptides had a strong ability to perturb membranes. The peptides were able to form cation-selective ion channels in planar asolectin lipid bilayers. The conductances of the ion channels were small (approximately 2 picosiemens for VRL8 and LRL8 and approximately 23 picosiemens for ARL8), suggesting that the peptides produce narrow pores or wider pores with certain permeable barriers that are a portion of the whole channels. The differences in their conductances depend possibly on the sizes of the side chains of Ala, Val, and Leu residues. However, non of the peptides showed antimicrobial activity (minimum inhibitory concentrations, > 50 micrograms/ml). Here, we present the first evidence that the peptides can form 3(10)-helical structures with long chain lengths in a lipid bilayer environment.
Pharmacokinetics and Sedative Effects of Intranasal Dexmedetomidine in Ambulatory Pediatric Patients (2019)

Dexmedetomidine is relatively rapidly absorbed after IN administration and provides clinically meaningful but short-lasting sedation in pediatric patients.
HDTV down-conversion decoder (1996)

In the near future we assume that the advanced television (ATV) broadcasts will be a mixture of HDTV and SDTV. We propose a HDTV down-conversion decoder which can decode the Grand Alliance HDTV bitstreams and display them on SDTV or NTSC monitors. The key technique is a frequency synthesis which decompresses the HDTV bitstreams without full decoding or spatial sampling processes, instead of synthesizing a set of new 8/spl times/8 coefficients from the coefficients of four original 8/spl times/8 blocks. The intent is to provide high quality reconstructed video with lower spatial resolution and less complexity, and thus less computing and memory requirements.
Oxygen electrode-based single antibody amperometric biosensor for qualitative detection of E. coli and bacteria in water (2008)

Design and performance of an amperometric biosensor for E. coli O157:H7 that is based on a common dissolved oxygen probe is discussed. Anti-E. coli O157:H7 antibody was conjugated to horseradish peroxidase and immobilized on a nitrocellulose membrane that was placed over the oxygen probe membrane using a custom-fabricated polyvinyl chloride (PVC) insert. Upon bacterial cell binding, a decrease in enzyme activity resulted in a change in oxygen concentration that was detected with a Clark-type oxygen electrode probe. Validation experiments determined the effect of the outer membrane and insert on the Clarke electrode performance and linearity, and the effects of stirring on sensor response. The mechanism of enzymatic disruption is presumably steric hindrance due to binding of the bacterial cell and conformational change in antibody structure. Sampling various dilutions of heat-sterilized E. coli O157:H7 cells in water, as little as 50 bacterial cells/mL could be detected in approximately 20 minutes of sampling and processing procedures. Bacterial concentrations from 0 to 5000 cells/mL were tested, with 2.52 mg/L +/- 0.37 mg/L equivalents of oxygen produced from as few as 50 cells/mL, versus 6.26 +/- 0.64 mg/L when no cells were present in solution. Overall, the developed amperometric biosensor technology offered an efficient means of detection primarily due to its ease of use, cost-effectiveness, portability, and amenability to incorporation at existing water quality gaging stations.