gebhart/patrepeval huggingface dataset:
Protease inhibitors decrease rabbit cartilage degradation after meniscectomy (1988)

In vitro proteoglycan (PG) synthesis and release were measured on cartilage removed from rabbit knees within 1 week of meniscectomy. Three days following partial lateral meniscectomy, 72% of the femurs and 82% of the tibias had visible ulcers. Cartilage from the weight-bearing areas incorporated 2.0-2.9 times more 35S-sulfate in vitro than cartilage from the opposite, unoperated knees. 3H-thymidine incorporation was 2.5-3.4 times higher for surgical than control groups. 35S-sulfate incorporation by the surgical group was inhibited by 22% in the presence of 10(-4) M U24522, an inhibitor of rabbit chondrocyte metalloprotease (CMP). 3H-thymidine incorporation by the surgical group was inhibited by 28% by 10(-4) M U24522. In vitro PG release from cartilage removed 2 days after surgery was 1.6-3.7 times higher for the surgical than the control group. PG release by the surgical group after 22 h of incubation was reduced to the control level by three CMP inhibitors, U24278, U24279, and U24522. PG release by cartilage from the nonsurgical group was also reduced by these compounds at 22 h. These results suggest that both the anabolic and catabolic processes that are stimulated by surgery can be isolated in vitro and that CMP may be involved in the catabolic process.
In silico Platform for Prediction of N-, O- and C-Glycosites in Eukaryotic Protein Sequences (2013)

Glycosylation is one of the most abundant and an important post-translational modification of proteins. Glycosylated proteins (glycoproteins) are involved in various cellular biological functions like protein folding, cell-cell interactions, cell recognition and host-pathogen interactions. A large number of eukaryotic glycoproteins also have therapeutic and potential technology applications. Therefore, characterization and analysis of glycosites (glycosylated residues) in these proteins is of great interest to biologists. In order to cater these needs a number of in silico tools have been developed over the years, however, a need to get even better prediction tools remains. Therefore, in this study we have developed a new webserver GlycoEP for more accurate prediction of N-linked, O-linked and C-linked glycosites in eukaryotic glycoproteins using two larger datasets, namely, standard and advanced datasets. In case of standard datasets no two glycosylated proteins are more similar than 40%; advanced datasets are highly non-redundant where no two glycosites' patterns (as defined in methods) have more than 60% similarity. Further, based on our results with several algorihtms developed using different machine-learning techniques, we found Support Vector Machine (SVM) as optimum tool to develop glycosite prediction models. Accordingly, using our more stringent and non-redundant advanced datasets, the SVM based models developed in this study achieved a prediction accuracy of 84.26%, 86.87% and 91.43% with corresponding MCC of 0.54, 0.20 and 0.78, for N-, O- and C-linked glycosites, respectively. The best performing models trained on advanced datasets were then implemented as a user-friendly web server GlycoEP (http://www.imtech.res.in/raghava/glycoep/). Additionally, this server provides prediction models developed on standard datasets and allows users to scan sequons in input protein sequences.
Using animal data to improve prediction of human decompression risk following air-saturation dives (2002)

To plan for any future rescue of personnel in a disabled and pressurized submarine, the US Navy needs a method for predicting risk of decompression sickness under possible scenarios for crew recovery. Such scenarios include direct ascent from compressed air exposures with risks too high for ethical human experiments. Animal data, however, with their extensive range of exposure pressures and incidence of decompression sickness, could improve prediction of high-risk human exposures. Hill equation dose-response models were fit, by using maximum likelihood, to 898 air-saturation, direct-ascent dives from humans, pigs, and rats, both individually and combined. Combining the species allowed estimation of one, more precise Hill equation exponent (steepness parameter), thus increasing the precision associated with human risk predictions. These predictions agreed more closely with the observed data at 2 ATA, compared with a current, more general, US Navy model, although the confidence limits of both models overlapped those of the data. However, the greatest benefit of adding animal data was observed after removal of the highest risk human exposures, requiring the models to extrapolate.
The CXC Chemokine Receptor Encoded by Herpesvirus saimiri, ECRF3, Shows Ligand-regulated Signaling through Gi, Gq, and G12/13 Proteins but Constitutive Signaling Only through Gi and G12/13 Proteins (2004)

Udgivelsesdato: 2004-Jul-30
The role of topography and plant functional traits in determining tropical reforestation success (2017)

Abstract Early establishment and sapling growth is a key phase in ensuring cost‐effective reforestation success in relation to biodiversity outcomes. Therefore, species selection must consider the interaction between plant functional traits and the often‐challenging and heterogeneous biophysical environment of degraded landscapes. In this study, we examine how microtopography (slope) results in spatial heterogeneity of soil nutrients, especially phosphorus (P) in a degraded tropical pasture landscape in Queensland, Australia. We then explore how this small‐scale heterogeneity influences the growth of two native tree species, Cardwellia (C.) sublimis (Proteaceae) and Flindersia (F.) brayleyana (Rutaceae), which differ in key nutrient‐acquisition strategies. The proteaceous C. sublimis was found to be buffered from possible P limitation in degraded soils due to its effective P acquisition by cluster roots. In contrast to C. sublimis, which showed no difference in growth after 5 years across a range of soil conditions, F. brayleyana was found to be highly responsive to soil conditions with increased growth in low‐slope, higher P availability areas. The ability of F. brayleyana to take advantage of high soil P levels, including the development of leaves with higher P concentrations, resulted in an apparent switch in competitive fitness between these two species across a landscape gradient. Synthesis and applications . In a detailed study of a landscape reforestation experiment in North Queensland, Australia, we demonstrate that site edaphic factors can vary within tens of metres due to topographic relief, and that species respond differently to these conditions. We therefore show the need to consider both the spatial heterogeneity of edaphic factors and the below‐ground functional traits of potential reforestation species when planning reforestation programmes.
Cloning the IKE Security Association in the Internet Key Exchange Protocol Version 2 (IKEv2) (2016)

This document considers a VPN end user establishing an IPsec Security
Association (SA) with a Security Gateway using the Internet Key
Exchange Protocol version 2 (IKEv2), where at least one of the peers
has multiple interfaces or where Security Gateway is a cluster with
each node having its own IP address. The protocol described allows a
peer to clone an IKEv2 SA, where an additional SA is derived from an
existing one. The newly created IKE SA is set without the IKEv2
authentication exchange. This IKE SA can later be assigned to another
interface or moved to another cluster node.
Diels-Alder Reactions of Furans. Synthesis of 7-Oxabicyclo[2.2.1]heptane Derivatives (1976)

New Diels-Alder reactions of furan and methylfurans with some dienonhiles were nerformed.The adduct from furan and nitroethvlene could be used for synthesizing other 7-oxabicyclo[2.2.l]heptane derivatives.Recent nublications (1,2) concerning Diels-Alder reactions of furan prompted us to reoort some of our results in this field.Several investigators ( 3 -5 ) examined the reaction of furan with methyl acrylate, which required long reaction times (1-2 months) in order to obtain reasonable yields of the adducts and 3 .we reasoned that these long reaction times might be avoided by using a more reactive dienophile like acryloyl chloride.Reaction of this dienophile with furan for a few days at r.t.produced in hiqh yield a mixture of endq-adduct & and z -a d d u c t 2b; their ratio dependinp on the reaction time.Reaction of & and & with methanol afforded the methyl esters la and 2, while reaction with water gave the carboxylic acids & and @, formerly obtained hv sa~onification of and a.The carboxylic acids % and @ can also be obtained by Diels-Alder reaction of furan with acrylic acid.This reaction nroceeded considerably
Correction: Genetic Networks of Liver Metabolism Revealed by Integration of Metabolic and Transcriptional Profiling (2008)

Although numerous quantitative trait loci (QTL) influencing disease-related phenotypes have been detected through gene mapping and positional cloning, identification of the individual gene(s) and molecular pathways leading to those phenotypes is often elusive. One way to improve understanding of genetic architecture is to classify phenotypes in greater depth by including transcriptional and metabolic profiling. In the current study, we have generated and analyzed mRNA expression and metabolic profiles in liver samples obtained in an F2 intercross between the diabetes-resistant C57BL/6 leptin ob/ob and the diabetes-susceptible BTBR leptin ob/ob mouse strains. This cross, which segregates for genotype and physiological traits, was previously used to identify several diabetes-related QTL. Our current investigation includes microarray analysis of over 40,000 probe sets, plus quantitative mass spectrometry-based measurements of sixty-seven intermediary metabolites in three different classes (amino acids, organic acids, and acyl-carnitines). We show that liver metabolites map to distinct genetic regions, thereby indicating that tissue metabolites are heritable. We also demonstrate that genomic analysis can be integrated with liver mRNA expression and metabolite profiling data to construct causal networks for control of specific metabolic processes in liver. As a proof of principle of the practical significance of this integrative approach, we illustrate the construction of a specific causal network that links gene expression and metabolic changes in the context of glutamate metabolism, and demonstrate its validity by showing that genes in the network respond to changes in glutamine and glutamate availability. Thus, the methods described here have the potential to reveal regulatory networks that contribute to chronic, complex, and highly prevalent diseases and conditions such as obesity and diabetes.
Image-guided endoscopic surgery for spontaneous supratentorial intracerebral hematoma (2016)

OBJECTIVE Endoscopic removal of intracerebral hematomas is becoming increasingly common, but there is no standard technique. The authors explored the use of a simple image-guided endoscopic method for removal of spontaneous supratentorial hematomas. METHODS Virtual reality technology based on a hospital picture archiving and communications systems (PACS) was used in 3D hematoma visualization and surgical planning. Augmented reality based on an Android smartphone app, Sina neurosurgical assist, allowed a projection of the hematoma to be seen on the patient's scalp to facilitate selection of the best trajectory to the center of the hematoma. A obturator and transparent sheath were used to establish a working channel, and an endoscope and a metal suction apparatus were used to remove the hematoma. RESULTS A total of 25 patients were included in the study, including 18 with putamen hemorrhages and 7 with lobar cerebral hemorrhages. Virtual reality combined with augmented reality helped in achieving the desired position with the obturator and sheath. The median time from the initial surgical incision to completion of closure was 50 minutes (range 40-70 minutes). The actual endoscopic operating time was 30 (range 15-50) minutes. The median blood loss was 80 (range 40-150) ml. No patient experienced postoperative rebleeding. The average hematoma evacuation rate was 97%. The mean (± SD) preoperative Glasgow Coma Scale (GCS) score was 6.7 ± 3.2; 1 week after hematoma evacuation the mean GCS score had improved to 11.9 ± 3.1 (p < 0.01). CONCLUSIONS Virtual reality using hospital PACS and augmented reality with a smartphone app helped precisely localize hematomas and plan the appropriate endoscopic approach. A transparent sheath helped establish a surgical channel, and an endoscope enabled observation of the hematoma's location to achieve satisfactory hematoma removal.
Nickel–Silicide Colloid Prepared under Mild Conditions as a Versatile Ni Precursor for More Efficient CO<sub>2</sub> Reforming of CH<sub>4</sub> Catalysts (2012)

Preparing highly active and stable non-noble-metal-based dry reforming catalysts remains a challenge today. In this context, supported nickel nanoparticles with sizes of 1.3 ± 0.2 and 2.1 ± 0.2 nm were synthesized on silica and ceria, respectively, via a two-step colloidal approach. First, 2-nm nickel-silicide colloids were synthesized from Ni(COD)(2) and octylsilane at low temperature; they were subsequently dispersed onto supports prior to reduction under H(2). The resulting catalysts display high activity in dry reforming compared to their analogues prepared using conventional approaches, ceria providing greatly improved catalyst stability.
Reliable systems: Design and tests (1981)

A repetitive cycle of modeling, testing, and redesign through final production specifications is crucial to eliminating a system's weak links.
Acetone and Isoprene Concentrations in Exhaled Breath in Healthy Subjects (2008)

We measured the concentrations of acetone and isoprene in the exhaled breath from students to evaluate their lifestyles for the annual medical checkup at our university. 451 students were examined for both gases simultaneously by a gas analysis device, Biogas Acetone Analyzer (BAS-2000). The average concentrations of acetone and isoprene in the breath were 0.53±0.45 ppm and 0.065±0.058 ppm, respectively, and the frequency of the abnormal high levels by judging the cut-off values of 1.5 and 0.20 ppm were 3.5% and 2.7% of them, respectively. Acetone concentration in the breath was higher in students having no breakfast in the day of the medical checkup than those having breakfast. Furthermore, acetone concentration was significantly correlated inversely with body fat percentage in students who took the medical checkup in the morning and significantly higher in students with body mass index (BMI) under 25 than obese students with BMI over 25. On the other hand, isoprene concentration was higher in male students than female students, and also higher in smokers than nonsmokers. However, isoprene level was not affected by ingestion of breakfast in the day. Acetone and isoprene concentrations were correlated positively with each other, although the relationship was not affected by having breakfast. The results suggest that the measurement of acetone and isoprene concentrations in the breath is useful for evaluating lifestyles such as lack of breakfast, smoking and obesity in students.
Computer-aided organic synthesis (2005)

It is tempting for those in the field of organic synthesis to liken the process of retrosynthesis to a game of chess. That the world chess champion was recently defeated by a computer leads us to think that perhaps new and powerful computing methods could be applied to synthetic problems. Here the analogy between synthesis and chess is outlined. Achievements in the 35-year history of computer-aided synthetic design are described, followed by some more recent developments.
Optical and structural studies in InGaN quantum well structure laser diodes (2001)

An InGaN multiple-quantum-well laser diode wafer that lased at around 400 nm was shown to have the InN mole fraction, x, of only 6% in the wells. Nanometer-probe compositional analysis showed that the fluctuation of x was as small as 1% or less, which is the resolution limit. However, the wells exhibited a Stokes-like shift (SS) of 49 meV at 300 K, which was approximately 65% of the luminescence linewidth, and effective localization depth, E0, was estimated to be 35 meV at 300 K. Since the effective electric field due to polarization in the wells was estimated to be as small as 300 kV/cm, SS was considered to originate from effective band-gap inhomogeneity. Because the well thickness fluctuation was insufficient to reproduce SS or E0 and bulk cubic In0.02Ga0.98N that does not suffer any polarization field or thickness fluctuation effect exhibited a SS of 140 meV at 77 K, the exciton localization is considered to be an intrinsic phenomenon in InGaN, which is due to the large band-gap bowing and In clustering in InGaN material. The spontaneous emission from the InGaN wells was thus assigned as being due to the recombination of excitons localized at the exponential tail-type potential minima in the density of states. The upper bound of the lateral localization size has been estimated to be 50 nm. Such shallow and low density localized states are leveled by injecting high density carriers under the lasing conditions.
Organometallic anticancer complexes of lapachol: metal centre-dependent formation of reactive oxygen species and correlation with cytotoxicity (2013)

Organometallic Ru(II), Os(II) and Rh(III) complexes of lapachol induce apoptosis in human tumour cell lines in the low μM range by a mode of action involving oxidative stress, especially in the case of the ruthenium compound.
Removal of stimulus-induced artifacts in functional spinal cord imaging (2013)

This paper develops a novel method to reduce the influence of stimulus-induced artifacts in functional spinal cord imaging. The developed method employes a two-step procedure. The first step acquires artifact data, which contain artifacts but do not contain spinal cord evoked magnetic field (SCEF). The second step applies a method called common-mode subspace projection (CSP). The effectiveness of the developed method is validated using SCEF data measured from a healthy volunteer.
Neuronal Avalanches Are Diverse and Precise Activity Patterns That Are Stable for Many Hours in Cortical Slice Cultures (2004)

A major goal of neuroscience is to elucidate mechanisms of cortical information processing and storage. Previous work from our laboratory (Beggs and Plenz, 2003) revealed that propagation of local field potentials (LFPs) in cortical circuits could be described by the same equations that govern avalanches. Whereas modeling studies suggested that these "neuronal avalanches" were optimal for information transmission, it was not clear what role they could play in information storage. Work from numerous other laboratories has shown that cortical structures can generate reproducible spatiotemporal patterns of activity that could be used as a substrate for memory. Here, we show that although neuronal avalanches lasted only a few milliseconds, their spatiotemporal patterns were also stable and significantly repeatable even many hours later. To investigate these issues, we cultured coronal slices of rat cortex for 4 weeks on 60-channel microelectrode arrays and recorded spontaneous extracellular LFPs continuously for 10 hr. Using correlation-based clustering and a global contrast function, we found that each cortical culture spontaneously produced 4736 +/- 2769 (mean +/- SD) neuronal avalanches per hour that clustered into 30 +/- 14 statistically significant families of spatiotemporal patterns. In 10 hr of recording, over 98% of the mutual information shared by these avalanche patterns were retained. Additionally, jittering analysis revealed that the correlations between avalanches were temporally precise to within +/-4 msec. The long-term stability, diversity, and temporal precision of these avalanches indicate that they fulfill many of the requirements expected of a substrate for memory and suggest that they play a central role in both information transmission and storage within cortical networks.
A Formal Framework for Linguistic Annotation (revised version) (2000)

`Linguistic annotation' covers any descriptive or analytic notations applied to raw language data. The basic data may be in the form of time functions - audio, video and/or physiological recordings - or it may be textual. The added notations may include transcriptions of all sorts (from phonetic features to discourse structures), part-of-speech and sense tagging, syntactic analysis, `named entity' identification, co-reference annotation, and so on. While there are several ongoing efforts to provide formats and tools for such annotations and to publish annotated linguistic databases, the lack of widely accepted standards is becoming a critical problem. Proposed standards, to the extent they exist, have focused on file formats. This paper focuses instead on the logical structure of linguistic annotations. We survey a wide variety of existing annotation formats and demonstrate a common conceptual core, the annotation graph. This provides a formal framework for constructing, maintaining and searching linguistic annotations, while remaining consistent with many alternative data structures and file formats.
Recent progress in the direct synthesis of hierarchical zeolites: synthetic strategies and characterization methods (2017)

Hierarchically structured zeolites combine the merits of microporous zeolites and mesoporous materials to offer enhanced molecular diffusion and mass transfer without compromising the inherent catalytic activities and selectivity of zeolites.
Traumatic Brain Injury – Modeling Neuropsychiatric Symptoms in Rodents (2013)

Each year in the US, ∼1.5 million people sustain a traumatic brain injury (TBI). Victims of TBI can suffer from chronic post-TBI symptoms, such as sensory and motor deficits, cognitive impairments including problems with memory, learning, and attention, and neuropsychiatric symptoms such as depression, anxiety, irritability, aggression, and suicidal rumination. Although partially associated with the site and severity of injury, the biological mechanisms associated with many of these symptoms - and why some patients experience differing assortments of persistent maladies - are largely unknown. The use of animal models is a promising strategy for elucidation of the mechanisms of impairment and treatment, and learning, memory, sensory, and motor tests have widespread utility in rodent models of TBI and psychopharmacology. Comparatively, behavioral tests for the evaluation of neuropsychiatric symptomatology are rarely employed in animal models of TBI and, as determined in this review, the results have been inconsistent. Animal behavioral studies contribute to the understanding of the biological mechanisms by which TBI is associated with neurobehavioral symptoms and offer a powerful means for pre-clinical treatment validation. Therefore, further exploration of the utility of animal behavioral tests for the study of injury mechanisms and therapeutic strategies for the alleviation of emotional symptoms are relevant and essential.
On-chip photonic tweezers for photonics, microfluidics, and biology (2017)

Near-field optical forces arise from evanescent electromagnetic fields and can be advantageously used for on-chip optical trapping. In this work, we investigate how evanescent fields at the surface of photonic cavities can efficiently trap micro-objects such as polystyrene particles and bacteria. We study first the influence of trapped particle’s size on the trapping potential and introduce an original optofluidic near-field optical microscopy technique. Then we analyze the rotational motion of trapped clusters of microparticles and investigate their possible use as microfluidic micro-tools such as integrated micro-flow vane. Eventually, we demonstrate efficient on-chip optical trapping of various kinds of bacteria.