gebhart/patrepeval huggingface dataset:
Viral Clades (2011)

Abstract Despite the rapid transglobal spread of HIV-1 infection, it has emerged as distinct subtypes or clades in different geographical regions. This sequence diversity seems to have profound effects in the spread of the virus, its ability to infect various cells types, the efficiency of viral replication, the propensity to develop drug resistance and their ability to cause neurocognitive disorders. While clade B virus is the still the best studied, it is becoming evident that clade D infected individuals have higher rates of neurocognitive disorders while the converse may be true for clade C infected individuals. This chapter reviews the evidence and the molecular basis for these clade differences.
Functional analysis of the evolutionarily conserved proline 53 residue in <i>Proteus mirabilis</i> glutathione transferase B1‐1 (1999)

The role of the evolutionarily conserved residue Pro‐53 in Proteus mirabilis glutathione transferase B1‐1 has been examined by replacing it with a serine residue using site‐directed mutagenesis. The effect of the replacement on the activity, thermal stability and antibiotic binding capacity of the enzyme was examined. The results presented support the view that Pro‐53 participates in the maintenance of the proper conformation of the enzyme fold rather than playing a direct role in the catalytic reaction. Furthermore, this residue appears to be an important determinant of the antibiotic binding to the enzyme. Experiments with wild type and mutated enzymes provide evidence that glutathione transferases may play an important role in antibiotic resistance exhibited by bacteria.
Cover Image, Volume 28, Issue 10 (2017)

On the cover: The cover image, by Gordon Ho MD et al., is based on the Original Article Rotors exhibit greater surface ECG variation during ventricular fibrillation than focal sources due to wavebreak, secondary rotors, and meander, DOI: 10.1111/jce.13283.
Bisphenol A Diglycidyl Ether Induces Adipogenic Differentiation of Multipotent Stromal Stem Cells through a Peroxisome Proliferator–Activated Receptor Gamma-Independent Mechanism (2012)

BADGE can induce adipogenic differentiation in both MSCs and in preadipocytes at low nanomolar concentrations comparable to those that have been observed in limited human biomonitoring. BADGE probably acts through a mechanism that is downstream of, or parallel to, PPARγ.
Changes in bacterial composition and enzymatic activity in ileostomy and ileal reservoir during intermittent occlusion: a study using dogs (1992)

Bacterial flora, activities of 10 potential mucus- and dietary polysaccharide-degrading enzymes, blood group antigenicity of the intestinal glycoproteins, and proteolytic activity in the output from experimentally colectomized dogs with conventional ileostomies and dogs with valveless ileal reservoirs (pouches) were determined. The ileostomies of dogs with conventional surgery (group II) and with pouches (group III) were occluded intermittently during a 6-week period. The duration of occlusion was progressively increased. Group I, five dogs with conventional ileostomies, served as a control group. After occlusion of the ileal pouch for 7 h, total numbers of bacteria increased threefold, glycosidase activity increased fivefold, and blood group antigenicity of the intestinal glycoproteins, which was high in the output from the nonoccluded pouch, was no longer detectable. Proteolytic activity was not influenced by occlusion of the pouch. Significantly lower numbers of bacteria, only minor glycosidase activity, high blood group antigenicities of the intestinal glycoproteins, and higher proteolytic activity were found in ileostomy effluents from groups I and II. Histopathological examination showed chronic inflammation and changes in crypt-villus ratio in all dogs with ileal reservoirs; the ileal mucosa from the dogs with conventional ileostomies did not show any abnormalities. Consequences of the flora-related enzyme activities for the ileal mucosa are discussed.
Compressed sensing based intensity non-uniformity correction (2011)

We present a compressed sensing based approach to remove gain field from magnetic resonance (MR) images of the human brain. During image acquisition, the inhomogeneity present in the radio-frequency (RF) coil appears as shading artifact in the intensity image. The inhomogeneity poses problem in any automatic algorithm that uses intensity as a feature. It has been shown that at low field strength, the shading can be assumed to be a smooth field that is composed of low frequency components. Thus most inhomogeneity correction algorithms assume some kind of explicit smoothness criteria on the field. This sometimes limits the performance of the algorithms if the actual inhomogeneity is not smooth, which is the case at higher field strength. We describe a model-free, non-parametric patch-based approach that uses compressed sensing for the correction. We show that these features enable our algorithm to perform comparably with a current state of the art method N3 on images acquired at low field, while outperforming N3 when the image has non-smooth inhomogeneity, such as 7T images.
Fitting Age Related Reference Intervals to Ocular Axial Length in Children Using a Four-Parameter Curve Family (1998)

There exist a number of methods to determine age dependent reference intervals. Some of those are based on standard parametric classes of distributions like normal or lognormal and standard parametric classes of age functions like linear or polynomial of some order. Others are based on more flexible distribution classes like Box-Cox transformation of the normal distribution, which allows for skewness. There exist also purely nonparametric methods, where the bounds of the reference intervals are only assumed to be nondecreasing and they are directly estimated by a suitable error function without any distributional assumption. In this paper we propose a flexible four-parameter age function class for the reference interval bounds and a method to estimate those. The four parameters in the class have concrete meanings; starting value at age 0, asymptotic value at increasing age, time scale and shape. The function class satisfies some desirable properties, which are discussed. The estimation of the parameters in the model uses the same type of error function as in the purely nonparametric methods. With our method we also get an estimate of the distributional position of an observation for a new individual given its age. The method is illustrated by an application example, where a 90% reference interval for ocular axis length of children up to age 18 years are determined.
The sorbicillinoid family of natural products: Isolation, biosynthesis, and synthetic studies (2011)

The sorbicillinoids are a family of hexaketide metabolites that have been isolated from a variety of fungal sources, collected from both marine and terrestrial sources. Since 1948, the family has grown in size to include over 50 members, many of which have complex, highly oxygenated, bicyclic and tricyclic frameworks. In conjunction with their biological activity, the structural complexity of these structures has inspired several synthetic campaigns and has also led to controversy surrounding the biosynthetic pathway responsible for the natural production of these compounds. Through this review, we aim to give a historical perspective to each of these areas and hope to inspire new avenues of research for addressing the knowledge gaps that still exist.
Repeated Low-Dose Mucosal Simian Immunodeficiency Virus SIVmac239 Challenge Results in the Same Viral and Immunological Kinetics as High-Dose Challenge: a Model for the Evaluation of Vaccine Efficacy in Nonhuman Primates (2004)

Simian immunodeficiency virus (SIV) challenge of rhesus macaques provides a relevant model for the assessment of human immunodeficiency virus (HIV) vaccine strategies. To ensure that all macaques become infected, the vaccinees and controls are exposed to large doses of pathogenic SIV. These nonphysiological high-dose challenges may adversely affect vaccine evaluation by overwhelming potentially efficacious vaccine responses. To determine whether a more physiologically relevant low-dose challenge can initiate infection and cause disease in Indian rhesus macaques, we used a repeated low-dose challenge strategy designed to reduce the viral inoculum to more physiologically relevant doses. In an attempt to more closely mimic challenge with HIV, we administered repeated mucosal challenges with 30, 300, and 3,000 50% tissue culture infective doses (TCID(50)) of pathogenic SIVmac239 to six animals in three groups. Infection was assessed by sensitive quantitative reverse transcription-PCR and was achieved following a mean of 8, 5.5, and 1 challenge(s) in the 30, 300, and 3,000 TCID(50) groups, respectively. Mortality, humoral immune responses, and peak plasma viral kinetics were similar in five of six animals, regardless of challenge dose. Interestingly, macaques challenged with lower doses of SIVmac239 developed broad T-cell immune responses as assessed by ELISPOT assay. This low-dose repeated challenge may be a valuable tool in the evaluation of potential vaccine regimes and offers a more physiologically relevant regimen for pathogenic SIVmac239 challenge experiments.
Ultra high spatial and temporal resolution breast imaging at 7T (2012)

There is a need to obtain higher specificity in the detection of breast lesions using MRI. To address this need, Dynamic Contrast-Enhanced (DCE) MRI has been combined with other structural and functional MRI techniques. Unfortunately, owing to time constraints structural images at ultra-high spatial resolution can generally not be obtained during contrast uptake, whereas the relatively low spatial resolution of functional imaging (e.g. diffusion and perfusion) limits the detection of small lesions. To be able to increase spatial as well as temporal resolution simultaneously, the sensitivity of MR detection needs to increase as well as the ability to effectively accelerate the acquisition. The required gain in signal-to-noise ratio (SNR) can be obtained at 7T, whereas acceleration can be obtained with high-density receiver coil arrays. In this case, morphological imaging can be merged with DCE-MRI, and other functional techniques can be obtained at higher spatial resolution, and with less distortion [e.g. Diffusion Weighted Imaging (DWI)]. To test the feasibility of this concept, we developed a unilateral breast coil for 7T. It comprises a volume optimized dual-channel transmit coil combined with a 30-channel receive array coil. The high density of small coil elements enabled efficient acceleration in any direction to acquire ultra high spatial resolution MRI of close to 0.6 mm isotropic detail within a temporal resolution of 69 s, high spatial resolution MRI of 1.5 mm isotropic within an ultra high temporal resolution of 6.7 s and low distortion DWI at 7T, all validated in phantoms, healthy volunteers and a patient with a lesion in the right breast classified as Breast Imaging Reporting and Data System (BI-RADS) IV.
ROSMETER: A Bioinformatic Tool for the Identification of Transcriptomic Imprints Related to Reactive Oxygen Species Type and Origin Provides New Insights into Stress Responses (2013)

The chemical identity of the reactive oxygen species (ROS) and its subcellular origin will leave a specific imprint on the transcriptome response. In order to facilitate the appreciation of ROS signaling, we developed a tool that is tuned to qualify this imprint. Transcriptome data from experiments in Arabidopsis (Arabidopsis thaliana) for which the ROS type and organelle origin are known were compiled into indices and made accessible by a Web-based interface called ROSMETER. The ROSMETER algorithm uses a vector-based algorithm to portray the ROS signature for a given transcriptome. The ROSMETER platform was applied to identify the ROS signatures profiles in transcriptomes of senescing plants and of those exposed to abiotic and biotic stresses. An unexpected highly significant ROS transcriptome signature of mitochondrial stress was detected during the early presymptomatic stages of leaf senescence, which was accompanied by the specific oxidation of mitochondria-targeted redox-sensitive green fluorescent protein probe. The ROSMETER analysis of diverse stresses revealed both commonalties and prominent differences between various abiotic stress conditions, such as salt, cold, ultraviolet light, drought, heat, and pathogens. Interestingly, early responses to the various abiotic stresses clustered together, independent of later responses, and exhibited negative correlations to several ROS indices. In general, the ROS transcriptome signature of abiotic stresses showed limited correlation to a few indices, while biotic stresses showed broad correlation with multiple indices. The ROSMETER platform can assist in formulating hypotheses to delineate the role of ROS in plant acclimation to environmental stress conditions and to elucidate the molecular mechanisms of the oxidative stress response in plants.
Osteoporosis: the role of calcium intake and supplementation (1988)

The role of calcium in age-related bone loss still is controversial. However, evidence is accumulating to support the hypothesis that an adequate calcium intake early in life, because of its relationship to peak bone mass, may be of greater importance than is the calcium intake in later life. Calcium intake would appear to be declining with age due to the changing food habits that are associated with social and technological change. This is explained partly by the increasing concern about obesity in Western society, with the trend for women to restrict their energy intake, rather than to increase their energy expenditure, to control weight. Thus, low energy intakes and the avoidance of dairy foods have contributed to the declining intakes of calcium and other minerals. Health educational programmes, which are designed to prevent osteoporosis and which identify women who are most at risk of the disease, should provide sensible nutritional advice on an adequate calcium intake and regular weight-bearing exercise among other life-style changes.
Sublocalization of an ataxia-telangiectasia gene distal to D11S384 by ancestral haplotyping in Costa Rican families. (1995)

In an effort to localize a gene for ataxia-telangiectasia (A-T), we have genotyped 27 affected Costa Rican families, with 13 markers, in the chromosome 11q22-23 region. Significant linkage disequilibrium was detected for 9/13 markers between D11S1816 and D11S1391. Recombination events observed in these pedigrees places A-T between D11S1819 and D11S1960. One ancestral haplotype is common to 24/54 affected chromosomes and roughly two-thirds of the families. Inferred (ancestral) recombination events involving this common haplotype in earlier generations suggest that A-T is distal to D11S384 and proximal to D11S1960. Several other common haplotypes were identified, consistent with multiple mutations in a single gene. When considered together with all other evidence, this study further sublocalizes the major A-T locus to approximately 200 kb, between markers S384 and S535.
Organic Nano-Floating-Gate Memory with Polymer:[6,6]-Phenyl-C<sub>61</sub> Butyric Acid Methyl Ester Composite Films (2010)

Here, we report on a pentacene-based, nonvolatile transistor memory device with poly(4-vinyl phenol) (PVP):[6,6]-phenyl-C 61 butyric acid methyl ester (PCBM) nano-composite films as the charge storage site. Incorporation of PCBM molecules into PVP dielectric materials as charge storage sites for electrons resulted in a reversible shift in the threshold voltage ( V Th ) and reliable memory characteristics. The characteristics of the pentacene memory device were as follows: a relatively high field-effect mobility (µ FET ) (0.2–0.3 cm 2 V -1 s -1 ) with a large memory window ( ca. 20 V), a high on/off ratio (∼10 4 ) during writing and erasing with application of an operating gate voltage of 60 V for a short duration time (∼1 ms), and a retention time of about 40 h.
Human Complement Factor H Is a Reductase for Large Soluble von Willebrand Factor Multimers—Brief Report (2013)

FH contributes to the reduction of large soluble vWF multimers.
Plasma Levels of Procalcitonin and Neopterin in Multiple Trauma Patients with or without Brain Injury (2003)

Clinical and experimental evidence suggests that traumatic brain injury (TBI) leads to a systemic immune response. To examine whether TBI causes a release of procalcitonin (PCT) or neopterin (NT) into the circulation, we compared plasmatic mediator levels among multiple injured patients with or without TBI. In total, 98 trauma patients (24 with TBI only, 39 with extracranial injuries excluding TBI, and 35 with combined injuries) and 35 healthy volunteers were studied. Blood was sampled at 15 predefined time points within 132 h after injury and analysed for NT and PCT. Multivariate statistical comparisons were adjusted for different severity of head, thorax, abdomen and extremity injuries, as quantified by the Abbreviated Injury Scale (AIS). PCT was normal 3 h after trauma, but 24 h after extracranial injuries a massive release (median 3 ng/mL) was observed. Significant positive associations between injury severity and posttraumatic PCT levels were found for abdominal and extremity, but not for cranial or thoracic injuries. Only modest changes of marginal statistical significance were detected for NT. The maximum increase per AIS point was 9% (95% confidence intervals [CI]: 3-16%). The effect of TBI on NT release was significant only at 108 h posttrauma with a 5% (95% CI: 1-10%) increase per AIS point. TBI induces a release of PCT and NT into the plasma, but this effect seems to be smaller for intra- than for extracranial injuries, probably due to more extensive surgery for abdominal and extremity injuries.
Target diagnostics for intense lithium ion hohlraum experiments on Particle Beam Fusion Accelerator II (1995)

A review of the diagnostics used at Sandia National Laboratories to measure the parameters of intense lithium ion-beam hohlraum target experiments on Particle Beam Fusion Accelerator II will be presented. This diagnostic package contains an extensive suite of x-ray spectral and imaging diagnostics that enable measurements of target temperature and x-ray output. The x-ray diagnostics include time-integrated and time-resolved pinhole cameras, energy-resolved one-dimensional streaked imaging diagnostics, time-integrated and time-resolved grazing incidence spectrographs, a transmission grating spectrograph, an elliptical crystal spectrograph, a bolometer array, an 11- element x-ray diode array, and an 11-element PIN diode detector array. The incident Li beam symmetry and an estimate of incident Li beam power density can be measured from ion beam-induced characteristic x-ray line emission and neutron emission.
ChemInform Abstract: Alkynyl Halides in Ruthenium(II)‐Catalyzed [2 + 2] Cycloadditions of Bicyclic Alkenes. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Compatible cartridges for magnetic tapes (1960)

Magnetic tape may be offered in cartridge form at a price competitive with phonograph disks. Cartridges of different sizes are designed either for high quality or for maximum tape economy. All of these will operate on present-day machines, as well as on automatic designs. A cartridge changer allows records to be played in sequence. The erase feature offers interesting possibilities for sale of pure music separate from the sale of cartridges.
Effects of an oat bran concentrate on serum lipids in free-living men with mild to moderate hypercholesterolaemia. (1992)

An oat bran concentrate was prepared by removing non-fibre components by cold-water wet-milling, resulting in a 2- to 3-fold concentration of soluble fibre, with beta-D-glucan as its main component. The concentrate was baked in bread which was consumed for 8 weeks by free-living men with mild to moderate hypercholesterolaemia. The effects on serum lipids were assessed in a randomized, double-blind, placebo-controlled trial. Despite the large daily dose (11.2 g) of beta-glucan, the beta-glucan-enriched bread had only a small and statistically non-significant effect on serum lipid concentrations. Probable reasons for the weakness of the effect could be the poor solubility of beta-glucan in the preparation, its enzymatic hydrolysis after ingestion, and the consequently low viscosity in the intestine.
Motion interference detection in mobile robots (2012)

As mobile robots become better equipped to autonomously navigate in human-populated environments, they need to become able to recognize internal and external factors that may interfere with successful motion execution. Even when these robots are equipped with appropriate obstacle avoidance algorithms, collisions and other forms of motion interference might be inevitable: there may be obstacles in the environment that are invisible to the robot's sensors, or there may be people who could interfere with the robot's motion. We present a Hidden Markov Model-based model for detecting such events in mobile robots that do not include special sensors for specific motion interference. We identify the robot observable sensory data and model the states of the robot. Our algorithm is motivated and implemented on an omnidirectional mobile service robot equipped with a depth-camera. Our experiments show that our algorithm can detect over 90% of motion interference events while avoiding false positive detections.
Amino acid metabolism in acetic acid bacteria. V. Purification and characterization of L-leucine-.ALPHA.-ketoglutarate transaminase from Acetobacter suboxydans. (1976)

L-Leucine-α-ketoglutarate (α-KGA) transaminase from Acetobacter suboxydans was purified to the state of homogeneity by the criteria of ultracentrifugation and electrophoresis on a cellulose acetate membrane. The molecular weight was about 80, 000 and one mole of pyridoxal 5'-phosphate was bound per mole of enzyme as a coenzyme. The enzyme exhibited absorption maxima at 280, 337 and 414 nm. The branched-chain amino acids and αa-KGA were specific as amino donors and an acceptor. L-Leucine-α-KGA transaminase is suggested to correspond to the enzyme so-called Transaminase B.