gebhart/patrepeval huggingface dataset:
Engineering Embryonic Stem-Cell Aggregation Allows an Enhanced Osteogenic Differentiation In Vitro (2009)

Pluripotent embryonic stem (ES) cells hold great promise for the field of tissue engineering, with numerous studies investigating differentiation into various cell types including cardiomyocytes, chondrocytes, and osteoblasts. Previous studies have detailed osteogenic differentiation via dissociated embryoid body (EB) culture in osteoinductive media comprising of ascorbic acid, beta-glycerophosphate, and dexamethasone. It is hoped that these osteogenic cultures will have clinical application in bone tissue repair and regeneration and pharmacological testing. However, differentiation remains highly inefficient and generates heterogeneous populations. We have previously reported an engineered three-dimensional culture system for controlled ES cell-ES cell interaction via the avidin-biotin binding complex. Here we investigate the effect of such engineering on ES cell differentiation. Engineered EBs exhibit enhanced osteogenic differentiation assessed by cadherin-11, Runx2, and osteopontin expression, alkaline phosphatase activity, and bone nodule formation. Results show that cultures produced from intact EBs aggregated for 3 days generated the greatest levels of osteogenic differentiation when cultured in osteoinductive media. However, when cultured in control media, only engineered samples appeared to exhibit bone nodule formation. In addition, polymerase chain reaction analysis revealed a decrease in endoderm and ectoderm expression within engineered samples. This suggests that engineered ES cell aggregation has increased mesoderm homogeneity, contributing to enhanced osteogenic differentiation.
Water Quality Sensor Placement in Water Networks with Budget Constraints (2005)

In recent years, several integer programming models have been proposed to place sensors in municipal water networks in order to detect intentional or accidental contamination. Although these initial models assumed that it is equally costly to place a sensor at any place in the network, there clearly are practical cost constraints that would impact a sensor placement decision. Such constraints include not only labor costs but also the general accessibility of a sensor placement location. In this paper, we extend our integer program to explicitly model the cost of sensor placement. We partition network locations into groups of varying placement cost, and we consider the public health impacts of contamination events under varying budget constraints. Thus our models permit cost/benefit analyses for differing sensor placement designs. As a control for our optimization experiments, we compare the set of sensor locations selected by the optimimzation models to a set of manually-selected sensor locations.
System analysis of metabolism and the transcriptome in Arabidopsis thaliana roots reveals differential co‐regulation upon iron, sulfur and potassium deficiency (2016)

Deprivation of mineral nutrients causes significant retardation of plant growth. This retardation is associated with nutrient-specific and general stress-induced transcriptional responses. In this study, we adjusted the external supply of iron, potassium and sulfur to cause the same retardation of shoot growth. Nevertheless, limitation by individual nutrients resulted in specific morphological adaptations and distinct shifts within the root metabolite fingerprint. The metabolic shifts affected key metabolites of primary metabolism and the stress-related phytohormones, jasmonic, salicylic and abscisic acid. These phytohormone signatures contributed to specific nutrient deficiency-induced transcriptional regulation. Limitation by the micronutrient iron caused the strongest regulation and affected 18% of the root transcriptome. Only 130 genes were regulated by all nutrients. Specific co-regulation between the iron and sulfur metabolic routes upon iron or sulfur deficiency was observed. Interestingly, iron deficiency caused regulation of a different set of genes of the sulfur assimilation pathway compared with sulfur deficiency itself, which demonstrates the presence of specific signal-transduction systems for the cross-regulation of the pathways. Combined iron and sulfur starvation experiments demonstrated that a requirement for a specific nutrient can overrule this cross-regulation. The comparative metabolomics and transcriptomics approach used dissected general stress from nutrient-specific regulation in roots of Arabidopsis.
A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response (2022)

Listeria monocytogenes strain 10403S harbors two phage elements in its chromosome; one produces infective virions and the other tailocins. It was previously demonstrated that induction of the two elements is coordinated, as they are regulated by the same anti-repressor. In this study, we identified AriS as another phage regulator that controls the two elements, bearing the capacity to inhibit their lytic induction under SOS conditions. AriS is a two-domain protein that possesses two distinct activities, one regulating the genes of its encoding phage and the other downregulating the bacterial SOS response. While the first activity associates with the AriS N-terminal AntA/AntB domain, the second associates with its C-terminal ANT/KilAC domain. The ANT/KilAC domain is conserved in many AriS-like proteins of listerial and non-listerial prophages, suggesting that temperate phages acquired such dual-function regulators to align their response with the other phage elements that cohabit the genome.
Identification of Modified Atropaldehyde Mercapturic Acids in Rat and Human Urine after Felbamate Administration (1997)

3-Carbamoyl-2-phenylpropionaldehyde has recently been proposed [Thompson et al. (1996) Chem. Res. Toxicol. 9, 1225-1229] as a potential reactive metabolite of the anti-epileptic drug felbamate. This aldehyde was found to undergo rapid elimination to generate 2-phenylpropenal and reversible cyclization to generate 4-hydroxy-5-phenyltetrahydro-1,3-oxazin-2-one at physiological pH. 2-Phenylpropenal, an alpha,beta-unsaturated aldehyde commonly termed atropaldehyde, is a potent electrophile and undergoes rapid conjugation with glutathione. We sought to demonstrate the formation of atropaldehyde in vivo through the identification of mercapturic acids in rat and human urine after felbamate administration. In this paper, we describe the identification of both the reduced (N-acetyl-S-(2-phenylpropan-3-ol)-L-cysteine) and oxidized (N-acetyl-S-(2-phenyl-3-propanoic acid)-L-cysteine) mercapturic acids of atropaldehyde in rat and human urine. The reduced species was the more abundant in human (approximately 2:1) and rat (approximately 6:1) urine. These findings establish the possibility that atropaldehyde is formed from felbamate in vivo, undergoes glutathione conjugation, and is ultimately excreted in urine in the form of mercapturic acids. Thus, the proposed pathway of felbamate biotransformation, if confirmed in patients, could contribute to our understanding of the toxicities observed during felbamate treatment.
Key directions in parallelism and distribution in database system (panel session) (1990)

No abstract available.
Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat (2020)

Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
Physiological data including evaluation of immuno-response in relation to anabolic effects on veal calves. (1976)

In a series of experiments with a total of 1480 veal calves, different aspects of treating calves with anabolic steroids were examined. The anabolics used were 17beta-estradiol (E), trenbolone acetate (T), progesterone (P), testosterone (Te), C+T, E+P, E+Te and zeranole (Z). The N-retention was estimated by examining the urea: creatinine ratio in single urine specimens during the course of two feeding trials. Increased gain due to the treatment with E (20 mg implanted/calf) + P (200 mg) and Te (200 mg), respectively, E + T (140 mg) or Z (36 mg) was during the whole experimental period. The extra gain, due to anabolics seems to contain even more protein. This conclusion may be supported by the crude protein content of meat samples. The antibody production of a total of 311 male and female calves was investigated after the application of the following steroids: E (20 mg), T (200 mg), T (200 mg), E + T, P (200 mg), Te (200 mg), E + P, E + Te, and Z. Eleven days after the implantation of the steroids the animals were immunized with alumprecipitated human serumalbumin. Antibody-titres were determined by the Antigen-Binding-Capacity Test on day 14 following immunization. In nearly all groups the antibody-titres of female calves exceeded those of male calves on the average by 75%. The immune response of all experimental groups did not differ significantly from that of the corresponding control groups. However, the results indicate that both E + T and its single components E and T exert an immunodepressive effect in male calves. While the humoral antibody formation in the calf appears not to be influenced by anabolic steroids, it cannot be decided presently whether these substances effect cell-mediated immune reactions and/or unspecific mechanisms of resistance. When estradiol (20, 200, and 500 mg) and trenbolone acetate (140, 1400, 3500 mg) alone and in combination were implanted in female calves, blood glucose, GOT, GPT, alkaline phosphatase, LDH, cholesterine and bilirubine; Hb, PVC, quick value; urine density and pH were not affected by treatment. Some criteria of the mineral metabolism (Ca- and P-levels in serum and bone) was not altered by treatment. Trenbolone (1 400 and 3 500 mg), especially with estradiol, caused a decrease of the serum Mg-level and of the Mg-deposition in the bone. It is discussed that Trenbolone affects the dig-metabolism of calves. Some morphological findings are worth mentioning. The weight of uterus was not affected by the different doses of E or T, but a combination E + T led to a surprising weight increase. The proliferation of uterine glandular cells was responsible for the increased uterine size. The lumen of uterus was partially filled with a watery liquid. The reduction of the ovarian weight was accompanied by a diminution of follicular size for all treated calves, most evident for E (200, 500 mg) + T (1400, 3500 mg). A decrease in the number of follicles was also found for these two groups. T (3500 mg) caused an abnormal size of the clitoris and led to a reduction of the size of thymus.
Cellular RNA homologous to the Abelson murine leukemia virus transforming gene: expression and relationship to the viral sequence. (1983)

To examine the expression of the cellular homolog of the Abelson murine leukemia virus transforming gene (the v-abl sequence), a DNA probe representing the v-abl sequence was prepared. The probe detected two cytoplasmic polyadenylic acid-containing c-abl RNAs of about 6.5 and 5.5 kilobases in a variety of rodent cells, and slightly larger RNAs were detected in human cells. These two RNA species were found in all normal tissues or cell lines examined, but at differing concentrations: liver cells had the least, fibroblastic cell lines had the most. By using a probe able to detect the cellular but not the viral gene, the two RNAs were shown to be present in Abelson murine leukemia virus-transformed cells at levels found either in their untransformed counterparts or in similar cell types transformed by other means. The target cells of the virus have a somewhat elevated level of the two RNAs although expression of the c-abl gene is not restricted to these cells. The v-abl sequence lacks 0.35 and 0.85 kilobases of the c-abl RNA on the 5' and 3' ends, respectively. Thus, the Abelson murine leukemia virus transforming gene is an internal fragment of the transcript of a normal cellular gene.
Reduktion von Epoxiden, α,β‐ungesättigten Aldehyden und vicinalen Diketonen mit „reaktivem Titanocen” (1988)

Die Desoxygenierung von Epoxiden 2 zu Alkenen 3 gelingt mit „reaktivem Titanocen”︁ stereoselektiv in hoher Ausbeute. Das Reagens wird aus 1 in situ erzeugt. Aus den beiden anderen Titelverbindungen sind Bis(allylalkohole) oder Bis(allyl)ether bzw. Acyloine, Ketone oder Vinylencarbonate zugänglich. magnified image
Structure and potential function of γ‐aminobutyrate type A receptor‐associated protein (2009)

The gamma-aminobutyrate type A receptor-associated protein (GABARAP) is a ubiquitin-like modifier, and is implicated in a variety of membrane trafficking and fusion events that are crucial to synaptic plasticity, autophagy and apoptosis. However, important aspects of GABARAP function and regulation remain poorly understood. We review the current state of knowledge about GABARAP, highlighting newly-identified GABARAP ligands, and discuss the possible physiological relevance of each ligand interaction.
Image-Guided Robotics for Standardized and Automated Biopsy and Ablation (2021)

Image-guided robotics for biopsy and ablation aims to minimize procedure times, reduce needle manipulations, radiation, and complications, and enable treatment of larger and more complex tumors, while facilitating standardization for more uniform and improved outcomes. Robotic navigation of needles enables standardized and uniform procedures which enhance reproducibility via real-time precision feedback, while avoiding radiation exposure to the operator. Robots can be integrated with computed tomography (CT), cone beam CT, magnetic resonance imaging, and ultrasound and through various techniques, including stereotaxy, table-mounted, floor-mounted, and patient-mounted robots. The history, challenges, solutions, and questions facing the field of interventional radiology (IR) and interventional oncology are reviewed, to enable responsible clinical adoption and value definition via ergonomics, workflows, business models, and outcome data. IR-integrated robotics is ready for broader adoption. The robots are coming!
Supplementary Figures 1 - 8 from The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies (2023)

&lt;p&gt;Figure S1. Genomic analysis of SWI/SNF alterations in human cancer. Figure S2. SMARCA4-deficient lung cancer cells depend on SMARCA2 expression for growth. Figure S3. In-situ cell extraction assay for PFI-3 treatment. Figure S4. SMARCA2/4 bromodomain inhibitor does not alter growth of lung cancer cells. Figure S5. Analysis of SMARCA4 target gene expression and promoter occupancy following prolonged treatment with PFI-3. Figure S6. Pharmacological PFI-3 inhibitor studies in leukemia cells. Figure S7. Pharmacological EZH2 inhibitor studies. Figure S8. Genome-wide microarray analysis of SMARCA2 knockdown in A549 cells reconstituted with SMARCA4 cDNAs. Table S1: Survey of genomic lesions in SWI/SNF across different cancer types. Table S2: Sequence information of shRNA's and siRNA's used in the study. Table S3. BROMOScan (DiscoveRx) profiling of PFI-3 (at 2uM) against 32 bromodomains. Table S4. Definition of gene sets (i.e. SMARCA2 knockdown signatures) from SMARCA4 rescue experiments in A549 cells. Table S5. Summary of GSEA normalized enrichment scores (NES) and false discovery rate (FDR) for rescue experiment using ATP-Dead, BRD-Mut and vector control and compared to WT.&lt;/p&gt;
Supplementary Table from GSK-3β Governs Inflammation-Induced NFATc2 Signaling Hubs to Promote Pancreatic Cancer Progression (2023)

&lt;p&gt;Tissue microarray analysis of NFATc2 and Stat3&lt;/p&gt;
Novel Genotyping and Quantitative Analysis of Neuraminidase Inhibitor Resistance-Associated Mutations in Influenza A Viruses by Single-Nucleotide Polymorphism Analysis (2011)

Neuraminidase (NA) inhibitors are among the first line of defense against influenza virus infection. With the increased worldwide use of the drugs, antiviral susceptibility surveillance is increasingly important for effective clinical management and for public health epidemiology. Effective monitoring requires effective resistance detection methods. We have developed and validated a novel genotyping method for rapid detection of established NA inhibitor resistance markers in influenza viruses by single nucleotide polymorphism (SNP) analysis. The multi- or monoplex SNP analysis based on single nucleotide extension assays was developed to detect NA mutations H275Y and I223R/V in pandemic H1N1 viruses, H275Y in seasonal H1N1 viruses, E119V and R292K in seasonal H3N2 viruses, and H275Y and N295S in H5N1 viruses. The SNP analysis demonstrated high sensitivity for low-content NA amplicons (0.1 to 1 ng/μl) and showed 100% accordant results against a panel of defined clinical isolates. The monoplex assays for the H275Y NA mutation allowed precise and accurate quantification of the proportions of wild-type and mutant genotypes in virus mixtures (5% to 10% discrimination), with results comparable to those of pyrosequencing. The SNP analysis revealed the lower growth fitness of an H275Y mutant compared to the wild-type pandemic H1N1 virus by quantitatively genotyping progeny viruses grown in normal human bronchial epithelial cells. This novel method offers high-throughput screening capacity, relatively low costs, and the wide availability of the necessary equipment, and thus it could provide a much-needed approach for genotypic screening of NA inhibitor resistance in influenza viruses.
Demosaicing on the TriMedia 3270 (2007)

electronic version (7 pp.)
Spectroscopic evidence of cerebral axonopathy in patients with “pure” adrenomyeloneuropathy (2005)

(1)H-MR spectroscopic imaging is able to detect biochemical abnormalities suggestive of axonal damage even in the brains of patients with pure adrenomyeloneuropathy. The axonopathy is most prominent in internal capsule and parieto-occipital white matter and may contribute to clinical disability.
ChemInform Abstract: First Synthesis of 7‐Amido‐[1,2,4]triazolo[1,5‐a]pyrimidines Using Halogen—Metal Exchange (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.
The Orthopedic Examination (2020)

This chapter details the small animal orthopedic examination including history and signalment, visual examination, and palpation (subjective gait analysis is discussed in Chapter 1). A video of the entire examination and a step-by-step outline is provided.
A SARS-CoV-2 spike binding DNA aptamer that inhibits pseudovirus infection in vitro by an RBD independent mechanism (2020)

Abstract The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS-CoV-2 (CoV2-S) binds to the human angiotensin converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2-S. The aptamer does not bind to the RBD of CoV2-S and does not block the interaction of CoV2-S with ACE2. Notwithstanding, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS-CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.
Synthesis and Activity of a New Series of Antileishmanial Agents (2017)

We have determined that tetrahydroindazoles such as <b>1</b> show potent activity against <i>Leishmania donovani</i>, the causative agent of leishmaniasis. While the Hsp90 activity and anticancer properties of <b>1</b> have previously been explored, we present here our efforts to optimize their activity against <i>L. donovani</i> via the synthesis of novel analogues designed to probe the hydrophobic pocket of the protozoan Hsp90 orthologue, specifically through the auspices of functionalization of an amine embedded into the scaffold.
Predicting types of failures in wireless sensor networks using an adaptive neuro-fuzzy inference system (2016)

In this paper, Adaptive Neuro-Fuzzy Interference System (ANFIS) technique is used to develop models to predict two conditions commonly found in a Wireless Sensor Network's deployment; these conditions are failure due to (i) poorly deployed environment and (ii) human movements. ANFIS models are trained using parameters obtained from actual ZigBee PRO nodes' Neighbour Table experimented under the influence of associated network challenges. These parameters are Mean RSSI, Standard Deviation RSSI, Average Coefficient of Variation RSSI and Neighbour Table Connectivity. The individual and combined effects of parameters are investigated in-depth. Results showed the mean RSSI is a critical parameter and the combination of mean RSSI, ACV RSSI and NTC produced the best prediction results (~92%) for all ANFIS models.
Construction of a Pseudomonas hybrid strain that mineralizes 2,4,6-trinitrotoluene (1993)

A bacterium, Pseudomonas sp. strain C1S1, able to grow on 2,4,6-trinitrotoluene (TNT), 2,4- and 2,6-dinitrotoluene, and 2-nitrotoluene as N sources, was isolated. The bacterium grew at 30 degrees C with fructose as a C source and accumulated nitrite. Through batch culture enrichment, we isolated a derivative strain, called Pseudomonas sp. clone A, which grew faster on TNT and did not accumulate nitrite in the culture medium. Use of TNT by these two strains as an N source involved the successive removal of nitro groups to yield 2,4- and 2,6-dinitrotoluene, 2-nitrotoluene, and toluene. Transfer of the Pseudomonas putida TOL plasmid pWW0-Km to Pseudomonas sp. clone A allowed the transconjugant bacteria to grow on TNT as the sole C and N source. All bacteria in this study, in addition to removing nitro groups from TNT, reduced nitro groups on the aromatic ring via hydroxylamine to amino derivatives. Azoxy dimers probably resulting from the condensation of partially reduced TNT derivatives were also found.