gebhart/patrepeval huggingface dataset:
Robo1/Robo4: Differential expression of angiogenic markers in colorectal cancer (2006)

The family of roundabout (Robo) proteins is related to the transmembrane receptors and plays a major role in the process of axonal guidance in neurogenesis. It has recently been shown that Robo proteins are also associated with tumor angiogenesis with Slit2 acting as the corresponding ligand. The aim of this study was to validate the differential expression by means of microarray analysis and real-time PCR and to analyze the in situ expression of Robo1 and Robo4 in colorectal cancer. Quantitative analyses of Robo1, Robo4 and Slit2 mRNA expression measured by large scale gene expression studies (Affymetrix U133A) showed a significant up-regulation of Robo1 in tumor vs. normal tissue, whereas Robo4 and Slit2 showed no significant deregulation. For subsequent real-time PCR experiments, paired colorectal tissue samples from cancerous and corresponding non-cancerous tissues were obtained from 50 colorectal cancer patients who underwent surgical resection. Robo1 mRNA overexpression in cancerous tissue compared with normal counterparts was observed in 80% of the patients with a 4-fold expression in 45% and a 12-fold expression in 15%. For Robo4, an up-regulation was detected in >70% (36/50). For Slit2, no differential expression was observed. The overexpression of Robo1 and Robo4 in tumor vs. normal tissue was verified using real-time PCR. The histological analysis revealed an expression of Robo1 mainly in tumor cells, whereas Robo4 is located primarily in endothelial cells of tumor vessels. Therefore, the Robo proteins provide potential target structures for the anti-tumorigenic and anti-angiogenic therapy of colorectal carcinoma.
ChemInform Abstract: Nucleosides and Nucleotides. Part 95. Improved Synthesis of 1‐(2‐Azido‐ 2‐deoxy‐β‐D‐arabinofuranosyl)cytosine (Cytarazid) and ‐thymine. Inhibitory Spectrum of Cytarazid on the Growth of Various Human Tumor Cells in vitro. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Accuracy of Inferior Vena Cava Ultrasound for Predicting Dehydration in Children with Acute Diarrhea in Resource-Limited Settings (2016)

Point-of-care ultrasound of the aorta-to-IVC ratio was statistically associated with volume status, but was not accurate enough to be used as an independent screening tool for dehydration in children under five years presenting with acute diarrhea in a resource-limited setting.
Comparative Performance Analysis of CAC Reward Optimization Algorithms in Wireless Networks (2009)

In this paper, we perform a comparative analysis of a set of call admission control (CAC) algorithms designed for servicing multiple priority classes in wireless networks with quality of service (QoS) guarantees. We evaluate the performance of partitioning, threshold-based, spillover, and elastic-threshold CAC algorithms in terms of the maximum number of mobile users the system is able to support with QoS satisfaction while maximizing the "reward" obtainable from servicing multiple priority classes with distinct QoS requirements. We compare these algorithms thoroughly with test cases generated through a combination of user workload, mobility, location, and population. We verify analytical results via simulation validation using real mobility trace data to model user mobility. We also analyze the tradeoff between solution optimality vs. solution efficiency in designing CAC algorithms for reward optimization and QoS satisfaction when servicing multiple service classes with distinct QoS requirements in wireless networks.
The serum protein binding of pharmacologically active gallium(III) compounds assessed by hyphenated CE‐MS techniques (2009)

Transition metal-based drugs exhibit high affinity to the soft donors of human serum proteins, especially of the high-abundance protein HSA and of transferrin (Tf), whereas Ga(III) salts are known to bind to Tf and other iron-containing metalloproteins, thereby interfering with the iron metabolism. Herein, the utilization of CE-MS methods for studying the binding behavior of a therapeutic gallium nitrate formulation and the anticancer drug candidate Tris(8-oxyquinolinato)gallium(III) to Tf and HSA under simulated physiological conditions is described. Both the Ga(III) salt and the complex were found to bind to Tf exclusively in the presence of carbonate, however, at different kinetics and to a different extent. Fe(III) induces the release of the Ga ions due to the higher affinity constant and also prevents the Ga(III) species from accessing the iron-binding pockets of Tf. In contrast, only low affinity to HSA was observed and even when present at ca. 20-fold excess, the majority of the Ga was attached to Tf.
Natality of ruffed grouse <i>Bonasa umbellus</i> in central Wisconsin, USA (1996)

Radio‐marked female ruffed grouse Bonasa umbellus were monitored in central Wisconsin, USA, during 1983–1988 to estimate nesting rates (the percentage of hens that initiate a clutch), clutch size, nest success, and the prevalence and success of renests. All 23 radio‐marked females initiated a clutch, 22 completed a first clutch; the remaining hen was killed by a predator during laying. Mean clutch size of first nests was 11.0 ± 0.5 eggs (range = 7–13). Five of nine (56%) hens attempted to renest with a mean clutch size of 7.4 ± 1.3 eggs (range = 6–9). Mean nest success was 46%; 43% for yearlings and 60% for adults. First nests produced the large majority of eggs that hatched (86.1%) compared to renests (13.9%). Productivity was estimated at 5.8 chicks hatched for each hen alive on 20 April, the mean date of the first egg laid.
Physical and chemical modifications of collagen gels: Impact on diffusion (2007)

The extracellular matrix (ECM) represents a major barrier for delivery of therapeutic drugs, and the transport is determined by the ECM composition, structure, and distribution. Because of the high interstitial fluid pressure in tumors, diffusion becomes the main transport mechanism through ECM. The purpose of this work was to study the impact of the structure of the collagen network on diffusion, by studying to what extent the orientation and chemical modification of the collagen network influenced diffusion. Collagen gels with a concentration of 0.2-2.0% that is comparable with the amount of collagen in the tumor ECM were used as a model system for ECM. Collagen gels were aligned in a low-strength magnetic field and geometrical confinement, and chemically modified by adding decorin or hyaluronan. Diffusion of dextran 2-MDa molecules in the collagen gels was measured using fluorescence recovery after photobleaching. Alignment of the collagen fibers in our gels was found to have no impact on the diffusion coefficient. Adding decorin reduced the diameter of the collagen fibers, but no effect on diffusion was observed. Hyaluronan also reduced the fiber diameter, and high concentration of hyaluronan (2.5 mg/ml) increased the diffusion coefficient. The results indicate that the structure of the collagen network is not a major factor in determining the diffusion through the ECM. Rather, increasing the concentration of collagen was found to reduce the diffusion coefficient. Concentration of the collagen network is more important than the structure in determining the diffusion coefficient.
High resolution HLA matching associated with decreased mortality after unrelated bone marrow transplantation (1996)

As compared with related HLA-identical sibling donors, bone marrow transplantation (BMT) with phenotypically HLA ABDR-compatible unrelated donors is associated with increased mortality. This may be due to hidden HLA incompatibilities not detected by conventional typing. We have analyzed 44 unrelated patient-donor pairs who were matched for HLA-A, -B, and -DR by routine tissue typing. Our comprehensive HLA typing approach consisted of serology, cytotoxic T-cell precursor (CTLp) tests, T-cell cloning, oligotyping, and DNA sequencing. Using these techniques, we identified numerous HLA allele mismatches not detected by the previously applied routine typing. Twenty-four patient-donor pairs were highly matched and had a low CTLp frequency, whereas the remaining 20 pairs were allele-mismatched for HLA-A, -B, -C, -DR, -DQ antigens and/or had a positive result of the CTLp test. Patient and donor age, diagnosis, and treatment did not differ significantly between the matched and mismatched transplants. The probability for severe acute graft-versus-host disease grades III-IV was 21% in the matched and 47% in the mismatched patients (P = .0464). Transplant-related mortality was 21% and 57% (P = .0072) and actuarial patient survival rates at 3 years were 61% and 13% (P = .0005). We conclude that both HLA class I and class II allele mismatches between unrelated phenotypically ABDR-compatible patient-donor pairs are frequent and associated with increased incidence of posttransplant complications.
Autonomous Zebrafish Embryo Injection Using a Microrobotic System (2007)

As an important embodiment of biomanipulation, injection of foreign materials (e.g., DNA, RNAi, sperms, proteins, and drug compounds) into individual cells has significant implications in genetics, transgenics, assisted reproduction, and drug discovery. This paper presents a microrobotic system for fully automated zebrafish embryo injection, which overcomes the problems inherent in manual operation, such as human fatigue and large variations in success rates due to poor reproducibility. Based on computer vision and motion control, the microrobotic system performs injection at a speed of 15 zebrafish embryos (chorion unremoved) per minute, with a survival rate of 98% (350 embryos), a success rate of 99% (350 embryos), and a phenotypic rate of 98.5% (210 embryos). The sample preparation technique and microrobotic control method are applicable to other biological injection applications such as the injection of mouse oocytes/embryos and Drosophila embryos to enable high-throughput biological and pharmaceutical research.
Distinct EBV and CMV reactivation patterns following antibody-based immunosuppressive regimens in patients with severe aplastic anemia (2006)

The natural history of EBV and CMV reactivation and the potential for serious complications following antibody-based immunosuppressive treatment for bone marrow failure syndromes in the absence of transplantation is not known. We monitored blood for EBV and CMV reactivation by polymerase chain reaction (PCR) weekly in 78 consecutive patients (total of 99 immunosuppressive courses) with aplastic anemia. Four regimens were studied: (1) HC, horse ATG/cyclosporine; (2) HCS, horse ATG/CsA/sirolimus; (3) RC, rabbit ATG/CsA; and (4) CP, alemtuzumab. There were no cases of EBV or CMV disease, but EBV reactivation occurred in 82 (87%) of 94 and CMV reactivation in 19 (33%) of 57 seropositive patients after starting immunosuppression. The median peak EBV copies were higher in the RC group when compared with HC, HCS, and alemtuzumab (P < .001). The median duration of PCR positivity for EBV was higher in the RC group compared with HC, HCS, and alemtuzumab (P = .001). Subclinical reactivation of both EBV and CMV is common and nearly always self-limited in patients with bone marrow failure receiving immunosuppression; different regimens are associated with different intensity of immunosuppression as measured by viral load and lymphocyte count; and viral reactivation patterns differ according to immunosuppressive regimens.
Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition (2016)

Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or "slow" substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors.
Relation between the number of myelin lamellae and axon circumference in fibers of vagus and sciatic nerves of mice (1967)

Abstract Nerve fiber populations of the vagus and sciatic nerves of mice were classified according to the number of myelin lamellae present in the sheaths. This method for classifying fiber populations was superior to others used previously since it provided a more sensitive procedure for the analysis of individual fibers and better control over the technical factors involved in tissue processing. The relationship of the number of myelin lamellae in the sheath to axon circumference was found to be linear. In fresh tissue there was one myelin lamella for every 0.24 μ increase in axon circumference above da value of 2.32 μ (the mean circumference of an average‐sized nonmyelinated fiber). A formula was proposed which may be useful for understanding how axons control myelin development and interpreting developmental stages, as well as for evaluating pathologic conditions affecting the peripheral nervous system. The critical diameter above which fibers were found to be myelinated was about 0.8 μ for fixed nerve and 1.1 μ for fresh nerve. The ratio of axon diameter to fiber diameter ranged between 0.5 and 0.9 and was not related to fiber size.
179. A new synthesis of fluoro-ketones (1956)

A. Sykes, J. C. Tatlow and C. R. Thomas, J. Chem. Soc., 1956, 835 DOI: 10.1039/JR9560000835
Stereoretentive Suzuki−Miyaura Coupling of Haloallenes Enables Fully Stereocontrolled Access to (−)-Peridinin (2010)

Stimulated by the substantial challenge of synthesizing the complex and sensitive stereogenic allene-containing core of (-)-peridinin, the first stereocontrolled coupling of haloallenes with boronic acids has been achieved. This new method and the principles that emerged during its development stand to enable the more efficient and flexible preparation of a wide range of natural products, pharmaceuticals, and intermediates that possess a stereogenic allene motif. This new reaction was harnessed to achieve the first completely stereocontrolled total synthesis of (-)-peridinin. This synthesis was accomplished using only one reaction iteratively to assemble four fully functionalized building blocks with complete stereoretention at each initial halide or boron-bearing carbon. This synthesis elevates the capacity of the iterative cross-coupling strategy to an unprecedented benchmark. Moreover, the efficient and highly modular nature of this synthesis promises to enable systematic dissection of the heretofore enigmatic structure/function relationships that underlie the protein-like antilipoperoxidant activities of this remarkable small molecule natural product.
Selection of Cathode Materials for Electrochemical Degradation of Hexachlorobenzene in Simulated Contaminated Soil Rinsing Effluent (2011)

A lab-scaled experiment was conducted for selecting effective cathode materials used in degrading hexachlorobenzene(HCB)-containing solution using electro-chemical method.HCB-containing solution referred to simulated HCB contaminated soil rinsing effluent.With an anode made of RuO2 /Ti being used,cathode made of zinc(a web),stainless-steel(a plate),graphite and RuO2 /Ti were tested in electrochemical removal of HCB from the solution,respectively.The result showed that with respect to HCB removal,zinc ranked first followed by stainless steel,graphite and then RuO2/Ti;the products in de-chlorination of HCB on the cathodes made of above four materials were different according to the analysis by use of gas chromatography.
Assimilation of surface velocity data into a primitive equation coastal ocean model (2002)

A data assimilation system (DAS) of the wind‐driven, mesoscale shelf circulation off the Oregon coast is developed. The DAS assimilates low‐pass filtered surface velocity measurements, obtained from land‐based high‐frequency coastal radar arrays, into a primitive equation coastal ocean model using a sequential optimal interpolation scheme. Inhomogeneous and anisotropic estimates of the forecast error covariances required for the assimilation are assumed to be proportional to typical cross‐correlations between modeled variables. These correlations are estimated from an ensemble of model simulations for 18 different summers. Similarly, the observation error covariances are assumed to be proportional to the actual covariances of the observations. A time‐distributed averaging procedure (TDAP) that effectively low‐pass filters the model forecast for comparison with the observations and introduces the corrections to the model state gradually over time is used in order to overcome problems of data compatibility and initialization. The correlations between direct subsurface current measurements and subsurface currents obtained from model‐only and assimilation experiments for the summer of 1998 are 0.42 and 0.78, respectively, demonstrating the effectiveness of the DAS. Our estimates of the error covariances are shown to be appropriate through a series of objective statistical tests. Analysis of the term balances of the model equations show that the dominant modeled dynamical balances are preserved by the DAS and that uncertainties in the spatial variability of the wind forcing are likely to be one source of model error. By varying the relative magnitudes of the estimated forecast and observation error covariances the DAS is shown to be most effective when approximately 80% of the analysis is made up of the model solution.
Conjunctival expression of thymosin-beta4 in vernal keratoconjunctivitis. (2006)

Our data provides the first evidence of Tbeta4 expression in the conjunctival tissues. The upregulation of both Tbeta4 mRNA and protein in the conjunctival stroma, and its peculiar localization in eosinophils and myofibroblasts populating VKC lesions, suggest a possible role for Tbeta4 in tissue inflammation and remodeling occurring in VKC.
Crystal structures of human pancreatic α-amylase in complex with carbohydrate and proteinaceous inhibitors (2000)

Crystal structures of human pancreatic α-amylase (HPA) in complex with naturally occurring inhibitors have been solved. The tetrasaccharide acarbose and a pseudo-pentasaccharide of the trestatin family produced identical continuous electron densities corresponding to a pentasaccharide species, spanning the -3 to +2 subsites of the enzyme, presumably resulting from transglycosylation. Binding of the acarviosine core linked to a glucose residue at subsites -1 to +2 appears to be a critical part of the interaction process between α-amylases and trestatin-derived inhibitors. Two crystal forms, obtained at different values of pH, for the complex of HPA with the protein inhibitor from Phaseolus vulgaris (α-amylase inhibitor) have been solved. The flexible loop typical of the mammalian α-amylases was shown to exist in two different conformations, suggesting that loop closure is pH-sensitive. Structural information is provided for the important inhibitor residue, Arg-74, which has not been observed previously in structural analyses.
Optimal buffering policy for downloading music in heterogeneous wireless networks (2003)

We consider a heterogeneous network of wireless LAN providing cheap, high speed coverage to local areas and wide area cellular networks providing a more expensive and slower coverage to a wider region. The movement of the mobile is modeled with a two state continuous time Markov chain. We consider the application where the mobile wants to download and listen to music. To reduce the download cost, the mobile downloads and buffers a lot of music in the lower cost area and plays it when it is in the more expensive areas. We formulate a mathematical model for this problem and present the optimal buffering policy for the mobile.
Synthesis and X-ray Crystal Structure of the Novel Organotin Dication [<i>n</i>-Bu<sub>2</sub>Sn(H<sub>2</sub>O)<sub>4</sub>]<sup>2+</sup>:  A Lamellar Layered Structure Assisted by Intermolecular Hydrogen Bonding (2002)

The reaction of n-Bu2SnO with 2,5-dimethylbenzenesulfonic acid affords the stable monomeric tin complex [n-Bu2Sn(H2O)4]2+[2,5-Me2-C6H3SO3]-2. The solid-state structure of the molecule reveals that the hydrogen-bonding interaction between the coordinated water and the sulfonate anion moieties leads to an unprecedented two-dimensional layered structure with a planar array of tin atoms. Further, the Lewis acidic dication complex is an extremely good catalyst for acylation of alcohols and phenols.
Thermal imaging for landmine detection (1998)

A thermal imaging technique for landmine detection is described. The technique uses microwave radiation and infrared detection, and works best for soil moisture levels of around 5%. Thermal images obtained in the laboratory show that the technique can be used to locate buried landmines and completely nonmetallic minelike objects.
Interleukin-1β Promotes Skeletal Colonization and Progression of Metastatic Prostate Cancer Cells with Neuroendocrine Features (2013)

Despite the progress made in the early detection and treatment of prostate adenocarcinoma, the metastatic lesions from this tumor are incurable. We used genome-wide expression analysis of human prostate cancer cells with different metastatic behavior in animal models to reveal that bone-tropic phenotypes upregulate three genes encoding for the cytokine interleukin-1β (IL-1β), the chemokine CXCL6 (GCP-2), and the protease inhibitor elafin (PI3). The Oncomine database revealed that these three genes are significantly upregulated in human prostate cancer versus normal tissue and correlate with Gleason scores ≥7. This correlation was further validated for IL-1β by immunodetection in prostate tissue arrays. Our study also shows that the exogenous overexpression of IL-1β in nonmetastatic cancer cells promotes their growth into large skeletal lesions in mice, whereas its knockdown significantly impairs the bone progression of highly metastatic cells. In addition, IL-1β secreted by metastatic cells induced the overexpression of COX-2 (PTGS2) in human bone mesenchymal cells treated with conditioned media from bone metastatic prostate cancer cells. Finally, we inspected human tissue specimens from skeletal metastases and detected prostate cancer cells positive for both IL-1β and synaptophysin while concurrently lacking prostate-specific antigen (PSA, KLK3) expression. Collectively, these findings indicate that IL-1β supports the skeletal colonization and metastatic progression of prostate cancer cells with an acquired neuroendocrine phenotype.