gebhart/patrepeval huggingface dataset:
Pterostilbene attenuates acute kidney injury in septic mice (2018)

Acute kidney injury (AKI) is a severe complication of sepsis with a high mortality and morbidity. Pterostilbene (Pte) has been suggested to confer anti-apoptotic and anti-inflammatory effects. In the current study, the effects of Pte on AKI were evaluated in septic mice. Cecal ligation and puncture surgery was performed to induce sepsis. The results suggested that Pte administration significantly decreased the levels of serum urea nitrogen and creatinine, and improved the survival rate of septic mice. Additionally, the renal injury induced by sepsis was attenuated by pterostilbene treatment. Notably, pterostilbene reduced Bcl-2-associated X protein expression, and levels of interleukin-1β and tumor necrosis factor-α, and upregulated B-cell lymphoma 2 expression. The results indicate that pterostilbene may serve as a potential therapeutic candidate for the treatment of AKI induced by sepsis.
T1 COLORECTAL CANCERS TREATED BY ENDOSCOPIC RESECTION: TUMOR SIZE AS A NEW PROGNOSTIC FACTOR? (2022)

Aims Tumor size seems to be an important prognostic factor in colorectal cancers, especially in T1. The objective of this study was to compare the rate of lymph node involvment between small≤20mm T1 colorectal tumors and those of larger size>20mm.
Understanding the Phase Transitions of theNi2MnGaMagnetic Shape Memory System from First Principles (2009)

The free energies of the austenite, the (modulated) premartensite and the unmodulated martensite of Ni2MnGa are determined using density functional theory and including quasiharmonic phonons and fixed-spin-moment magnons. This approach very well reproduces the complete phase sequence (martensite<-->premartensite<-->austenite) of stoichiometric Ni2MnGa as a function of temperature. By analyzing the relevant free energy contributions, we also understand the delicate interplay of phonons and magnons driving both phase transitions.
HYDROXYAPATITE IN REVISION OF TOTAL HIP REPLACEMENTS WITH MASSIVE ACETABULAR DEFECTS (1997)

Hydroxyapatite (HA) granules of 100 to 300 μm, 0.9 to 1.2 mm and 3.0 to 5.0 mm were mixed in a ratio of 10:45:45 and packed into massive bone deficiencies in revision operations for total hip arthroplasty. We did not use additional graft or cup support for deficiencies of the lateral and medial wall. The procedure was carried out in 40 hips between 1986 and 1992. The radiographic spaces seen at the interface between HA and bone immediately after surgery disappeared within three months. Some spaces appeared between HA granules near the bone in the lateral part of two joints, and three sockets migrated in patients with severe segmental and cavitary deficiencies. Direct bonding of HA to bone was observed radiologically without morphological changes, except in the three joints with migration. All patients could walk without pain but the three with definite loosening needed crutches.
How high can you jump? Children's Perception of Affordances for Self and Others with Different Abilities (2013)

The current study investigated whether children and adults can distinguish between actions they are afforded and those afforded to an actor.Participants judged the maximum height they could reach while jumping and they judged the maximum height that the actor could reach while jumping.They did so with and without a weighted backpack, and they did so with and without walking several laps.Results show that before the addition of the weighted backpack, participants rated the actor's abilities as much closer to their own.While wearing the weighted backpack and then walking with it, participants' estimates decreased for themselves, but remained mostly unchanged for the adult.
An analytical framework for interpretable and generalizable ‘quasilinear’ single-cell data analysis (2020)

Abstract Scaling single-cell data exploratory analysis with the rapidly growing diversity and quantity of single-cell omics datasets demands more interpretable and robust data representation that is generalizable across datasets. To address this challenge, here we developed a novel ‘quasilinear’ framework that combines the interpretability and transferability of linear methods with the representational power of nonlinear methods. Within this framework, we introduce a data representation and visualization method, GraphDR, and a structure discovery method, StructDR, that unifies cluster, trajectory, and surface estimation and allows their confidence set inference. We applied both methods to diverse single-cell RNA-seq datasets from whole embryos and tissues. Unlike PCA and t-SNE, GraphDR and StructDR generated representations that both distinguished highly specific cell types and were comparable across datasets. In addition, GraphDR is at least an order of magnitude faster than commonly used nonlinear methods. Our visualizations of scRNA-seq data from developing zebrafish and Xenopus embryos revealed extruding branches of lineages from a continuum of cell states, suggesting that the current branch view of cell specification may be oversimplified. Moreover, StructDR identified a novel neuronal population using scRNA-seq data from mouse hippocampus. An open-source python library and a user-friendly graphical interface for 3D data visualization and analysis with these methods are available at https://github.com/jzthree/quasildr .
Development of a Double-Lumen Cannula for a Percutaneous RVAD (2015)

The objectives were to design/fabricate a double-lumen cannula (DLC) for a percutaneous right ventricular assist device (pRVAD) and to test the feasibility/performance of this pRVAD system. A 27 Fr DLC prototype was made and tested in six adult sheep. The pRVAD DLC was inserted into the right jugular vein; advanced through the superior vena cava, the right atrium (RA), the right ventricle (RV); ending in the pulmonary artery (PA). A CentriMag pump and optional gas exchanger were connected to the DLC. Blood was withdrawn from RA, pumped through gas exchanger, and perfused PA. Maximal pumping flow was maintained for 2 hours. The pRVAD DLC was successfully deployed in all six sheep. In first three sheep, maximal average pumping flow was less than 3 L/min because the DLC was advanced too far with drainage opening against RA side wall. In last three sheep with well-positioned DLC, average maximal flow was more than 3.5 L/min. The gas exchanger provided up to 230 ml/min CO2 removal and 174 ml/min O2 transfer. Our DLC-based pRVAD system is feasible for percutaneous right heart and respiratory assistance through a single cannulation. The pRVAD DLC can be easily placed prophylactically during left ventricular assist device implantation and removed as needed without additional open chest procedures.
On-demand routing in large ad hoc wireless networks with passive clustering (2002)

This paper presents on-demand routing scalability improvements achieved using a "passive" clustering. Any on-demand routing typically requires some form of flooding. Clustering can dramatically reduce transmission overhead during flooding. In fact, by using clustering, we restrict the set of forwarding nodes during flood search and thus reduce the energy cost and traffic overhead of routing in dynamic traffic and topology environments. However existing "active" clustering mechanisms require periodic refresh of neighborhood information and tend to introduce quite a large amount of communication maintenance overhead. We introduce a passive clustering protocol scheme which is mostly supported/maintained by user data packets instead of explicit control packets. The passive scheme is consistent with the on-demand routing philosophy. Simulation results show significant performance improvements when passive clustering is used.
ChemInform Abstract: Synthesis of Enantiomerically Enriched Homoallylic Alcohols and of 1,2‐Dien‐4‐ols Using Chiral Tin(IV) Complexes Containing Diethyl Tartrate as an Auxiliary Ligand. (1988)

Abstract The homoallylic alcohols (VI) are prepared via the allylic tin(IV) complexes (IV) which are coupled with the aldehydes (V).
Vascular endothelial growth factor +405 G/C,−460 T/C and −2578 A/C polymorphisms are not associated with insulin resistance in polycystic ovary syndrome (2010)

Insulin resistance (IR) and pancreatic beta-cell dysfunction are usual comorbidities in polycystic ovary syndrome (PCOS). Vascular endothelial growth factor (VEGF) is known to play an important role in the pathogenesis of PCOS. This study examined firstly the possible association of common +405 G/C,-460 T/C and -2578 A/C polymorphisms of VEGF gene with fasting glucose, fasting insulin and the indices of IR [glucose/insulin ratio (GIR), homoeostasis model assessment (HOMA) and quantitative insulin sensitivity check index (QUICKI)] in 137 patients with PCOS. None of the studied polymorphisms were found to affect IR indices significantly. However, there was a trend towards higher HOMA in +405 G and -460 T allele carriers in comparison with homozygotes +405 CC and -460 CC, respectively. With regard to -2578 A/C polymorphism, although not significant, in -2578 C carriers HOMA was lower, and GIR was higher in comparison with -2578 AA genotype. Alteration of QUICKI between genotypes was minimal and varied from 4% to 7%. Because of the relatively small sample size, more studies with greater number of cases are necessary to confirm our observations before any statement can be made about the relationship between VEGF gene polymorphism and IR parameters in PCOS.
Lysosomal Enzymes and Their Receptors (1986)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Parallel routing algorithms in Benes-Clos networks (2002)

A new parallel algorithm for route assignment in Benes-Clos network is studied. In packet switching systems, switch fabrics must be able to provide internally conflict-free paths simultaneously and to accommodate packets requesting for connections in real-time as they arrive at the inputs. Most known sequential route assignment algorithms, such as the looping algorithm for Benes (1962) networks or Clos (1953) networks, are designed for circuit switching systems where the switching configuration can be rearranged at a relatively low speed. Most existing parallel routing algorithms are not practical for packet switching because they either assume the set of connection requests is a full permutation or fail to deal with output contentions among the set of input packets. We develop a parallel routing algorithm by solving a set of Boolean equations which are derived from the connection requests and the symmetric structure of the Benes network. Our approach can handle both the partial permutations and the output contention problem easily. The time complexity of our algorithm is O(log/sup 2/N), where N is the network size. Furthermore, we extend the algorithm and show that it can be applied to the Clos network if the number of central modules is a power of two.
Enzyme Replacement Therapy for Lysosomal Storage Diseases (2008)

Lysosomal storage diseases (LSD) are a heterogenous group of more than 40 inborn errors of metabolism that are due to specific defects of lysosomal en-zymes, lysosomal membrane proteins or transporters respectively. All LSD are inherited autosomal recessively with the exception of MPS II (M. Hunter), Fabry Disease and Danon Disease that are inherited as X chromosomal traits. Although individually rare their cumulative prevalence may be as high as 1:800 in certain ethnic populations. LSD in general are progressive multiorgan disorder with about 50% having significant central nervous involvement. Each LSD comprises a more or less unique clinical spectrum with patients at the more severe end showing in-creased morbidity and mortality whereas patients at the milder end of the spectrum having only subtle clinical signs. Patients with mild disease may of-ten go unrecognized for many years. Therapy of LSD consisted mainly of palliative treatment until the recent de-velopment of enzyme replacement therapies for Gaucher, Pompe and Fabry Diseases as well as Mucopolysaccharidosis types I and II (MPS I/II) Lysosomes are intracellular organelles that encompass numerous hy-drolases and other enzymes that break down different compounds derived from intermediary metabolism such as complex lipids, carbohydrates and others. During the last years the interest for the LSD has significantly increased due to the development of novel therapies including enzyme replacement thera-pies (ERT) and substrate inhibition therapy. Additional therapies such as chaperone therapy are currently evaluated in phase I and II trials. Currently ERT are available for MPS I, II, VI, Fabry, Pompe and Gaucher diseases. In ad-dition SRT has been licensed for Gaucher disease. The aim of this paper is to give a brief overview of the treatable LSD, to summarise the guidelines for diagnosis, treatment and disease management, to summarise data from ERT registers and to analyse eventual fields of con-flict. For this purpose a thorough Medline search up to August 2008 was per-formed using the following key words: MPS I, MPS II, MPS VI, Pompe, Fabry, Gaucher, enzyme replacement therapy, treatment and registry respectively. In addition all pharmaceutical companies involved in manufacturing recom-binant enzyme and/or substrate inhibition therapies were contacted for fur-ther information. These companies included Actelion, Biomarin, Genzyme and Shire.
Induction of AhR transactivation by PBDD/Fs and PCDD/Fs using a novel human-relevant, high-throughput DRhuman CALUX reporter gene assay (2020)

Polychlorinated dioxins and dibenzofurans (PCDD/Fs) are highly toxic contaminants that are strictly regulated and monitored in the environment and food to reduce human exposure. Recently, the increasing occurrence of polybrominated dioxins and dibenzofurans (PBDD/Fs) in the environment is raising concerns about the impact on human health by the combined exposure to chlorinated and brominated analogues of dioxins. Toxicological properties of PBDD/Fs relative to PCDD/Fs have not been firmly established, and brominated dioxins are not included in routine monitoring programs. In this study, we set out to determine human-relevant congener-specific potency values for a range of brominated and chlorinated dioxin congeners, based on their aryl hydrocarbon receptor (AhR)-mediated mode of toxic action. Transactivation of the AhR was measured using dioxin-responsive (DR) CALUX reporter gene assays. Because of known species-differences in dioxin-mediated toxicity, we developed and used a HepG2 human liver cell-based DR human CALUX assay that is a variant of the rodent-based DR CALUX. The assay was found to be highly inducible and stable, with low variations between independent measurements. Using both DR CALUX assays in an automated high-throughput mode we found that overall PBDD/Fs were as potent as PCDD/Fs in inducing AhR transactivation, but congener-specific differences were observed. We also observed species-specific differences in sensitivity and potency when comparing DR human REP values to those obtained in the rat-based DR CALUX. Finally, we observed significant differences between WHO-TEF values and DR human REP values, suggesting that actual WHO-TEF values may underestimate the hazards associated with exposure of humans to dioxins.
Genetic and Immunological Studies of Bacteriophage T4 Thymidylate Synthetase (1973)

Thymidylate synthetase, which appears after infection of Escherichia coli with bacteriophage T4, has been partially purified. The phage enzyme is immunologically distinct from the host enzyme and has a molecular weight of 50,000 in comparison to 68,000 for the host enzyme. A system has been developed to characterize T4 td mutants previously known to have impaired expression of phage thymidylate synthetase. For this system, an E. coli host lacking thymidylate synthetase was isolated. Known genetic suppressors were transduced into this host. The resulting isogenic hosts were infected with phage T4 td mutants. The specific activities and amounts of cross-reacting material induced by several different types of phage mutants under conditions of suppression or non-suppression have been examined. The results show that the phage carries the structural gene specifying the thymidylate synthetase which appears after phage infection, and that the combination of plaque morphology, enzyme activity assays, and an assay for immunologically cross-reacting material provides a means for identifying true amber mutants of the phage gene.
Designing interpolation kernels for SAR data resampling (2012)

It is fairly common in radar signal processing that sampled data is not sampled precisely at the desired positions within a function. Resampling the data to more advantageous sample locations entails interpolation of the data. The radar engineer often picks a resampling or an interpolation technique that "is handy", or "seems to work", without any analytical justification for his choice. However, understanding the science and mathematics that underpin interpolation can avoid unexpected and undesirable side effects from a suboptimal choice. This paper details interpolation kernel characteristics, allowing intelligent choices for algorithm design, tailored for radar signal processing applications.
A Rational Framework for Selecting Modes of Ventilation (2012)

Mechanical ventilation is a life-saving intervention for respiratory failure and thus has become the cornerstone of the practice of critical care medicine. A mechanical ventilation mode describes the predetermined pattern of patient-ventilator interaction. In recent years there has been a dizzying proliferation of mechanical ventilation modes, driven by technological advances and market pressures, rather than clinical data. The comparison of these modes is hampered by the sheer number of combinations that need to be tested against one another, as well as the lack of a coherent, logical nomenclature that accurately describes a mode. In this paper we propose a logical nomenclature for mechanical ventilation modes, akin to biological taxonomy. Accordingly, the control variable, breath sequence, and targeting schemes for the primary and secondary breaths represent the order, family, genus, and species, respectively, for the described mode. To distinguish unique operational algorithms, a fifth level of distinction, termed variety, is utilized. We posit that such coherent ordering would facilitate comparison and understanding of modes. Next we suggest that the clinical goals of mechanical ventilation may be simplified into 3 broad categories: provision of safe gas exchange; provision of comfort; and promotion of liberation from mechanical ventilation. Safety is achieved via optimization of ventilation-perfusion matching and pressure-volume relationship of the lungs. Comfort is provided by fostering patient-ventilator synchrony. Liberation is promoted by optimization of the weaning experience. Then we follow a paradigm that matches the technological capacity of a particular mode to achieving a specific clinical goal. Finally, we provide the reader with a comparison of existing modes based on these principles. The status quo in mechanical ventilation mode nomenclature impedes communication and comparison of existing mechanical ventilation modes. The proposed model, utilizing a systematic nomenclature, provides a useful framework to address this unmet need.
Mr.Tree: Multiple Realities in Tree-based Monitoring Overlays for Peer-to-Peer Networks (2018)

Peer-to-peer systems are difficult to manage due to their decentralized nature and the lack of a central controlling instance. Thus, establishing a quality of service is a challenging task. In the last decade, decentralized monitoring approaches have been proposed, which are either precise or fault-tolerant. Tree-based approaches, which belong to the former category, are prone to churn as the structure needs to reorganize itself on node failures. In this paper, we propose the monitoring approach Mr.Tree, a protocol that enhances the robustness of existing tree-based approaches by introducing multiple realities, through building up multiple trees, and smartly replicating and maintaining aggregated data. Three modes are proposed to fit individual scenarios and needs. The evaluation shows a significant decrease of the error in completeness of monitoring data while keeping the costs relatively low. The error of the extended protocol under heavy churn is in the magnitude of the original protocol under low churn conditions, which is 8%, whereby the error of the original protocol under heavy churn raises to a value above 22%. The superior precision cancels out the increased costs already in scenarios with moderate churn.
Changes in the kinetics of inositol transport during TPA‐induced differentiation of HL60 cells towards monocytes (1991)

When exposed to the phorbol ester TPA, HL60 cells undergo growth arrest and differentiate towards monocytes. During TPA-induced differentiation there was a 2.6-fold increase in the rate of inositol transport (Vmax), a 2.1-fold increase in intracellular inositol and a 1.5-fold increase in inositol lipid. An increase in the Vmax of inositol transport did not occur when the variant cell line HL60Ast3 was exposed to TPA, which has been shown in this cell line to induce growth arrest but not differentiation. This observation suggests that the change in inositol transport during HL60 monocyte differentiation is specifically associated with the process of cell differentiation as opposed to growth arrest.
Supplementary Tables 1-2 from Genetic Variation in <i>TYMS</i> in the One-Carbon Transfer Pathway Is Associated with Ovarian Carcinoma Types in the Ovarian Cancer Association Consortium (2023)

Supplementary Tables 1-2 from Genetic Variation in &lt;i&gt;TYMS&lt;/i&gt; in the One-Carbon Transfer Pathway Is Associated with Ovarian Carcinoma Types in the Ovarian Cancer Association Consortium
Channels formed by M2 peptides of a putative glutamate receptor subunit of locust (1993)

A cDNA encoding part of a polypeptide (Loc1) that exhibits similarity to the corresponding portion of the rat GluR1 subunit has been identified by screening an amplified locust cDNA library. This polypeptide is deduced to be missing about 200 amino acids of the amino-terminus and about 100 amino acids of the carboxy-terminus. cDNAs encoding two other glutamate receptor-like polypeptides (Loc2 and Loc3), which both exhibit good sequence homology with Loc1, have also been identified. So far, there is no evidence for 'flip' and 'flop' variants of Loc1, 2 and 3. A 27-mer peptide including the M1 sequence of Loc1 and a 25-mer peptide including the M2 sequence of this putative glutamate receptor subunit have been synthesised and incorporated into artificial bilayers. Channel openings, of minimum conductance 20 pS, were seen more frequently with the M2 peptide. These studies are designed to lead to the isolation of full-length cDNAs for Loc1, 2 and 3 and to the electrophysiological characterisation of their ion transport properties.