gebhart/patrepeval huggingface dataset:
Gut microbiome signatures distinguish type 2 diabetes mellitus from non-alcoholic fatty liver disease (2021)

Non-alcoholic fatty liver disease (NAFLD) is closely associated with type 2 diabetes mellitus (T2D), and these two metabolic diseases demonstrate bidirectional influences. The identification of microbiome profiles that are specific to liver injury or impaired glucose metabolism may assist understanding of the role of the gut microbiota in the relationship between NAFLD and T2D. Here, we studied a biopsy-proven Asian NAFLD cohort (n = 329; 187 participants with NAFLD, 101 with NAFLD and T2D, and 41 with neither) and identified <i>Enterobacter</i>, <i>Romboutsia</i>, and <i>Clostridium sensu stricto</i> as the principal taxa associated with the severity of NAFLD and T2D, whereas <i>Ruminococcus</i> and <i>Megamonas</i> were specific to NAFLD. In particular, the taxa that were associated with both severe liver pathology and T2D were also significantly associated with markers of diabetes, such as fasting blood glucose and Hb1Ac. Enterotype analysis demonstrated that participants with NAFLD had a significantly higher proportion of <i>Bacteroides</i> and a lower proportion of <i>Ruminococcus</i> than a Korean healthy twin cohort (n = 756). However, T2D could not be clearly distinguished from NAFLD. Analysis of an independent T2D cohort (n = 185) permitted us to validate the T2D-specific bacterial signature identified in the NAFLD cohort. Functional inference analysis revealed that endotoxin biosynthesis pathways were significantly enriched in participants with NAFLD and T2D, compared with those with NAFLD alone. These findings may assist with the development of effective therapeutic approaches for metabolic diseases that are associated with specific bacterial signatures.
Java Management Extensions (2002)

From the Publisher:
Steve Perry has spent his time in the trenches. I've been paged at 3:00 am to provide support because the system wasn't doing what it should and no one had a clue how to figure out why. I've scrolled through endless logfiles to decipher system problems, when a management solution could have presented an operator with a warning message hours earlier! Wanting other developers to be able to learn from his experiences, Steve wrote Java Management Extensions.
Java Management Extensions is a practical, hands-on guide to using the JMX APIs, Sun Microsystem's new Java-based tool for managing enterprise applications. This one-of-a kind book is a complete treatment of the JMX architecture (both the instrumentation level and the agent level), and it's loaded with real-world examples for implementing Management Extensions. It also contains useful information at the higher level about JMX (the big picture) to help technical managers and architects who are evaluating various application management approaches and are considering JMX. 
The JMX technology is very new, and according to Steve, still has a few potholes in it. This book takes developers through it step by step, pointing out the gotchas before they have a chance to trip up smooth operation of the application. The author, a member of the expert group developing the JMX specification, points out that as J2EE becomes more widely adopted, the Java standard for management (JMX) becomes more and more crucial to avoid splinter standards where each vendor has their own distinct, arguably successful, way of doing things. In my own company we have already identified and are tackling the problem of managing our Java applications. It's my belief that other companies will follow, as they come to realize the power that a standard manageability solution (ie, JMX) gives them. 
The book is divided into the following sections: 
Part I: Introduction and overview
Part II: the JMX Instrumentation Level
Standard MBeans
Dynamic MBeans
Model Mbeans
Part III: The JMX Agent Level
The Mbean Server
The JMX Notification Model
Dynamic Loading
Monitors
Timer Services 
Relation Services
Appendix: Related Technologies
Index
Upregulation of tissue kallikrein, kinin B1 receptor, and kinin B2 receptor in mast and giant cells infiltrating oesophageal squamous cell carcinoma (2005)

This is the first demonstration that TK1 and kinin B(1) and B(2) receptors are expressed in oesophageal carcinoma. Because TK1 released from tumour cells enzymatically generates mitogenic kinins from its endogenous substrate, kininogen, it is possible that third generation kinin receptor antagonists, which have been shown to be cytotoxic to cancer cells, may be useful therapeutic agents in this disease.
Distinctive T Cell Suppressive Signals from Nuclearized Type 1 Sphingosine 1‐Phosphate G Protein‐Coupled Receptors (2007)

Sphingosine 1‐phosphate (S1P) from innate immune cells regulates lymphoid organ traffic and tissue migration of T cells through the type 1 S1P G protein‐coupled receptor (S1P 1 ). However, effects of the S1P‐S1P 1 axis on T cell proliferation are highly dependent on the timing of introduction of S1P. We now show that antigen receptor (TCR)‐mediated activation of CD4 T cells translocates plasma membrane (PM) S1P 1 to nuclear membranes along with Gi/o, extracellular signal‐regulated kinase (Erk) ½ and some other signaling proteins. By isolating T cell nuclei with intact membrane envelopes and stimulating them with known intracellular concentrations of S1P, we demonstrated that nuclear S1P 1 and PM S1P 1 transduce opposite effects on T cell signals relevant to proliferation. Nuclear p‐Erk levels are decreased by a mean of 70% when 1μM S1P was added to nuclear S1P 1, but increased 3‐fold by adding 1μM S1P to PM S1P 1 . TCR‐mediated activation of T cells therefore not only eliminates migration responses to S1P by downregulation of PM S1P 1 , but also translocates the S1P‐ S1P 1 axis into the nucleus where S1P may control proliferation, survival and other non‐migration functions. (Grant support from NIH HL‐31809.)
Predicting the probability of pT3 or higher pathological stage at radical prostatectomy: COVID19-specific considerations (2022)

The newly developed, externally validated nomogram predicts presence of pT3-4/pN1 better than NCCN risk group stratification and allows to focus radical prostatectomy treatment on individuals at highest risk of pT3-4/pN1.
Generalization and specialization of multiple scattering theory for Gaussian beam model of heavy charged particles in radiotherapy (2008)

This study provides an accurate, efficient, and simple multiple scattering formulation for heavy charged particles such as protons and heavier ions with a new form of scattering power that is a key quantity for beam transport in matter. The Highland formula for multiple scattering angle was modified to a scattering-power formula to be used within the Fermi-Eyges theory in the presence of heterogeneity. An analytical formula for RMS end-point displacement in homogeneous matter was also derived for arbitrary ions. The formulation was examined in terms of RMS angles and displacements in comparison with other formulations and measurements. The results for protons, helium ions, and carbon ions in water agreed with them at a level of 2% or the differences were discussed.
On the Perturbation of the H-Bonding Interaction in Ethylene Glycol Clusters upon Hydration (2012)

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.
Effect of Follicle Size on Cumulus-Expansion, In Vitro Fertilization and Development of Porcine Follicular Oocytes. (2001)

The aim of the present experiment was to investigate the effect of follicular size on oocyte cumulus-expansion, in vitro fertilization and subsequent developmental competence. After maturation culture, the rates of porcine oocytes with expanded cumulus derived from antral follicles ≥5 mm, 4-4.9 mm, 3-3.9 mm and 2-2.9 mm in diameter were 90.5%, 89.7%, 85.4% and 67.4%, respectively. After in vitro fertilization, the developmental competence of oocytes dependently increased with follicular size. Higher cleavage rates and higher proportions of 3-4-cell embryos were obtained from ≥4 mm follicles compared to 2-2.9 mm follicles (P<0.05). Although the proportions of 6-8-cell and 12-16-cell embryos obtained from ≥5 mm, 4-4.9 mm, 3-3.9 mm and 2-2.9 mm follicles showed no significant differences, embryos obtained from 2-2.9 mm follicles showed a complete failure to develop beyond the 8-cell stage, embryos obtained from 3-3.9 mm follicles failed to develop beyond the 16-cell stage and none of embryos developed beyond the early stage of morula. The percentages of expanded cumulus-oocyte complexes (COCs) and 2-cell cleavage rates of oocytes derived from 2-2.9 mm follicles were not significantly different when the oocytes were matured for 36 h , 42 h and 48 h in vitro. The exposure to 5% or 15% porcine follicular fluid (PFF) from the large follicles during in vitro maturation (IVM) had no significant effect on the cleavage and subsequent developmental rates of porcine oocytes compared to PFF from small follicles.
Prohisin, New Thiol Protease Inhibitor Produced byCephalosporiumsp. KM 388 (1984)

Journal Article Prohisin, New Thiol Protease Inhibitor Produced by Cephalosporium sp. KM 388 Get access Tetsu Kimura, Tetsu Kimura Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-02, Japan Search for other works by this author on: Oxford Academic Google Scholar Katsumi Tsuchiya, Katsumi Tsuchiya Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-02, Japan Search for other works by this author on: Oxford Academic Google Scholar Satoshi ōmura Satoshi ōmura School of Pharmaceutical Sciences, Kitasato University and The Kitasato Institute, Minato-ku, Tokyo 108, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 48, Issue 6, 1 June 1984, Pages 1685–1686, https://doi.org/10.1080/00021369.1984.10866384 Published: 01 June 1984 Article history Received: 30 January 1984 Published: 01 June 1984
Sequence-specific cleavage of chromatin by staphylococcal nuclease can generate an atypical nuclesome pattern (1982)

We have investigated the nucleosomal organization of ribosomal genes in the acellular slime mold Physarum polycephalum. When probed with staphylococcal nuclease, the ribosomal genes appear to be uniformly packed in nucleosomes, in an arrangement which is indistinguishable from the pattern obtained with bulk chromatin. During this study, an unusual pattern of digestion was obtained from a DNA region immediately upstream of the initiation site of rRNA transcription, in addition to the nucleosomal profile, a second regular ladder of fragments with a repeat length of 30-40 basepairs was generated from this region. We established that this pattern of degradation reflects the strong preference of staphylococcal nuclease for certain nucleotide arrangements on the DNA, rather than a particular chromatin configuration. These observations clearly show that great caution needs to be exerted whenever data from staphylococcal nuclease digestions are interpreted in terms of chromatin structure.
P-239 Complementary effects of AV and VV-delay on interventricular asynchrony and cardiac pump function during BIV pacing in canine LBBB hearts (2003)

elevation in these families suggests that an unknown mutation(s) in the genes that encode cardiac ion channels may be involved.
Impact of Ti Interfacial Layer on Resistive Switching Characteristics at sub-µA Current Level in SiOx-Based Flexible Cross-Point RRAM (2019)

The impact of Ti interfacial layer on resistive switching characteristics in 5×5 μm 2 Ni/Ti/SiO x /Ni flexible cross-point resistive random access memory (RRAM) structure for the first time. Devices with Ti buffer layer exhibits bipolar resistive switching (BRS) with large memory window (HRS/LRS) of > 10 3 at 500 nA current compliance (CC). Thin 4-nm Ti interfacial layer regulates the migration of oxygen ions (O -2 ) and controls BRS process. Highly non-linear (non-linearity of > 22) switching (rectifying ratio i.e, RR of >4×10 3 ) is obtained from reference sample without (W/O) Ti buffer layer.
A Functionally Superior Second-Generation Vector Expressing an Aurora Kinase-A-Specific T-Cell Receptor for Anti-Leukaemia Adoptive Immunotherapy (2016)

Aurora Kinase A is a cancer-associated protein normally involved in the regulation of mitosis. Being over-expressed in a range of cancers, it is a suitable target for cell-based immunotherapy. Gene transfer of T-cell receptor sequences cognisant of HLA-A*0201-restricted Aurora Kinase A antigen has previously been shown to transfer specific immunoreactivity against the target peptide in a Human Lymphocyte Antigen-restricted manner. While T cell receptor gene-transfer has great potential in overcoming the difficulties of isolating and expanding tumour-reactive lymphocytes from a patient's own cells, one hurdle is potential mispairing and competition between exogenous and endogenous T cell receptor chains. We have used a retroviral vector design bearing a short-interfering RNA that downregulates endogenous T cell receptor chains, without affecting expression of the transgenic T cell receptor sequences. The T cell receptor expression cassette also includes a 2A self-cleaving peptide, resulting in equimolar expression of the T cell receptor alpha and beta chains, further enhancing formation of the desired T cell receptor. Via a simple, modular cloning method, we have cloned the alpha and beta chains of the anti-Aurora Kinase A-reactive T cell receptor into this 'siTCR' vector. We then compared the activity of this vector against the original, 'conventional' vector across a panel of assays. T cell receptors expressed from the siTCR-vector retained the cytotoxic functionality of the original vector, with evidence of reduced off-target reactivity. The rate of expression of correctly-formed T cell receptors was superior using the siTCR design, and this was achieved at lower vector copy numbers. Maintaining T cell receptor efficacy with a reduced vector copy number reduces the risk of genotoxicity. The siTCR design also reduces the risk of mispairing and cross-reactivity, while increasing the functional titre. Such improvements in the safety of T cell receptor gene-transfer will be crucial for clinical applications of this technology.
How far can we go? Towards Realistic Software-Defined Wireless Networking Experiments (2017)

International audience
Information programming for personal user interfaces (2002)

With widespread access to e-mail, the world-wide web, and other information sources, people now use computers more for managing information than for managing applications. To support how people naturally and routinely organize information, computers ought to be able to reflect the categories, relationships, and cues that people rely on when thinking about and remembering facts. Toward this end, we created an Information Programming Toolkit (IPtk) that collects application-independent properties, indexes documents along many dimensions to create a personal record of information use, and provides convenient means for information access. The IPtk enables the development of smart user interfaces that automatically tailor information to a user's history and context of information use.
Effect of a Longitudinally Applied Voltage Upon the Growth of Zea mays Seedlings (1988)

The electrical parameters that affect young seedling growth were investigated. Voltages ranging from 5 to 40 volts were applied longitudinally along the mesocotyl region of 4-day old Zea mays L. (cv Silver Queen) seedlings for periods of 3 or 4 hours. It was determined that: (a) making the tips of the seedlings electrically positive relative to the base strongly inhibited shoot growth at 5 volts, whereas the reverse polarity had no effect; (b) at higher voltages, making the tip of the seedlings negative caused less growth inhibition than the reverse polarity at each voltage level; (c) the higher the applied voltage the greater the degree of inhibition; and, (d) the more growth inhibition experienced by the plants the poorer, and slower, their recovery. Previous observations of a relationship between the amount of free indole-3-acetic acid in the mesocotyl cortex and the growth rate of the mesocotyl and of gravitropism-induced movement of labeled indole-3-acetic acid from the seed to the shoot lead to the prediction of a voltage-dependent gating of the movement of indole-3-acetic acid from the stele to the cortex. This provided the basis for attempting to alter the growth rate of seedlings by means of an applied voltage.
Studies on the modulation of DNA damage. 1: A simple kinetic model for radioprotection of DNA in aqueous solution. (1997)

A simple kinetic model, based on the assumption that direct and indirect interactions of ionising radiations with DNA lead to formation of DNA-radicals which are precursors of single strand break (ssb) and double strand break (dsb) is presented. Considering accessibility of OH attack on DNA and assuming homogenous kinetics, the model has been validated by using experimental data on radiation-induced strand break formation in presence of methanol (MeOH) and glutathione (GSH). Fitting the D37 values for ssb in aqueous solution of pBR322 DNA in the presence of the predominantly A-T minor groove-ligand Hoechst 33258, the value of the rate constant of OH scavenging by DNA-bound Hoechst was estimated by Martin and his group as 2.7 x 10(11) dm3 mol-1 s-1 (Martin, R.F. and Denison, L. (1992), Int. J. Radiat. Oncol. Biol. Phys., 23, 578-584). Using aqueous solution of calf thymus DNA in the presence of Hoechst this rate constant has been determined by pulse radiolysis as 1.1 x 10(9) dm3 mol-1 s-1. The yield of strand breaks has also been measured by low angle laser light scattering. Using the experimentally measured value of the rate constant of OH scavenging by DNA-bound Hoechst in the model, calculations show that OH scavenging alone could not explain the overall protection provided by Hoechst; there should be quenching of DNA-radicals by Hoechst. Fitting the yield of radiation-induced ssb (G(ssb)) obtained for CT DNA and pBR322 DNA, the rate constant of this DNA-radical quenching has been calculated as 10(6) dm3 mol-1 s-1, which agrees with pulse radiolytic data. Using these rate constant values, calculations show that the protection against radiation-induced dsb formation provided by the combination of Hoechst with GSH is more than that by the combination of MeOH with GSH.
A Hierarchical Bayesian Framework For Score-Informed Source Separation Of Piano Music Signals. (2015)

[TODO] Add abstract here.
Design and comparison of mode-set adaptive IMM algorithms for maneuvering target tracking (1999)

The variable-structure multiple model (MM) state estimation approach is utilized for maneuvering aircraft (MA) radar tracking. Two adaptive time-varying mode-set interacting multiple model (IMM) tracking filters are designed and investigated: switching grid (SG) IMM and adaptive grid (AG) IMM algorithms, By Monte Carlo simulations the performances of the algorithms and the respective fixed grid (FG) IMM filter are evaluated and compared over different flight scenarios. It is shown that for the considered specific maneuvering target tracking problem, the SGIMM and AGIMM tracking filters significantly outperform the corresponding fixed structure version (the FGIMM filter) with respect to performance-to-computational load ratio.
3,5-Dicyanopyridine motifs for electron-transporting semiconductors: from design and synthesis to efficient organic light-emitting diodes (2023)

Proposing 3,5-dicyanopyridine motifs for the design of electroactive materials for optoelectronic devices, three electron-transporting semiconductors are synthesised. The best performance was observed for OLED containing FPDD as a host (EQE = 21.9%).
How Female Mice Attract Males: A Urinary Volatile Amine Activates a Trace Amine-Associated Receptor That Induces Male Sexual Interest (2018)

Individuals of many species rely on odors to communicate, find breeding partners, locate resources and sense dangers. In vertebrates, odorants are detected by chemosensory receptors of the olfactory system. One class of these receptors, the trace amine-associated receptors (TAARs), was recently suggested to mediate male sexual interest and mate choice. Here we tested this hypothesis in mice by generating a cluster deletion mouse (<i>Taar2-9</i><sup>-/-</sup>) lacking all TAARs expressed in the olfactory epithelium, and evaluating transduction pathways from odorants to TAARs, neural activity and behaviors reflecting sexual interest. We found that a urinary volatile amine, isobutylamine (IBA), was a potent ligand for TAAR3 (but not TAAR1, 4, 5, and 6). When males were exposed to IBA, brain regions associated with sexual behaviors were less active in <i>Taar2-9</i><sup>-/-</sup> than in wild type males. Accordingly, <i>Taar2-9</i><sup>-/-</sup> males spent less time sniffing both the urine of females and pure IBA than wild type males. This is the first demonstration of a comprehensive transduction pathway linking odorants to TAARs and male sexual interest. Interestingly, the concentration of IBA in female urine varied across the estrus cycle with a peak during estrus. This variation in IBA concentration may represent a simple olfactory cue for males to recognize receptive females. Our results are consistent with the hypothesis that IBA and TAARs play an important role in the recognition of breeding partners and mate choice.
Synthesis and Evaluation of 3-Aroylindoles as Anticancer Agents: Metabolite Approach (2009)

BPR0L075 (2) is a potential anticancer drug candidate designed from Combretastatin A-4 (1) based on the bioisosterism principle. Metabolites of 2, proposed from in vitro human microsome studies, were synthesized, leading to the identification of metabolite-derived analogue 10 with 40-350 pM potency against various cancer cell lines. Insights gained from the major inactive metabolite of 2 led to the development of 29, with better pharmacokinetics and improved potency in the tumor xenograft model than 2.