gebhart/patrepeval huggingface dataset:
An upper arm model for simulated weightlessness (2000)

This investigation examined the effects of 4 weeks of non-dominant arm unloading on the functional and structural characteristics of the triceps brachii muscle of six normo-active college-age males (age: 23 +/- 1 years, height: 176 +/- 4 cm, weight: 76 +/- 6 kg). The primary intention of this study was to determine if arm unloading is an effective analogue for simulating the effects of weightlessness on human skeletal muscle. Subjects were tested 2-3 days preceding unloading in a standard arm sling and following removal of the sling. The sling was worn during waking hours to unload the arm. Subjects were allowed to remove the sling during sleep and bathing. Torque production (Nm) during maximal isometric extension at 90 degrees significantly declined (P < 0.05) in response to unloading (53.93 +/- 5.07 to 47.90 +/- 5.92; 12%). There was no significant change (P > 0.05) in the force-velocity attributes of the triceps over the other measured velocities (1.05, 1.57, 2.09, 3.14, 4.19, 5.24 rad.s-1). Cross-sectional muscle area (CSA) of the upper arm was smaller (44.3 +/- 2.7 to 42.4 +/- 2.5 cm2; 4%) following 4 weeks of unloading (P < 0.05). Histochemical analysis of individual muscle fibres demonstrated reductions in fibre CSA of 27 and 18% for type I and type II fibres, respectively. However, these changes were not statistically significant. Electrophoretic analysis of muscle samples revealed a significant increase (40 +/- 7 to 58 +/- 4%, pre- and post-, respectively) in myosin heavy chain (MHC) type II isoforms following unloading. Reductions in type I MHC isoform composition failed to reach statistical significance (P < 0.08). Amplitude of the integrated electromyographic (IEMG) signal during maximal isometric contraction of the long head of the triceps decreased by 21% in response to the 4-week unloading period (P < 0.05). The changes in triceps, muscle structure and function found with arm unloading are similar in magnitude and direction to data obtained from humans following exposure to real and simulated weightlessness. These findings demonstrate that arm unloading produces some of the effects seen in response to weightlessness in muscles of the upper arm and provides potential for an additional model to simulate the effects of microgravity on human skeletal muscle.
Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids (2014)

We investigated the influence of the gut microbiota and microbially produced short-chain fatty acids (SCFAs) on gut functioning. Many commensal bacteria in the gut produce SCFAs, particularly butyrate, acetate, and propionate, which have been demonstrated to reduce the risk of gastrointestinal disorders. Organoids-small crypt-villus structures grown from ileal intestinal stem cells-were exposed to SCFAs and two specific gut bacteria. Akkermansia muciniphila, found in the intestinal mucus, was recently shown to have a favorable effect on the disrupted metabolism associated with obesity. Faecalibacterium prausnitzii is a commensal gut bacterium, the absence of which may be associated with Crohn's disease. We showed that in our model, A. muciniphila induces stronger effects on the host than F. prausnitzii. We observed that A. muciniphila and propionate affect the expression of genes involved in host lipid metabolism and epigenetic activation or silencing of gene expression. We demonstrated that organoids provide a powerful tool for host-microbe interaction studies.
Chromaticity and color temperature for achitectural lighting (2002)

HBLEDs bring a new dimension to architectural lighting design: color. Compared to traditional "white" light sources such as fluorescent and metal halide lamps, HBLEDs offer lighting designers unprecedented control over color temperature and lamp chromaticity. This raises two important questions: 1) How should the correlated color temperature metric used by lamp manufacturers be applied to HBLED-based light sources; and 2) What are appropriate limits on chromaticity variances for LED clusters and arrays? The answers to these questions will influence the acceptance of HBLEDs by architectural lighting designers.
The Albatross Project: Parallel Application Support for Computational Grids. (2000)

The aim of the Albatross project is to study applications and programming environments for computational grids consisting of multiple clusters that are connected by wide-area networks. Parallel processing on such systems is useful but challenging, given the large differences in latency and bandwidth between LANs and WANs. We provide efficient algorithms and programming environments that exploit the hierarchical structure of wide-area clusters to minimize communication over the WANs. In addition, we use highly efficient local-area communication protocols. We illustrate this approach using the Manta high-performance Java system and the MagPIe MPI library, both of which are implemented on a collection of four Myrinet-based clusters connected by wide-area ATM networks. Our sample applications obtain high speedups on this wide-area system. 1 Introduction As computational grids become more widely available, it becomes feasible to run parallel applications on multiple clusters at d...
Apoptosis Promotes a Caspase-induced Amino-terminal Truncation of IκBα That Functions as a Stable Inhibitor of NF-κB (1999)

Caspases are cell death cysteine proteases that are activated upon the induction of the apoptotic program and cleave target proteins in a sequence-specific manner to promote cell death. Recently, Barkett et al. (Barkett, M., Xue, D., Horvitz, H. R., and Gilmore, T. D. (1997) J. Biol. Chem. 272, 29419-29422) have shown that IkappaBalpha, the inhibitory subunit of the transcription factor NF-kappaB, can be cleaved by caspase-3 in vitro at a site that potentially produces a dominant inhibitory form of IkappaBalpha. The involvement of NF-kappaB in the inhibition of cell death led us to ask whether apoptotic stimuli would induce the caspase-mediated cleavage of IkappaBalpha in vivo. In this study, we show that apoptosis leads to the caspase-mediated amino-terminal truncation of IkappaBalpha (DeltaN-IkappaBalpha). Our data show that DeltaN-IkappaBalpha can bind NF-kappaB, suppress NF-kappaB activation, and sensitize cells to death. Since activated NF-kappaB plays a role in the inhibition of cell death, these data suggest that caspase-mediated cleavage of IkappaBalpha may be a mechanism to suppress NF-kappaB and its associated antiapoptotic activity.
Nitric Oxide Mechanism of Protection in Ischemia and Reperfusion Injury (2009)

In 1992 nitric oxide (NO) was declared molecule of the year by Science magazine, and ever since research on this molecule continues to increase. Following this award, NO was shown to be a mediator/protector of ischemia and reperfusion injury in many organs, such as the heart, liver, lungs, and kidneys. Controversy has existed concerning the actual protective effects of NO. However, literature from the past 15 years seems to reinforce the consensus that NO is indeed protective. Some of the protective actions of NO in ischemia and reperfusion are due to its potential as an antioxidant and anti-inflammatory agent, along with its beneficial effects on cell signaling and inhibition of nuclear proteins, such as NF-kappa B and AP-1. New therapeutic potentials for this drug are also continuously emerging. Exogenous NO and endogenous NO may both play protective roles during ischemia and reperfusion injury. Sodium nitroprusside and nitroglycerin have been used clinically with much success; though only recently have they been tested and proven effective in attenuating some of the injuries associated with ischemia and reperfusion. NO inhalation has, in the past, mostly been used for its pulmonary effects, but has also recently been shown to be protective in other organs. The potential of NO in the treatment of ischemic disease is only just being realized. Elucidation of the mechanism by which NO exerts its protective effects needs further investigation. Therefore, this paper will focus on the mechanistic actions of NO in ischemia and reperfusion injury, along with the compound's potential therapeutic benefits.
Modulation of Conventional Outflow Facility by the Adenosine A1AgonistN6-Cyclohexyladenosine (2005)

These studies demonstrate that the adenosine agonist CHA significantly increases conventional outflow facility in the perfused bovine eye. Analysis of the CHA concentration-response curve and inhibition of the CHA-induced increase in outflow facility by the adenosine A(1) antagonist confirms that this response is mediated by the activation of adenosine A(1) receptors. The inhibition of the CHA-induced increase in outflow facility by the MMP inhibitor GM-6001 provides evidence that the secretion and activation of MMPs within the conventional outflow pathway play a central role in the ocular hypotensive action of adenosine A(1) agonists.
Expression, assembly competence and antigenic properties of hepatitis B virus core gene deletion variants from infected liver cells. (1999)

Previous studies have shown that the progression of hepatitis B virus-related liver disease in long-term immunosuppressed kidney transplant recipients is associated with the accumulation of virus variants carrying in-frame deletions in the central part of the core gene. A set of naturally occurring core protein variants was expressed in Escherichia coli in order to investigate their stability and assembly competence and to characterize their antigenic and immunogenic properties. In addition, a library of core gene variants generated in vitro with deletions including the major immunodominant region (MIR) of the core protein was investigated. The position and length of deletions determined the behaviour of mutant core proteins in E. coli and their assignment to one of the three groups: (i) assembly-competent, (ii) stable but assembly-incompetent and (iii) unstable proteins. In vivo core variants with MIR deletions between amino acids 77 and 93 belong to the first group. Only proteins with the shortest deletion (amino acids 86-93) showed stability and self-assembly at the same level as wild-type cores, and they showed reduced antigenicity and immunogenicity. Mutants with deletions extending N-terminally beyond residue G73 or C-terminally beyond G94 were found to be assembly-incompetent. We suggest that G73 and G94 are involved in the folding and the native assembly of core molecules, whereas the intervening sequence determines the antibody response. Depending on their ability to form stable proteins or to assemble into particles, core mutants could contribute to liver cell pathogenesis in different ways.
A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma (2019)

This three-factor model includes genomic (SNV count >9) and clinical (NLR <5, lack of visceral metastasis) variables predictive for benefit to ICI but not taxane therapy for mUC. External validation of these hypothesis-generating results is warranted to enable use in routine clinical care.
Potent Cyclic Monomeric and Dimeric Peptide Inhibitors of VLA-4 (?4?1 Integrin)-Mediated Cell Adhesion Based on the Ile-Leu-Asp-Val Tetrapeptide (2000)

Potent monomeric and dimeric cyclic peptide very late antigen-4 (VLA-4) inhibitors have been designed based on a tetrapeptide (Ile-Leu-Asp-Val) sequence present in a 25-amino acid peptide (CS-1) reported in the literature. The peptides, synthesized by the SPPS techniques, were evaluated in the in vitro cell adhesion assays and in the in vivo inflammation models. The N- to C-terminal cyclic peptides such as cyclo(Ile-Leu-Asp-Val-NH-(CH2)2-S-(CH2)2-CO) (28) and cyclo(MeIle-Leu-Asp-Val-D-Ala-D-Ala) (31), monomeric and dimeric peptides containing piperazine (Pip) or homopiperazine (hPip) residues as linking groups, e.g. cyclo(MeIle-Leu-Asp-Val-Pip-CH2CO-NH-(CH2)2-S-CH2-CO) (49) and cyclo(MeIle-Leu-Asp-Val hPip-CH2CO-MeIle-Leu-Asp-Val-hPip-CH2CO) (58) and cyclic peptides containing an amide bond between the side chain amino group of an amino acid such as Lys and the C-terminal Val carboxyl group, e.g. Ac-cyclo(D-Lys-D-Ile-Leu-Asp-Val) (62) and beta-Ala-cyclo(D-Lys-D-Leu-Leu-Asp-Val) (68) were more potent than CS-1 in inhibiting the adhesion of the VLA-4-expressing MOLT-4 cells to fibronectin. The more potent compounds were highly selective and did not affect U937 cell adhesion to fibronectin (VLA-5), PMA-differentiated U937 cell adhesion to intercellular cell adhesion molecule- 1-expressing Chinese hamster ovary cells (LFA-1) and ADP-induced platelet aggregation (GPIIb/IIIa). A number of the more potent compounds inhibited ovalbumin-induced delayed type hypersensitivity in mice and some were 100-300 times more potent (ED50 = 0.003-0.009 mg/kg/day, s.c.) than CS-1. Two peptides, Ac-cyclo(D-Lys D-Ile-Leu-Asp-Val) (62) and cyclo(CH2CO-Ile-Leu-Asp-Val-Pip-CH2CO-Ile-Leu-Asp-Val-Pip) (55), were formulated in poly(DL-lactide-co-glycolide) depots and the release profile was investigated in vitro over a 30-day period.
Renal Blood Flow Dynamics and Arterial Pressure Lability in the Conscious Rat (2001)

It is not known whether renal blood flow (RBF) is still autoregulated when the kidney is exposed to large transient blood pressure (BP) fluctuations such as those occurring spontaneously in conscious sinoaortic baroreceptor-denervated (SAD) rats. In this study, BP and RBF were simultaneously recorded in 8 SAD rats (2 weeks before study) and 8 baroreceptor-intact rats during approximately 3 hours of spontaneous activity. The kidney used for RBF recordings was denervated to prevent the interference of changes in renal sympathetic tone with autoregulatory mechanisms. In intact rats, RBF variability (coefficient of variation 9.1+/-0.8%) was larger (P<0.02) than BP variability (5.9+/-0.2%). This was mainly because of slow changes in RBF that were unrelated to BP and also to a prominent oscillation of RBF of approximately 0.25-Hz frequency. Autoregulatory patterns were identified at frequencies <0.1 Hz and provided a modest attenuation of BP fluctuations. In SAD rats, RBF variability (12.4+/-1.6%) was lower (P<0.02) than BP variability (18.2+/-1.1%). Autoregulation powerfully attenuated BP changes <0.1 Hz (normalized transfer gain 0.21+/-0.02 in the 0.0015- to 0.01-Hz frequency range) but at the expense of an oscillation located at approximately 0.05 Hz that possibly reflected the operation of the tubuloglomerular feedback. Large transient hypertensive episodes were not translated into RBF changes in SAD rats. We conclude that autoregulatory mechanisms have an ample capacity to protect the kidney against spontaneous BP fluctuations in the conscious rat. This capacity is not fully used under normal conditions of low BP variability.
Correlation between Interferon‐γ Secretion and Cytotoxicity, in Virus‐Specific Memory T Cells (2004)

ELISpot and intracellular cytokine staining are replacing the traditional cytolytic ((51)Cr release) assay method in vaccine trials using human immunodeficiency virus (HIV)-1, and it is widely assumed that the number of interferon (IFN)- gamma -secreting T cells is a surrogate for the level of cytolytic activity. Thus, we sought to determine whether the detection of IFN- gamma in CD8(+) T cells correlates with cytolytic ability in vitro. In 29 (69.0%) of 42 HIV-1-seronegative immunocompetent individuals (22 unvaccinated and 20 vaccinated), virus-specific T cell responses recognizing cytomegalovirus, Epstein-Barr virus, and influenza and HIV-1 Gag epitopes were detected by at least 1 assay method (ELISpot, intracellular cytokine staining, and/or (51)Cr release), and 18 (62.1%) of these 29 demonstrated both IFN- gamma secretion and cytolysis. There was strong correlation between the results of IFN- gamma ELISpot and those of IFN- gamma intracellular cytokine staining ( rho =0.88) and between the results of (51)Cr release and those of intracellular cytokine staining ( rho =0.81); although the correlation is not absolute, intracellular cytokine staining can be used--and is superior to ELISpot--as a surrogate for cytolytic assays.
Characterization and evidence of mobilization of the LEE pathogenicity island of rabbit‐specific strains of enteropathogenic Escherichia coli (2002)

We have characterized the LEE pathogenicity islands (PAIs) of two rabbit-specific strains of enteropathogenic E. coli (REPEC), 83/39 (serotype O15:H-) and 84/110-1 (O103:H2), and have compared them to homologous loci from the human enteropathogenic and enterohaemorrhagic E. coli strains, E2348/69 and EDL933, and another REPEC strain, RDEC-1. All five PAIs contain a 34 kb core region that is highly conserved in gene order and nucleotide sequence. However, the LEE of 83/39 is significantly larger (59 540 basepairs) than those of the human strains, which are less than 44 kb, and has inserted into pheU tRNA. The regions flanking the 34 kb core of 83/39 contain homologues of two putative virulence determinants, efa1/lifA and senA. The LEE of 84/110-1 is approximately 85 kb and is located at pheV tRNA. Its core is almost identical to those of 83/39 and RDEC-1, apart from a larger espF gene, but its flanking regions contain trcA, a putative virulence determinant of EPEC. All three REPEC LEE PAIs contain a gene for an integrase, Int-phe. The LEE PAI of 84/110-1 is also flanked by short direct repeats (representing the 3'-end of pheV tRNA), suggesting that it may be unstable. To investigate this possibility, we constructed a LEE::sacB derivative of 84/110-1 and showed that the PAI was capable of spontaneous deletion. We also showed that Int-phe can mediate site-specific integration of foreign DNA at the pheU tRNA locus of E. coli DH1. Together these results indicate possible mechanisms of mobilization and integration of the LEE PAI.
Effects of Chromatic Illumination on Cyanobacterial Phycobilisomes (1981)

Pseudanabaena 7409 is a chromatically cyanobacterium which photocontrols the synthesis of both phycoerythrin and phycocyanin [Tandeau de Marsac (1977) J. Bacteriol. 130, 82--91]. Phycobilisomes, isolated from cells grown in either green or red light, have been dissociated and the component biliproteins purified and characterized. Phycobilisomes isolated from cells grown in green light were composed of allophycocyanin B, allophycocyanin, two phycocyanin subunits (one alpha-type and one beta-type subunit), phycoerythrin and eight uncolored polypeptides. When dissociated phycobilisomes were chromatographed on DEAE-cellulose at pH 5.5, most of the phycocyanin was recovered as part of a large (17.3 S) multiprotein complex with phycoerythrin (molar ratio 1 : 1). This complex also contained five of the uncolored polypeptides found in intact phycobilisomes isolated from cells grown in green light. Phycobilisomes isolated from cells grown in red light were composed of allophycocyanin B, allophycocyanin, four phycocyanin subunits (two alpha-type and two beta-type subunits), and six uncolored polypeptides. When these phycobilisomes were dissociated, the phycocyanin was recovered as a large (21.0 S) multiprotein complex which was composed of the four phycocyanin subunits types and four uncolored polypeptides. This complex was morphologically identical to the rod-like stacks of discs about 6 x 12 nm which form the peripheral rods of intact phycobilisomes. Each of the four phycocyanin subunits found in the complex isolated from the phycobilisomes of cells grown in red light was purified to homogeneity and characterized. Amino acid compositions of the four subunits indicated that each subunit was a unique gene product. Two of the subunits of the complex were apparently identical to those of the phycocyanin purified from phycobilisomes isolated from cells grown in green light. These studies suggest that one pair of phycocyanin subunits was synthesized constitutively (i.e. irrespective of the light wavelength to which the cells were exposed during growth) while the synthesis of the second pair of phycocyanin subunits was specifically induced during growth in red light.
Diode-laser array modes: discrete and continuous models and their stability (1991)

A new class of mode profiles appropriate to large one-dimensional evanescently coupled laser diode arrays can be conveniently approximated by solutions to a Riccatti equation derived from a continuous model of the discrete array. Solutions of the latter model are shown to agree with the continuous solutions in the large-N limit. The continuous model has the advantage that new types of discrete array modes can readily be identified. Stability analyses of the discrete array modes as a function of increasing N confirm that these laser systems are intrinsically unstable in the free-running mode.
The Theory of Bacterial Constant Growth Apparatus (1955)

Recent work in bacterial genetics has emphasised the usefulness of apparatus whose purpose is to maintain a constant population of bacteria in a state of active growth. Several such devices have been described for example by Monod (1950), Novick and Szilard (1950), and Perret (1954). It seems worthwhile to give a short account of the underlying theory as a guide to the problems of design likely to be encountered with organisms of different growth characteristics; or under various conditions of culture. Mathematically the problem may be stated as follows:-Consider an organism growing freely in a limited, conistant volume of nutrient. After some period of growth factors come into play which depress the power of the organism, to divide and eventually stop it growing altogether. These factors may be of several different kinds: for example, exhaustion of nutrient, insufficiency of oxygen, or production of some toxic metabolite, the general effect however, is that the growth rate of the population at any time is a function of its size (n) so that
Controls of Hair Follicle Cycling (2001)

Nearly 50 years ago, Chase published a review of hair cycling in which he detailed hair growth in the mouse and integrated hair biology with the biology of his day. In this review we have used Chase as our model and tried to put the adult hair follicle growth cycle in perspective. We have tried to sketch the adult hair follicle cycle, as we know it today and what needs to be known. Above all, we hope that this work will serve as an introduction to basic biologists who are looking for a defined biological system that illustrates many of the challenges of modern biology: cell differentiation, epithelial-mesenchymal interactions, stem cell biology, pattern formation, apoptosis, cell and organ growth cycles, and pigmentation. The most important theme in studying the cycling hair follicle is that the follicle is a regenerating system. By traversing the phases of the cycle (growth, regression, resting, shedding, then growth again), the follicle demonstrates the unusual ability to completely regenerate itself. The basis for this regeneration rests in the unique follicular epithelial and mesenchymal components and their interactions. Recently, some of the molecular signals making up these interactions have been defined. They involve gene families also found in other regenerating systems such as fibroblast growth factor, transforming growth factor-beta, Wnt pathway, Sonic hedgehog, neurotrophins, and homeobox. For the immediate future, our challenge is to define the molecular basis for hair follicle growth control, to regenerate a mature hair follicle in vitro from defined populations, and to offer real solutions to our patients' problems.