gebhart/patrepeval huggingface dataset:
Learning Deep Boltzmann Machines using Adaptive MCMC (2010)

When modeling high-dimensional richly structured data, it is often the case that the distribution defined by the Deep Boltzmann Machine (DBM) has a rough energy landscape with many local minima separated by high energy barriers. The commonly used Gibbs sampler tends to get trapped in one local mode, which often results in unstable learning dynamics and leads to poor parameter estimates. In this paper, we concentrate on learning DBM’s using adaptive MCMC algorithms. We first show a close connection between Fast PCD and adaptive MCMC. We then develop a Coupled Adaptive Simulated Tempering algorithm that can be used to better explore a highly multimodal energy landscape. Finally, we demonstrate that the proposed algorithm considerably improves parameter estimates, particularly when learning large-scale DBM’s. 1.
Diffusion‐weighted magnetic resonance imaging (1992)

We examined serial changes of diffusion- (DWI) and T2-weighted (T2WI) magnetic resonance images 30 minutes to 3 hours after intraluminal suture occlusion of the middle cerebral artery (MCA) in eight rats and after sham occlusion in four. We correlated the abnormal areas on DWI and T2WI with postmortem areas of infarction determined by 2,3,5-triphenyltetrazolium chloride (TTC), 24 hours after the operation. The 30-minute DWI in each MCA-occluded rat demonstrated increased signal intensity in the ipsilateral MCA territory, while T2WI showed no changes. At 3 hours, the ipsilateral DWI signal intensity increased further and the area of abnormality slightly increased. In some animals, the 3-hour T2WI disclosed an area of hyperintensity significantly smaller than that seen on the 30-minute DWI. TTC staining demonstrated an extensive MCA infarction in all rats with permanent MCA occlusion, confirmed by hematoxylin and eosin staining. The percent infarcted area of coronal brain sections, as determined by TTC staining, correlated significantly with areas on similar DWI sections at both 30 minutes and 3 hours. Sham-occluded control animals did not display any changes on DWI, T2WI, or TTC staining. The present study suggests that DWI is a very sensitive modality for detecting early ischemic brain injury, being highly correlated with post-mortem area of infarction, and may be useful to assess pharmacologic intervention.
hCLCA2 Is a p53-Inducible Inhibitor of Breast Cancer Cell Proliferation (2009)

hCLCA2 is frequently down-regulated in breast cancer and is a candidate tumor suppressor gene. We show here that the hCLCA2 gene is strongly induced by p53 in response to DNA damage. Adenoviral expression of p53 induces hCLCA2 in a variety of breast cell lines. Further, we find that p53 binds to consensus elements in the hCLCA2 promoter and mutation of these sites abolishes p53-responsiveness and induction by DNA damage. Adenoviral transduction of hCLCA2 into immortalized cells induces p53, CDK inhibitors p21 and p27, and cell cycle arrest by 24 hours, and caspase induction and apoptosis by 40 hours postinfection. Transduction of the malignant tumor cell line BT549 on the other hand does not induce p53, p21, or p27 but instead induces apoptosis directly and more rapidly. Knockout and knockdown studies indicate that growth inhibition and apoptosis are signaled via multiple pathways. Conversely, suppression of hCLCA2 by RNA interference enhances proliferation of MCF10A and reduces sensitivity to doxorubicin. Gene expression profiles indicate that hCLCA2 levels are strongly predictive of tumor cell sensitivity to doxorubicin and other chemotherapeutics. Because certain Cl(-) channels are proposed to promote apoptosis by reducing intracellular pH, we tested whether, and established that, hCLCA2 enhances Cl(-) current in breast cancer cells and reduces pH to approximately 6.7. These results reveal hCLCA2 as a novel p53-inducible growth inhibitor, explain how its down-regulation confers a survival advantage to tumor cells, and suggest both prognostic and therapeutic applications.
Regeneration of Transected Sciatic Nerves Through Semi-Permeable Nerve Guidance Channels (1986)

AEBISCHER, PATRICK; VALENTINI, ROBERT F.; WINN, SHELLEY R.; KUNZ, SANDRA; SASKEN, HARVEY; GALLETTI, PIERRE M.
The Effect of Ethylene on the Growth and Development of Wild-type and Mutant Arabidopsis thaliana (L.) Heynh (1991)

Some developmental responses of wild-type and mutant strains of Arabidopsis thaliana to ethylene have been investigated (shoot and root elongation, isodiametric cell expansion, plumular hook angle, ethylene biosynthesis, peroxidase activity). One such mutant (eti 5) shows little or no response to ethylene at concentrations up to 10000 μl 1−1 in any test; the other mutants show reduced responses. The ability of germinated seedlings to emerge through sand is directly proportional to their sensitivity to ethylene. It is suggested that this finding supports the hypothesis that increased ethylene production in response to mechanical impedance is involved, via its effects on stem thickening and hook closure, in the emergence process.
3D Traction Forces in Cancer Cell Invasion (2012)

Cell invasion through a dense three-dimensional (3D) matrix is believed to depend on the ability of cells to generate traction forces. To quantify the role of cell tractions during invasion in 3D, we present a technique to measure the elastic strain energy stored in the matrix due to traction-induced deformations. The matrix deformations around a cell were measured by tracking the 3D positions of fluorescent beads tightly embedded in the matrix. The bead positions served as nodes for a finite element tessellation. From the strain in each element and the known matrix elasticity, we computed the local strain energy in the matrix surrounding the cell. We applied the technique to measure the strain energy of highly invasive MDA-MB-231 breast carcinoma and A-125 lung carcinoma cells in collagen gels. The results were compared to the strain energy generated by non-invasive MCF-7 breast and A-549 lung carcinoma cells. In all cases, cells locally contracted the matrix. Invasive breast and lung carcinoma cells showed a significantly higher contractility compared to non-invasive cells. Higher contractility, however, was not universally associated with higher invasiveness. For instance, non-invasive A-431 vulva carcinoma cells were the most contractile cells among all cell lines tested. As a universal feature, however, we found that invasive cells assumed an elongated spindle-like morphology as opposed to a more spherical shape of non-invasive cells. Accordingly, the distribution of strain energy density around invasive cells followed patterns of increased complexity and anisotropy. These results suggest that not so much the magnitude of traction generation but their directionality is important for cancer cell invasion.
Mechanism of thrombin inactivation by immobilized heparin (1996)

The ability of heparin to interact with plasma proteins, in particular antithrombin III (ATIII) and thrombin, is its primary mechanism as an anticoagulant drug. Research efforts have focused on the biological activity of heparin under three conditions: in solution as a free molecule, chemically coupled directly onto a polymer surface, and coupled onto a polymer surface using hydrophilic spacer groups. Each of these conditions yields altered biological activity, presumably a result of differing binding interactions with ATIII and thrombin. In this report, insights into binding interaction of direct versus polyethylene oxide space immobilized heparin with ATIII, thrombin, and the generation of the thrombin-antithrombin complex will be presented.
THE REACTION OF DIARYLFORMAMIDINES WITH ETHYL MALONATE1 (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE REACTION OF DIARYLFORMAMIDINES WITH ETHYL MALONATE1ROYSTON M. ROBERTSCite this: J. Org. Chem. 1949, 14, 2, 277–284Publication Date (Print):March 1, 1949Publication History Published online1 May 2002Published inissue 1 March 1949https://pubs.acs.org/doi/10.1021/jo01154a013https://doi.org/10.1021/jo01154a013research-articleACS PublicationsRequest reuse permissionsArticle Views1460Altmetric-Citations95LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
In Vivo Antitumor Activity of Tumor-Infiltrating Lymphocytes Expanded in Recombinant Interleukin-2 (1987)

A method was described for the generation of cells from tumor-bearing mice; these cells were capable of exhibiting significant antitumor reactivity when adoptively transferred into tumor-bearing hosts. Tumor cell suspensions from a variety of tumors were able to be separated using enzymatic techniques and they were cultured in medium containing recombinant interleukin-2. Activated infiltrating lymphocytes within these tumors expanded; and, by 6-8 days after initiation of culture, lymphocytes predominated and were able to grow to large numbers. The adoptive transfer of these tumor-infiltrating lymphocytes (TILs) made possible mediation of the reduction of established 3-day pulmonary micrometastases from 5 of 7 tumors tested, including two 3-methylcholanthrene (CAS: 56-49-5)-induced sarcomas, one 1,2-dimethylhydrazine (CAS: 540-73-8)-induced colon carcinoma, and the B16 melanoma, all in C57BL/6 mice, as well as the 1660 bladder carcinoma in BALB/c mice. Approximately 2-4 X 10(6) transferred cells were capable of totally eliminating 3-day established metastases. These cells were thus 50 to 100 times more effective than lymphokine-activated killer cells in reducing established metastases; however, they could not be generated from all tumors. The concomitant administration of recombinant interleukin-2 enhanced, by approximately fivefold, the in vivo activity of these cells. The specificity of action of TILs in vivo was different from that determined by classic amputation rechallenge experiments. The tumor-infiltrating lymphocytes that developed this antitumor reactivity appeared to be Thy-1+ and did not bear the asialo GM1 antigen. The potent antitumor effect of these TILs, when transferred in vivo to tumor-bearing hosts, raises the possibility of utilizing similar approaches for the isolation and therapeutic use of lymphocytes with antitumor reactivity from human tumors.
Characterization of nonlymphoid cells derived from rat peripheral lymph (1983)

Mesenteric lymphadenectomy in rats is followed by union of peripheral and central lymphatics, allowing the collection of intestine-derived peripheral lymph cells via the thoracic duct for several days. These cells include a proportion of nonlymphoid cells (NLC) that show irregular and heterogeneous surface morphology including long pseudopodia and veils. They stain variably for nonspecific esterase and acid phosphatase and are ATPase-positive. Their nuclei are irregular and some contain cytoplasmic inclusions, some of which show peroxidase activity and/or contain DNA. NLC have a range of densitites generally lower than that of lymphocytes. Freshly collected NLC express the leukocyte-common antigen (defined by monoclonal antibody MRC Ox 1) and Ia antigens (I-A and I-E subregion products defined by monoclonal antibodies) but they show a relative lack of other surface markers normally found on rat B or T lymphocytes (W3/13, W3/25, MRC Ox 12 (sIg), MRC Ox 19) or rat macrophages (FcR, C'R, mannose R, W3/25). In general NLC are only weakly adherent to glass or plastic. Although a subpopulation of NLC appear to have had a phagocytic past, freshly collected NLC fail to phagocytose a variety of test particles in vitro. NLC also appear incapable of pinocytosis in vitro. This heterogeneity may represent distinct subpopulations of NLC or different stages in the development of a single cell lineage. Direct cannulation of mesenteric lacteals shows that the majority of NLC are derived from the small intestine and their precursors appear to be present both in lamina propria and Peyer's patches. Kinetic studies, following irradiation or intravenous tritiated thymidine, show that the majority of NLC turn over rapidly in the intestine with a modal time of 3-5 d. Studies with bone marrow chimeras show that they are derived from a rapidly dividing precursor present in normal bone marrow. NLC occur at very low frequencies in normal thoracic duct lymph at all times following cannulation. The evidence presented suggests that NLC closely resemble mouse lymphoid dendritic cells. This conclusion is supported by evidence already obtained showing that NLC are potent stimulators of the semi-allogeneic rat primary mixed leukocyte reaction. In addition to the ceils resembling dendritic cells rare monocytoid cells are found in thoracic duct lymph of lymphadenectomized specific pathogen-free rats. The proportion of these cells increases greatly when the animals are conventionally housed. It seems probable that the physiological function of NLC is to act as accessory cells in the lymph nodes to which they normally drain. Methods for enriching NLC and thus facilitating analysis of their functions are discussed.
Fast capacitance extraction of general three-dimensional structures (1992)

K. Nabors and J. White (1991) presented a boundary-element-based algorithm for computing the capacitance of three-dimensional m-conductor structures whose computational complexity grows nearly as mn, where n is the number of elements used to discretize the conductor surfaces. In that algorithm, a generalized conjugate residual iterative technique is used to solve the n*n linear system arising from the discretization, and a multipole algorithm is used to compute the iterates. Several improvements to that algorithm are described which make the approach applicable and computationally efficient for almost any geometry of conductors in a homogeneous dielectric. Results using these techniques in a program which computes the capacitance of general 3D structures are presented to demonstrate that the new algorithm is nearly as accurate as the more standard direct factorization approach, and is more than two orders of magnitude faster for large examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mitochondria‐Targeted Pharmaceutical Nanocarriers (2010)

This chapter contains sections titled: Introduction Intracellular Barriers for Mitochondria - Targeted Drug and DNA Delivery Mitochondria - Targeted Nanocarriers Conclusion References
On the Perils of Financial Intermediaries Setting Security Prices: The Mutual Fund Wild Card Option (2001)

ABSTRACT Economic distortions can arise when financial claims trade at prices set by an intermediary rather than direct negotiation between principals. We demonstrate the problem in a specific context, the exchange of open‐end mutual fund shares. Mutual funds typically set fund share price (NAV) using an algorithm that fails to account for nonsynchronous trading in the fund's underlying securities. This results in predictable changes in NAV, which lead to exploitable trading opportunities. A modification to the pricing algorithm that corrects for nonsynchronous trading eliminates much of the predictability. However, there are many other potential sources of distortion when intermediaries set prices.
Parallelism-Aware Batch Scheduling: Enhancing both Performance and Fairness of Shared DRAM Systems (2008)

In a chip-multiprocessor (CMP) system, the DRAM system is shared among cores. In a shared DRAM system, requests from a thread can not only delay requests from other threads by causing bank/bus/row-buffer conflicts but they can also destroy other threadspsilaDRAM-bank-level parallelism. Requests whose latencies would otherwise have been overlapped could effectively become serialized. As are sult both fairness and system throughput degrade, and some thread scan starve for long time periods. This paper proposes a fundamentally new approach to designing a shared DRAM controller that provides quality of service to threads,while also improving system throughput. Our parallelism-aware batch scheduler (PAR-BS) design is based on two key ideas. First, PARBS processes DRAM requests in batches to provide fairness and to avoid starvation of requests. Second, to optimize system throughput,PAR-BS employs a parallelism-aware DRAM scheduling policy that aims to process requests from a thread in parallel in the DRAM banks, thereby reducing the memory-related stall-time experienced by the thread. PAR-BS seamlessly incorporates support for system-level thread priorities and can provide different service levels, including purely opportunistic service, to threads with different priorities.We evaluate the design trade-offs involved in PAR-BS and compare it to four previously proposed DRAM scheduler designs on 4-, 8-, and16-core systems. Our evaluations show that, averaged over 100 4-core workloads, PAR-BS improves fairness by 1.11X and system through put by 8.3% compared to the best previous scheduling technique, Stall-Time Fair Memory (STFM) scheduling. Based on simple request prioritization rules, PAR-BS is also simpler to implement than STFM.
Quantitative MR imaging of lumbar intervertebral disks and vertebral bodies: influence of diurnal water content variations. (1993)

The influence of diurnal water content variation on T1 and T2 and relative proton density (Nr) in intervertebral disks and vertebral bodies was studied in 10 healthy adult volunteers. T1, T2, and Nr were calculated from a set of 20 images obtained at 1.5 T with five single-section, multiecho sequences at different repetition times. Volunteers were randomized into study (one measurement in the morning and one in the evening) and control (two consecutive measurements in the morning) groups. In the study group, evening mean T1 and Nr in intervertebral disks and in vertebral bodies were significantly (P < .001) less than measured in the morning. Mean T2 in vertebral bodies significantly (P < .05) increased between morning and evening measurements. Diurnal variations were significantly less pronounced in degenerative than in normal intervertebral disks. No significant changes occurred in the control group. Relaxation time and Nr measurements allow sufficiently accurate estimation of diurnal water content variation in cohorts of vertebral bodies and intervertebral disks.
Effects of androgen deficiency and replacement on prostate zonal volumes (2001)

We conclude that, during mid-life, chronic androgen deficiency due to hypogonadism is associated with reduced central, peripheral and total prostate volumes. Reduced prostate volumes persist even during long-term maintenance of effective androgen replacement therapy with physiological testosterone concentrations until the fourth decade of life. After that, prostate volumes increase with age regardless of androgen deficiency or replacement. These findings suggest that, during mid-life, age is a more important determinant of prostate growth than ambient testosterone concentrations maintained in the physiological range. The persistently subnormal prostate volumes despite adequate androgen replacement therapy may explain the apparent paucity of cases of overt prostate disease among testosterone-treated androgen deficient men who retain protection against prostate disease despite physiological androgen replacement therapy.
Metallographic Cooling Rate of IVA Irons Revisited (2005)

There is long standing problem reconciling the chemical evidence that the IVA iron meteorites formed in a core with the diverse cooling rates reported by several researchers. This large inferred range of cooling rates suggests that the IVA irons were distributed at different depths in a parent body with a complex structure when the Widmanstatten pattern formed. On the other hand, some researchers argued that the diverse cooling rates in group IVA result from inaccurate model parameters such as phase diagram, interdiffusion coefficients, and kamacite nucleation and growth mechanisms. In addition, the measured cooling rates may not apply for the same cooling temperature ranges, and the variation in the crystallographic orientations of the Widmanstatten plates on the analysis surface may result in inaccurate measurements of widths needed for the computer simulation models. We have revaluated the major parameters in computer model developed by Hopfe and Goldstein and measured cooling rates for the IVA irons. Such data are useful in evaluating whether these meteorites were part of a single core of a parent body during the formation of the Widmanstatten pattern.
Molecular structure of a major insulin/mitogen-activated 70-kDa S6 protein kinase. (1990)

The molecular structure of a rat hepatoma 70-kDa insulin/mitogen-stimulated S6 protein kinase, obtained by molecular cloning, is compared to that of a rat homolog of the 85-kDa Xenopus S6 protein kinase alpha; both kinases were cloned from H4 hepatoma cDNA libraries. The 70-kDa S6 kinase (calculated molecular mass of 59,186 Da) exhibits a single catalytic domain that is most closely related in amino acid sequence (56% identity) to the amino-terminal, kinase C-like domain of the rat p85 S6 kinase (calculated molecular mass of 82,695 Da); strong similarity extends through a further 67 residues carboxyl-terminal to the catalytic domain (40% identity), corresponding to a region also conserved among the kinase C family. Outside of this segment of approximately 330 amino acids, the structures of the p70 and p85 S6 kinases diverge substantially. The p70 S6 kinase is known to be activated through serine/threonine phosphorylation by unidentified insulin/mitogen-activated protein kinases. A model for the regulation of p70 S6 protein kinase activity is proposed wherein the low activity of the unphosphorylated enzyme results from the binding of a basic, inhibitory pseudosubstrate site (located carboxyl-terminal to the extended catalytic domain) to an acidic substrate binding region (located amino-terminal to the catalytic domain); substrate binding is thereby prevented. S6 kinase activation requires displacement of this inhibitory segment, which is proposed to occur consequent to its multiple phosphorylation. The putative autoinhibitory segment contains several serine and threonine residues, each followed directly by a proline residue. This motif may prevent autophosphorylation but permit transphosphorylation; two of these serine residues reside in a maturation promoting factor (MPF)/cdc-2 consensus motif. Thus, hormonal regulation of S6 kinase may involve the action of MPF/cdc-2 or protein kinases with related substrate specificity.