gebhart/patrepeval huggingface dataset:
Supporting fine-grained synchronization on a simultaneous multithreading processor (1999)

This paper proposes and evaluates new synchronization schemes for a simultaneous multithreaded processor. We present a scalable mechanism that permits threads to cheaply synchronize within the processor, with blocked threads consuming no processor resources. We also introduce the concept of lock release prediction, which gains an additional improvement of 40%. Overall, we show that these improvements in synchronization cost enable parallelization of code that could not be effectively parallelized using traditional techniques.
Regulating the Beta Cell Mass as a Strategy for Type-2 Diabetes Treatment (2015)

The incidence of type 2 diabetes (T2D) increases dramatically worldwide and has created an enormous health care burden. Obesity, dyslipidemia and insulin resistance are major risk factors for the development of T2D, but the major factor leading to the disease is failure of the insulin-producing beta cell mass to compensate for increasing insulin demands of the body. Progression of the disease further diminishes the beta cell mass as a result of lipotoxicity and glucotoxicity for which beta cells are particularly sensitive. Hence, treatment aiming to prevent beta cell loss or increase the number of beta cells could inhibit diabetes progression or lead to restoration of normal metabolism. Whereas current and new antidiabetic drugs are mainly targeting insulin secretion and action or glucose uptake, newer interventions must be found that prevent beta cell loss or increase beta cell number. The targets for this are beta cell proliferation, neogenesis and survival. This review examines major evidence from animal experiments suggesting that it is feasible to regulate the beta cell mass by bioactive compounds like growth factors, cytokines, hormones, phytochemicals and small molecules. Often the mode of action remains unclear due to inadequate methods to assess the effects of the compounds on the beta cell dynamics. Furthermore, a major challenge is to identify compounds with sufficient specificity in order to avoid unwanted effects on other cell types. Provided such safety issues can be solved, this may provide a curative approach for diabetes treatment.
Early exit from an above market lease (2005)

Purpose – This paper aims to examine an unwinding of a lease obligation, where the in‐place rental rate exceeds current market. Design/methodology/approach – The paper examines some of the critical variables in mitigating lease obligations, and uses a case study of a 2003 transaction near San Jose, California to elaborate. Findings – After a 3 year period of vacancy increases and rental declines, the lease is a liability to a company with no projected need for the premises. The passive Landlord has little incentive to settle the lease in these market conditions, but is eager to avoid potential further credit erosion, and tests the market in a sales process. Originality/value – The paper provides information of value to all parties interested or involved in property leasing decisions.
Endothelin Stimulates Ciliary Beat Frequency and Chloride Secretion in Canine Cultured Tracheal Epithelium (1991)

Endothelin, an endothelium-derived vasoconstrictor peptide, has recently been reported to exist in airway epithelial cells. To elucidate a possible role of endothelin on epithelial functions, we studied the effects of this peptide on ciliary beat frequency (CBF) and electrical properties of canine cultured tracheal epithelium by a microphoto-oscillation method and Ussing's short-circuited technique, respectively. Endothelin dose-dependently increased CBF, the maximal increase above the baseline value and EC50 being 32.3 +/- 4.0% (P less than 0.001) and 3 nM, respectively. This effect was moderately attenuated by pretreatment of cells with indomethacin and greatly reduced by Ca2(+)-free medium. Addition of endothelin (10(-6) M) to the mucosal bath of Ussing chamber increased short-circuit current from 5.1 +/- 1.2 to 9.4 +/- 1.7 microA/cm2 (P less than 0.05) and potential difference from 2.9 +/- 0.4 to 5.0 +/- 0.9 mV (P less than 0.05), an effect that was inhibited by indomethacin or Ca2(+)-deficiency and was abolished by the Cl transport inhibitor bumetanide or substitution of Cl with iodide in the medium. These results indicate that endothelin stimulates ciliary motility and Cl secretion probably through an increase in cytosolic Ca2+ and partially a prostaglandin synthesis in canine tracheal epithelium, and suggest that this peptide might play a role in modulating airway mucociliary transport functions.
Excited-State Lifetime Assay for Protein Detection on Gold Colloids−Fluorophore Complexes (2009)

The interaction of the surface plasmons of gold nanoparticles (NP) a few nanometers in size with fluorophores can be used to engineer their fluorescence properties. This possibility can be exploited in principle to obtain nanodevices for protein−protein recognition. We studied different types of constructs based on gold NPs on which derivatives of fluorescein were bound. The interaction of this fluorophore with the gold surface plasmon resonances, mainly occurring through quenching, affects its excited-state lifetime that is measured by fluorescence burst analysis in standard solutions. The binding of proteins to the gold NPs through antigen−antibody recognition further modifies the dye excited-state lifetime. This change can therefore be used to measure the protein concentration. The data reported here indicate that one can measure the concentration of bovine serum albumine in solution with an apparent limit of detection of 5 ± 2 pM.
Analysis of the Role of Calmodulin Binding and Sequestration in Neuromodulin (GAP-43) Function (1996)

We demonstrated previously that forced expression of the neuronal phosphoprotein neuromodulin (also known as GAP-43, F1, B-50, and p57) in mouse anterior pituitary AtT-20 cells enhances depolarization-mediated secretion and alters cellular morphology. Here we analyze the role of calmodulin binding by neuromodulin in these responses. In cells expressing wild-type neuromodulin, a complex with calmodulin that is sensitive to intracellular calcium and phosphorylation is localized to the plasma membrane. Transfection of several mutant forms of neuromodulin shows that the effects of this protein on secretion are dependent on both calmodulin binding and association with the plasma membrane. In contrast, the morphological changes depend only on membrane association. Thus, the multitude of effects of neuromodulin noted in previous studies may result from divergent properties of this protein.
<title>Three-dimensional silicone microfluidic interconnection scheme using sacrificial wax filaments</title> (2000)

A very simple room-temperature procedure is presented herein for formation of true three-dimensionality of microplumbing in plastic (silicone elastomer in this case), by molding the plastic to simply encapsulate a pre-formed network of sacrificial wax threads or other connected wax configurations which are ultimately to become micro channels and cavities in the plastic motherboard. When these wax sacrificial areas are etched away with acetone, precise cavities, channels, and capillaries results with direct arbitrary three- dimensionality for the first time. This method leads also to a simple and effective external interconnect scheme where ordinary fused silica tubes may be press-fitted into the surface opening to withstand high pressure. This method may be extended for connection of multiple levels of silicone motherboards together using small sections of fused silica tubing, with no loss of stacking volume because of the lack of any connector lips or bosses. An array of micro channels having circular cross sections with diameters of 100, 150 and 200 microns were molded on silicone elastomer using wax thread. The wax thread was dissolved in acetone after the silicon elastometer became components (motherboards) while being able to control the channel lengths within the stacks as desired. Mixing chambers were also molded in a single silicone elastomer layer, because true three-dimensionality is trivially possible without the complexity of multi stacked lithography.
Volume slicing display (2009)

The Volume Slicing Display enables interactive exploration of volumetric data (for example, medical images) using a piece of plexiglass (or paper) that functions both as a control interface and a passive, untethered projection screen.
Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing (2012)

Voltage-gated sodium channels are vital membrane proteins essential for electrical signalling; in humans, they are key targets for the development of pharmaceutical drugs. Here we report the crystal structure of an open-channel conformation of NavMs, the bacterial channel pore from the marine bacterium Magnetococcus sp. (strain MC-1). It differs from the recently published crystal structure of a closed form of a related bacterial sodium channel (NavAb) by having its internal cavity accessible to the cytoplasmic surface as a result of a bend/rotation about a central residue in the carboxy-terminal transmembrane segment. This produces an open activation gate of sufficient diameter to allow hydrated sodium ions to pass through. Comparison of the open and closed structures provides new insight into the features of the functional states present in the activation cycles of sodium channels and the mechanism of channel opening and closing.
A Levinson Algorithm Based on an Isometric Transformation of Durbin's (2008)

Starting from the Durbin algorithm in polynomial space with an inner product defined by the signal autocorrelation matrix, an isometric transformation is defined that maps this vector space into another one where the Levinson algorithm is performed. Alternatively, for iterative algorithms such as discrete all-pole (DAP), an efficient implementation of a Gohberg-Semencul (GS) relation is developed for the inversion of the autocorrelation matrix which considers its centrosymmetry. In the solution of the autocorrelation equations, the Levinson algorithm is found to be less complex operationally than the procedures based on GS inversion for up to a minimum of five iterations at various linear prediction (LP) orders.
Upregulated Expression of Toll-Like Receptor 4 in Monocytes Correlates with Severity of Acute Cerebral Infarction (2008)

In the present study, we observed the expression of toll-like receptor 4 (TLR4) and its downstream signal pathway in peripheral blood monocytes (PBMs) from patients with acute cerebral infarct (ACI). The expression of TLR4 and MyD88 by PBMs was determined by flow cytometry and reverse transcriptase-polymerase chain reaction, and nuclear factor-kappaB (NF-kappaB) activity was detected by electrophoretic mobility shift assay. Ischemia/reperfusion injury-induced cerebral edema, infarction area, and neurologic impairment scores were determined in MyD88 gene knockout mice. The results indicated a significant increase in circulating TLR4(+) monocytes in ACI patients as compared with the control group and the transient ischemia attack (TIA) group. This change paralleled an elevation in TLR4mRNA transcription and serum tumor necrosis factor-alpha (TNF-alpha) and interleukin (IL)-6 in the ACI and TIA groups. Correlation analysis showed TLR4 expression to significantly correlate with cytokine levels and stroke severity. MyD88mRNA differed insignificantly among the three groups. Compared with wild-type mice, 6 h of cerebral ischemia followed by 24 h of reperfusion did not significantly change cerebral edema, cerebral infarction area, and neurologic impairment scores in MyD88 gene knockout mice. Compared with the control group, serum heat shock protein (HSP) 60 increased significantly in the ACI and TIA groups, leading to NF-kappaB activation in TLR4/CD14-transfected HEK293 cells. It is suggested that upregulated TLR4 expression on PMBs may act as one of the peripheral mechanisms of inflammatory injury after ACI. Moreover, circulating HSP60 may be a ligand for TLR4, which is involved in the peripheral mechanism of inflammatory injury after ACI, possibly through an MyD88-independent signal pathway.
<title>Real-time image histogram equalization using FPGA</title> (1998)

A new hardware implementation of histogram equalization by means of Field Programmable Gate Array (FPGA) is presented. Histogram equalization is an effective means of image enhancement. Its real-time processing requires a great deal of memory and very high processing speed. The logic cell nature of XC4000 family's FPGA is most suitable for performing real-time pixel-level image processing operations such as histogram equalization. A core is constructed to complete this histogram statistics and histogram equalization. As a result, the chip makes circuits and system more effective than ever, and it takes very short time to complete the calculation and generate the look-up table. The equalizing technique is described and implementation results using a Xilinx XC4010 FPGA are presented.
Amoxicillin, clarithromycin, and omeprazole based targeted nanoparticles for the treatment of<i>H. pylori</i> (2009)

The aim of the present study was to develop and characterize targeted sustained release nanoparticles of chitosan-glutamic acid conjugates containing triple therapy for Helicobacter pylori to improve its therapeutic effect and reduce its dose-related side effect. The chitosan-glutamate nanoparticles were prepared by using the ionotropic gelation method. The particle sizes of systems ranged between 550 nm and 900 nm. Percent drug entrapment and release profiles of amoxicillin, clarithromycin, and omeprazole in simulated gastric fluid (pH 1.2) were determined using high-performance liquid chromatography. The maximum % drug entrapment and % yield of formulations were about 60-90% and 73-88%, respectively. The stability of the drugs was assessed in simulated gastric fluid (pH 1.2). In vitro antibacterial efficacy of optimized formulations containing monotherapy and triple therapy on isolated culture of H. pylori was assessed. In vivo clearance study and histopathological study were also carried out on Swiss albino mice to evaluate the efficacy of triple therapy containing targeted nanosystem for the treatment of H. pylori. The proposed delivery system holds promise at optimizing the treatment of H. pylori.
On the Origin of Deep Learning (2017)

This paper is a review of the evolutionary history of deep learning models. It covers from the genesis of neural networks when associationism modeling of the brain is studied, to the models that dominate the last decade of research in deep learning like convolutional neural networks, deep belief networks, and recurrent neural networks. In addition to a review of these models, this paper primarily focuses on the precedents of the models above, examining how the initial ideas are assembled to construct the early models and how these preliminary models are developed into their current forms. Many of these evolutionary paths last more than half a century and have a diversity of directions. For example, CNN is built on prior knowledge of biological vision system; DBN is evolved from a trade-off of modeling power and computation complexity of graphical models and many nowadays models are neural counterparts of ancient linear models. This paper reviews these evolutionary paths and offers a concise thought flow of how these models are developed, and aims to provide a thorough background for deep learning. More importantly, along with the path, this paper summarizes the gist behind these milestones and proposes many directions to guide the future research of deep learning.
The Influence of Hydrogen Bonding Side-Groups on Viscoelastic Behavior of Linear and Network Polymers (2014)

Polymers containing hydrogen-bonding side groups (HBGs) can form transient supramolecular networks that exhibit technologically useful viscoelastic properties. Here, we investigate how dynamic behavior of functional poly(n-butyl acrylate) melts and cross-linked networks is influenced by different HBGs. Random copolymers containing weak and strong HBGs were synthesized and subjected to thermal and dynamic mechanical analysis. The glass transition temperature (Tg) increased nearly linearly with the HBG concentration, and this effect was similar for both weak and strong binding groups. Copolymers containing weak HBGs behaved as unentangled melts and exhibited higher storage and loss modulus with increasing amounts of binding group. In contrast, copolymers containing strong HBGs behaved like entangled networks. Flow activation energies increased linearly with comonomer content; and, for weak hydrogen-bonding groups, they depended only on the departure from Tg. Similar behavior was observed in cross-linked films. Differences between weak and strong HBGs were also apparent from shape memory cycles.
Randomized phase II study of perifosine in combination with capecitabine versus capecitabine alone in patients with second- or third-line metastatic colon cancer (2009)

4081 Background: Perifosine (Peri), a synthetic alkylphospholipid, inhibits or modifies a number of different signal transduction pathways (AKT, MAPK and JNK). Peri as a single agent or in combination with other cytotoxic agents, has shown clinical benefit with a manageable safety profile. In a phase I solid tumor trial, Peri was safely combined with capecitabine (Cap) and demonstrated interesting activity in patients (pts) with metastatic colorectal cancer (mCRC), with one patient progression-free for 49 weeks (wks). To assess the true effect of Peri, a phase II was initiated as an exploratory randomized double-blind, placebo controlled study where mCRC pts received Cap in combination with Peri or placebo. Methods: Pts with 2 nd or 3 rd line mCRC, not previously treated with single agent Cap. ECOG PS 0–1, normal organ/marrow function required. Dose for Cap was 825 mg/m 2 BID d 1–14 q 3 weeks. Dose for Peri or placebo was 50 mg qd. Primary outcome analyses included median time to progression (TTP) and response rate (CR+PR). Results: 37 pts have been randomized. Median age 68 (range 32–83) and 57% were male. Median prior Rx was 2 (range 1 - 5). For the analyses, 25 pts were unblinded (12 too early) with 22/25 pts evaluable for response (2 pts off for toxicity at d 14, 46 and 1 patient off at d 4 for other disease; all 3 pts were on Cap + placebo). Results in table below. The log-rank p-value comparing active to placebo for TTP is 0.01. As of 12/08, all unblinded pts are off treatment and 11/12 that were too early remain on treatment with enrollment ongoing. Most frequent (>5%) grade 3 /4 adverse events for Cap + Peri was hand/foot syndrome (16%) and anemia (8%); for Cap + placebo was fatigue (8%). Conclusions: Perifosine in combination with capecitabine was well tolerated, clinically active and more than doubled median TTP over capecitabine alone in pts with advanced, metastatic CRC. [Table: see text] [Table: see text]
Isoquinoline Alkaloids. 2. Preparation of <i>d,l</i>-Glaucine 1.5 Phosphate from <i>d,l</i>-Laudanosoline Hydrobromide (1997)

A high-yield, commercially viable synthesis of d,l-glaucine 1.5 phosphate (1) from d,l-laudanosoline hydrobromide (2) is described. Oxidation of 2 with ferric chloride in ethanol/ water buffered with sodium acetate gave d,l-1,2,9,10-tetrahydroxyaporphine hydrochloride (3) in 76−83% yield. This was converted to the free base, 4, which was methylated with phenyltrimethylammonium hydroxide (5) in 1,2-dichlorobenzene to give, after precipitation with 48% hydrobromic acid, crude d,l-glaucine hydrobromide (6) in 74% yield. The crude 6 was purified by recrystallization from 50/50 (v/v) ethanol/water to remove by-product 1-(2-(dimethylamino)ethyl)-3,4,6,7-tetramethoxyphenanthrene hydrobromide (7). The purified 6 was converted to 1 in 86−88% yield by formation of the free base followed by treatment with 85% phosphoric acid in 80% ethanol and subsequent crystal digestion for 6 h.
compareFinRaw.r – an R program to measure the difference between datasets (2012)

In every data-related research it is essential to have knowledge about potential disparity of the data in use.There might be differences between modification stages of a single dataset or between distinct datasets.Either way the researcher has to be aware of these differences in order to draw proper conclusions that might be affected by different data properties.This report describes an adaptable solution to cope with that problem by using the statistical software R [R 2011].The program compareFinRaw.r is a suitable automatic tool to measure differences of two datasets by computing distances for all relevant variable (column) pairs of the datasets on two levels.Two excerpts of the R-internal dataset Seatbelts [R 2011[R , Harvey 1986] serve as an illustrative data example.
ProgNet: Covid-19 prognosis using recurrent and convolutional neural networks (2020)

Abstract —Humanity is facing nowadays a dramatic pandemic episode with the Coronavirus propagation over all continents. The Covid-19 disease is still not well characterized, and many research teams all over the world are working on either therapeutic or vaccination issues. Massive testing is one of the main recommendations. In addition to laboratory tests, imagery-based tools are being widely investigated. Artificial intelligence is therefore contributing to the efforts made to face this pandemic phase. Regarding patients in hospitals, it is important to monitor the evolution of lung pathologies due to the virus. A prognosis is therefore of great interest for doctors to adapt their care strategy. In this paper, we propose a method for Covid-19 prognosis based on deep learning architectures. The proposed method is based on the combination of a convolutional and recurrent neural networks to classify multi-temporal chest X-ray images and predict the evolution of the observed lung pathology. When applied to radiological time-series, promising results are obtained with an accuracy rates higher than 92%.
Ultrathin thermoresponsive self-folding 3D graphene (2017)

Graphene and other two-dimensional materials have unique physical and chemical properties of broad relevance. It has been suggested that the transformation of these atomically planar materials to three-dimensional (3D) geometries by bending, wrinkling, or folding could significantly alter their properties and lead to novel structures and devices with compact form factors, but strategies to enable this shape change remain limited. We report a benign thermally responsive method to fold and unfold monolayer graphene into predesigned, ordered 3D structures. The methodology involves the surface functionalization of monolayer graphene using ultrathin noncovalently bonded mussel-inspired polydopamine and thermoresponsive poly(<i>N</i>-isopropylacrylamide) brushes. The functionalized graphene is micropatterned and self-folds into ordered 3D structures with reversible deformation under a full control by temperature. The structures are characterized using spectroscopy and microscopy, and self-folding is rationalized using a multiscale molecular dynamics model. Our work demonstrates the potential to design and fabricate ordered 3D graphene structures with predictable shape and dynamics. We highlight applicability by encapsulating live cells and creating nonlinear resistor and creased transistor devices.