gebhart/patrepeval huggingface dataset:
Highly efficient small molecule multi-junction organic photovoltaic cells (2023)

A highly efficient multi junction photovoltaic device, such as a two, three, or four junction device, is disclosed. The multi-junction device may include a first subcell comprising a first photoactive region and a second subcell comprising a second photoactive region. The first and second photoactive regions are designed to minimize spectral overlap and maximize photocurrent across a broad absorption spectra, such as wavelengths ranging from 400 nm to 900 nm. The device may further include an inter-connecting layer, disposed between the first subcell and the second subcell, that is at least substantially transparent. By introducing a transparent interconnecting layer, a dual element (tandem) cell achieves a power conversion efficiency of 10.0±0.5%. By adding an additional (3rd) sub-cell that absorbs at the second order optical interference maximum within the stack. The triple junction cell significantly improves the quantum efficiency at shorter wavelengths, achieving a power conversion efficiency of 11.1±0.5%. Adding additional sub-cells has been shown to increase power conversion efficiency above 12%.
B-tree indexes for high update rates (2006)

In some applications, data capture dominates query processing. For example, monitoring moving objects often requires more insertions and updates than queries. Data gathering using automated sensors often exhibits this imbalance. More generally, indexing streams is considered an unsolved problem.For those applications, B-tree indexes are good choices if some trade-off decisions are tilted towards optimization of updates rather than towards optimization of queries. This paper surveys some techniques that let B-trees sustain very high update rates, up to multiple orders of magnitude higher than traditional B-trees, at the expense of query processing performance. Not surprisingly, some of these techniques are reminiscent of those employed during index creation, index rebuild, etc., while other techniques are derived from well known technologies such as differential files and log-structured file systems.
Identification of the DAG Lipase alpha‐1 and beta‐1 mRNA transcripts in Human Tissues. (2008)

Using human DAG lipase α and β specific RT‐PCR, we identified two alternatively spliced variants of human DAG lipase mRNAs, DAG lipase α–1 and β‐1, in human multiple tissues. The alternative splicing of DAG lipase α‐1 occurred at +206 (Gene bank: NM_006133 ), spliced out 212 bp (+206 to +418 bp) of the coding region, and encoded a 956 amino acid DAG lipase α‐1 protein. The N‐terminus of DAG lipase α–1 differed from that of DAG lipase α. The alternative splicing of DAG lipase β‐1 occurred at 360 (Gene bank: NM_139179 ), spliced out 552 bp (+360 to +912 bp) of the coding region, and encoded a 391 amino acid DAG lipase β‐1 protein with a 281 amino acid N‐terminal deletion. This study is the first to document alternative splicing of DAG lipase genes. We therefore studied DAG lipase α‐1 and DAG lipase β‐1 mRNA distribution in human tissues (heart, kidney, brain, lung, liver, spleen, and small intestine). DAG lipase α‐1 mRNA was highly expressed in heart, kidney, brain, liver, spleen, small intestine and smooth muscle, but not lung. DAG lipase β‐1 mRNA was highly expressed in kidney, brain, spleen, small intestine and smooth muscle, but not heart, liver, and lung. DAG lipase α‐1 and DAG lipase β‐1 were not found in rat and mouse tissues, indicating species specificity of the alternative splicing variants of DAG lipase mRNA expression. When recombinant DAG lipase α‐1 and DAG lipase β‐1 were expressed in HEK293/EBNA cells, DAG lipase α‐1 was present almost exclusively in membrane, whereas DAG lipase β‐1 was present in cytosolic fractions. The data suggest that the N‐terminus of DAG lipases may be important for this protein translocating to the cell membrane, and alternative splicing variants of DAG lipase α or β may play an unique role in the regulation of “on‐demand” 2‐AG production in human tissues.
Pillars article: Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 1992. 255: 1261-1263. (2007)

Antigens recognized by T cells are expressed as peptides bound to major histocompatibility complex (MHC) molecules. Microcapillary high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry was used to fractionate and sequence subpicomolar amounts of peptides isolated from the MHC molecule HLA-A2.1. Of 200 different species quantitated, eight were sequenced and four were found in cellular proteins. All were nine residues long and shared a distinct structural motif. The sensitivity and speed of this approach should enhance the analysis of peptides from small quantities of virally infected and transformed cells as well as those associated with autoimmune disease states.
The Polycyclic Flavonoid, Maackiain, Arrests Cell Cycle Progression in LNCaP and PC‐3 Human Prostate Cancer Cells and Repairs DNA Damage in PC‐3 and NHPrE Cells (2010)

The effect of maackiain, a potent polycyclic flavonoid with anticarcinogenic activities found in red clover, on cell proliferation, cell cycle progression and tumor suppressor gene expression was examined in human derived prostate cancer LNCaP and PC‐3 cells as well as normal human prostate epithelial (NHPrE) cells. The treatment of as low as 10 μM maackiain in LNCaP and PC‐3 cells for 3 days resulted in 20% inhibition of cell proliferation. The highest dosage of 100 uM resulted in 40% of growth inhibition in PC‐3 cells but 70% in LNCaP cells after 6 days treatment. Most importantly, for NHPrE cells, maackiain just began to be effective only at the highest concentration of 100 μM. The growth inhibition in maackiain treated LNCaP and PC‐3 cells was associated with cell cycle arrest at the G0/G1 and G2/M phases, respectively, in a dosage dependent manner without induction of apoptosis or senescence. The cell cycle arrest in maackiain treated PC‐3 cells was found to be resulted from enhanced expression of p21, p27 and hypophos‐Rb and suppressed expression of cyclin B and phos‐Rb. Immunofluorescence study using γH2A.X (phosphor S139) and DNA PKcs (phosphor T2647) antibodies indicated that maackiain treatments enhanced DNA damage repair both in PC‐3 and NHPrE cells without the activation of ATM or ATR signaling pathway. Our data suggest that maackiain may serve as a potential chemopreventitive agent against prostate cancer.
Heartbeat of a nest (2010)

We present a scalable end-to-end system for vision-based monitoring of natural environments, and illustrate its use for the analysis of avian nesting cycles. Our system enables automated analysis of thousands of images, where manual processing would be infeasible. We automate the analysis of raw imaging data using statistics that are tailored to the task of interest. These “features” are a representation to be fed to classifiers that exploit spatial and temporal consistencies. Our testbed can detect the presence or absence of a bird with an accuracy of 82%, count eggs with an accuracy of 84%, and detect the inception of the nesting stage within a day. Our results demonstrate the challenges and potential benefits of using imagers as biological sensors. An exploration of system performance under varying image resolution and frame rate suggest that an in situ adaptive vision system is technically feasible.
[SMANCS/TAE for hepatocellular carcinoma: comparison with SMANCS/TAI]. (1998)

To evaluate the effects of SMANCS/TAE for hepatocellular carcinoma, AFP reduction rates, tumor reduction rates of SMANCS/TAE were compared with those of SMANCS/TAI. SMANCS is a stylene-maleic acid neocarzinostatin. TAE means transcatheter arterial embolization with gelatin sponge after SMANCS infusion and TAI means transcatheter arterial infusion of only SMANCS-iodized oil suspension. For evaluation of the AFP reduction rate, 13 SMANCS/TAEs were compared with 32 SMANCS/TAIs. In these cases, pretreatment serum AFP levels were higher or equal to 100 ng/ ml. The average dose of SMANCS/TAE was 4.2 +/- 1.8 (S. D) mg and that of SMANCS/TAI was 3.9 +/- 1.8 (S. D) mg (N. S: t-test, p = 0.59). Student's t-test revealed that the AFP reduction rate of SMANCS/TAE was not significantly superior to that of SMANCS/TAI (p = 0.78), and both AFP reduction rate of SMANCS/TAE and SMANCS/ TAI were not correlated with the dose of SMANCS. Tumor reduction rates of 12 SMANCS/TAEs and 14 SMANCS/TAIs on CT examination were calculated. The average dose of SMANCS/TAE was 4.5 +/- 1.9 (S. D) mg and that of SMANCS/TAI was 3.8 +/- 2.1 (S. D) mg (N. S: t-test, p = 0.29). The average tumor reduction rate of SMANCS/TAE was 25.3 +/- 30.1 (S. D)% and of SMANCS/TAI was 13.8 +/- 29.1%. Student's t-test revealed the tumor reduction rate of SMANCS/TAE was not significantly larger than that of SMANCS/TAI (p = 0.33). AFP reduction rate and tumor reduction rate of SMANCS/TAE were not significantly different from those of SMANCS/TAI. Although the number of cases was not enough, these results suggest SMANCS/TAI should be applied for treatment of hepatocellular carcinoma rather than SMANCS/ TAE.
Crosslinked poly(N‐isopropylacrylamide) gel for electrophoretic separation and recovery of substances (1994)

Abstract Crosslinked poly(N‐isopropylacrylamide) gel was tested on the feasibility for a preparative electrophoretic matrix. Horse heart myoglobin and bovine hemoglobin were well separated on the gel matrix electrophoretically by molecular sieving effect of the gel network. Relative mobilities of those proteins in the gel were larger than those in a crosslinked polyacrylamide gel of the same polymer concentration. After the separation, the protein‐containing portion of the gel underwent swelling at 4°C and deswelling at 37°C, alternatively. As a result of the deswelling, each protein was recovered in a discharged solution out of the gel at almost 100% yield.
Ada's derived types and units of measure (1985)

Abstract Types in programming languages cannot model many properties of real world objects and quantities. Consequently, many errors resulting from the inconsistent usage of program objects representing real world objects and quantities cannot be detected automatically. For example, the real variables PRICE and WEIGHT, representing the price of diesel fuel and the weight of a person, may be inadvertently added, giving a non‐sensical value; such an error cannot be detected by a compiler. The programming language Ada introduces the concept of derived types to tackle this problem. An alternative solution to this problem is the incorporation of units of measure as a new data attribute. Derived types only partially solve the problem of detecting the inconsistent usage of objects; some valid usages of objects are also not allowed. Moreover, the solution is inelegant and inconvenient to use. On the other hand, specification of units of measure solves the problem elegantly and conveniently. The two solutions are compared and analysed. Several ways to implement units of measure in Ada are examined.
Stochastic Dynamics of Inclined Risers Induced by Pulsating Internal Fluid Flow (2022)

International audience
Performance Evaluation for Hybrid Architectures (2007)

In this dissertation we discuss methologies for estimating the performance of applications on hybrid architectures, systems that include various types of computing resources (e.g. traditional general-purpose processors, chip multiprocessors, reconfigurable hardware). A common use of hybrid architectures will be to deploy coarse pipeline stages of application on "suitable" compute units with communication path for transferring data. The first problem we focus on relates to the sizing the data queues between the different processing elements of an hybrid system. Much of the discussion centers on our analytical models that can be used to derive performance metrics of interest such as, throughput and stalling probability for networks of processing elements with finite data buffering between them. We then discuss to the reliability of performance models. There we start by presenting scenarios where our analytical model is reliable, and introduce tests that can detect their inapplicability. As we transition into the question of reliability of performance models, we access the accuracy and applicability of various evaluation methods. We present results from our experiments to show the need for measuring and accounting for operating system effects in architectural modeling and estimation.
Spacing cells protects and enhances utilization of ATM network links (1992)

It is shown that peak cell rate policing can be combined with fast reservation protocols for achieving statistical multiplexing in asynchronous transfer mode (ATM) networks. A cell spacer-controller architecture which smooths out cell clusters according to the original period both at the user network interface (UNI) and at network node interface (NNI) is proposed. A performance evaluation of the spacer-controller is presented. The evaluation involves modeling the spacer-controller, dimensioning a virtual scheduling algorithm, and the impact on cell delay variation (CDV). It is shown that large CDVs may induce severe degradation in the accuracy of usage parameter control/network parameter control mechanisms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of cancer testis genes in human brain tumors. (2000)

Cancer-testis (CT) genes are expressed in a variety of human cancers but not in normal tissues, except for testis tissue, and represent promising targets for immunotherapeutic and gene therapeutic approaches. Because little is known about their composite expression in human brain tumors, we investigated the expression of seven CT genes (MAGE-3, NY-ESO-1, HOM-MEL-40/SSX-2, SSX-1, SSX-4,HOM-TES-14/SCP-1, and HOM-TES-85) in 88 human brain tumor specimens. Meningiomas expressed only HOM-TES-14/SCP-1 (18% of meningiomas were HOM-TES-14/SCP-1 positive) and did not express any other CT genes. One ependymoma was negative for all CT genes tested. SSX-4 was the only CT gene expressed in oligodendrogliomas (2 of 5 cases), and it was also expressed in oligoastrocytomas (3 of 4 cases) and astrocytomas (10 of 37 cases). Astrocytomas were most frequently positive for HOM-TES-14/SCP-1 (40%) and SSX-4 (27%), followed by HOM-TES-85 (13%), SSX-2 (11%), and MAGE-3 (7%). Whereas MAGE-3 was detected only in grade IV astrocytomas, the expression of the other CT genes showed no clear correlation with histological grade. Of 39 astrocytomas, 60% expressed at least one CT gene, 21% expressed two CT genes, and 8% coexpressed three CT genes of the seven CT genes investigated. We conclude that a majority of oligoastrocytomas and astrocytomas might be amenable to specific immunotherapeutic interventions. However, the identification of additional tu-mor-specific antigens with a frequent expression in gliomas is warranted to allow for the development of widely applicable polyvalent glioma vaccines.
Development of gas and liquid optical sensor materials using combinatorial screening techniques (2005)

We developed combinatorial screening techniques for the efficient design and optimization of sensor materials formulations for gas and liquid optical sensors. Our approach is based on the fabrication and performance screening of discrete and gradient sensor materials arrays. Simultaneous formation of multiple sensor coatings into discrete arrays and their screening provides not only a well-recognized acceleration in the screening rate, but also considerably reduces or even eliminates sources of variability, which are randomly affecting sensors response during a conventional one-at-a-time sensor coating evaluation. The application of gradient sensor arrays provides additional capabilities for rapid finding of the optimal formulation parameters.
A High-Content Screening (HCS) Assay for the Identification of Chemical Inducers of PML Oncogenic Domains (PODs) (2011)

PML is a multi-functional protein with roles in tumor suppression and host defense against viruses. When active, PML localizes to subnuclear structures named PML oncogenic domains (PODs) or PML nuclear bodies (PML-NBs), whereas inactive PML is located diffusely throughout the nucleus of cells. The objective of the current study was to develop a high content screening (HCS) assay for the identification of chemical activators of PML. We describe methods for automated analysis of POD formation using high throughput microscopy (HTM) to localize PML immunofluorescence in conjunction with image analysis software for POD quantification. Using this HCS assay in 384 well format, we performed pilot screens of a small synthetic chemical library and mixture-based combinatorial libraries, demonstrating the robust performance of the assay. HCS counter-screening assays were also developed for hit characterization, based on immunofluorescence analyses of the subcellular location of phosphorylated H2AX or phosphorylated CHK1, which increase in a punctate nuclear pattern in response to DNA damage. Thus, the HCS assay devised here represents a high throughput screen that can be utilized to discover POD-inducing compounds that may restore the tumor suppressor activity of PML in cancers or possibly promote anti-viral states.
Heavyweight Pattern Mining in Attributed Flow Graphs (2014)

This paper defines a new problem - heavyweight pattern mining in attributed flow graphs. The problem can be described as the discovery of patterns in flow graphs that have sets of attributes associated with their nodes. A connection between nodes is represented as a directed edge. The amount of load that goes through a path between nodes, or the frequency of transmission of such load between nodes, is represented as edge weights. A heavyweight pattern is a sub-set of attributes, found in a dataset of attributed flow graphs, that are connected by edges and have a computed weight higher than an user-defined threshold. A new algorithm called AFG Miner is introduced, the first one to our knowledge that finds heavyweight patterns in a dataset of attributed flow graphs and associates each pattern with its occurrences. The paper also describes a new tool for compiler engineers, HEP Miner, that applies the AFG Miner algorithm to Profile-based Program Analysis modeled as a heavyweight pattern mining problem.
Intracellular recording from cardiac ganglion neurons receiving functional vagal inputs (2009)

Cardiac vagal tone is an important indicator of cardiovascular health, and its loss is an independent risk factor for arrhythmias and cardiac mortality. Thus, it is important to elucidate the factors that modulate cardiac vagal ganglionic transmission. Using the working heart‐ brainstem preparation (Paton 1996, J.Neurosci Meth. 65, 63‐), we report the first intracellular recordings from functionally connected cardiac vagal ganglion cells in situ . The atria were dissected from the ventricles, pinned out, stabilized with a nylon mesh foot, and ganglion cells (n=33) were impaled with sharp microelectrodes (0.5M KCl; 80‐120 MOhm). Spontaneous EPSPs and action potentials (AP) occurred most commonly in post‐inspiration. Activation of bradycardic reflexes (baro‐, chemo‐, nasotrigeminal) increased dramatically EPSP frequency producing AP and atrial rhythm slowing. Spontaneous and reflexly‐evoked AP were mostly triggered by suprathreshold unitary EPSPs rather than by summation of subthreshold EPSPs. Stimulation of the right cervical vagus evoked EPSPs with a latency of 30‐40 ms. Thus, it is possible to record intracellularly from functionally intact cardiac vagal ganglion cells, which exhibit appropriate patterns of ongoing and reflex excitatory synaptic drives. Future studies will elucidate how cardiac vagal transmission may be modified in health and disease. RMcA holds an NHMRC Principal Research Fellowship; JFRP holds a Royal Society Wolfson Research Merit Award; AEP is a Wellcome Trust Advanced Clinical Fellow
OMAC: An Opportunistic Medium Access Control Protocol for IEEE 802.11 Wireless Networks (2015)

The ambitious goal of the upcoming IEEE 802.11ax (HEW) standard for wireless LANs (WLANs) to enhance throughput by four times (and beyond), compared with IEEE 802.11ac, demands a radical improvement of present medium access control (MAC) functionality. To this end, a promising paradigm would be a graceful migration towards new MAC protocols which incorporate higher certainty in their decisions. However, this requires adequate information to be available to the devices, which in turn incurs excessive costs due to information exchange between devices. Also, scalability becomes an issue for emerging dense networks. In this paper, we take a step forward by proposing an opportunistic MAC (OMAC), which restrains these costs, while increasing throughput of the new generation HEW. OMAC eliminates overhead costs by solely relying on the local capability of devices in measuring signal activities in the channel. A particular OMAC node continually collects and records the received signal strengths (RSS) overheard from the channel, and regards each individual RSS level as being transmitted by a unique node without the need to know the actual identity of the node. The OMAC node uses this knowledge to select a recorded RSS as its reference, and triggers a desired transmission policy whenever a transmission with an RSS sufficiently close to this reference RSS is detected. Our results, obtained using simulations, indicate that OMAC improves the throughput performance significantly, and that the performance gain increases with an increase in network density.
The epichaperome is a mediator of toxic hippocampal stress and leads to protein connectivity-based dysfunction (2020)

Optimal functioning of neuronal networks is critical to the complex cognitive processes of memory and executive function that deteriorate in Alzheimer's disease (AD). Here we use cellular and animal models as well as human biospecimens to show that AD-related stressors mediate global disturbances in dynamic intra- and inter-neuronal networks through pathologic rewiring of the chaperome system into epichaperomes. These structures provide the backbone upon which proteome-wide connectivity, and in turn, protein networks become disturbed and ultimately dysfunctional. We introduce the term protein connectivity-based dysfunction (PCBD) to define this mechanism. Among most sensitive to PCBD are pathways with key roles in synaptic plasticity. We show at cellular and target organ levels that network connectivity and functional imbalances revert to normal levels upon epichaperome inhibition. In conclusion, we provide proof-of-principle to propose AD is a PCBDopathy, a disease of proteome-wide connectivity defects mediated by maladaptive epichaperomes.