gebhart/patrepeval huggingface dataset:
LPA4 regulates blood and lymphatic vessel formation during mouse embryogenesis (2010)

Lysophosphatidic acid (LPA) is a potent lipid mediator with a wide variety of biological actions mediated through G protein-coupled receptors (LPA(1-6)). LPA(4) has been identified as a G(13) protein-coupled receptor, but its physiological role is unknown. Here we show that a subset of LPA(4)-deficient embryos did not survive gestation and displayed hemorrhages and/or edema in many organs at multiple embryonic stages. The blood vessels of bleeding LPA(4)-deficient embryos were often dilated. The recruitment of mural cells, namely smooth muscle cells and pericytes, was impaired. Consistently, Matrigel plug assays showed decreased mural cell coverage of endothelial cells in the neovessels of LPA(4)-deficient adult mice. In situ hybridization detected Lpa4 mRNA in the endothelium of some vasculatures. Similarly, the lymphatic vessels of edematous embryos were dilated. These results suggest that LPA(4) regulates establishment of the structure and function of blood and lymphatic vessels during mouse embryogenesis. Considering the critical role of autotaxin (an enzyme involved in LPA production) and Gα(13) in vascular development, we suggest that LPA(4) provides a link between these 2 molecules.
A Suboptimal Multiuser-Pairing Algorithm With Low Complexity for Virtual MIMO Systems (2014)

In virtual multiple-input-multiple-output (V-MIMO) systems, employing a user-pairing algorithm can significantly improve system capacity and spectral efficiency using multiuser diversity. The optimal pairing algorithm can achieve optimal system performance, but it is not feasible to implement in practice due to its huge complexity. To solve the problem, an efficient suboptimal pairing algorithm with lower complexity is proposed, which maximizes the system throughput by selecting users one by one. Furthermore, to achieve a good balance between throughput and user fairness, a novel pairing algorithm is derived, which combines the advantages of the suboptimal pairing algorithm and proportional fair (PF) criteria. Simulation results show that the proposed algorithm achieves better fairness and higher system throughput than the double PF (D-PF) algorithm, and has much lower complexity than the optimal pairing algorithm.
Contribution of Na<sup>+</sup>-glucose cotransport to the short-circuit current in the pigmented rabbit conjunctiva (1996)

The objective of this study was to determine whether Na(+)-glucose cotransport contributed to the residual short-circuit current (Isc) in the pigmented rabbit conjunctiva not accounted for by Cl- secretion. The Isc of the pigmented rabbit conjunctiva was measured following exposure of its mucosal or serosal side to varying concentrations of D-glucose or phloridzin in a glutathione-bicarbonated Ringer's solution (GBR). Addition of D-glucose to the mucosal side of the conjunctiva bathed in glucose-free GBR elevated Isc up to 26 +/- 6% in a dose-dependent manner (K0.5 = 1.2 mM), while mucosal (but not serosal) addition of phloridzin reduced the Isc (IC50 = 0.05 mM) of the conjunctiva bathed in regular GBR. In a mucosal Na(+)-free medium, neither 20 mM D-glucose nor 0.5 mM phloridzin was effective. In a mucosal glucose-containing medium, deletion of Na+ reduced Isc up to 27 +/- 4%. It was, however, restored to its initial value upon the addition of 17.5-141 mM Na+ to a medium containing 5 mM D-glucose. Hill plot analysis of Isc elevation at 141 mM Na+ in the presence of varying D-glucose concentrations in the mucosal bathing fluid yielded a Hill coefficient of 0.86. There is, therefore, evidence for the apical localization of phloridzin-sensitive Na(+)-coupled D-glucose transport that exhibits apparent 1:1 stoichiometry, being responsible for the maximal 26% increase in the Isc.
shi lun xian xue hou jiao qi fa si wei shi ke tang jiao xue de gou jian (2013)

在先学后教,启发思维教学模式的实验中,抓好课前准备、课堂参与、课后练习巩固三个阶段.改变教师以“教”为主的教学模式,形成以学生“学”为主,以启发思维性为主的课堂模式,树立教师的课改理念,提高学生的学业成就.
Recognizing Biomedical Named Entities Using Skip-Chain Conditional Random Fields (2010)

Linear-chain Conditional Random Fields (CRF) has been applied to perform the Named Entity Recognition (NER) task in many biomedical text mining and information extraction systems. However, the linear-chain CRF cannot capture long distance dependency, which is very common in the biomedical literature. In this paper, we propose a novel study of capturing such long distance dependency by defining two principles of constructing skip-edges for a skip-chain CRF: linking similar words and linking words having typed dependencies. The approach is applied to recognize gene/protein mentions in the literature. When tested on the BioCreAtIvE II Gene Mention dataset and GENIA corpus, the approach contributes significant improvements over the linear-chain CRF. We also present in-depth error analysis on inconsistent labeling and study the influence of the quality of skip edges on the labeling performance.
Inorganic coordination polymers. XI. A new family of chromium(III) bis(phosphinate) polymers, [Cr(OH)(OPRR′O)<sub>2</sub>]<sub><i>x</i></sub> (1971)

Abstract Heating hydroxyaquochromium(III) bis(phosphinates) at temperatures up to 200°C under vacuum yields the corresponding anhydrous polymers [Cr(OH)(OPRR'O) 2 ] x . The infrared and visible spectra and solution properties lead to the following conclusions. When R and R′ are phenyl groups, the hydroxyl groups appear to bridge between adjacent chromium atoms in the chain together with the phosphinate ligands to yield a linear, triple‐bridged polymer. When at least one substituent on the phosphorus is an alkyl group, some of the hydroxyl groups crosslink between chains to yield less soluble polymers. Comparison of the properties of these new polymers with the parent polymers suggests that the latter should be formulated [Cr(H 2 O) n (OH)(OPRR′O) 2 ] x · p H 2 O and that they contain more than one kind of monomer unit. The parent polymers can be readily prepared by a new method which involves reaction of a soluble chromium(III) salt with alkali metal phosphinates or of chromium(III) hydroxide with phosphinic acids in a water–tetrahydrofuran mixture.
ConvBERT: Improving BERT with Span-based Dynamic Convolution (2020)

Pre-trained language models like BERT and its variants have recently achieved impressive performance in various natural language understanding tasks. However, BERT heavily relies on the global self-attention block and thus suffers large memory footprint and computation cost. Although all its attention heads query on the whole input sequence for generating the attention map from a global perspective, we observe some heads only need to learn local dependencies, which means the existence of computation redundancy. We therefore propose a novel span-based dynamic convolution to replace these self-attention heads to directly model local dependencies. The novel convolution heads, together with the rest self-attention heads, form a new mixed attention block that is more efficient at both global and local context learning. We equip BERT with this mixed attention design and build a ConvBERT model. Experiments have shown that ConvBERT significantly outperforms BERT and its variants in various downstream tasks, with lower training cost and fewer model parameters. Remarkably, ConvBERTbase model achieves 86.4 GLUE score, 0.7 higher than ELECTRAbase, while using less than 1/4 training cost. Code and pre-trained models will be released.
Precision Learning: Reconstruction Filter Kernel Discretization (2017)

In this paper, we present substantial evidence that a deep neural network will intrinsically learn the appropriate way to discretize the ideal continuous reconstruction filter. Currently, the Ram-Lak filter or heuristic filters which impose different noise assumptions are used for filtered back-projection. All of these, however, inhibit a fully data-driven reconstruction deep learning approach. In addition, the heuristic filters are not chosen in an optimal sense. To tackle this issue, we propose a formulation to directly learn the reconstruction filter. The filter is initialized with the ideal Ramp filter as a strong pre-training and learned in frequency domain. We compare the learned filter with the Ram-Lak and the Ramp filter on a numerical phantom as well as on a real CT dataset. The results show that the network properly discretizes the continuous Ramp filter and converges towards the Ram-Lak solution. In our view these observations are interesting to gain a better understanding of deep learning techniques and traditional analytic techniques such as Wiener filtering and discretization theory. Furthermore, this will allow fully trainable data-driven reconstruction deep learning approaches.
Bioinspired hole-conducting polymers for application in organic light-emitting diodes (2012)

A novel uracil-functionalized poly(3-thiophene) as a hole-injecting/transporting layer in an organic light-emitting device is able to form physical crosslinkages resulting in high thermal stability, non-corrosion, excellent hole injection/transport and electron-blocking capabilities in the solid state, and it achieves up to 10 times higher performance than that of conventional poly(3-thiophene)s under similar experimental conditions.
Nucleation and Growth of Gas Hydrate Crystals in Relation to Kinetic Inhibition (1996)

Pour des raisons d'économie et de protection de l'environnement, on attache de plus en plus d'importance à la méthode de contrôle des hydrates, dite cinétique, qui cherche à empêcher l'agglomération des hydrates pendant les phases de traitement et/ou de transport du pétrole ou du gaz. On recourt au terme d' inhibition cinétique . L'objet du présent article est d'étudier la cristallisation des hydrates par rapport au problème de la nécessité d'intervenir pour assurer le contrôle des hydrates. L'étude est menée sous divers angles à savoir : la corrélation entre les espèces dissoutes, la nucléation et la croissance des cristaux qui en découle, et les configurations de croissance macroscopiques. L'étude analyse également les résultats du nombre restreint de données expérimentales dont on dispose.
Evaluation of segmentation methods on head and neck <scp>CT</scp>: Auto‐segmentation challenge 2015 (2017)

The Head and Neck Auto-Segmentation Challenge 2015 was a good opportunity to assess the current state-of-the-art in segmentation of organs at risk for radiotherapy treatment. Participating teams had the possibility to compare their approaches to other methods under unbiased and standardized circumstances. The results demonstrate a clear tendency toward more general purpose and fewer structure-specific segmentation algorithms.
An Application of Reinforcement Learning to Aerobatic Helicopter Flight (2007)

Autonomous helicopter flight is widely regarded to be a highly challenging control problem. This paper presents the first successful autonomous completion on a real RC helicopter of the following four aerobatic maneuvers: forward flip and sideways roll at low speed, tail-in funnel, and nose-in funnel. Our experimental results significantly extend the state of the art in autonomous helicopter flight. We used the following approach: First we had a pilot fly the helicopter to help us find a helicopter dynamics model and a reward (cost) function. Then we used a reinforcement learning (optimal control) algorithm to find a controller that is optimized for the resulting model and reward function. More specifically, we used differential dynamic programming (DDP), an extension of the linear quadratic regulator (LQR).
Simple, Inexpensive Technique for High-Quality Smartphone Fundus Photography in Human and Animal Eyes (2013)

Purpose. We describe in detail a relatively simple technique of fundus photography in human and rabbit eyes using a smartphone, an inexpensive app for the smartphone, and instruments that are readily available in an ophthalmic practice. Methods. Fundus images were captured with a smartphone and a 20D lens with or without a Koeppe lens. By using the coaxial light source of the phone, this system works as an indirect ophthalmoscope that creates a digital image of the fundus. The application whose software allows for independent control of focus, exposure, and light intensity during video filming was used. With this app, we recorded high-definition videos of the fundus and subsequently extracted high-quality, still images from the video clip. Results. The described technique of smartphone fundus photography was able to capture excellent high-quality fundus images in both children under anesthesia and in awake adults. Excellent images were acquired with the 20D lens alone in the clinic, and the addition of the Koeppe lens in the operating room resulted in the best quality images. Successful photodocumentation of rabbit fundus was achieved in control and experimental eyes. Conclusion. The currently described system was able to take consistently high-quality fundus photographs in patients and in animals using readily available instruments that are portable with simple power sources. It is relatively simple to master, is relatively inexpensive, and can take advantage of the expanding mobile-telephone networks for telemedicine.
De Novo peptide sequencing via tandem mass spectrometry (1999)

Peptide sequencing via tandem mass spectrometry (MS/MS) is one of the most powerful tools in proteomics for identifying proteins.
Scalability of a Parallel JPEG Encoder on Shared Memory Architectures (2010)

Embedded multimedia systems are expected to fully embrace the future many-core wave. As a consequence parallel programming is being revamped as the only way to exploit the power of coming chips. While waiting for them we try to extrapolate some lessons learned from current multi-cores to influence future architectures and programming methods. In this paper we investigate the parallelism and scalability of a JPEG image encoder, which is a typical embedded application, on several shared memory machines using the OpenMP programming framework. We identify the Huffman coding as the bottleneck that blocks the application from scaling above a 7x factor. We propose a strategy to parallelize the Huffman coding, which introduces a small degradation in some parts of the image, allowing to reach higher speedup factors. A factor of 18.8x has been reached in SGI Altix 4700 using 22 threads. Contrasting these results with some previous works using message passing architectures we consider that the use of OpenMP on top of shared memory architectures should be reconsidered for future chips in favor of message passing architectures and programming models.
Syzygium aromaticum extracts as good source of betulinic acid and potential anti-breast cancer (2011)

Syzygium aromaticum (L.) Merr. & L.M. Perry, Myrtaceae, is an evergreen tree with anticarcinogenic, antimutagenic, aphrodisiac, antimicrobial, antioxidant and antiinflammatory properties. This study aims to investigate the anti-breast cancer effect of extracts from leaves, stem and bark of S. aromaticum and to develop a method for preparation of betulinic acid fraction from the leaves. Betulinic acid, ursolic acid and oleanolic acid contents of the extracts were determined by HPLC. A betulinic acid fraction was prepared by simple crystallization of leaves extract and was characterized by HPLC and mass analysis. Anti-breast cancer effects were studied on MCF-7 and MDA-MB-231 cells. The extracts were found to contain high levels of betulinic acid particularly the leaves extract which contained 17% wt/wt. The betulinic acid fraction contains 75% betulinic acid. Cytotoxicity testing reveals high and selective cytotoxic effect of the stem extract on MCF-7 cells with IC50 33±1.6 µg/mL. Cytotoxic effect of the stem extract was due to activation of apoptotic machinery of cell death. Combination studies of stem extract with tamoxifen reveals antagonistic effect at high concentration of tamoxifen and enhancement effect at low concentration. The selective cytotoxicity of the stem extract of S. aromaticum on MCF-7 is not due to betulinic acid but due to other constituents yet to be discovered.
Mapping, Complementation, and Targets of the Cysteine Protease Actinidin in Kiwifruit       (2011)

Cysteine proteases (CPs) accumulate to high concentration in many fruit, where they are believed to play a role in fungal and insect defense. The fruit of Actinidia species (kiwifruit) exhibit a range of CP activities (e.g. the Actinidia chinensis variety YellowA shows less than 2% of the activity of Actinidia deliciosa variety Hayward). A major quantitative trait locus for CP activity was mapped to linkage group 16 in a segregating population of A. chinensis. This quantitative trait locus colocated with the gene encoding actinidin, the major acidic CP in ripe Hayward fruit encoded by the ACT1A-1 allele. Sequence analysis indicated that the ACT1A locus in the segregating A. chinensis population contained one functional allele (A-2) and three nonfunctional alleles (a-3, a-4, and a-5) each containing a unique frameshift mutation. YellowA kiwifruit contained two further alleles: a-6, which was nonfunctional because of a large insertion, and a-7, which produced an inactive enzyme. Site-directed mutagenesis of the act1a-7 protein revealed a residue that restored CP activity. Expression of the functional ACT1A-1 cDNA in transgenic plants complemented the natural YellowA mutations and partially restored CP activity in fruit. Two consequences of the increase in CP activity were enhanced degradation of gelatin-based jellies in vitro and an increase in the processing of a class IV chitinase in planta. These results provide new insight into key residues required for CP activity and the in vivo protein targets of actinidin.
Oligonucleotide-based systems: DNA, microRNAs, DNA/RNA aptamers (2016)

There are an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or a synthetic analogue of naturally occurring nucleic acids. This review will shed light on various types of nucleic acids such as DNA and RNA (particularly microRNAs), their role and their application in biosensing. It will also cover DNA/RNA aptamers, which can be used as bioreceptors for a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides such as peptide nucleic acid (PNA) or locked nucleic acid (LNA) has pushed the limits of molecular biology and biosensor development to new perspectives. These technologies are very promising albeit still in need of development in order to bridge the gap between the laboratory-based status and the reality of biomedical applications.
Chondramides A - D, New Antifungal and Cytostatic Depsipeptides from Chondromyces crocatus (Myxobacteria). Production, Physico-chemical and Biological Properties. (1995)

Novel depsipeptides, named chondramides were produced at levels up to 4.3 mg/liter by several myxobacteria of the genus Chondromyces. The compounds are structurally closely related to jaspamide/jasplakinolide from marine sponges of the genus Jaspis. Initially the chondramides were detected in acetone extracts of the biomass of Chondromyces crocatus, strain Cm c2. So far, four structural variants could be characterized, the chondramides A approximately D. They inhibited the growth of a few yeasts and showed high cytostatic activity against cultivated human and animal cells.
Effect of flow regime on the architecture of a <i>Pseudomonas fluorescens</i> biofilm (2002)

A comparison of the effects of laminar versus turbulent flow regime on the characteristics of a single-species biofilm is presented. The study was carried out by growing Pseudomonas fluorescens biofilms in a flow cell and studying the different layers of the biological matrix with a confocal laser-scanning microscope. The following conclusions were obtained: i) a higher concentration of cells was found in the upper layers of the microbial films than in their inner layers, regardless of the flow regime; ii) the fraction of cells in the overall biofilm mass decreased with time as the film grew; and iii) under laminar flow the total number of cells was higher than in biofilms formed under turbulent flow, but the latter had a higher number of cells per unit volume. Such conclusions, together with the fact that the biofilms were more dense and stable when formed in contact with turbulent flows, favor the design of more compact and efficient biofilm reactors operating in turbulent conditions.
Pain in ambulatory AIDS patients. II: Impact of pain on psychological functioning and quality of life (1996)

The relationships among pain, psychological distress and other quality of life concerns were examined through a prospective cross-sectional survey of 438 ambulatory AIDS patients recruited from health care facilities in New York City. In this sample, 274 (62.6%) patients reported frequent or persistent pain during the prior 2 wks. Patients with and without pain completed a questionnaire packet that included measures of psychological symptom distress (Brief Symptom Inventory and the Psychological Distress Subscale of the Memorial Symptom Assessment Scale), depression (Beck Depression Inventory and Beck Hopelessness Scale), social support (Social Support Questionnaire), and overall quality of life (Functional Living Index-Cancer, modified for AIDS). Multivariate analyses (MANOVA, multiple regression) revealed significant associations between the presence and intensity of pain and scores on the measures of psychological distress, depression, hopelessness, and quality of life (P < 0.0001 for most analyses). Perceived adequacy of social support was also significantly associated with lower levels of psychological distress and depression, and better quality of life. These results demonstrate the significant relationships between pain, psychological well-being, and quality of life, and affirm the need to provide adequate treatment of pain in patients with AIDS.
Coordination of Ribosomal Protein and Ribosomal RNA Gene Expression in Response to TOR Signaling (2009)

Cells grow in response to nutrients or growth factors, whose presence is detected and communicated by elaborate signaling pathways. Protein kinases play crucial roles in processes such as cell cycle progression and gene expression, and misregulation of such pathways has been correlated with various diseased states. Signals intended to promote cell growth converge on ribosome biogenesis, as the ability to produce cellular proteins is intimately tied to cell growth. Part of the response to growth signals is therefore the coordinate expression of genes encoding ribosomal RNA (rRNA) and ribosomal proteins (RP). A key player in regulating cell growth is the Target of Rapamycin (TOR) kinase, one of the gatekeepers that prevent cell cycle progression from G1 to S under conditions of nutritional stress. TOR is structurally and functionally conserved in all eukaryotes. Under favorable growth conditions, TOR is active and cells maintain a robust rate of ribosome biogenesis, translation initiation and nutrient import. Under stress conditions, TOR signaling is suppressed, leading to cell cycle arrest, while the failure of TOR to respond appropriately to environmental or nutritional signals leads to uncontrolled cell growth. Emerging evidence from Saccharomyces cerevisiae indicates that High Mobility Group (HMGB) proteins, non-sequence-specific chromosomal proteins, participate in mediating responses to growth signals. As HMGB proteins are distinguished by their ability to alter DNA topology, they frequently function in the assembly of higher-order nucleoprotein complexes. We review here recent evidence, which suggests that HMGB proteins may function to coordinate TOR-dependent regulation of rRNA and RP gene expression.