gebhart/patrepeval huggingface dataset:
Chemical labelling for visualizing native AMPA receptors in live neurons (2017)

The location and number of neurotransmitter receptors are dynamically regulated at postsynaptic sites. However, currently available methods for visualizing receptor trafficking require the introduction of genetically engineered receptors into neurons, which can disrupt the normal functioning and processing of the original receptor. Here we report a powerful method for visualizing native α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors (AMPARs) which are essential for cognitive functions without any genetic manipulation. This is based on a covalent chemical labelling strategy driven by selective ligand-protein recognition to tether small fluorophores to AMPARs using chemical AMPAR modification (CAM) reagents. The high penetrability of CAM reagents enables visualization of native AMPARs deep in brain tissues without affecting receptor function. Moreover, CAM reagents are used to characterize the diffusion dynamics of endogenous AMPARs in both cultured neurons and hippocampal slices. This method will help clarify the involvement of AMPAR trafficking in various neuropsychiatric and neurodevelopmental disorders.
Periodontitis: a host‐mediated disruption of microbial homeostasis. Unlearning learned concepts (2013)

Abstract New concepts evolve when existing ones fail to address known factors adequately or are invalidated by new evidence. For decades periodontitis has been considered to be caused by specific bacteria or groups of bacteria and, accordingly, treatment protocols have largely been based on anti‐infective therapies. However, close inspection of current data leads one to question whether these bacteria are the cause or the result of periodontitis. Good evidence is emerging to suggest that it is indeed the host response to oral bacteria that leads to the tissue changes noted in gingivitis. These changes lead to an altered subgingival environment that favors the emergence of ‘periodontal pathogens’ and the subsequent development of periodontitis if the genetic and external environmental conditions are favorable for disease development. Thus, it seems that it is indeed the initial early host‐inflammatory and immune responses occurring during the development of gingivitis, and not specific bacteria or their so‐called virulence factors, which determine whether periodontitis develops and progresses. In this review we consider these concepts and their potential to change the way in which we view and manage the inflammatory periodontal diseases.
URES (2006)

Most information extraction systems either use hand written extraction patterns or use a machine learning algorithm that is trained on a manually annotated corpus. Both of these approaches require massive human effort and hence prevent information extraction from becoming more widely applicable. In this paper we present URES (Unsupervised Relation Extraction System), which extracts relations from the Web in a totally unsupervised way. It takes as input the descriptions of the target relations, which include the names of the predicates, the types of their attributes, and several seed instances of the relations. Then the system downloads from the Web a large collection of pages that are likely to contain instances of the target relations. From those pages, utilizing the known seed instances, the system learns the relation patterns, which are then used for extraction. We present several experiments in which we learn patterns and extract instances of a set of several common IE relations, comparing several pattern learning and filtering setups. We demonstrate that using simple noun phrase tagger is sufficient as a base for accurate patterns. However, having a named entity recognizer, which is able to recognize the types of the relation attributes significantly, enhances the extraction performance. We also compare our approach with KnowItAll's fixed generic patterns.
Cut and Paste: Efficient Homology-Directed Repair of a Dominant Negative KRT14 Mutation via CRISPR/Cas9 Nickases (2017)

With the ability to induce rapid and efficient repair of disease-causing mutations, CRISPR/Cas9 technology is ideally suited for gene therapy approaches for recessively and dominantly inherited monogenic disorders. In this study, we have corrected a causal hotspot mutation in exon 6 of the keratin 14 gene (KRT14) that results in generalized severe epidermolysis bullosa simplex (EBS-gen sev), using a double-nicking strategy targeting intron 7, followed by homology-directed repair (HDR). Co-delivery into EBS keratinocytes of a Cas9 D10A nickase (Cas9n), a predicted single guide RNA pair specific for intron 7, and a minicircle donor vector harboring the homology donor template resulted in a recombination efficiency of >30% and correction of the mutant KRT14 allele. Phenotypic correction of EBS-gen sev keratinocytes was demonstrated by immunofluorescence analysis, revealing the absence of disease-associated K14 aggregates within the cytoplasm. We achieved a promising safety profile for the CRISPR/Cas9 double-nicking approach, with no detectable off-target activity for a set of predicted off-target genes as confirmed by next generation sequencing. In conclusion, we demonstrate a highly efficient and specific gene-editing approach for KRT14, offering a causal treatment option for EBS.
Evaluation of gas chromatography coupled with ion mobility spectrometry for monitoring vinyl chloride and other chlorinated and aromatic compounds in air samples (1996)

Abstract The objective of this research was to evaluate, in the laboratory, the potential of gas chromatography/ion mobility spectrometry (GC/IMS) for monitoring vinyl chloride and other organic compounds in air samples in the field. It was determined that GC/IMS has the potential to directly detect vinyl chloride in air at the 2 ppbv level, and when concentrated on an adsorbent trap from a 1 L sample of air, detection could be lowered to the 0.02 ppbv level. From a comparative investigation of 18 EPA priority pollutants and 34 common vapor‐phase organic compounds, many compounds were found to provide a more sensitive response in IMS than vinyl chloride, indicating that GC/IMS would be broadly applicable to the direct detection of vapor‐phase organics in air. Operating parameters including drift gas, spectrometer temperature, and sample‐inlet position were evaluated and discussed with respect to sensitivity and resolution. High temperature dramatically increased sensitivity to vinyl chloride. Vinyl chloride was shown to produce both negative and positive ion mobility spectra, with the negative‐mode spectra resulting from electron‐capture dissociation of the vinyl chloride. The limit of detection for vinyl chloride was found to be 7 pg/s. Limits of detection for 18 EPA priority pollutants were determined and compared to vinyl chloride. The responses of 34 other vapor‐phase organic compounds were also compared to that of vinyl chloride. Non‐selective, positive‐ion detection of 30 of the 34 compounds was demonstrated along with selective, electron‐capture‐type detection of 29 of them. Chloride‐specific and bromide‐specific detection illustrated the advantages of selected‐ion monitoring in IMS.
Multi-Resource Fair Allocation in Heterogeneous Cloud Computing Systems (2014)

We study the multi-resource allocation problem in cloud computing systems where the resource pool is constructed from a large number of heterogeneous servers, representing different points in the configuration space of resources such as processing, memory, and storage. We design a multi-resource allocation mechanism, called DRFH, that generalizes the notion of Dominant Resource Fairness (DRF) from a single server to multiple heterogeneous servers. DRFH provides a number of highly desirable properties. With DRFH, no user prefers the allocation of another user; no one can improve its allocation without decreasing that of the others; and more importantly, no coalition behavior of misreporting resource demands can benefit all its members. DRFH also ensures some level of service isolation among the users. As a direct application, we design a simple heuristic that implements DRFH in real-world systems. Large-scale simulations driven by Google cluster traces show that DRFH significantly outperforms the traditional slot-based scheduler, leading to much higher resource utilization with substantially shorter job completion times.
Activation-induced NK cell death triggered by CD2 stimulation (1998)

Both T cells and natural killer (NK) cells express CD2, the target of an alternative activation pathway that induces the proliferation of both cell types. The mitogenic response to CD2 ligation requires the co-expression of CD3 : TCR in T cells and FcγRIII in NK cells, suggesting that these receptors are involved in transducing the response initiated by CD2. The ability of FcγRIII to trigger the activation-induced death of IL-2-primed NK cells led us to investigate the potential for CD2 to trigger activation-induced NK cell death. Our results reveal that the same anti-CD2 monoclonal antibodies (mAb) that activate freshly isolated NK cells induce apoptosis in IL-2-primed NK cells. CD2-induced apoptosis results in chromatin condensation, DNA fragmentation and cleavage of caspase-3. Activation-induced NK cell death triggered by CD2 ligation is extremely rapid (DNA fragmentation is first observed at 90 min) and it is not inhibited by neutralizing antibodies reactive with TNF-α or Fas ligand. Whereas mAb reactive with distinct CD2 epitopes (i.e. T11.1, T11.2, and T11.3) are required for activation-induced T cell death, mAb reactive with a single CD2 epitope are sufficient for activation-induced NK cell death. The ability of CD2, CD16, and CD94 to induce apoptosis in IL-2-primed lymphocytes suggests that cytokine priming changes the response to a signaling cascade that is common to each of these activation receptors.
Ammonium Removal by the Oxygen-Limited Autotrophic Nitrification-Denitrification System (1998)

The present lab-scale research reveals the potential of implementation of an oxygen-limited autotrophic nitrification-denitrification (OLAND) system with normal nitrifying sludge as the biocatalyst for the removal of nitrogen from nitrogen-rich wastewater in one step. In a sequential batch reactor, synthetic wastewater containing 1 g of NH4+-N liter-1 and minerals was treated. Oxygen supply to the reactor was double-controlled with a pH controller and a timer. At a volumetric loading rate (Bv) of 0. 13 g of NH4+-N liter-1 day-1, about 22% of the fed NH4+-N was converted to NO2--N or NO3--N, 38% remained as NH4+-N, and the other 40% was removed mainly as N2. The specific removal rate of nitrogen was on the order of 50 mg of N liter-1 day-1, corresponding to 16 mg of N g of volatile suspended solids-1 day-1. The microorganisms which catalyzed the OLAND process are assumed to be normal nitrifiers dominated by ammonium oxidizers. The loss of nitrogen in the OLAND system is presumed to occur via the oxidation of NH4+ to N2 with NO2- as the electron acceptor. Hydroxylamine stimulated the removal of NH4+ and NO2-. Hydroxylamine oxidoreductase (HAO) or an HAO-related enzyme might be responsible for the loss of nitrogen.
Kira Radinsky [Resources Tools] (2015)

Presents information on the latest computer and engineering technologies and products.
High Zinc Supplementation of Rainbow Trout Diets (1983)

Abstract Zinc in the form of zinc sulfate or chelated as zinc proteinate was fed in increasing levels (4 to 1,700 µg/g zinc) in an egg-white based diet to fingerling rainbow trout (Salmo gairdneri) to determine potential toxicity. Zinc sulfate was fed for the first 55 days and zinc proteinate for the last 118 days of a 173-day test. Fish fed the lowest level of zinc (4 µg/g zinc, a zinc-deficient diet) had poor growth and high mortalities, while the lowest level of added zinc (90 µg/g) reduced mortalities and markedly improved growth. Higher levels of supplemented zinc, up to 1,700 µg/g, had no further effect on growth or survival. Zinc concentration in liver, blood, and gills increased with dietary levels of zinc above 90 µg/g. Trout showed no signs of zinc toxicity during feeding with levels of dietary zinc as high as 1,700 µg/g.
Direct writing of electronics based on alloy and metal （DREAM） ink： A newly emerging area and its impact on energy, environment and health sciences (2012)

电子学例如印刷电路董事会(聚氯联苯)，晶体管，收音机频率鉴定( RFID )，器官的轻射出二极管( OLED )，太阳能电池，电子显示，一个薄片( LOC )上的实验室，传感器，致动器，并且变换器等等在民族日报生活正在起日益重要的作用。向集成电路(IC ) 的常规制造策略，请求至少六工作走，通常消费太多精力，材料和水，并且不是环境地友好的。在蚀刻的过程期间，大量原料不得不被抛弃。而且，平版印刷术和 microfabrication 典型地在限制 IC 制造的地点并且导致高生产费用的 Cleanroom 被执行。作为一种选择，打印电子学的最新新兴的墨水喷气逐渐地正在塑造现代电子工业和它的相关区域，由于由聚合物矩阵，传导性的 fillers，溶剂和添加剂组成的一系列传导性的墨水的发明。不过，当前可得到的方法也由于低 electroconductivity，复杂 sythesis 和墨水的 sintering 过程遇到一些技术麻烦。作为一种选择，根本上不同的策略最近被作者实验室向通过用低融化的点液体金属或它的合金做的传导性的墨水的一个新班的介绍的电子学的真正直接的写建议。当基于合金和金属(梦) 墨水的电子学的直接的写，方法被说出。一系列功能的电路，传感器，电子元素和设备一会儿能容易因此在各种各样的软或僵硬的底层上被写。与被保留的发现沿着这使范畴成为了的越来越技术的进步和基础， DREAM 墨水电子学启用的一个新区域是新兴的，这被发现，它将在未来精力和环境科学上有巨大的影响。以便沿着这个方向支持研究和发展，现在的论文被奉献由总结它的很基本的特征和原则在 DREAM 墨水技术上起草一幅全面图画。一些重要的低融化点金属墨水候选人，特别房间温度液体金属象镓那样和它的合金，被收集，列出并且分析。在常规打印电子学和新直接作品方法之�
Mesenchymal stem cells and neovascularization: role of platelet‐derived growth factor receptors (2007)

There is now accumulating evidence that bone marrow-derived mesenchymal stem cells (MSCs) make an important contribution to postnatal vasculogenesis, especially during tissue ischaemia and tumour vascularization. Identifying mechanisms which regulate the role of MSCs in vasculogenesis is a key therapeutic objective, since while increased neovascularization can be advantageous during tissue ischaemia, it is deleterious during tumourigenesis. The potent angiogenic stimulant vascular endothelial growth factor (VEGF) is known to regulate MSC mobilization and recruitment to sites of neovascularization, as well as directing the differentiation of MSCs to a vascular cell fate. Despite the fact that MSCs did not express VEGF receptors, we have recently identified that VEGF-A can stimulate platelet-derived growth factor (PDGF) receptors, which regulates MSC migration and proliferation. This review focuses on the role of PDGF receptors in regulating the vascular cell fate of MSCs, with emphasis on the function of the novel VEGF-A/PDGF receptor signalling mechanism.
Identification of differentially expressed genes in human bladder cancer through genome-wide gene expression profiling (2006)

Large-scale gene expression profiling is an effective strategy for understanding the progression of bladder cancer (BC). The aim of this study was to identify genes that are expressed differently in the course of BC progression and to establish new biomarkers for BC. Specimens from 21 patients with pathologically confirmed superficial (n = 10) or invasive (n = 11) BC and 4 normal bladder samples were studied; samples from 14 of the 21 BC samples were subjected to microarray analysis. The validity of the microarray results was verified by real-time RT-PCR. Of the 136 up-regulated genes we detected, 21 were present in all 14 BCs examined (100%), 44 in 13 (92.9%), and the other 71 in 12 BCs (85.7%). Of 69 down-regulated genes, 25 were found in all 14 BCs (100%), 22 in 13 (92.9%), and the other 22 in 12 BCs (85.7%). Functional annotation revealed that of the up-regulated genes, 36% were involved in metabolism and 14% in transcription and processing; 25% of the down-regulated genes were linked to cell adhesion/surface and 21% to cytoskeleton/cell membrane. Real-time RT-PCR confirmed the microarray results obtained for the 6 most highly up- and the 2 most highly down-regulated genes. Among the 6 most highly up-regulated genes, CKS2 was the only gene with a significantly greater level of up-regulation in invasive than in superficial BC (p = 0.04). To confirm this result, we subjected all 21 BC samples to real-time PCR assay for CKS2. We found a considerable difference between superficial and invasive BC (p = 0.001). Interestingly, there was a considerable difference between the normal bladder and invasive BC (p = 0.001) and less difference between the normal bladder and superficial BC (p = 0.005). We identified several genes as promising candidates for diagnostic biomarkers of human BC and the CKS2 gene not only as a potential biomarker for diagnosing, but also for staging human BC. This is the first report demonstrating that CKS2 expression is strongly correlated with the progression of human BC.
Quad list quad trees: a geometrical data structure with improved performance for large region queries (1989)

A data structure is presented for the storage of graphical information. It is a modified multiple storage quad tree, with four lists in each leaf quad. A substantial improvement is obtained for region queries, in particular on large windows, and for tree traversal. On the other hand, only an insignificant increase of memory requirement is noticed in particular situations. The method is not complicated, so it can easily be programmed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Epitaxial regrowth of Ar-implanted amorphous silicon (1978)

The influence of Ar on the recrystallization of implanted amorphous silicon layers has been studied. Investigation of the growth kinetics at temperatures up to 575 °C showed that epitaxial regrowth of silicon is halted if the Ar concentration at the amorphous–single-crystal interface reaches about 1.5×1020 cm−3. Further regrowth could be obtained by higher-temperature annealings, during which the Ar concentration profile was changed and part of the Ar diffused out. TEM analysis showed, that in samples with a dose of 6×1015 Ar ions/cm2, the formation of Ar bubbles occurred during implantation. During annealing the Ar bubbles grew about a factor of 6 in diameter. The epitaxially regrown silicon layers contained a large amount of microtwins. We present a model which relates the occurrence of microtwins to the existence of Ar bubbles.
Real-time finite element based virtual tissue cutting. (2006)

Tool-tissue interaction is most accurately modeled as an imposed displacement constraint, thus augmenting the traditional finite element equation, Ku=f, to a 2 x 2 block system. This augmentation does two things: it enlarges the system, and it introduces the Schur complement(S) during the solution. This research has focused on efficient methods to update the Schur complement and it's inverse during displacement constraint removal and addition to allow for soft-tissue cutting to occur in real-time. By taking advantage of how the constraints impact the Schur complement, removal and addition of these constraints are handled by either performing a rank-2 or rank-1 update on S(-1), respectively. This greatly reduces the computational load on the CPU; and through use of timing tests shows that the update frequencies are well within an acceptable range for tactile feedback. To further solidify this method as being highly useful, a prototypical simulator has been developed that allows users to haptically perform bi-manual soft-tissue cutting.
Awake Craniotomy with Dexmedetomidine in Pediatric Patients (2003)

We present our experience with the use of dexmedetomidine, an alpha2 agonist, in two children undergoing awake craniotomy. General anesthesia with the laryngeal mask airway was used for parts of the procedure not requiring patient cooperation to reduce the duration of wakefulness and abolish the discomfort of surgical stimulation. Dexmedetomidine was used as a primary anesthetic for brain mapping of the cortical speech area. The asleep-awake-sleep technique provided adequate sedation and analgesia throughout the surgery and allowed the patient to complete the necessary neuropsychological tests. To our knowledge, ours is the first description of the use of dexmedetomidine in pediatric neurosurgery.
Simulating Whole Supercomputer Applications (2011)

Detailed simulations of large scale message-passing interface parallel applications are extremely time consuming and resource intensive. A new methodology that combines signal processing and data mining techniques plus a multilevel simulation reduces the simulated data by various orders of magnitude. This reduction makes possible detailed software performance analysis and accurate performance predictions in a reasonable time.
Breast cancer: age-specific growth rates and screening strategies. (1986)

In an earlier work, the author and colleagues predicted that the lead time gained by mammographic screening of an asymptomatic, randomly selected population of women was 2 years +/- 0.5 for women aged 35-49 years and 3.5 years +/- 0.5 for those over age 50. At the completion of long-term follow-up of 10,530 women (with a total of 111,087 "person years"), the resultant lead time actually gained seems to be 12-24 months for women aged 35-49 years at entry and 3.5-4 years for older women. Failure to take this lead time into account in the design of controlled trials may well result in failure to decrease mortality due to breast cancer. The results of the present study and those of recent Dutch and Swedish trials suggest that the most effective screening strategy may be annual mammographic and clinical examinations for women aged 40-49 years and biennial examinations thereafter.
Anisotropic local tomography (2008)

Abstract Local tomography is interactive, ray-based, residual-interval-parameter analysis for updating background anisotropic velocity parameters. The method operates directly on image gathers generated by anisotropic curved-ray Kirchhoff time migration. A locally 1D, spatially varying, vertical transversely isotropic model is assumed. The background anisotropy parameters are the instantaneous (interval) vertical compression velocity VP and the two Thomsen anisotropy parameters, δ and ε. The interval velocity δ is updated from short-offset reflection events, and ε is updated from available long-offset data. The medium parameters are updated from the top down both vertically and by layers, one parameter at a time. The picked residual-anisotropy parameters correspond to the residual-moveout (RMO) curves that best fit the migrated reflection events. The method is based on splitting the contribution to the computed RMO at a given point into two parts: from overburden residual parameters and from the actual picked residual parameter. This approach allows for direct residual-interval-parameter analysis to be applied in the same way we perform the commonly used residual-effective-parameter analysis. The local tomography enables a controlled interactive estimation of the long-wavelength anisotropy parameters. The reliable anisotropy parameters estimated by the local approach are used as a background (guiding) model for a global tomography. This makes it possible to successfully apply a global constrained inversion that is performed simultaneously for all parameters of all output intervals using detailed RMO information.