gebhart/patrepeval huggingface dataset:
Applications of Animal Models of Infectious Arthritis in Drug Discovery:A focus on Alphaviral Disease (2011)

Animal models, which mimic human disease, are invaluable tools for understanding the mechanisms of disease pathogenesis and development of treatment strategies. In particular, animal models play important roles in the area of infectious arthritis. Alphaviruses, including Ross River virus (RRV), o'nyong-nyong virus, chikungunya virus (CHIKV), mayaro virus, Semliki Forest virus and sindbis virus, are globally distributed and cause transient illness characterized by fever, rash, myalgia, arthralgia and arthritis in humans. Severe forms of the disease result in chronic incapacitating arthralgia and arthritis. The mechanisms of how these viruses cause musculoskeletal disease are ill defined. In recent years, the use of a mouse model for RRV-induced disease has assisted in unraveling the pathobiology of infection and in discovering novel drugs to ameliorate disease. RRV as an infection model has the potential to provide key insights into such disease processes, particularly as many viruses, other than alphaviruses, are known to cause infectious arthritides. The emergence and outbreak of CHIKV in many parts of the world has necessitated the need to develop animal models of CHIKV disease. The development of non-human primate models of CHIKV disease has given insights into viral tropism and disease pathogenesis and facilitated the development of new treatment strategies. This review highlights the application of animal models of alphaviral diseases in the fundamental understanding of the mechanisms that contribute to disease and for defining the role that the immune response may have on disease pathogenesis, with the view of providing the foundation for new treatments.
Velocity and flow quantitation in the superior sagittal sinus with ungated and cine (gated) phase‐contrast MR imaging (1994)

Normal blood flow and velocity in the superior sagittal sinus were measured in 30 patients. A fast two-dimensional ungated phase-contrast (PC) pulse sequence was compared with a peripherally gated cine PC technique for velocity and flow quantitation. The same imaging parameters were used for both methods. Measured values for mean velocity and flow obtained with the two methods were compared by using regression analysis and t testing. For blood flow, the correlation coefficient was .976. For velocity measurements, r was .950. Mean flow was 285 mL/min +/- 19 with the ungated PC method and 281 mL/min +/- 19 with the cine PC method. The mean velocities measured with the two methods were 12.94 cm/sec +/- 1.1 and 13.59 cm/sec +/- 1.1, respectively. There was no significant difference (paired t test) between the methods for mean flow or velocity data. This was true even though flow in the superior sagittal sinus is moderately pulsatile, as shown with the cine PC technique. The ungated PC method provided these data in 13 seconds versus 3.5 minutes for the cine PC method.
High-speed transmission (2002)

Service providers are struggling to meet the unprecedented growth of data services in today's telecommunications networks and are currently limited by a public backbone network optimally designed for circuit (voice) transmission. In the future, networks will continue to be shared between static voice circuits and increasing amounts of dynamic traffic that is often referred to as packet, IP, or data traffic. This mixture of traffic puts new requirements on the design of core public networks and stresses their ability to scale to meet capacity demand at backbone distances. When bandwidth hungry applications such as cable modem, Storage Area Networks (SANs), and peer-to-peer networking become commonplace in access networks, the wide-area network or core network will need to respond by operating much more like a LAN in terms of being flexible and data ready. These future networks must support high capacity IP networking across backbone distances, and system vendors must provide reliable and cost-effective ultrafast long haul optical transmission as the first step to realizing the promise of flexible optical networking.
High-Density Sodium and Lithium Ion Battery Anodes from Banana Peels (2014)

Banana peel pseudographite (BPPG) offers superb dual functionality for sodium ion battery (NIB) and lithium ion battery (LIB) anodes. The materials possess low surface areas (19-217 m(2) g(-1)) and a relatively high electrode packing density (0.75 g cm(-3) vs ∼1 g cm(-3) for graphite). Tested against Na, BPPG delivers a gravimetric (and volumetric) capacity of 355 mAh g(-1) (by active material ∼700 mAh cm(-3), by electrode volume ∼270 mAh cm(-3)) after 10 cycles at 50 mA g(-1). A nearly flat ∼200 mAh g(-1) plateau that is below 0.1 V and a minimal charge/discharge voltage hysteresis make BPPG a direct electrochemical analogue to graphite but with Na. A charge capacity of 221 mAh g(-1) at 500 mA g(-1) is degraded by 7% after 600 cycles, while a capacity of 336 mAh g(-1) at 100 mAg(-1) is degraded by 11% after 300 cycles, in both cases with ∼100% cycling Coulombic efficiency. For LIB applications BPPG offers a gravimetric (volumetric) capacity of 1090 mAh g(-1) (by material ∼2200 mAh cm(-3), by electrode ∼900 mAh cm(-3)) at 50 mA g(-1). The reason that BPPG works so well for both NIBs and LIBs is that it uniquely contains three essential features: (a) dilated intergraphene spacing for Na intercalation at low voltages; (b) highly accessible near-surface nanopores for Li metal filling at low voltages; and (c) substantial defect content in the graphene planes for Li adsorption at higher voltages. The <0.1 V charge storage mechanism is fundamentally different for Na versus for Li. A combination of XRD and XPS demonstrates highly reversible Na intercalation rather than metal underpotential deposition. By contrast, the same analysis proves the presence of metallic Li in the pores, with intercalation being much less pronounced.
Sleep and Brain Energy Levels: ATP Changes during Sleep (2010)

Sleep is one of the most pervasive biological phenomena, but one whose function remains elusive. Although many theories of function, indirect evidence, and even common sense suggest sleep is needed for an increase in brain energy, brain energy levels have not been directly measured with modern technology. We here report that ATP levels, the energy currency of brain cells, show a surge in the initial hours of spontaneous sleep in wake-active but not in sleep-active brain regions of rat. The surge is dependent on sleep but not time of day, since preventing sleep by gentle handling of rats for 3 or 6 h also prevents the surge in ATP. A significant positive correlation was observed between the surge in ATP and EEG non-rapid eye movement delta activity (0.5-4.5 Hz) during spontaneous sleep. Inducing sleep and delta activity by adenosine infusion into basal forebrain during the normally active dark period also increases ATP. Together, these observations suggest that the surge in ATP occurs when the neuronal activity is reduced, as occurs during sleep. The levels of phosphorylated AMP-activated protein kinase (P-AMPK), well known for its role in cellular energy sensing and regulation, and ATP show reciprocal changes. P-AMPK levels are lower during the sleep-induced ATP surge than during wake or sleep deprivation. Together, these results suggest that sleep-induced surge in ATP and the decrease in P-AMPK levels set the stage for increased anabolic processes during sleep and provide insight into the molecular events leading to the restorative biosynthetic processes occurring during sleep.
Cutting Edge: The ST2 Ligand IL-33 Potently Activates and Drives Maturation of Human Mast Cells (2007)

IL-33, the natural ligand of the IL-1 receptor family member ST2L, is known to enhance experimental allergic-type inflammatory responses by costimulating the production of cytokines from activated Th2 lymphocytes. Although ST2L has long been known to be expressed by mast cells, its role in their biology has not been explored. In this study we report that IL-33 directly stimulates primary human mast cells (MCs) to produce several proinflammatory cytokines and chemokines and also exerts a permissive effect on the MCs response to thymic stromal lymphopoietin, a recently described potent MCs activator. IL-33 also acts both alone and in concert with thymic stromal lymphopoietin to accelerate the in vitro maturation of CD34(+) MC precursors and induce the secretion of Th2 cytokines and Th2-attracting chemokines. Taken together, these results suggest that IL-33 may play an important role in mast cell-mediated inflammation and further emphasize the role of innate immunity in allergic diseases.
What Should Be Done about Difficult Brand Expansion? : Effect of Regulatory Focus (2020)

기업에게 신제품은 지속가능성을 높이려는 매력적인 대안이 될 수 있다. 그렇지만 유행이 빠르게 변하고 소비자 욕구가 다양해짐에 따라 신제품의 성공을 담보 할 수 없게 되었다. 이에 따라 신제품에 의한 효과성이 갈수록 감소하고 있다. 신제품 출시가 기업의 지속가능성을 해하는 일도 있다. 시장에서 신제품의 약 20% 정도만이 성공한다고 하니, 신제품의 출시를 긍정적인 시각으로만 바라볼 수 없게 되었다. 그럼에도 불구하고 신제품 출시는 여전히 기업을 주목시키고 기업의 매력도를 높이는 중요한 과업이다. 기업은 신제품의 성공률을 높이기 위해 브랜드 확장 전 략을 적극적으로 활용한다. 그러나 브랜드 확장 전략이 항상 쉬운 길은 아니다. 어려운 브랜드 확장 상황(모브랜드와 거리가 있는 확장 영역, 제조 난이도가 높은 확장 제품)이 있다. 본 연구는 어려운 상황에서의 효과적인 브랜드 확장 전략을 제안하기 위해 실행되었다. 주요 연구결과는 다음과 같다. 첫째, 예방 초점의 소비자에게는 직접 확장보다 순차적 확장이 효과적이었다. 둘째, 향상 초점의 소비자에게는 제조난이도가 낮 은 확장보다 높은 확장이 더 효과적이다. 그러나 예방 초점의 소비자에게는 제조 난이도가 높은 확장보다 낮은 확장이 효과적이다. 셋째, 제조 난이도가 높은 확장 에는 직접 확장보다 순차적 확장이 더 효과적이었다.
Omnidirectional Square Loop Segmented Antenna (2015)

A square loop antenna of circumference about one free-space wavelength displays an omnidirectional radiation pattern when its conductor is partitioned into five segments that are interconnected by four small capacitances. The optimization process for determining the capacitances values is described in detail. The required four capacitances are created by overlapping the conductor segments on the opposite sides of the substrate. The far field of the antenna resembles the one of an elementary magnetic dipole. At the center frequency of 956 MHz, the measured maximum gain is 2 dBi, and the measured antenna efficiency is 94%.
A user-adaptive indexing model of structured documents (2005)

In this paper we present an indexing model of multimedia documents having a hierarchical structure; this model allows users to generate personal document representations. The documents are organised into logical (thematic) sections where the index terms play a distinct role as descriptors of the documents' information contents. The indexed archive can be heterogeneous, i.e. it may contain documents with distinct logical structures. The proposed indexing model is adaptive to the user, who can indicate in the retrieval phase the preferred sections of documents, i.e. those which they estimate to bear the most interesting information, and can linguistically quantify the number of sections which determine the global potential interest of the documents. The adaptation is carried out by a flexible query language for expressing the aforementioned soft selection conditions on the structured documents.
Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies (2013)

The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease modeling by mapping named-entities mentions to terminologies and clustering semantically related terms. EHR corpora, however, exhibit specific statistical and linguistic characteristics when compared with corpora in the biomedical literature domain. We focus on copy-and-paste redundancy: clinicians typically copy and paste information from previous notes when documenting a current patient encounter. Thus, within a longitudinal patient record, one expects to observe heavy redundancy. In this paper, we ask three research questions: (i) How can redundancy be quantified in large-scale text corpora? (ii) Conventional wisdom is that larger corpora yield better results in text mining. But how does the observed EHR redundancy affect text mining? Does such redundancy introduce a bias that distorts learned models? Or does the redundancy introduce benefits by highlighting stable and important subsets of the corpus? (iii) How can one mitigate the impact of redundancy on text mining? We analyze a large-scale EHR corpus and quantify redundancy both in terms of word and semantic concept repetition. We observe redundancy levels of about 30% and non-standard distribution of both words and concepts. We measure the impact of redundancy on two standard text-mining applications: collocation identification and topic modeling. We compare the results of these methods on synthetic data with controlled levels of redundancy and observe significant performance variation. Finally, we compare two mitigation strategies to avoid redundancy-induced bias: (i) a baseline strategy, keeping only the last note for each patient in the corpus; (ii) removing redundant notes with an efficient fingerprinting-based algorithm. aFor text mining, preprocessing the EHR corpus with fingerprinting yields significantly better results. Before applying text-mining techniques, one must pay careful attention to the structure of the analyzed corpora. While the importance of data cleaning has been known for low-level text characteristics (e.g., encoding and spelling), high-level and difficult-to-quantify corpus characteristics, such as naturally occurring redundancy, can also hurt text mining. Fingerprinting enables text-mining techniques to leverage available data in the EHR corpus, while avoiding the bias introduced by redundancy.
Neutrophil Extracellular Traps in Pulmonary Diseases: Too Much of a Good Thing? (2016)

Neutrophil extracellular traps (NETs) arise from the release of granular and nuclear contents of neutrophils in the extracellular space in response to different classes of microorganisms, soluble factors, and host molecules. NETs are composed by decondensed chromatin fibers coated with antimicrobial granular and cytoplasmic proteins, such as myeloperoxidase, neutrophil elastase (NE), and α-defensins. Besides being expressed on NET fibers, NE and MPO also regulate NET formation. Furthermore, histone deimination by peptidylarginine deiminase 4 (PAD4) is a central step to NET formation. NET formation has been widely demonstrated to be an effective mechanism to fight against invading microorganisms, as deficiency in NET release or dismantling NET backbone by bacterial DNases renders the host susceptible to infections. Therefore, the primary role of NETs is to prevent microbial dissemination, avoiding overwhelming infections. However, an excess of NET formation has a dark side. The pathogenic role of NETs has been described for many human diseases, infectious and non-infectious. The detrimental effect of excessive NET release is particularly important to lung diseases, because NETs can expand more easily in the pulmonary alveoli, causing lung injury. Moreover, NETs and its associated molecules are able to directly induce epithelial and endothelial cell death. In this regard, massive NET formation has been reported in several pulmonary diseases, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, respiratory syncytial virus bronchiolitis, influenza, bacterial pneumonia, and tuberculosis, among others. Thus, NET formation must be tightly regulated in order to avoid NET-mediated tissue damage. Recent development of therapies targeting NETs in pulmonary diseases includes DNA disintegration with recombinant human DNase, neutralization of NET proteins, with anti-histone antibodies and protease inhibitors. In this review, we summarize the recent knowledge on the pathophysiological role of NETs in pulmonary diseases as well as some experimental and clinical approaches to modulate their detrimental effects.
Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform (2007)

An innovative reconfigurable supercomputing platform -- XD1000 is developed by XtremeData Inc. to exploit the rapid progress of FPGA technology and the high-performance of Hyper-Transport interconnection. In this paper, we present the implementations of the Smith-Waterman algorithm for both DNA and protein sequences on the platform. The main features include: (1) we bring forward a multistage PE (processing element) design which significantly reduces the FPGA resource usage and hence allows more parallelism to be exploited; (2) our design features a pipelined control mechanism with uneven stage latencies -- a key to minimize the overall PE pipeline cycle time; (3) we also put forward a compressed substitution matrix storage structure, resulting in substantial decrease of the on-chip SRAM usage. Finally, we implement a 384-PE systolic array running at 66.7MHz, which can achieve 25.6GCUPS peak performance. Compared with the 2.2GHz AMD Opteron host processor, the FPGA coprocessor speedups 185X and 250X respectively.
Application of sim-hash algorithm and big data analysis in spam email detection system (2014)

Currently, there are many effective techniques that are used for filtering spam emails. However, spammers have mostly identified the weakness of those methods in order to bypass current detection systems. In this paper, we propose a novel similarity-based method that implements the fingerprinting technique on parallel processing framework. Furthermore, meet-in-the-middle approach is used in our method to achieve a higher accuracy in the spam email detection system. Our experimental result demonstrates the improved efficiency of this study.
Robust Resource Allocations in Parallel Computing Systems: Model and Heuristics (2006)

The resources in parallel computer systems (including heterogeneous clusters) should be allocated to the computational applications in a way that maximizes some system performance measure. However, allocation decisions and associated performance prediction are often based on estimated values of application and system parameters. The actual values of these parameters may differ from the estimates; for example, the estimates may represent only average values, the models used to generate the estimates may have limited accuracy, and there may be changes in the environment. Thus, an important research problem is the development of resource management strategies that can guarantee a particular system performance given such uncertainties. To address this problem, we have designed a model for deriving the degree of robustness of a resource allocation-the maximum amount of collective uncertainty in system parameters within which a user-specified level of system performance (QoS) can be guaranteed. The model is presented and we demonstrate its ability to select the most robust resource allocation from among those that otherwise perform similarly (based oh the primary performance criterion). The model's use in allocation heuristics is also demonstrated. This model is applicable to different types of computing and communication environments, including parallel, distributed, cluster; grid, Internet, embedded, and wireless.
Tumor-specific Ab-mediated targeting of MHC-peptide complexes induces regression of human tumor xenografts<i>in vivo</i> (2004)

A cancer immunotherapy strategy is described herein that combines the advantage of the well established tumor targeting capabilities of high-affinity recombinant fragments of Abs with the known efficient, specific, and potent killing ability of CD8 T lymphocytes directed against highly antigenic MHC-peptide complexes. Structurally, it consists of a previously uncharacterized class of recombinant chimerical molecules created by the genetic fusion of single-chain (sc) Fv Ab fragments, specific for tumor cell surface antigens, to monomeric scHLA-A2 complexes containing immunodominant tumor- or viral-specific peptides. The fusion protein can induce very efficiently tumor cell lysis, regardless of the expression of self peptide-MHC complexes. Moreover, these molecules exhibited very potent antitumor activity in vivo in nude mice bearing preestablished human tumor xenografts. These in vitro and in vivo results suggest that recombinant scFv-MHC-peptide fusion molecules could represent an approach to immunotherapy, bridging Ab and T lymphocyte attack on cancer cells.
Order batching to minimize total travel time in a parallel-aisle warehouse (2004)

Although the picking of items may make up as much as 60% of all labor activities in a warehouse and may account for as much as 65% of all operating expenses, many order picking problems are still not well understood. Indeed, usually simple rules of thumb or straightforward constructive heuristics are used in practice, even in state-of-the-art warehouse management systems, however, it might well be that more attractive algorithmic alternatives could be developed. We address one such a fundamental materials handling problem: the batching of orders in a parallel-aisle warehouse so as to minimize the total traveling time needed to pick all items. Many heuristics have been proposed for this problem, however, a fundamental analysis of the problem is still lacking. In this paper, we first address the computational complexity of the problem. We prove that this problem is NP-hard in the strong sense but that it is solvable in polynomial time if no batch contains more than two orders. This result is not really surprising but it justifies the development of approximation and/or enumerative optimization algorithms for the general case. Our primary goal is to develop a branch-and-price optimization algorithm for the problem. To this end, we model the problem as a generalized set partitioning problem and present a column generation algorithm to solve its linear programming relaxation. Furthermore, we develop a new approximation algorithm for the problem. Finally, we test the performance of the branch-and-price algorithm and the approximation algorithm on a comprehensive set of instances. The computational experiments show the compelling performance of both algorithms.
Quantitative assessment of tear production: A review of methods and utility in dry eye drug discovery (2008)

The successful development of a therapeutic agent targeting treatment of dry eye syndrome necessitates the demonstration of drug efficacy for both sign and symptom endpoints. As numerous therapeutic strategies incorporate a secretagogue function into their overall mechanism of action, the quantitative assessment of tear production serves as a logical endpoint to anchor "sign" efficacy. Although several methods including the Schirmer, the phenol red thread and tear clearance tests exist, their utility in clinical evaluations of novel therapeutics is unclear. The purpose of this review is to summarize findings and conclusions describing the performance of each of these tests so as to gain insight into which, if any, is most applicable for use in discovering new dry eye therapeutics.