gebhart/patrepeval huggingface dataset:
Cell Surface Capturing Technologies for the Surfaceome Discovery of Hepatocytes (2012)

Proteins expressed at the cell surface define how cells can functionally interact with their microenvironment in time and space. The cell surface subproteome, or surfaceome, represents a cellular information gateway not only enabling the processing of environmental molecular cues but also limiting cellular interaction capacities. Therefore, the array of antibody-detectable cell surface proteins is widely used to phenotype and categorize cells. Quantitative differences in surfaceome markers can not only indicate different developmental cellular stages but also serve as markers of disease. In fact, cell surface proteins are promising biomarker candidates, since they are often, apart from their plasma membrane expression, secreted, shed, or released otherwise from the tissue into the bloodstream. From minute amounts of blood these informative proteins can be detected and quantified by ELISA or highly sensitive state-of-the art targeted mass spectrometric techniques. However, the identification of the complete surfaceome and its constituents is hampered by a lack of suitable technologies to detect these proteins at the cell surface location. Antibodies for the detection of cell surface proteins are only available for a subset of the potentially expressed surfaceome members. The mass spectrometry-based cell surface capturing (CSC) technology and recently developed variants overcome these limitations by selectively enriching and identifying cell surface proteins that are either N-glycosylated (Glyco-CSC, Cys-Glyco-CSC), or have an extracellularly exposed and conformationally available lysine (Lys-CSC). Here, we outline the CSC technology and its variants in a detailed step-by-step protocol for soluble and adherent cells. Representative results from the application of the CSC technologies to the hepatocyte cell line Hepa1-6 illustrate the complementary nature of the CSC technologies, which enables a systems biology view of the surfaceome.
The TOPHITS Model for Higher-Order Web Link Analysis∗ (2006)

As the size of the web increases, it becomes more and more important to analyze link structure while also considering context. Multilinear algebra provides a novel tool for incorporating anchor text and other information into the authority computation used by link analysis methods such as HITS. Our recently proposed TOPHITS method uses a higher-order analogue of the matrix singular value decomposition called the PARAFAC model to analyze a three-way representation of web data. We compute hubs and authorities together with the terms that are used in the anchor text of the links between them. Adding a third dimension to the data greatly extends the applicability of HITS because the TOPHITS analysis can be performed in advance and offline. Like HITS, the TOPHITS model reveals latent groupings of pages, but TOPHITS also includes latent term information. In this paper, we describe a faster mathematical algorithm for computing the TOPHITS model on sparse data, and Web data is used to compare HITS and TOPHITS. We also discuss how the TOPHITS model can be used in queries, such as computing context-sensitive authorities and hubs. We describe different query response methodologies and present experimental results.
Adult Neural Stem Cells From the Subventricular Zone: A Review of the Neurosphere Assay (2013)

The possibility of obtaining large numbers of cells with potential to become functional neurons implies a great advance in regenerative medicine. A source of cells for therapy is the subventricular zone (SVZ) where adult neural stem cells (NSCs) retain the ability to proliferate, self-renew, and differentiate into several mature cell types. The neurosphere assay, a method to isolate, maintain, and expand these cells has been extensively utilized by research groups to analyze the biological properties of aNSCs and to graft into injured brains from animal models. In this review we briefly describe the neurosphere assay and its limitations, the methods to optimize culture conditions, the identity and the morphology of aNSC-derived neurospheres (including new ultrastructural data). The controversy regarding the identity and "stemness" of cells within the neurosphere is revised. The fine morphology of neurospheres, described thoroughly, allows for phenotypical characterization of cells in the neurospheres and may reveal slight changes that indirectly inform about cell integrity, cell damage, or oncogenic transformation. Along this review we largely highlight the critical points that researchers have to keep in mind before extrapolating results or translating experimental transplantation of neurosphere-derived cells to the clinical setting.
Understanding the pedagogic discourse of assessment in Physical Education (2011)

In recent years, various scholars have expounded on the notable pedagogic work that assessment plays in educational contexts, describing its capacity to convey powerful messages on the valued aspect of education knowledge, impacting upon how and what students learn in these contexts. However, not many studies have sought to gain an insight into what and how discourses are reproduced or produced in the classroom through assessment, or the pedagogic consequences that may arise. The pilot study presented in this article provided some insights into the aforementioned issues in the field of Physical Education (PE) at the middle and senior phases of learning in Queensland schools. The findings show that the messages that were transmitted and acquired through assessment may not be in alignment with the official intended discourse, and that systemic accountability mechanisms not only influence the rigour of assessment that is conducted in PE, but also influence the consistency of teachers' and students' awareness of the valued elements of subject matter.
A concept for a biologically derived, parabolic implant design. (2002)

It has become widely accepted that modern titanium dental implants are successful and predictable. However, there is bone loss in relation to any interface (microgap) that occurs between the implant parts when the microgap is in proximity or apical to the osseous crest. The principle of biologic width may be responsible for such bone remodeling in an apical manner. A new, biologically derived implant design that conceptually may minimize bone remodeling and promote better bone and overlying gingival contours and stability is suggested. The parabolic occlusal platform of this design is in harmony with the biologic width of the soft tissue around the circumference of the implant when the proximal bone is occlusal to the facial and lingual bone. Preservation of proximal bone for an isolated implant, and between implants, will help support and maintain physiologic and cosmetic gingival contours and papillae. This is of particular importance in esthetic areas, where interproximal bone loss between implants or between an implant and an adjacent tooth may cause a reduction in gingival papilla height.
UCLA Loneliness Scale (Version 3): Reliability, Validity, and Factor Structure (1996)

In this article I evaluated the psychometric properties of the UCLA Loneliness Scale (Version 3). Using data from prior studies of college students, nurses, teachers, and the elderly, analyses of the reliability, validity, and factor structure of this new version of the UCLA Loneliness Scale were conducted. Results indicated that the measure was highly reliable, both in terms of internal consistency (coefficient alpha ranging from .89 to .94) and test-retest reliability over a 1-year period (r = .73). Convergent validity for the scale was indicated by significant correlations with other measures of loneliness. Construct validity was supported by significant relations with measures of the adequacy of the individual's interpersonal relationships, and by correlations between loneliness and measures of health and well-being. Confirmatory factor analyses indicated that a model incorporating a global bipolar loneliness factor along with two method factor reflecting direction of item wording provided a very good fit to the data across samples. Implications of these results for future measurement research on loneliness are discussed.
Large‐scale carbohydrate analysis by capillary array electrophoresis: Part 2. Data normalization and quantification (2004)

Automated 96-capillary array electrophoresis (CAE) methodology described in the first part of the present work offered large-scale high-performance profiling of oligo- and monosaccharides to fulfill the needs of bioindustrial laboratories. Sensitivity at low nanomolar concentration, good resolving power and reliability achieved in the experiments is invaluable for monitoring reaction products from enzymatic polysaccharide digestion with numerous applications in agricultural, chemical and food industries. In addition to optimization of mono- and oligosaccharide separations in CAE system and necessary operational protocol modifications, capillary-to-capillary and run-to-run variation in migration time and signal intensity necessitated development of data normalization tools. Internal fluorescent standards have been incorporated into the analysis aiding migration time normalization and CAE trace alignment. Data processing, visualization, and programming tools have been developed along with quantification approaches.
Synthesis of a Room‐Temperature‐Stable Dimeric Copper(I) Hydride (2010)

CAACs are not NHCs! (NHC)CuH cannot be stored at room temperature, whereas a (CAAC)CuH is stable for weeks both in solution and in the solid state. In the presence of an additional L ligand, the hydride migrates to the carbene carbon, thus affording (CAAC,H)CuL complexes. CAAC=cyclic (alkyl)(amino)carbene; NHC=N-heterocyclic carbene.
UPDATED LIST OF MEALYBUGS AND PUTOIDS FROM COLOMBIA (HEMIPTERA: PSEUDOCOCCIDAE AND PUTOIDAE) (2011)

Collecting localities, plant hosts and associated ants of 34 species of mealybugs and putoids (Hemiptera: Coccoidea: Pseudococcidae and Putoidae) in Colombia collected during 1995–2008 are provided. Brief notes on their biology, taxonomy and distribution are given. Eleven species, Dysmicoccus sp., Ferrisia sp., Maconellicoccus hirsutus (Green), Nipaecoccus sp. 1, Nipaecoccus sp. 2, Phenacoccus solani Ferris, Ph. solenopsis Tinsley, Planococcus halli Ezzat & McConnell, Prorhizoecus sp., Pseudococcus calceolariae (Maskell), and Rhizoecus mayanus (Hambleton) are newly recorded from Colombia. An updated list of 78 mealybug species from Colombia is given.
Distributed data warehouses-the role of adaptive information agents (2002)

One of the greatest challenges facing the information age is the discovery of relevant information. Current approaches to the problem fall short in several respects. We propose a scalable, self-organising model for online distributed data warehouses. The prime feature of the model is a population of adaptive agents, one per Web site. These agents produce reports by distributing elements of a query to appropriate resources or to other agents in the population, Queries are couched in a specialised scripting language, based on XML. Agents adapt by converting new queries into functions and by recording new resources.
Hippocampal Volume in Patients With Alcohol Dependence (1999)

In chronic alcoholism, the reduction of hippocampal volume is proportional to the reduction of the brain volume. Alcohol consumption should be accounted for in studies of hippocampal damage.
Longitudinal Evaluation of Neonatal Nosocomial Infections: Association of Infection With a Blood Pressure Cuff (1978)

Nosocomial infections acquired in a special care nursery were surveyed longitudinally. The rates of acquired infection were determined, allowing the evaluation of specific infection control measures. A blood pressure cuff, utilized for all infants in the nursery, was associated with an increased rate of infection.
Botnet Identification in DDoS Attacks With Multiple Emulation Dictionaries (2021)

In a Distributed Denial of Service (DDoS) attack, a network (botnet) of dispersed agents (bots) sends requests to a website to saturate its resources. Since the requests are sent by automata, the typical way to detect them is to look for some repetition pattern or commonalities between requests of the same user or from different users. For this reason, recent DDoS variants exploit communication layers that offer broader possibility in terms of admissible request patterns, such as, e.g., the application layer. In this case, the malicious agents can pick legitimate messages from an emulation dictionary, and each individual agent sends a relatively low number of admissible requests, so as to make its activity non suspicious. This problem has been recently addressed under the assumption that all the members of the botnet use the same emulation dictionary. This situation is an idealization of what occurs in practice, since different clusters of agents are typically sharing only part of a global emulation dictionary. The diversity among the emulation dictionaries across different clusters introduces significant complexity in the botnet identification challenge. This work tackles this issue and provides the following main contributions. We obtain an analytical characterization of the message innovation rate of the DDoS attack with multiple emulation dictionaries. Exploiting this result, we design a botnet identification algorithm equipped with a cluster expurgation rule, which, under appropriate technical conditions, is shown to provide exact classification of bots and normal users as the observation window size increases. Then, an experimental campaign over real network traces is conducted to assess the validity of the theoretical analysis, as well as to examine the effect of a number of non-ideal effects that are unavoidably observed in practical scenarios.
Enhancement of Dopamine Release In Vivo from the Rat Striatum by Dialytic Perfusion of 6<i>R</i>‐<scp>l</scp>‐<i>erythro</i>‐5,6,7,8‐Tetrahydrobiopterin (1990)

We have previously reported that intracerebroventricular administration of 6R-L-erythro-5,6,7,8-tetrahydrobiopterin (6R-BH4), a cofactor for tyrosine hydroxylase, enhances biosynthesis of 3,4-dihydroxyphenylethylamine (dopamine) in the rat brain. In the present study, we have more precisely examined the effects of 6R-BH4 on dopamine release in vivo from the rat striatum using brain microdialysis. The amount of dopamine collected in striatal dialysates was determined using HPLC with electrochemical detection after purification with an alumina batch method. When the striatum was dialyzed with Ringer solution containing various concentrations of 6R-BH4 (0.25, 0.5, and 1.0 mM), dopamine levels in striatal dialysates increased in a concentration-dependent manner. Biopterin had little effect on dopamine levels in dialysates. The 6R-BH4-induced increase in dopamine levels in dialysates was abolished after pretreatment with tetrodotoxin (50 microM) added to the perfusion fluid, but after pretreatment with nomifensine (100 mg/kg, intraperitoneal injection), an inhibitor of dopamine uptake mechanism, a larger increase was observed. After inhibition of tyrosine hydroxylase by pretreatment with alpha-methyl-p-tyrosine (250 mg/kg, intraperitoneal injection), most of the increase persisted. These results suggest that 6R-BH4 has a dopamine-releasing action, which is not dependent on biosynthesis of dopamine.
1,1,3,3-Tetramethylguanidine solvated lanthanide aryloxides: pre-catalysts for intramolecular hydroalkoxylation (2009)

The synthesis and structural characterization of six 1,1,3,3-tetramethylguanidine (H-TMG) solvated lanthanide aryloxide complexes are reported. Ln[N{Si(CH3)3}2]3 (Ln = Nd, La) was reacted with two equivalents of both H-TMG and HOAr {HOAr = HOC6H2(CMe3)2-2,6 (H-DBP) or HOC6H2(CMe3)2-2,6-CH3-4 (H-4MeDBP)} and one equivelent of ethanol (HOEt) to yield the corresponding [Nd(H-TMG)2(4MeDBP)2(OEt)] (1) and [La(H-TMG)2(DBP)2(OEt)] (2). Compounds 1 and 2 were further reacted with 4-pentyn-1-ol {HO(CH2)3C[triple bond]CH} to isolate [Nd(H-TMG)2(4MeDBP)2{O(CH2)3C[triple bond]CH}] (3) and [La(H-TMG)2(DBP)2{O(CH2)3C[triple bond]CH}] (4), respectively. Three equivalents of HOAr and one equivalent of H-TMG were additionally reacted with Ln[N{Si(CH3)3}2]3 to generate [Nd(4MeDBP)3(H-TMG)] (5) and [La(DBP)3(H-TMG)] (6). In order to examine the formation of 1-6, the interaction of H-TMG and HOAr was further examined in solution and the hydrogen bonded complexes (H-TMG:HOAr), 7 and 8, were isolated. Upon successful isolation of 1-6, the utility of 1, 2, 4 and 5 as pre-catalysts for the intramolecular hydroalkoxylation of 4-pentyn-1-ol was investigated. The bulk powders for all complexes were found to be in agreement with the crystal structures based on elemental analyses, FT-IR spectroscopy, and 1H and 13C NMR investigations.
Heterometal Incorporation in Metal-Exchanged Zeolites Enables Low-Temperature Catalytic Activity of NO<sub><i>x</i></sub>Reduction (2012)

A series of new heterobimetallic zeolites has been synthesized by incorporating a secondary metal cation M (Sc3+, Fe3+, In3+, and La3+) in Cu-exchanged ZSM-5, zeolite-β, and SSZ-13 zeolites under carefully controlled experimental conditions. Characterization by diffuse-reflectance ultraviolet–visible spectroscopy (UV–vis), X-ray powder diffraction (XRD), extended X-ray absorption fine structure spectroscopy (EXAFS), and electron paramagnetic resonance spectroscopy (EPR) does not permit conclusive structural determination but supports the proposal that M3+ is hosted in zeolite structures in the vicinity of Cu(II), resulting in high NOx conversion activity at 150 °C. Among various zeolites reported here, CuFe-SSZ-13 offers the best NOx conversion activity in the 150–650 °C range and is hydrothermally stable when tested under accelerated aging conditions. Mechanistic studies employing stopped-flow diffuse reflectance FT-IR spectroscopy (DRIFTS) suggest that the high concentration of NO+ generated by heterobimetallic zeolites is probably responsible for their superior low-temperature NOx activity.
Synthesis, Structure, and Reactivity of the Phosphinimide Complexes (<i>t-</i>Bu<sub>3</sub>PN)<i><sub>n</sub></i>MX<sub>4</sub><sub>-</sub><i><sub>n</sub></i> (M = Ti, Zr) (2000)

The phosphinimide complexes (t-Bu3PN)TiCl3 (1) and (t-Bu3PN)2TiCl2 (4) are readily prepared in high yields from the stoichiometric reaction of t-Bu3PNSiMe3 and TiCl4, while (t-Bu3PN)3TiCl (11) is readily obtained from the reaction of t-Bu3PNLi and TiCl4. The analogous 1:1 or 2:1 reactions of ZrCl4 and t-Bu3PNLi afford mixtures of products, although in the 3:1 stoichiometric ratio (t-Bu3PN)3ZrCl (12) is isolable. These complexes are readily alkylated with a variety of reagents to give (t-Bu3PN)TiMe3 (2), (t-Bu3PN)Ti(CH2Ph)3 (3), (t-Bu3PN)2TiMe2 (5), (t-Bu3PN)2Ti(η3-C3H5)2 (6), (t-Bu3PN)2Ti(CH2Ph)2 (7), (t-Bu3PN)2TiPh2 (8), (t-Bu3PN)2Ti(η5-Cp)Cl (9), (t-Bu3PN)2Ti(η5-Cp)Me (10), (t-Bu3PN)3TiMe (13), (t-Bu3PN)3TiPh (14), (t-Bu3PN)3ZrMe (15), (t-Bu3PN)3Zr(CH2Ph) (16), and (t-Bu3PN)3Zr(η5-Cp) (17). Subsequent reactions of some of these alkyl derivatives with [PhNMe2H][B(C6F5)4], [Ph3C][B(C6F5)4], or B(C6F5)3 are investigated. A number of zwitterionic and cationic species complexes have been characterized. These include [(t-Bu3PN)Ti(CH2Ph)2(PhCH2)B(C6F5)3] (18), [(t-Bu3PN)2TiMe(PMe3)][B(C6F5)4] (19), (t-Bu3PN)2TiMe (μ-MeB(C6F5)3) (20), (t-Bu3PN)2Ti(μ-MeB(C6F5)3)2 (21), and (t-Bu3PN)2Ti(C6F5)2 (22). The implications of this chemistry are considered. Structural data for 1, 4, 5, 12, 16, 21, and 22 are described.
Security in wireless actor &amp; sensor networks (WASN): towards a hierarchical re-keying design (2005)

Our work aims to address the challenging security issues in an important information infrastructure - large-scale and low-energy wireless actuator and sensor networks (WASN). Since WASNs have specific network constraints and data transmission requirements compared to general ad hoc networks and other wireless/wired networks, the security issues need to be tackled accordingly. We propose to seamlessly integrate WASN security with a promising routing architecture that is scalable and energy-efficient. To protect from active attacks in mobile sensor networks, we propose two-level re-keying/re-routing schemes that can not only adapt to a dynamic network topology but also securely update keys for each data transmission session. Moreover, to provide the security for the in-networking processing such as data aggregation in WASNs, we define a multiple-key management scheme in conjunction with the proposed tree-ripple-zone (TRZ) routing architecture.
DETECTING ANOMALY REGIONS IN SATELLITE IMAGE TIME SERIES BASED ON SESAONAL AUTOCORRELATION ANALYSIS (2016)

Anomaly regions in satellite images can reflect unexpected changes of land cover caused by flood, fire, landslide, etc. Detecting anomaly regions in satellite image time series is important for studying the dynamic processes of land cover changes as well as for disaster monitoring. Although several methods have been developed to detect land cover changes using satellite image time series, they are generally designed for detecting inter-annual or abrupt land cover changes, but are not focusing on detecting spatial-temporal changes in continuous images. In order to identify spatial-temporal dynamic processes of unexpected changes of land cover, this study proposes a method for detecting anomaly regions in each image of satellite image time series based on seasonal autocorrelation analysis. The method was validated with a case study to detect spatial-temporal processes of a severe flooding using Terra/MODIS image time series. Experiments demonstrated the advantages of the method that (1) it can effectively detect anomaly regions in each of satellite image time series, showing spatial-temporal varying process of anomaly regions, (2) it is flexible to meet some requirement (e.g., z-value or significance level) of detection accuracies with overall accuracy being up to 89% and precision above than 90%, and (3) it does not need time series smoothing and can detect anomaly regions in noisy satellite images with a high reliability.
Practical implementation of a 16-channel C-band phased array radar receiver (2015)

This paper presents the practical implementation of a 16 channel, C-band FMCW radar phased array receiver developed for the purpose of imaging flowing avalanches. The phased array is designed for a 30° field of view to give full coverage of an avalanche track. A fully populated, uniform linear array design is achieved using overlapping sub-arrays of 2A spacing, and with 16 elements, the beamwidth of the array is 1.6°. The phased array is arranged on a three layer PCB that is split into four panels due to its large physical width (1.95 m). The array is mounted on plastic pillars screwed to an aluminium base in a watertight radome to provide mechanical strength. Radio absorbent material between the PCB's and the aluminium base prevent back lobe reflections. A continuous ground across the PCB panels is maintained using grounded copper sheet bridges. Initial laboratory measurements of the phased array show that its performance agrees well with predictions.