Miracle-dz/UniFAR-FTUs huggingface dataset:
Detachment of cultured cells from the substratum induced by the neutrophil-derived oxidant NH2Cl: synergistic role of phosphotyrosine and intracellular Ca2+ concentration

The neutrophil-derived, membrane-permeating oxidant, NH2Cl, (but not the non-membrane-permeating chloramine, taurine-NHCl) induced detachment of fetal mouse cardiac myocytes and other cell types (fibroblasts, epithelial cells, and endothelial cells) from the culture dish, concomitant with cell shrinkage ("peeling off"). Stimulated human neutrophils also induced peeling off of cultured mouse cardiac myocytes when the latter were pretreated with inhibitors of . OH and elastase. Immunofluorescence microscopy revealed that the NH2Cl-induced peeling off of WI-38 fibroblasts is accompanied by disorganization of integrin alpha 5 beta 1, vinculin, stress fibers, and phosphotyrosine (p-Tyr)- containing proteins. Decrease in the content of the p-Tyr-containing proteins of the NH2Cl-treated cells was analyzed by immunoblotting techniques. Coating of fibronectin on the culture dish prevented both NH2Cl-induced peeling off and a decrease in p-Tyr content. Preincubation with a protein-tyrosine phosphatase inhibitor, sodium orthovanadate (Na3VO4), also prevented NH2Cl-induced peeling off, suggesting that dephosphorylation of p-Tyr is necessary for peeling off. NH2Cl-induced peeling off was accompanied by an increase in intracellular Ca2+ concentration ([Ca2+]i) in mouse cardiac myocytes and WI-38 fibroblasts. The absence of extracellular Ca2+ prevented both NH2Cl-induced peeling off and increased [Ca2+]i, both of which did occur on subsequent incubation of the cells in Ca2+-containing medium. These observations suggest that an increase in [Ca2+]i is also necessary for peeling off. Depletion of microsomal and cytosolic Ca2+ by incubation with the microsomal Ca2+-ATPase inhibitor 2',5'-di(tert- butyl)-1,4-benzohydroquinone (BHQ) plus EGTA prevented both NH2Cl- induced increases in [Ca2+]i and peeling off. Direct inhibition of microsomal Ca2+ pump activity by NH2Cl may participate in the NH2Cl- induced [Ca2+]i increment. A combination of p-Tyr dephosphorylation by genistein (an inhibitor of tyrosine kinase) and an increase in [Ca2+]i by BHQ could also induce peeling off. All these observations suggest a synergism between p-Tyr dephosphorylation and increased [Ca2+]i in NH2Cl-induced peeling off.
A Single Chromosome Unexpectedly Links Highly Divergent Isolates of Toxoplasma gondii

ABSTRACT Toxoplasma gondii is an obligate intracellular parasite that can cause disease in all warm-blooded animals studied to date, including humans. Over a billion people have been infected with this parasite worldwide. In Europe and North America, Toxoplasma has a clonal population structure, where only three lineages are highly dominant (strain types I, II, and III). Khan et al. [mBio 2(6): e00228-11, 2011] have carried out phylogenetic analyses on a large number of diverse strains from outside of these lineages and found evidence for a significant split between the clonal North American/European lineages and those in South America. In contrast to most of the genome, nearly all North American/European strains sampled, and the majority of South American strains sampled, harbored at least portions of a monomorphic chromosome Ia (Ia*). In contrast to previous models, these data suggest that the monomorphic haplotype originated in South America and migrated to the North. These authors propose that South American haplotype 12 was a precursor to modern-day type II, while South American haplotypes 6 and 9 crossed with haplotype 12 to give rise to the type I and III lineages, respectively. However, the findings reported by Khan et al. complicate the origin of chromosome Ia, since there are members of haplotypes 9 and 12 with nearly complete versions of Ia* and members of haplotypes 6 and 12 with over 50% of Ia*. This unexpected finding raises exciting new questions about how an entire common chromosome can be found within strains that are highly divergent at most other genomic loci.
The Effect of Personality on Adults' Perceived Benefit of Speech Therapy: A Pilot Study

Title of Thesis: THE EFFECT OF PERSONALITY ON ADULTS’ PERCEIVED BENEFIT OF SPEECH THERAPY: A PILOT STUDY Andrea M. Krcmar, Master of Arts, 2006 Thesis Directed By: Assistant Professor Rochelle Newman Department of Hearing and Speech Sciences Professor Nan Bernstein Ratner Department of Hearing and Speech Sciences Associate Professor Froma Roth Department of Hearing and Speech Sciences Previous research has found a link between personality and many aspects of life, including health issues, ability to cope with stress, career satisfaction, and hearing aid satisfaction. The effects of personality in the field of speech therapy have not yet been determined. It was the purpose of this study to evaluate the effect of personality on adults’ perceived benefit from speech therapy. Eleven current and former speech therapy clients participated in this study. Each were administered the Myers Briggs Type Indicator and a questionnaire assessing perceived benefit from therapy via telephone. The results indicated that personality does not affect one’s perception of benefit from therapy; however, several factors may have limited the results of the study, including the small sample size and the limited number of participants who clearly fit each personality type. THE EFFECT OF PERSONALITY ON ADULTS’ PERCEIVED BENEFIT OF SPEECH THERAPY: A PILOT STUDY by Andrea Marie Krcmar Thesis submitted to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Master of Arts 2006 Advisory Committee: Assistant Professor Rochelle Newman, Chair Professor Nan Bernstein Ratner Associate Professor Froma Roth
Isoaspartyl Formation in Creatine Kinase B Is Associated with Loss of Enzymatic Activity; Implications for the Linkage of Isoaspartate Accumulation and Neurological Dysfunction in the PIMT Knockout Mouse

Isoaspartate (isoAsp) formation is a common type of spontaneous protein damage that is normally kept in check by the repair enzyme protein-L-isoaspartyl methyltransferase (PIMT). PIMT-KO (knockout) mice exhibit a pronounced neuropathology highlighted by death from an epileptic seizure at 30 to 60 days after birth. The mechanisms by which isoaspartyl damage disrupts normal brain function are incompletely understood. Proteomic analysis of the PIMT-KO mouse brain has shown that a number of key neuronal proteins accumulate high levels of isoAsp, but the extent to which their cellular functions is altered has yet to be determined. One of the major neuronal targets of PIMT is creatine kinase B (CKB), a well-characterized enzyme whose activity is relatively easy to assay. We show here that (1) the specific activity of CKB is significantly reduced in the brains of PIMT-deficient mice, (2) that in vitro aging of recombinant CKB results in significant accumulation of isoAsp sites with concomitant loss of enzymatic activity, and (3) that incubation of in vitro aged CKB with PIMT and its methyl donor S-adenosyl-L-methionine substantially repairs the aged CKB with regard to both its isoAsp content and its enzymatic activity. These results, combined with similarity in phenotypes of PIMT-KO and CKB-KO mice, suggests that loss of normal CKB structure and function contributes to the mechanisms by which isoAsp accumulation leads to CNS dysfunction in the PIMT-KO mouse.
Three-Dimensional Coculture Model to Analyze the Cross Talk Between Endothelial and Smooth Muscle Cells

The response of blood vessels to physiological and pathological stimuli partly depends on the cross talk between endothelial cells (EC) lining the luminal side and smooth muscle cells (SMC) building the inner part of the vascular wall. Thus, the in vitro analysis of the pathophysiology of blood vessels requires coculture systems of EC and SMC. We have developed and validated a modified three-dimensional sandwich coculture (3D SW-CC) of EC and SMC using open μ-Slides with a thin glass bottom allowing direct imaging. The culture dish comprises an intermediate plate to minimize the meniscus resulting in homogenous cell distribution. Human umbilical artery SMC were sandwiched between coatings of rat tail collagen I. Following SMC quiescence, human umbilical vein EC were seeded on top of SMC and cultivated until confluence. By day 7, EC had formed a confluent monolayer and continuous vascular endothelial (VE)-cadherin-positive cell/cell contacts. Below, spindle-shaped SMC had formed parallel bundles and showed increased calponin expression compared to day 1. EC and SMC were interspaced by a matrix consisting of laminin, collagen IV, and perlecan. Basal messenger RNA (mRNA) expression levels of E-selectin, angiopoietin-1, calponin, and intercellular adhesion molecule 1 (ICAM-1) of the 3D SW-CC was comparable to that of a freshly isolated mouse inferior vena cava. Addition of tumor necrosis factor alpha (TNF α) to the 3D SW-CC induced E-selectin and ICAM-1 mRNA and protein induction, comparable to the EC and SMC monolayers. In contrast, the addition of activated platelets induced a significantly delayed but more pronounced activation in the 3D SW-CC compared to EC and SMC monolayers. Thus, this 3D SW-CC permits analyzing the cross talk between EC and SMC that mediate cellular quiescence as well as the response to complex activation signals.
Preoperative pulmonary evaluation and therapy for surgery patients.

Simple pulmonary function studies can be utilized successfully for diagnosis of pulmonary problems in surgery patients preoperatively. In the present study, randomly selected "poor risk" patients were treated preoperatively and postoperatively with cessation of smoking, bronchodilator drugs, antibiotics, inhalation of humidified gases, segmental postural drainage, and chest physiotherapy. When compared to nontreated poor risk patients, the treated patients had a marked reduction in postoperative morbidity and mortality due to pulmonary complications. Although the frequency and the severity of pulmonary complications were somewhat greater in the treated patients than in a group of "good risk" patients who were considerably younger in age, the differences were not significant. Extension of these simple therapeutic measures to large numbers of poor risk patients should reduce postoperative morbidity and mortality, allow earlier discharge, and lower the costs of patient care.
Testing with Feedback Yields Potent, but Piecewise, Learning of History and Biology Facts.

Does correctly answering a test question about a multiterm fact enhance memory for the entire fact? We explored that issue in 4 experiments. Subjects first studied Advanced Placement History or Biology facts. Half of those facts were then restudied, whereas the remainder were tested using “5 W” (i.e., who, what, when, where, or why) or analogous questions. Each question assessed a specific critical term of the fact. In the first 3 experiments, 1 test question was posed per tested fact; in the fourth experiment, up to 3 different test questions were posed per tested fact. After a delay of at least 24 hr, a final test involved questions that assessed the same terms that were tested during training, as well as questions that assessed a different term from that previously tested. Results showed that testing produced piecewise fact learning: Tested terms benefited relative to restudy, but untested terms did not. That pattern held when either fill-in-the-blank or multiple-choice questions were used during training, when 1 or 2 test trials were used during training, for both history and biology facts, and when more than 1 term from each fact was tested during training. Thus, across a range of circumstances, taking tests on complex facts results in a selective memory benefit for tested terms. In analogous applied settings, testing on multiple response terms should promote more comprehensive retention. (PsycINFO Database Record (c) 2016 APA, all rights reserved)
Laryngeal Features Are Phonetically Abstract: Mismatch Negativity Evidence from Arabic, English, and Russian

Many theories of phonology assume that the sound structure of language is made up of distinctive features, but there is considerable debate about how much articulatory detail distinctive features encode in long-term memory. Laryngeal features such as voicing provide a unique window into this question: while many languages have two-way contrasts that can be given a simple binary feature account [±VOICE], the precise articulatory details underlying these contrasts can vary significantly across languages. Here, we investigate a series of two-way voicing contrasts in English, Arabic, and Russian, three languages that implement their voicing contrasts very differently at the articulatory-phonetic level. In three event-related potential experiments contrasting English, Arabic, and Russian fricatives along with Russian stops, we observe a consistent pattern of asymmetric mismatch negativity (MMN) effects that is compatible with an articulatorily abstract and cross-linguistically uniform way of marking two-way voicing contrasts, as opposed to an articulatorily precise and cross-linguistically diverse way of encoding them. Regardless of whether a language is theorized to encode [VOICE] over [SPREAD GLOTTIS], the data is consistent with a universal marking of the [SPREAD GLOTTIS] feature.
INCREASE AND DECREASE OF THE EFFECTIVE CONDUCTIVITY OF TWO PHASE COMPOSITES DUE TO POLYDISPERSITY

We present a two–dimensional mathematical model of a composite material with conducting inclusions (fibers) embedded in a matrix. Our main objective is to study how polydispersity (two different sizes of particles) affects the overall conductivity of the composite. If the conductivity of inclusions is higher than the conductivity of the matrix, then previous studies suggest an increase of the effective conductivity due to polydispersity. We show that for high volume fraction when inclusions are not well–separated and percolation effects play a significant role, polydispersity may result in either an increase or decrease of the effective conductivity. Our proof is based on the method of functional equations and it provides sufficient conditions for both the increase and the decrease of the effective conductivity.
NpPDR1, a Pleiotropic Drug Resistance-Type ATP-Binding Cassette Transporter from Nicotiana plumbaginifolia, Plays a Major Role in Plant Pathogen Defense1

Nicotiana plumbaginifolia NpPDR1, a plasma membrane pleiotropic drug resistance-type ATP-binding cassette transporter formerly named NpABC1, has been suggested to transport the diterpene sclareol, an antifungal compound. However, direct evidence for a role of pleiotropic drug resistance transporters in the plant defense is still lacking. In situ immunolocalization and histochemical analysis using the gusA reporter gene showed that NpPDR1 was constitutively expressed in the whole root, in the leaf glandular trichomes, and in the flower petals. However, NpPDR1 expression was induced in the whole leaf following infection with the fungus Botrytis cinerea, and the bacteria Pseudomonas syringae pv tabaci, Pseudomonas fluorescens, and Pseudomonas marginalis pv marginalis, which do not induce a hypersensitive response in N. plumbaginifolia, whereas a weaker response was observed using P. syringae pv syringae, which does induce a hypersensitive response. Induced NpPDR1 expression was more associated with the jasmonic acid than the salicylic acid signaling pathway. These data suggest that NpPDR1 is involved in both constitutive and jasmonic acid-dependent induced defense. Transgenic plants in which NpPDR1 expression was prevented by RNA interference showed increased sensitivity to sclareol and reduced resistance to B. cinerea. These data show that NpPDR1 is involved in pathogen resistance and thus demonstrate a new role for the ATP-binding cassette transporter family.
On the axiomatisability of priority

This paper studies the equational theory of bisimulation equivalence over the process algebra BCCSP extended with the priority operator of Baeten, Bergstra and Klop. We prove that, in the presence of an infinite set of actions, bisimulation equivalence has no finite, sound, ground-complete equational axiomatisation over that language. This negative result applies even if the syntax is extended with an arbitrary collection of auxiliary operators, and motivates the study of axiomatisations using equations with action predicates as conditions. In the presence of an infinite set of actions, it is shown that, in general, bisimulation equivalence has no finite, sound, ground-complete axiomatisation consisting of equations with action predicates as conditions over the language studied in this paper. Finally, sufficient conditions on the priority structure over actions are identified that lead to a finite, ground-complete axiomatisation of bisimulation equivalence using equations with action predicates as conditions.
Management of Cosmetic Embarrassment Caused by Malassezia spp. with Fruticose Lichen Cladia Using Phylogenetic Approach

During anti-Malassezia screening of plants by CLSI broth microdilution method, Cladia aggregata (Swartz) Nyl. (family Cladoniaceae), a fruticose lichen from Sikkim (northeast Himalayan region), has been found effective at minimum inhibitory concentrations (mg/mL) of 2.72, 0.63, and 1.28 against yeast-like fungi namely, M. furfur, M. globosa and M. sympodialis, respectively. These test pathogens are responsible for pityriasis versicolor (PV) and seborrheic dermatitis (SD) in humans. We tried to establish the reason for variable MICs against various Malassezia spp. using bioinformatical tools, thereby reducing the cost of the experimentation. This is the first report on anti-Malassezia activity of C. aggregata and thus can serve as a potential source for the development of cosmaceuticals.
Domain Adaptation for Statistical Machine Translation with Monolingual Resources

Domain adaptation has recently gained interest in statistical machine translation to cope with the performance drop observed when testing conditions deviate from training conditions. The basic idea is that in-domain training data can be exploited to adapt all components of an already developed system. Previous work showed small performance gains by adapting from limited in-domain bilingual data. Here, we aim instead at significant performance gains by exploiting large but cheap monolingual in-domain data, either in the source or in the target language. We propose to synthesize a bilingual corpus by translating the monolingual adaptation data into the counterpart language. Investigations were conducted on a state-of-the-art phrase-based system trained on the Spanish--English part of the UN corpus, and adapted on the corresponding Europarl data. Translation, re-ordering, and language models were estimated after translating in-domain texts with the baseline. By optimizing the interpolation of these models on a development set the BLEU score was improved from 22.60% to 28.10% on a test set.
Interfacial Shear Stress Distribution in Model Composites Part 2: Fragmentation Studies on Carbon Fibre/Epoxy Systems

The micromechanics of reinforcement of a model composite system con sisting of a continuous high-modulus (HM) carbon fibre embedded in an epoxy resin have been investigated. The composite was subjected to incremental tensile loading up to full fibre fragmentation, while the strain in the fibre was monitored at each level of load using a laser Raman spectroscopic (LRS) technique. The average strain in the fibre increased linearly with applied matrix strain up to a value of 0.8 %, when the first fibre fracture oc curred. After fracture, the strain in the fibre was found to build from the tips of the fibre breaks, reaching a maximum value in the middle of each fragment. The shape of the load transfer profiles at the locality of the fibre tips indicated that the stress transfer efficiency had been affected by the fracture process. The length of interfacial debonding at the point of fibre fracture was found to be driven by the strain energy of the fractured fragments. The interfacial shear stress (ISS) distributions at various levels of applied load along in dividual fragments, have been derived from the load transfer profiles using a balance of forces analysis. The shape of the ISS profiles confirmed that interfacial debonding initiated from the tips of the fibre breaks, whereas good fibre/matrix adhesion was retained around the mid-length of each fragment. By increasing the applied strain to 1.8%, the maximum ISS values also increased in spite of the presence of debonding at the fibre tips. An upper ISS limit of 42 MPa was calculated at this point. Further increases of the applied strain to 5% resulted in significant reductions in the values of the maximum ISS, as well as an in crease, of the frictional slip towards the middle of each fragment. Finally, by employing the assumptions of the conventional fragmentation test, the calculated value of the nominal interfacial shear strength at the point of full fragmentation was lower by a factor of 2 than the value measured by the LRS method.
Privacy Risk Assessment of Textual Publications in Social Networks

Recent studies have warned that, in Social Networks, users usually publish sensitive data that can be exploited by dishonest parties. Some mechanisms to preserve the privacy of the users of social networks have been proposed (i.e. controlling who can access to a certain published data); however, a still unsolved problem is the lack of proposals that enable the users to be aware of the sensitivity of the contents they publish. This situation is especially true in the case of unstructured textual publications (i.e., wall posts, tweets, etc.). These elements are considered to be particularly dangerous from the privacy point of view due to their dynamism and high informativeness. To tackle this problem, in this paper we present an automatic method to assess the sensitivity of the userâs textual publications according to her privacy requirements towards the other users in the social network. In this manner, users can have a clear picture of the privacy risks inherent to their publications and can take the appropriate countermeasures to mitigate them. The feasibility of the method is studied in a highly sensitive social network: PatientsLikeMe.
Impacts of temperature and pH on the distribution of archaeal lipids in Yunnan hot springs, China

In culture experiments and many low temperature environments, the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) commonly shows a strong correlation with temperature; however, this is often not the case in hot springs. We studied 26 hot springs in Yunnan, China, in order to determine whether temperature or other factors control the distribution of GDGTs in these environments. The hot springs ranged in temperature from 39.0 to 94.0°C, and in pH from 2.35 to 9.11. Water chemistry including nitrogen-, sulfur-, and iron species was also determined. Lipids from the samples were analyzed using liquid chromatography–mass spectrometry (LC–MS). Distributions of GDGTs in these hot springs were examined using cluster analysis, which resulted in two major groups. Group 1 was characterized by the lack of dominance of any individual GDGTs, while Group 2 was defined by the dominance of GDGT-0 or thaumarchaeol. Temperature was the main control on GDGT distribution in Group 1, whereas pH played an important role in the distribution of GDGTs in Group 2. However, no correlations were found between the distribution of GDGTs and any of the nitrogen-, sulfur-, or iron species. Results of this study indicate the dominance of temperature or pH control on archaeal lipid distribution, which can be better evaluated in the context of lipid classification.