Miracle-dz/UniFAR-FTUs huggingface dataset:
Ocean acidification induces biochemical and morphological changes in the calcification process of large benthic foraminifera

Large benthic foraminifera are significant contributors to sediment formation on coral reefs, yet they are vulnerable to ocean acidification. Here, we assessed the biochemical and morphological impacts of acidification on the calcification of Amphistegina lessonii and Marginopora vertebralis exposed to different pH conditions. We measured growth rates (surface area and buoyant weight) and Ca-ATPase and Mg-ATPase activities and calculated shell density using micro-computer tomography images. In A. lessonii, we detected a significant decrease in buoyant weight, a reduction in the density of inner skeletal chambers, and an increase of Ca-ATPase and Mg-ATPase activities at pH 7.6 when compared with ambient conditions of pH 8.1. By contrast, M. vertebralis showed an inhibition in Mg-ATPase activity under lowered pH, with growth rate and skeletal density remaining constant. While M. vertebralis is considered to be more sensitive than A. lessonii owing to its high-Mg-calcite skeleton, it appears to be less affected by changes in pH, based on the parameters assessed in this study. We suggest difference in biochemical pathways of calcification as the main factor influencing response to changes in pH levels, and that A. lessonii and M. vertebralis have the ability to regulate biochemical functions to cope with short-term increases in acidity.
Comparison of manual and automated quantification methods of 123I-ADAM

Summary: 123I-ADAM is a novel radioligand for imaging of the brain serotonin transporters (SERTs). Traditionally, the analysis of brain receptor studies has been based on observer-dependent manual region of interest definitions and visual interpretation. Our aim was to create a template for automated image registrations and volume of interest (VOI) quantifications and to show that an automated quantification method of 123I-ADAM is more repeatable than the manual method. Patients, methods: A template and a predefined VOI map was created from 123I-ADAM scans done for healthy volunteers (n = 15). Scans of another group of healthy persons (HS, n = 12) and patients with bulimia nervosa (BN, n = 10) were automatically fitted to the template and specific binding ratios (SBRs) were calculated by using the VOI map. Manual VOI definitions were done for the HS and BN groups by both one and two observers. The repeatability of the automated method was evaluated by using the BN group. Results: For the manual method, the interobserver coefficient of repeatability was 0.61 for the HS group and 1.00 for the BN group. The intraobserver coefficient of repeatability for the BN group was 0.70. For the automated method, the coefficient of repeatability was 0.13 for SBRs in midbrain. Conclusion: An automated quantification gives valuable information in addition to visual interpretation decreasing also the total image handling time and giving clear advantages for research work. An automated method for analysing 123I-ADAM binding to the brain SERT gives repeatable results for fitting the studies to the template and for calculating SBRs, and could therefore replace manual methods.
Isoelectric focusing in serial immobilized pH gradient gels to improve protein separation in proteomic analysis

We previously demonstrated the separation of proteins by isoelectric focusing (IEF) over pH 4–8 immobilized pH gradients (IPGs) over 54 cm (Poland et al., Electrophoresis 2003, 24, 1271). Here we show that similar results can be conveniently achieved using commercially available IPGs of appropriate pH ranges positioned end‐on‐end in series during electrophoresis, which we term ‘daisy chain IEF’. Proteins efficiently electrophorese from one IPG to another during IEF by traversing buffer‐filled porous bridges between the serial IPGs. A variety of materials can function as bridges, including paper, polyacrylamide gels or even IPGs. The quality of two‐dimensional (2‐D) protein patterns is not apparently worse than that generated by conventional IEF using the same individual IPGs. A major advantage of this method is that sample is consumed efficiently, without the requirement for preliminary steps, such as chamber IEF. This advantage is pronounced when working with extremely limited sources of samples, such as with clinical biopsies or cellular subfractions. The present study was limited by the commercial availability of suitable pH gradients. Proteomics analyses could be further improved if commercial vendors would manufacture IPGs with suitable pH ranges to achieve high resolution (∼100 cm) IEF separation of proteins in one electrophoretic step over the pH range 2–12.
Expression of p63 protein and mRNA in oral epithelial dysplasia.

BACKGROUND Abnormalities in the TP53 are regarded as the most consistent findings in oral squamous cell carcinoma. Two related members of the TP53 family, p73 and p63, have shown remarkable structural similarity to TP53, indicating possible functional and biological interactions. The aim of the present study was to investigate the expression of p63 protein and mRNA in oral epithelial dysplasia. METHODS Immunohistochemical p63 staining was compared for samples from 90 male patients with buccal epithelial dysplasias and 15 healthy individuals with normal buccal mucosa and 15 subjects with reactive epithelial hyperplasia of the oral mucosa secondary to traumatic insult. The buccal lesions consisted of mild, moderate and severe epithelial dysplasias (30 samples in each category). The mRNA expression using reverse transcription polymerase chain reaction (RT-PCR) was also included for a subset of available fresh tissue specimens (four samples in each category of mild and moderate epithelial dysplasia; five samples in severe epithelial dysplasia; five samples in each of normal and reactive epithelial hyperplasia). RESULTS Nuclear p63 staining was demonstrated predominantly in the basal layers of the epithelium of the normal buccal mucosa and reactive epithelial hyperplasia specimens. For epithelial dysplasia lesions, however, staining was not restricted to the basal layers, extending to the middle spinous layer for samples in the mild category, with p63 immunoexpression observed across almost the full thickness of the dysplastic epithelium for analogous moderate and severe specimens. Compared with normal/reactive hyperplastic mucosa, p63 staining in the dysplastic mucosa was significantly increased. The severity of dysplasia was increased with the increase of p63 staining. Furthermore, Delta Np63mRNA was identified in all of the fresh tissue samples whereas expression of transactivation (TA) isotype was not detected. A subset of moderate epithelial dysplasia and severe variant showing p63-positive staining has undergone malignant transformation to squamous cell carcinomas in about 5 years follow-up. CONCLUSION Our results indicate that impaired p63 immunoexpression (predominantly Delta N isoform) is associated with the severity of oral epithelial dysplasias and up-regulation of p63 may play a role in the early stage of human oral tumorigenesis.
The anthelmintic drug mebendazole induces mitotic arrest and apoptosis by depolymerizing tubulin in non-small cell lung cancer cells.

Microtubules have a critical role in cell division, and consequently various microtubule inhibitors have been developed as anticancer drugs. In this study, we assess mebendazole (MZ), a microtubule-disrupting anthelmintic that exhibits a potent antitumor property both in vitro and in vivo. Treatment of lung cancer cell lines with MZ caused mitotic arrest, followed by apoptotic cell death with the feature of caspase activation and cytochrome c release. MZ induces abnormal spindle formation in mitotic cancer cells and enhances the depolymerization of tubulin, but the efficacy of depolymerization by MZ is lower than that by nocodazole. Oral administration of MZ in mice elicited a strong antitumor effect in a s.c. model and reduced lung colonies in experimentally induced lung metastasis without any toxicity when compared with paclitaxel-treated mice. We speculate that tumor cells may be defective in one mitotic checkpoint function and sensitive to the spindle inhibitor MZ. Abnormal spindle formation may be the key factor determining whether a cell undergoes apoptosis, whereas strong microtubule inhibitors elicit toxicity even in normal cells.
Missile autopilot design via functional inversion and time-scaled transformation

This paper presents a new approach to acceleration control of STT (Skid-To-Turn) missiles. In the design and stability analysis of our autopilot, we assume perfect roll-stabilization but consider fully all other nonlinearities of the missile dynamics including the coupling effect due to bank angle. Our autopilot controller consists of a partial-linearizing controller and a dynamic compensator. The partial-linearizing controller along with a time scaled transformation can convert the nonlinear missile dynamics to the so-called normalized system which is completely independent of Mach number and almost independent of air density. The dynamic compensator is designed based on this normalized system. This normalized system greatly simplifies the design process of an autopilot controller regardless of flight conditions. Our autopilot controller can provide fast and exact set-point tracking performance but without the slow-varying conditions on angle of attack and side-slip angle required often in the prior works.
Positively charged filters for virus recovery from wastewater treatment plant effluents

Positively charged Zeta Plus filters were used to concentrate enteroviruses from 19 liters of effluent from activated sludge units. Neither the addition of salts nor the acidification of the effluent was required for adsorption of viruses to the filters. Viruses adsorbed to the filters were eluted by treating the filters with a solution of 4 M urea buffered at pH 9 with 0.05 M lysine. Eluted viruses were concentrated into final volumes of 1 to 2 ml by using a two-step concentration procedure that employed inorganic and organic flocculation. Approximately 50% of the viruses added to effluents could be recovered in the final sample. The procedure was used to monitor effluents from activated sludge units at two wastewater treatment plants for the presence of enteroviruses.
Shortening of the Symptom-Free Period in Rhesus Macaques Is Associated with Decreasing Nonsynonymous Variation in theenv Variable Regions of Simian Immunodeficiency Virus SIVsm during Passage

ABSTRACT During six blood passages of simian immunodeficiency virus SIVsm in rhesus macaques, the asymptomatic period shortened from 18 months to 1 month. To study SIVsm envelope gene (env) evolution during passage in rhesus macaques, the C1 to CD4 binding regions of multiple clones were sequenced at seroconversion and again at death. Theenv variation found during adaptation was almost completely confined to the variable regions. Intrasample sequence variation among clones at seroconversion was lower than the variation among clones at death. Intrasample variation among clones from a single time point as well as intersample variation decreased during the passage. In the variable regions, the mean number of intrasample nonsynonymous nucleotide substitutions decreased from the first passage (5.26 × 10−2 ± 0.6 × 10−2 per site) to the fifth passage (2.24 × 10−2 ± 0.4 × 10−2 per site), whereas in the constant regions, the mean number of intrasample nonsynonymous nucleotide substitutions differed less between the first and fifth passages (1.14 × 10−2 ± 0.27 × 10−2 and 0.80 × 10−2 ± 0.24 × 10−2 per site). Shortening of the asymptomatic period coincided with a rise in theKs/Ka ratio (ratio between the number of synonymous [Ks] and the number of nonsynonymous [Ka] substitutions) from 1.080 in passage one to 1.428 in passage five and mimicked the difference seen in the intrahost evolution between asymptomatic and fast-progressing individuals infected with human immunodeficiency virus type 1. The distribution of nonsynonymous substitutions was biphasic, with most of the adaptation ofenv variable regions occurring in the first three passages. This phase, in which the symptom-free period fell to 4 months, was followed by a plateau phase of apparently reduced adaptation. Analysis of codon usage revealed decreased codon redundancy in the variable regions. Overall, the results suggested a biphasic pattern of adaptation and evolution, with extremely rapid selection in the first three passages followed by an equilibrium or stabilization of the variation between env clones at different time points in passages four to six.
Risk factors for prolonged QTc among US adults: Third National Health and Nutrition Examination Survey

Background QT interval prolongation can lead to torsades de pointes, a potentially fatal arrhythmia. Although research exists on the relationship between QT prolongation and clinical outcome, few studies have described risk factors for prolonged QT interval in the general population. Methods The Third National Health and Nutrition Examination Survey (NHANES III) collected electrocardiogram interval data on 8561 subjects over 40 years of age and projected results to the US population. QT was corrected for heart rate using Fridericia's formula. Logistic regression analyses were performed to identify factors independently associated with prolonged QTc interval, defined as being in the upper 5% of the population QTc interval distribution. Analyses were conducted separately for women and men as a result of differences in the QT distribution between the sexes and also because of potential effect modification. Analytical variables included age, race/ethnicity, electrolyte measurements, body mass index, the recent use of QT-prolonging drugs and past medical histories of stroke, thyroid disease, hypertension, diabetes and myocardial infarction. Results Age, female sex, hypocalcemia (men), hypokalemia (women), and a history of thyroid disease and myocardial infarction (men) were associated with a prolonged QTc interval. In addition, taking QT-prolonging medications in the past month was associated with more than a twofold increase in the odds of prolonged QTc interval in both men and women. Conclusions Healthcare practitioners should be aware that a prolonged QTc interval is a potential indicator of cardiovascular risk, and should exercise caution in prescribing potentially QT-prolonging medications to certain patients.
Si3N4 nanobeam optomechanical crystals

We demonstrate sideband-resolved Si<sub>3</sub>N<sub>4</sub> optomechanical crystals supporting 10<sup>5</sup> quality factor optical modes at 980 nm, coupled to GHz frequency mechanical modes. We also develop slot-mode-based geometries for enhanced optomechanical coupling and multimode applications.
A Capital Structure Financial Analysis and Unmeasured Effect of each Countries Regime: the Real Estate Companies (REITS)

This article investigates the capital structure of Real Estate companies (REITS) and how it is connected with key financial ratios. Financial analysis provides significant insight of the company capital structure. Existing financial models accumulate the dynamics of different key factors that enhance or diminish the capabilities of a company to extend the debt finance. Previous literature review in trade-off theory, pecking order theory, agency costs and market timing hypothesis postulate the relation of capital structure with several financial measurements. The contribution of this research is to link debt to capital ratio with independent variables, which are important within the real estate business context. Panel data analysis of an adequate sample, from 2005 to 2010, of 371 international listed real estate companiesâ€™, materialize our assumptions of this linkage of debt ratio. The unmeasured effect of each countries regime is inherited into the equation with the incorporation of dummy variables. This valuation methodology is an easy accessible tool for professionals and practitioners engaged in real estate business.
Historical and modern medicinal plant uses — the example of the Ch'orti‘ Maya and Ladinos in Eastern Guatemala

Local empirical knowledge about medicinal properties of plants is the basis for their use as home remedies. Particularly in developing countries such remedies still are an indispensable resource for everyday health care. They form the basis for numerous studies on drugs from natural sources. Like other indigenous groups across the world, the Ch'orti' Maya in Eastern Guatemala are currently experiencing a phase of dramatic cultural change, with their traditional knowledge about plants being in great danger of disappearing. During 17 months of fieldwork, medicinal plant uses were documented using a semi‐quantitative approach and analysed using ethnopharmacological methods. The most important groups of illnesses treated with plants were gastrointestinal complaints and illnesses associated with pain and fever. Field data were compared with mostly unpublished historical data collected in the 1930s by the anthropologist Charles Wisdom. This comparison showed that medicinal plant uses that are more consistent over time are also shared by a larger number of people. A literature search on the most frequently mentioned medicinal plants showed that, even for widely used medicinal species, phytochemical and pharmacological data are insufficient for fully understanding their therapeutic profile. Whereas a few examples of potentially dangerous practices were encountered, the limited amount of information available mostly supports local medicinal plant usage.
Structural basis for the broad specificity to host-cell ligands by the pathogenic fungus Candida albicans

Candida albicans is the most prevalent fungal pathogen in humans and a major source of life-threatening nosocomial infections. The Als (agglutinin-like sequence) glycoproteins are an important virulence factor for this fungus and have been associated with binding of host-cell surface proteins and small peptides of random sequence, the formation of biofilms and amyloid fibers. High-resolution structures of N-terminal Als adhesins (NT-Als; up to 314 amino acids) show that ligand recognition relies on a motif capable of binding flexible C termini of peptides in extended conformation. Central to this mechanism is an invariant lysine that recognizes the C-terminal carboxylate of ligands at the end of a deep-binding cavity. In addition to several protein–peptide interactions, a network of water molecules runs parallel to one side of the ligand and contributes to the recognition of diverse peptide sequences. These data establish NT-Als adhesins as a separate family of peptide-binding proteins and an unexpected adhesion system for primary, widespread protein–protein interactions at the Candida/host-cell interface.
Diagnostic Immunohistochemistry: What can Go Wrong?

Although immunohistochemistry (IHC) has become an integral component of the surgical pathology laboratory and practice, it remains a subspecialty in search of a definition. The rapid expansion of this discipline is continually contributing to the struggle of interested pathologists and technologists to identify the proper working conditions of antibody reagents and the right choice of detection systems and instrumentations. Training programs have not, for the most part, successfully incorporated IHC in their curricula. Thus, pitfalls in diagnostic IHC, in our opinion, are becoming more frequent than they used to. In this review, we highlight and attempt to provide solutions for the most common pitfalls in diagnostic IHC as it relates to the routine practice of surgical pathology.
Green marketing strategies: how do they influence consumer-based brand equity?

This paper examines the effects of green marketing strategies on the dimensions of consumer-based brand equity (CBBE). This study addresses a gap in literature green consumers' stated pro-environmental beliefs and actual consumption behaviours of purportedly green consumers. Drawing upon relevant extant literature, the paper proposes a research model to evaluate the relationship between green marketing mix elements and the dimensions of CBBE. With data collected from consumers in Saudi Arabia, the research model is tested by a two-stage process. First stage is to assess reliability and validity of the measurement model. Second stage is to test the various hypotheses. The results of the conceptual analyses are presented. Managerial implications and limitations are discussed. This study makes a valuable contribution to literature given the growing importance of ecological and sustainability concerns and the efforts marketing firms have been making to have a better understanding of green consumers.
Optimization design of rotor structure for high speed permanent magnet machines

Permanent magnet (PM) machine is especially being employed in high speed machines due to its simple structure and high power density. Nowadays, the sintered neodymium-iron-boron (Nd-Fe-B) material is used in most of PM machines. This kind of PM material has large compression strength but small tensile strength, and can not withstand the large centrifugal force due to the high rotation speed. A nonmagnetic steel enclosure is needed to cover the PM material. The tensile press of PM can be reduced by pre-pressure applied to the outer surface of the PM through shrink-fitting into the enclosure. In this paper, the comprehensive optimization design of PM rotor structure is introduced with multiple constraints, such as deformation, stress and critical speed. The capacity of enclosure is the optimal goal. By finite element non-linear contact and optimization analysis, the optimized result for a high speed PM machine with rated speed of 60 000 rpm is presented.
A Web-Based Reference Architecture for Mobile Learning: Its Quality Aspects and Evaluation

This paper discusses the development process and evaluation of a reference software architecture within the field of mobile learning. The architecture implements the workflow of preparation – activity – analysis & reflection of (data collection) activities supported by mobile applications. A number of challenges, like portability, flexibility, or expandability are important to address in mobile learning. To overcome the mentioned challenges in this field, we are proposing a web-based architecture that is supposed to serve as a foundation for the development of software solutions in the field of mobile learning. We discuss scenario descriptions needed for the evaluation and present three implementations in this field that serve as candidate architectures. With the support of those candidates, the reference architecture is proposed. Important system quality attributes are identified and then applied for an evaluation of the architecture using the SAAM method. We conclude by discussing that the proposed architecture does not only fit the field of mobile learning but can also be adapted to a general solution regarding the workflow of: preparation – activity – analysis & reflection of mobile (data collection) applications.