Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of obligate and non-obligate complexes using desolvation energies in domain-domain interactions

Protein-protein interactions (PPI) are important in most biological processes and their study is crucial in many applications. Identification of types of protein complexes is a particular problem that has drawn the attention of the research community in the past few years. We focus on obligate and non-obligate complexes, their prediction and analysis. We propose a prediction model to distinguish between these two types of complexes, which uses desolvation energies of domain-domain interactions (DDI), pairs of atoms and amino acids present in the interfaces of such complexes. Principal components of the data were found and then the prediction is performed via linear dimensionality reduction (LDR) and support vector machines (SVM). Our results on a newly compiled dataset, namely binary-PPID, which is a joint and modified version of two well-known datasets consisting of 146 obligate and 169 non-obligate complexes, show that the best prediction is achieved with SVM (77.78%) when using desolvation energies of atom type features. Furthermore, a detailed analysis shows that different DDIs are present in obligate and non-obligate complexes, and that homo-DDIs are more likely to be present in obligate interactions.
Psychological distress among Cuban and Colombian immigrants in Miami: Considering the roles of acculturation and ethnic discrimination

Although researchers concerned with Hispanic American mental health have long recognized the roles of acculturation and ethnic discrimination in shaping health, many questions remain about the conditions under which these factors have their influence. To what extent do acculturation and discrimination matter for Hispanic American health in US contexts with strong Latin cultures? Can acculturation and ethnic discrimination explain Hispanic subgroup variation in distress? Using data from the Physical Challenge and Health study, the current investigation examines the roles of five dimensions of acculturation as well as perceived ethnic discrimination in predicting depressive symptoms among Colombian and Cuban adult immigrants in Miami (N=451). Cuban and Colombian immigrants represent an interesting comparison in this context because of similar reasons for migration and because both groups are relatively high in SES in comparison with other Hispanic immigrant groups. Results indicate that Colombian immigrants report higher mean levels of psychological distress than Cuban immigrants. While the indicators of acculturation together attenuate the observed elevation in Colombian distress relative to Cubans to some extent, there is a differential influence of level of American orientation across groups on distress. Specifically, stronger American orientation is beneficial for Cuban immigrant health but detrimental for Colombian immigrant health. Also, stronger ethnic identity is associated with less distress across immigrant groups. However, preference for socializing with others from within one’s ethnic group is associated with more distress. Finally, perceived ethnic discrimination is associated with higher levels of distress net of all dimensions of acculturation, social status considerations, and difficulties with the performance of functional activities. These findings support the conclusion that acculturation and discrimination are universal factors in Hispanic American mental health and reinforce the importance of assessing the independent contributions of multiple dimensions of acculturation in the study of Hispanic American mental health.
Serum Ferritin Is Inversely Correlated with Serum Adiponectin Level: Population-Based Cross-Sectional Study

Background: The serum concentrations of ferritin and adiponectin are associated with several metabolic disorders and have been used as predictors of insulin resistance and metabolic syndrome. But there have been no reports demonstrating a direct correlation between serum ferritin and adiponectin levels. We performed this study to evaluate the association between serum ferritin and adiponectin concentrations. Subjects and methods: We evaluated a total of 995 subjects from the Korea Rural Genomic Cohort Study in a population-based cross-sectional study. Extensive clinical and laboratory measurements, including adiponectin and ferritin concentrations, were recorded. Results: Univariate analysis revealed that the serum adiponectin level was correlated with age, sex, BMI, diastolic blood pressure, triglyceride, HDL-cholesterol, fasting blood glucose, fasting insulin, HOMA-IR, hs-CRP, and ferritin. Multivariate analysis demonstrated that the adiponectin concentration was correlated with age, BMI, fasting glucose, hs-CRP, and ferritin. The ferritin concentration was the most powerfully associated with serum adiponectin. In non-diabetic subgroups, the adiponectin level was correlated with BMI, triglyceride, HDL-cholesterol, fasting glucose, and ferritin level in multivariate analysis. In diabetic subgroups, the adiponectin level was correlated with BMI, triglyceride, hs-CRP, and ferritin level in multivariate analysis. Conclusions: The serum adiponectin concentration was correlated with conventional clinical variables, but the most powerfully associated factor was the serum ferritin level.
Accuracy of earnings forecasts: evidence from Ghana

This study examines the accuracy of the earnings forecasts contained in the prospectuses for initial public offerings (IPO) and rights offerings (RO) of public companies listed on the Ghana Stock Exchange during the period from 2004 to 2011. The study also examines the bias in those earnings forecasts and the association between the accuracy of the earnings forecasts and the following firm characteristics: age of the firm, firm size, auditor quality, forecast horizon and business risk. The results indicate that, overall, the earnings forecasts included in the prospectuses are not accurate and tend to be optimistic. However, comparing IPO with RO, the earnings forecasts for RO are more accurate and pessimistic while those for IPO are less accurate and optimistic. Also, whereas there is no significant difference in forecast accuracy between RO and IPO, the same is not true for auditor quality; the Big-4 auditing firms are associated with significant higher forecast accuracy than the Non-Big-4 auditing firms. Regarding relationships, significant inverse correlations exist between forecast accuracy and two of the firm characteristics: age and size of the firm. However, in explaining the variance in forecast accuracy, the firm characteristics that have significant effect are auditor quality, forecast horizon, and size of the firm. From these results, it is recommended that future investors pay more attention to the age of the firm, size of the firm and auditor quality in evaluating the accuracy of earnings forecasts contained in prospectuses issued for the Ghana Stock Exchange.
Proteomic differential display analysis identified upregulated astrocytic phosphoprotein PEA‐15 in human malignant pleural mesothelioma cell lines

We performed proteomic differential display analysis of human malignant pleural mesothelioma (MPM) cell lines and a human pleural mesothelial cell line by using 2‐DE and LC‐MS/MS. The human MPM cell lines were NCI‐H28, NCI‐H2052 and NCI‐H2452, and the human pleural mesothelial cell line was MeT‐5A. Between MeT‐5A and NCI‐H2052, we found 38 protein spots whose expression levels were different, from the results of 2‐DE; 28 protein spots appeared higher, and 10 other protein spots lower in NCI‐H2052 than in MeT‐5A. These spots were analyzed by LC‐MS/MS analysis and identified by a peptide sequence tag. However, from the results of 2‐DE of the other cell lines, there was only one consistently upregulated protein, astrocytic phosphoprotein PEA‐15, in all three MPM cell lines. Western blotting using specific antibodies against PEA‐15 confirmed the elevated expression level of PEA‐15 in all three MPM cell lines compared with MeT‐5A cells and normal pleura tissues from patients. PEA‐15 was knocked down in NCI‐H2052 cells, and the proliferation of PEA‐15‐silenced NCI‐H2052 cells was suppressed 7–15% compared with negative control cells. These results suggest that PEA‐15 expression is likely to be associated with the tumorigenesis of MPM.
Automatically generating citizen-focused brochures for public administration

This paper describes a collaborative effort to develop tailored informational brochures describing the programs offered by a public administration agency to the public it serves. The goal is to better communicate with the public by moving from brochures written for generic audiences, which must include careful discussions of the conditions distinguishing the various constituencies within the generic audience, to brochures written for individuals, which can be personalised to focus on the information relevant to one reader. This paper presents a scoping study that identified key requirements for the effort and a prototype application developed in response to the study. The paper pays particular attention to the forms of document tailoring appropriate in the eGovernment domain and on the information that must be represented to support this tailoring.
Personal History and Professional Impairment

ABSTRACT This paper examines the personal histories of social workers and investigates how these variables were related to diminished professional functioning (i.e., professional impairment). One thousand practicing NASW members were anonymously surveyed as part of the study “Work and Well-Being: A Study of North Carolina Social Workers. ” Social workers responded to 11 personal history questions, and an analysis found statistically significant differences in professional impairment scores for all but three of these variables. Regression analysis found that five personal history variables explained the most variance in professional impairment scores. This study's findings have important implications for organizations that employ social workers. Managers, supervisors, and administrators can create organizational conditions that make it safe for social workers to seek help for their problems. Professional impairment and concomitant personal history issues should be explored in social workers' formal education and subsequent training to prevent harm to clients and create a healthier workplace.
UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes

Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR) assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.
Ringtail: A Generalized Nowcasting System

Social media nowcasting--using online user activity to describe real-world phenomena--is an active area of research to supplement more traditional and costly data collection methods such as phone surveys. Given the potential impact of such research, we would expect general-purpose nowcasting systems to quickly become a standard tool among noncomputer scientists, yet it has largely remained a research topic. We believe a major obstacle to widespread adoption is the nowcasting feature selection problem. Typical nowcasting systems require the user to choose a handful of social media objects from a pool of billions of potential candidates, which can be a time-consuming and error-prone process. We have built RINGTAIL, a nowcasting system that helps the user by automatically suggesting high-quality signals. We demonstrate that RINGTALL can make nowcasting easier by suggesting relevant features for a range of topics. The user provides just a short topic query (e.g., unemployment) and a small conventional dataset in order for RINGTALL to quickly return a usable predictive nowcasting model.
Design Strategies for Aptamer-Based Biosensors

Aptamers have been widely used as recognition elements for biosensor construction, especially in the detection of proteins or small molecule targets, and regarded as promising alternatives for antibodies in bioassay areas. In this review, we present an overview of reported design strategies for the fabrication of biosensors and classify them into four basic modes: target-induced structure switching mode, sandwich or sandwich-like mode, target-induced dissociation/displacement mode and competitive replacement mode. In view of the unprecedented advantages brought about by aptamers and smart design strategies, aptamer-based biosensors are expected to be one of the most promising devices in bioassay related applications.
Structure and evolution of the Carlsberg Ridge: Evidence for non-stationary spreading on old and modern spreading centres

We present the results of magnetic and bathymetric data collected on board Russian vessels during the last decade. Our analysis shows that since late Cretaceous the proto-Carlsberg Ridge (CR) was spreading at a faster rate, prior to India's collision with Eurasia. Since Eocene, the present CR is characterized by slow spreading. Our results depict two discordant systems of linear magnetic anomalies. One corresponds with fast spreading with respect to latitude axis of the proto-ridge and the other with slow spreading with respect to modern axis of the CR, suggesting that the two spreading systems are asymmetric both relative to each other and relative to axial anomaly. We infer that during both these periods the structure and spreading on the CR was non-stationary.
An exploration into the palliative and end-of-life experiences of carers of people with Parkinson’s disease

Although most people with Parkinson’s disease are cared for in the community, little is known about family members’ lived experiences of palliative or end-of-life care. The aim of this study was to explore former carers’ lived experiences of palliative and end-of-life care. In total, 15 former family caregivers of patients who had died with Parkinson’s disease were interviewed using a semi-structured topic list. Findings indicated that some palliative and end-of-life care needs had not been fully addressed. Lack of communication, knowledge and coordination of services resulted in many people caring for someone with Parkinson’s disease not accessing specialist palliative care services. Participants also reflected upon the physical and psychological impact of caring in the advanced stage of Parkinson’s. A multi-disciplinary team-based approach was advocated by participants. These findings provide important insights into the experience of caregiving to patients with Parkinson’s disease in the home at the end-of-life stage. According to palliative care standards, patients and their carers are the unit of care; in reality, however, this standard is not being met.
Effects of Curcuma longa rhizome powder on egg quality, performance and some physiological indices of laying hens fed different levels of metabolizable energy.

BACKGROUND High-energy diets of laying hens may improve roductive performance, although some negative effects may also appear with respect to egg quality and physiological parameters. Curcuma longa rhizome powder (CRP) has beneficial effects on health indices of the birds through antioxidant and antimicrobial properties, especially when the birds experience nutritional stress. RESULTS Increasing dietary CRP enhanced egg quality by improving eggshell thickness and hardness but decreasing yolk cholesterol content (P < 0.05). The best feed conversion ratio was obtained in birds fed high-apparent metabolizable energy (AME) diets supplemented with 2.0 g kg-1 CRP (P < 0.05). Although increasing dietary AME elevated the serum concentration of triglycerides (P < 0.05) and enzymatic activities of alanine aminotransferase and aspartate aminotransferase (P < 0.05), dietary inclusion of CRP alleviates the blood levels of these enzymes (P < 0.01). Low level of dietary CRP boosted the immune responses to Newcastle virus (P < 0.01) and sheep red blood cells (P < 0.05) antigens but decreased the heterophil to lymphocyte ratio (P < 0.05). Inclusion of at least 2.0 g kg-1 CRP in the diet of laying decreased Escherichia coli enumerations in the ileal content (P < 0.01) and improved villus height, crypt depth and goblet cell numbers (P < 0.05). CONCLUSION An improvement in the productive performance of laying hens fed high-energy diets might be associated with decreasing health indices and product quality, which could potentially be amended by nutritional modifications such as incorporating medicinal herbs in the feed. © 2016 Society of Chemical Industry.
Molecular Procedure for Rapid Detection ofBurkholderia mallei and Burkholderia pseudomallei

ABSTRACT A PCR procedure for the discrimination of Burkholderia mallei and Burkholderia pseudomallei was developed. It is based on the nucleotide difference T 2143 C (T versus C at position 2143) between B. mallei and B. pseudomallei detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel.
Morphologic and molecular characteristics of Sarcocystis atraii n. sp. (Apicomplexa: Sarcocystidae) infecting the common coot (Fulica atra) from Egypt

A single morphologic type of Sarcocystis cysts found in two out of 43 examined common coots, Fulica atra, is considered to represent a new species for which the name Sarcocystis atraii n. sp. is proposed and its description is provided. Coots were hunted from the vicinity of Brolos Lake located at KafrElsheikh province, Egypt. The structural morphology of the revealed sarcocysts was described using light and transmission electron microscopy. Sarcocysts were found in the leg and thigh muscles. The cysts were microscopic and measured 165–850 µm in length × 50–85 µm in width. Histologically; the sarcocyst wall was wavy and had minute undulations. Ultrastructurally, it measured 1–3 µm in thickness and possessed many mushroom-like villar protrusions sometimes originating from other mushroom-like villar protrusions that measured approximately 0.5–2 µm in length and up to 2 µm in width, with the presence of electron dense ground substance of 300 nm to 1 µm thick. The brady-zoites were elongated, banana-shaped and measured 7.5–14 × 1.5–2.5 µm, with centrally or terminally located nuclei. The ultrastructural features of the cyst wall belonged to type 24. On the basis of sequencing and phylogenic analyses for 18S rRNA, 28S rRNA genes and ITS-1 region; S. atraii n. sp. is considered a genetically distinct species, being most closely related to avian Sarcocystis spp. whose definitive hosts are predatory mammals.
Embryo development after successful somatic cell nuclear transfer to in vitro matured human germinal vesicle oocytes.

BACKGROUND Somatic cell nuclear transfer (SCNT) involves the transfer of somatic cell nuclei into enucleated oocytes. Because human in vivo matured oocytes are scarcely available, we investigated whether in vitro matured (IVM) germinal vesicle (GV) oocytes could also support preimplantation development of human cloned embryos. METHODS Three groups were used for SCNT: in vitro matured GV oocytes (IVM oocytes), 'in vivo' matured oocytes (in vivo oocytes) and 'failed fertilized' oocytes after routine-ICSI (FF oocytes). After removal of the chromosome-spindle complex, cumulus cell nuclei were injected, and oocytes were artificially activated and cultured. RESULTS In total 61, 54 and 45 metaphase II oocytes were used for SCNT in the three groups, respectively. Survival and pronuclear rates were 59, 78 and 58% and 61, 64 and 50%, respectively. Of the 22 activated IVM oocytes, 13 cleaved to the 2-cell stage, whereby 2 morulae were formed. For the in vivo oocytes, 17 of 27 activated oocytes cleaved to the 2-cell stage and 1 morula was observed. Cleavage to the 2-cell stage in the group of FF oocytes was compromised. CONCLUSIONS To our knowledge, this is the first report describing development of cloned human embryos using IVM oocytes and non-autologous transfer using a conventional method of SCNT.
Incremental Slicing Revisited : Accelerated Volume Rendering Of Unstructured Meshes

We accelerate the incremental slicing method for near interactive volume rendering of unstructured grids with conventional polygon rendering hardware support. Our method uses less memory compared to the method of Yagel et al. [25], with significant improvements in rendering time. Using our method, a rendering performance gain of at least 400% was achieved for some datasets, e.g., the Blunt fin dataset. We completely eliminate sorting of edges as a preprocessing step. Further, we introduce a hierarchical z-region paradigm, which can be incorporated with the dataset-input module to get the depth information of the cells with no extra computational overhead. We argue that keeping an active edge list and an active cell list as data structures is redundant, because this information is inherent in the z-region paradigm in our method. In pursuit of accuracy, we explore the application of Nyquist’ s classical sampling theorem when slicing the datasets, and conclude that images of comparable visual quality can be obtained by relaxing this requirement, while maintaining the rendering performance. Finally, we conclude with the results of our method, and a discussion on how progressive refinement of 2-manifold triangular meshes (for 2D slices of cutting planes parallel to the view plane) can help to achieve additional interactivity in a volume visualization system. CR Categories: I.3. 5 [Computer Graphics]: Computational Geometry and Object Modeling – surfaces and object representations.
Design of a Beam Switching/Steering Butler Matrix for Phased Array System

A compact broadband 8-way Butler matrix integrated with tunable phase shifters is proposed to provide full beam switching/steering capability. The newly designed multilayer stripline Butler matrix exhibits an average insertion loss of 1.1 dB with amplitude variation less than ±2.2 dB and an average phase imbalance of less than 20.7° from 1.6 GHz to 2.8 GHz. The circuit size is only 160 × 100 mm2, which corresponds to an 85% size reduction compared with a comparable conventional microstrip 8-way Butler matrix. The stripline tunable phase shifter is designed based on the asymmetric reflection-type configuration, where a Chebyshev matching network is utilized to convert the port impedance from 50 ¿ to 25 ¿ so that a phase tuning range in excess of 120° can be obtained from 1.6 GHz to 2.8 GHz. To demonstrate the beam switching/steering functionality, the proposed tunable Butler matrix is applied to a 1 × 8 antenna array system. The measured radiation patterns show that the beam can be fully steered within a spatial range of 108°.