Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of a patient-derived antibody in complex with allergen reveals simultaneous conventional and superantigen-like recognition

Significance We have discovered that a human antibody can simultaneously bind two molecules of antigen, in this case a grass pollen allergen, one in a conventional manner and the other unconventionally. The two allergen molecules also bridge two identical antibodies. These observations challenge the dogma that one antibody recognizes only a single antigen/allergen epitope. The mechanism of antibody cross-linking seen here may explain the potency of certain allergens in triggering an allergic reaction, extending our understanding of the nature of allergenicity and informing the design of hypoallergenic molecules for allergen immunotherapy. This dual reactivity and potential for cross-linking surface immunoglobulin on B cells suggests mechanisms by which human autoimmune and other diseases might be initiated. Antibodies classically bind antigens via their complementarity-determining regions, but an alternative mode of interaction involving V-domain framework regions has been observed for some B cell “superantigens. ” We report the crystal structure of an antibody employing both modes of interaction simultaneously and binding two antigen molecules. This human antibody from an allergic individual binds to the grass pollen allergen Phl p 7. Not only are two allergen molecules bound to each antibody fragment (Fab) but also each allergen molecule is bound by two Fabs: One epitope is recognized classically, the other in a superantigen-like manner. A single allergen molecule thus cross-links two identical Fabs, contrary to the one-antibody–one-epitope dogma, which dictates that a dimeric allergen at least is required for this to occur. Allergens trigger immediate hypersensitivity reactions by cross-linking receptor-bound IgE molecules on effector cells. We found that monomeric Phl p 7 induced degranulation of basophils sensitized solely with this monoclonal antibody expressed as an IgE, demonstrating that the dual specificity has functional consequences. The monomeric state of Phl p 7 and two structurally related allergens was confirmed by size-exclusion chromatography and multiangle laser light scattering, and the results were supported by degranulation studies with the related allergens, a second patient-derived allergen-specific antibody lacking the nonclassical binding site, and mutagenesis of the nonclassically recognized allergen epitope. The antibody dual reactivity and cross-linking mechanism not only have implications for understanding allergenicity and allergen potency but, importantly, also have broader relevance to antigen recognition by membrane Ig and cross-linking of the B cell receptor.
Non-Invasive Endoscopy Technique - Virtual Colonoscopy

Colorectal carcinoma ranks third in frequency among all cancers. With regards to cancer related mortality, colorectal carcinoma is known as the second cause (Levin et al., 2003). This condition accounts for 10% of all cancer related mortalities in women and men. Overall, lifetime risk for the development of colorectal carcinoma is still 5%. (Eddy, 1990) The wellknown risk factors are age, inheritance, inflammatory bowel disease, and environmental and dietary factors. Despite these risk factors, any individual factors could not be demonstrated in 75-80% of cases. Nevertheless, it is reported that most of the colorectal cancers originate from polyps. Colonic polyps are described as overgrowths of colonic mucosa regardless of histological findings (Van Dan, 1995). Vast majority of colorectal carcinomas originate from adenomatous polyps. This theory called adenoma-carcinoma sequence has been widely accepted (Hawk & Levin, 2005). Colonic polyps are divided as: non-neoplastic, which has no risk or low risk of developing cancer (hamartomatous, inflammatory, hyperplastic); and neoplastic which has low risk of developing cancer (tubular adenoma, villous adenoma, tubulovillous adenoma). Histopathological analysis has an important place in the discrimination of polyps (Erdem et al., 2005; Netzer et al., 1998). The size of the polyps has an important role for the occurrence of invasive cancer (Altiparmak et al., 2001). Small polyps with size less than 1 cm have a low rate of developing invasive cancer. However, this rate increases, as the polyps get larger (Su et al., 2005; Yamaji et al., 2004). Colonic polyps are overgrowths with a slow progress that carry a small risk of malignant transformation. However, colonic polyps constitute an important predisposition to colon cancer, and therefore these neoplasms should be removed when detected. Understanding the fact that development of colorectal carcinoma starts with mucosal lesions, the visualization of colon, early diagnosis of the lesions and the initiation of treatment have gained much importance. The determination of precancerous adenomatous polyps and cancer at an early stage with screening reduces mortality and morbidity associated with colon cancer (Chao et al., 2004; Van Dan, 1995). Thus, American Cancer Association emphasized the importance of screening in colon cancer (Jemal et al., 2002). It is possible to detect and treat polyps at a very early stage with various screening methods. This feature different from some other types of cancer enables prevention or early
The social organisation and mating system of the Brown Kiwi (Apteryx mantelli)

i ACKNOWLEDGEMENTS . v CHAPTER 1 . 1 The evolution and variation of mating systems; implications for the social and the mating system of kiwi (Apteryx spp.) Sexual selection, sexual conflicts, and the evolution of sex roles . 3 Parental care and sex role reversal. 5 Social mating system . 6 Genetic mating system . 9 Ecological determinants of social organisation and mating system . 11 Research on Kiwi (Apteryx spp.) with emphasis on the Brown Kiwi (A. mantelli) . 16 Research objectives and thesis layout . 20 CHAPTER 2 . 25 Roosting behaviour, roost sharing and long-term social groups in a high-density population of Brown Kiwi (Apteryx mantelli) Abstract . 27 Introduction . 27 Methods . 29 Results . 34 Discussion . 40. 27 Introduction . 27 Methods . 29 Results . 34 Discussion . 40 CHAPTER 3 . 45 Spacing behaviour of the Brown Kiwi (Apteryx mantelli) in a high-density population: implications for the Brown Kiwi mating system Abstract . 47 Introduction . 48 Methods . 50 Results . 58. 47 Introduction . 48 Methods . 50 Results . 58 Discussion . 68 CHAPTER 4 . 75 Nesting success and breeding ecology in a high-density population of Brown Kiwi (Apteryx mantelli) Abstract . 77 Introduction . 77 Methods . 79 Results . 82.77 Introduction . 77 Methods . 79 Results . 82 CHAPTER 5 . 93 The genetic mating system and kinship of the Brown Kiwi (Apteryx mantelli) in two high-density populations Abstract . 95 Introduction . 95 Methods . 98 Results . 107 Discussion . 112.95 Introduction . 95 Methods . 98 Results . 107 Discussion . 112 CHAPTER 6 . 119 The social organisation and mating system of the Brown Kiwi (Apteryx mantelli); a general discussion Introduction . 121 Roosting behaviour and social associations between individuals . 122 Spacing systems and the implication on kiwi mating system . 125 Nesting success and breeding ecology . 126 Genetic mating system and kinship . 128 Limitations of this study . 133 Suggestions for future research . 134 REFERENCES.139 APPENDIX 1 . 163 APPENDIX 2 . 164
Association between birth weight and adolescent systolic blood pressure in a caucasian birth cohort differs according to skin type, CRH promoter or 11β-HSD2 genotype

Objective: To examine whether the inverse association between birth weight and blood pressure varies by skin pigmentation and/or related genotypes. Study design: 671 children from a predominantly caucasian birth cohort were followed-up to adolescence (mean (SD) age 14.4 (0.64)). Methods: Data on birth weight, socioeconomic status, maternal antenatal smoking, adolescent blood pressure and polymorphisms of candidate genes were obtained and analysed by multiple linear regression. Results: An increase in birth weight of 1 kg was associated with an non-significant difference in adolescent systolic blood pressure of –0.53 mm Hg (95% CI –1.72 to 0.66) per kg after adjustment for child age and cohort entry criteria. The inverse association between birth weight and systolic blood pressure was stronger for those with darker skin (⩾2% melanin) (difference in effect, p = 0.02), those with more copies of the C allele of corticotropin-releasing hormone (CRH) +T1273C (p = 0.06), and those with more copies of the short (⩽236 bp) form of the 11β-HSD2{CA}nrepeat microsatellite (p = 0.03). Conclusions: These findings add to the evidence that cortisol-related pathways may account for at least part of the observed birth weight–blood pressure associations.
3D CNN Design for the Classification of Alzheimer’s Disease Using Brain MRI and PET

Attempt to diagnose Alzheimer’s disease (AD) using imaging modalities is one of the scopes of deep learning. While considering the theoretical background from past studies, we are trying to identify convolutional neural network (CNN) behaviors moving from 2D to 3D architecture. This study aims to explore the output from a variety of CNN models implemented in the MRI or/and PET classification tasks for AD prediction while trying to summarize its characteristics with a variety of parameters that are tuned and changed. There are many architectures available; however, we are testing a basic architecture with a change in the reception area based on the convolutional layer’s kernel size and its strides. The architecture has been categorized as converging, diverging, or equivalent if the filter kernel size is unchanged. This investigation studies a simple encoder based CNN with a sequential flow of features from low-level to high-level feature extraction. The idea is to present a diverging reception area by increasing the filter size and stride from a lower to a higher level. As a result, the feature redundancy is reduced and the trivial features keep on diminishing. The proposed architecture is referred to as ‘divNet’, and several experiments were performed to determine how effective the architecture is in terms of the consumed memory, the number of parameters, running time, classification error, and the generalization error. This study surveys several related experiments by changing the hyper-parameters setting, the architecture selection based on the depth and area of the reception feature, and the data size.
Comparative Metabolome Analyses of Chinese Hickory Nut Kernels Highlight The Importance of Allocation Shift and Accumulation on Primary and Secondary Metabolites During In-Situ Germination

Background: Chinese hickory ( Carya cathayensis ) and pecan ( C. illinoinensis ) are popular nut trees with high economic value in the family Juglandaceae, due to the richness in nutrients and multiple health factors in their nut kernels. However, the considerable in-situ germination of the nut seeds severely impact the quality of the kernels. The fundamental meta bolic mechanism of in-situ germination has been widely reported in major crops but rare in nut crops. Results: We sampled non- and pre-sprouted Chinese hickory nut kernels and performed liquid chromatography-tandem mass spectrometry (LC–MS/MS)-based metabolomic analyses. Comparative metabolomic analyses revealed 35 6 significantly-changed metabolites during in-situ germination. Detailed analysis emphasized the increasing accumulation and dynamic changes in compounds of primary mechanism and energy supply for in-situ germination. The results highlighted the importance of allocation shift and accumulation on four classes of primary metabolites and their derivatives, and two secondary metabolite classes between the transitions of germination initiation and germination and seedling establishment during the process. Metabolites related to carbohydrates and nitrogen metabolism, and few harmful to human health also demonstrated increasing accumulation along the process. Conclusions: The findings flourish our understanding of the metabolic mechanisms of in-situ germination and will be useful for future application in molecular breeding in Chinese hickory.
AHA! The adaptive hypermedia architecture

AHA! , the "Adaptive Hypermedia Architecture", was originally developed to support an on-line course with some user guidance through conditional (extra) explanations and conditional link hiding. This paper describes the many extensions and tools that have turned AHA! into a versatile adaptive hypermedia platform. It also shows how AHA! can be used to add different adaptive "features" to applications such as on-line courses, museum sites, encyclopedia, etc. The architecture of AHA! is heavily inspired by the AHAM reference model.
Getting Back to the Future: A Grounded Theory Study of the Patient Perspective of Total Knee Joint Arthroplasty

PURPOSE The purpose of this study was to describe the experience of adults with osteoarthritis who had undergone a total knee joint arthroplasty. METHOD Grounded theory qualitative methodology was applied. SAMPLE Purposive and theoretical sample of nine participants. FINDINGS In managing the experience of total knee joint arthroplasty, participants expressed the basic psychosocial process, “Getting back to the future. ” There were three main categories identified within this process, “enduring,” “thinking twice,” and “keeping faith. ” “Enduring” conceptualized the way the participants lived their daily lives. “Thinking twice” captured the participants' processes of adaptation and problem solving. “Keeping faith” was the combination of determination, trust, and optimism that sustained participants as they progressed through the total knee joint arthroplasty experience to rehabilitation. CONCLUSION The study provides a grounded theory of the participants' perspectives of undergoing total knee joint arthroplasty, making the process more visible for those involved in their care. Prehabilitation, postoperative care, and discharge planning can facilitate the patients' optimism and motivation to self-help. Further research to explore the process from the perspective of patients with rheumatoid arthritis and patients who have complications is recommended.
Nurses' job satisfaction in their early career: is it the same for all branches of nursing?

AIM To develop an early career job satisfaction instrument that is valid and reliable across the four UK nursing branches. BACKGROUND Contemporary instruments are required to measure nurse job satisfaction and to explore potential links with quality of care and retention. METHOD(S) Factor analysis was used to explore and test the stability of job satisfaction components across branches and over time. RESULTS Seven components (client care, staffing, development, relationships, education, work-life interface, resources) of job satisfaction were identified common to the adult, child and mental health branches that explained over 70% of the variance. The factor structure remained reasonably stable across time within each branch. Some differences between branches emerged at 6 and 18 months. The instrument has similarities and differences with existing generic and nursing facet job satisfaction scales. CONCLUSION Findings support a generic instrument that can be used to measure the job satisfaction of adult, child and mental health nurses in their early career. IMPLICATIONS FOR NURSING MANAGEMENT The instrument could be used for appraisal, annual staff surveys, for understanding retention locally and nationally, as an early warning system to identify organizational problems and to measure the impact of policies over time.
Analysis of the Developmental Roles of the Arabidopsis Gibberellin 20-Oxidases Demonstrates That GA20ox1, -2, and -3 Are the Dominant Paralogs[C][W]

In a systematic study of the five Arabidopsis thaliana genes that encode the biosynthetic enzyme gibberellin 20-oxidase, we show by mutant analysis and examination of gene expression that three of the genes make the major contribution to plant height and fertility, with the other two genes playing minor roles. Gibberellin (GA) biosynthesis is necessary for normal plant development, with later GA biosynthetic stages being governed by multigene families. Arabidopsis thaliana contains five GA 20-oxidase (GA20ox) genes, and past work has demonstrated the importance of GA20ox1 and -2 for growth and fertility. Here, we show through systematic mutant analysis that GA20ox1, -2, and -3 are the dominant paralogs; their absence results in severe dwarfism and almost complete loss of fertility. In vitro analysis revealed that GA20ox4 has full GA20ox activity, but GA20ox5 catalyzes only the first two reactions of the sequence by which GA12 is converted to GA9. GA20ox3 functions almost entirely redundantly with GA20ox1 and -2 at most developmental stages, including the floral transition, while GA20ox4 and -5 have very minor roles. These results are supported by analysis of the gene expression patterns in promoter:β-glucuronidase reporter lines. We demonstrate that fertility is highly sensitive to GA concentration, that GA20ox1, -2, and -3 have significant effects on floral organ growth and anther development, and that both GA deficiency and overdose impact on fertility. Loss of GA20ox activity causes anther developmental arrest, with the tapetum failing to degrade. Some phenotypic recovery of late flowers in GA-deficient mutants, including ga1-3, indicated the involvement of non-GA pathways in floral development.
The Role of Attitudes and Awareness in Anti-Violence Education

Summary Most interventions for the prevention of violence in relationships aim at attitudes and awareness. Prevailing attitudes in our society already condemn violence, however, and wife assault is viewed as particularly serious. Some research shows that perpetrators have attitudes more supportive of violence than other people do, but the link between attitudes and behavior can be complex. Trying to persuade people to change their attitudes in one direction can lead instead to people taking more extreme versions of their existing attitudes. Some interventions that raise awareness and promote availability of services appear to teach participants to take the problem less seriously. Most students report neither undesirable attitudes nor low awareness of violence in relationships. But their behavior appears inconsistent with their reported attitudes and awareness. If interpersonal violence has its roots in a problem more fundamental than the views of contemporary society, then anti-violence education based on attitudes and awareness will have limited benefits, and possibly some harmful effects. This article encourages a cautious rethinking of assumptions underlying current anti-violence education and alternative theories of violent behavior. It offers some suggestions for ways to reduce violent behavior, and encourages integration of violence prevention efforts into regular curricula and extra-curricular activities.
Morphological and anatomical development in the Vitaceae. X. Comparative ontogeny and phylogenetic implications of Cissus quadrangularis L.

Although the grape family, Vitaceae, is of great economic importance, there is little understanding of the relationships between and within the genera. Recent DNA-based phylogenies of the Vitaceae have disagreed with traditional classifications by grouping some Cissus species (e.g., Cissus antarctica Vent.) in a clade with Vitis species, while placing other Cissus species (e.g., Cissus quadrangularis L.) in a monophyletic clade. This study investigates Cissus phylogeny using epi-illumination light microscopy and histological ontogenetic comparisons of vegetative and reproductive characters of Vitis rotundifolia (Forssk.) Vahl, Vitis ‘Ventura’, Vitis riparia Michx. , C. antarctica, and C. quadrangularis. Ten characters limited to the Cissus species (connection of stipules, precocious axillary bud initiation, prophyll growth not obviously unequal, timing of mature shoot architecture on axillary buds, lack of spiral inflorescence branching, absence of calyptra, petals closely enveloping anthers, large gynoeci.
M-Business: The Race to Mobility

From the Publisher: "Knowing a change is coming is one thing; predicting its shape and form is something else entirely. M-Business succeeds at both, exploring today's wireless revolution from a business perspective as it introduces practical strategies your business can use to adapt from tethered, PC-centric models to mobile, person-centric techniques and strategies. " M-Business focuses on the bottom line: how managers can begin to plan for and differentiate m-business investments. This hands-on book steers clear of the technical nuances of mobile protocols and advanced technology - covered exhaustively by others - to provide insight into the actual market drivers, enablers, and business applications.
Diversity and prevalence of endoparasites in domestic chickens across an elevation gradient

Abstract. Setyowati EA, Santoso S, Rokhmani, Rochmatino. 2022. Diversity and prevalence of endoparasites in domestic chickens across an elevation gradient. Biodiversitas 23: 3936-3942. The domestic chicken farm is negatively affected by endoparasites, which decrease immunity, egg production, and body weight. Although these effects are well understood in large-scale chicken farms, here we aimed to understand endoparasite diversity and prevalence in the context of local-scale domestic chicken farms conducted in Central Java, Indonesia, according to elevation. Chickens were sampled from three villages each in two regions; lowland in Banyumas District and highland in Purbalingga. The result showed that the diversity of endoparasite is very low (H' index: 1.3065-1.3773) and we detected only four endoparasite species (Ascaridia galli, Trichuris trichiura, Heterakis gallinarum (Nematoda), and Raillietina sp. (Cestoda) among a sample of 300 chickens. Endoparasite infection was significantly more prevalent in the lowland villages (70%) than in highland (48%,) (p < 0.05). Among endoparasites found, A. galli was the most prevalent species among all samples (50.0±0.0% of infections in the lowlands and 23.7±1.15% in the highlands) the second is H. gallinarum accounted for 38.3±7.64% of all infections in the highlands and 15.3±0.58% in the lowlands. Raillietina sp. accounted for 35.0±5.0% and 7.3±0.58% of all infections, and T. trichiura accounted for 25.0±5.0 % and 16.0±1.0%. The rate of endoparasite infection within the study area is currently moderate and mainly affected by methods of farm, our findings can serve as a baseline for controlling infection in domestic chickens.
Recognizability in S-adic shifts

We investigate questions related to the notion of recognizability of sequences of morphisms, a generalization of Moss{\'e}'s Theorem. We consider the most general class of morphisms including ones with erasable letters. The main result states that a sequence of morphisms with finite alphabet rank is eventually recognizable for aperiodic points, improving and simplifying a result of Berth{\'e} et al. (2019). This also provides a new simple proof for the recognizability of a single morphism on its shift space. The main ingredient of the proof are elementary morphisms.