bluuebunny/crossref_metadata_2025_split huggingface dataset:
Track-by-Day: A standardized approach to estrous cycle monitoring in biobehavioral research
Authors: Raimondi Gianna M. , Eng Ashley K. , Kenny Murphy P. , Britting Madison A. , Ostroff Linnaea E. 
Published: August 2022

AbstractDespite known sex differences in brain function and incidence of neurological disorders, female subjects are routinely excluded from preclinical neuroscience research, particularly behavioral studies in rats. A common rationale for excluding females is that the hormone fluctuations of the estrous cycle will increase variability in experimental data. Accounting for the estrous cycle as an experimental variable requires expert knowledge of cycle tracking methods, which presents a barrier to widespread inclusion of female subjects. Conventional tracking relies on qualitative interpretation of vaginal cytology smears, and the subjective nature of this approach combined with a lack of reporting standards likely underlies the conflicting literature on estrous cycle effects on behavior. The estrous cycle is traditionally divided into stages based on cytology, but most stages do not directly reflect hormonal events and are therefore of limited relevance to neuroscience experiments. Here we present a simple, streamlined approach to estrous cycle monitoring in rats that eliminates subjective staging. Our method instead indexes the days of the estrous cycle to the one event that is unambiguously reflected in vaginal cytology – the pre-ovulatory surge in 17β-estradiol and subsequent epithelial cornification. With this tracking method, we demonstrate that cycle length is robustly regular across conditions. We quantified long-term memory in a Pavlovian fear conditioning experiment and uterine histology in a large cohort of rats, and found that grouping subjects by day was more sensitive in detecting cycle effects than grouping by traditional cytology staging. We present several datasets demonstrating the logic and applicability of our method, and show that, in the Track-by-Day framework, the cycle is highly regular and predictable in the vast majority of rats across a range of experimental conditions.
Variability in training unlocks generalization in visual perceptual learning through invariant representations
Authors: Manenti Giorgio L. , Dizaji Aslan Satary , Schwiedrzik Caspar M. 
Published: August 2022

SummaryStimulus and location specificity are long considered hallmarks of visual perceptual learning. This renders visual perceptual learning distinct from other forms of learning, where generalization can be more easily attained, and unsuitable for practical applications, where generalization is key. Based on hypotheses derived from the structure of the visual system, we test here whether stimulus variability can unlock generalization in perceptual learning. We train subjects in orientation discrimination, while we vary the amount of variability in a task-irrelevant feature, spatial frequency. We find that independently of task difficulty, this manipulation enables generalization of learning to new stimuli and locations, while not negatively affecting the overall amount of learning on the task. We then use deep neural networks to investigate how variability unlocks generalization. We find that networks develop invariance to the task-irrelevant feature when trained with variable inputs. The degree of learned invariance strongly predicts generalization. A reliance on invariant representations can explain variability-induced generalization in visual perceptual learning, suggests new targets for understanding the neural basis of perceptual learning in high-order visual cortex, and presents an easy to implement modification of common training paradigms that may benefit practical applications.
Detection and typing of plasmids in Acinetobacter baumannii using rep genes encoding replication initiation proteins
Authors: Lam Margaret M.C. , Koong Jonathan , Holt Kathryn E. , Hall Ruth M. , Hamidian Mehrad 
Published: August 2022

ABSTRACTPlasmids found in Acinetobacter species contribute to the spread of antibiotic resistance genes. They appear to be largely confined to this genus and cannot be typed with available tools and databases. Here, a method for distinguishing and typing these plasmids was developed using a curated, non-redundant set of 621 complete sequences of plasmids from Acinetobacter baumannii. Plasmids were separated into three groups based on the Pfam domains of the encoded replication initiation (Rep) protein and a fourth group that lack an identifiable Rep protein. The rep genes of each Rep-encoding group (n=13 Rep_1, n=107 RepPriCT_1, n=351 Rep_3) were then clustered using a threshold of >95% nucleotide identity to define 80 distinct types. Five Rep_1 subgroups, designated R1_T1 to R1-T5, were identified and a sixth reported recently was added. Each R1 type corresponded to a conserved small plasmid sequence. The RepPriCT_1 plasmids fell into 5 subgroups, designated RP-T1 to RP-T5 and the Rep_3 plasmids comprised 69 distinct types (R3-T1 to R3-T69). Three R1, 2 RP and 32 R3 types are represented by only a single plasmid. Over half of the plasmids belong to the four most abundant types: the RP-T1 plasmids (n=97), which include conjugation genes and are often associated with various acquired antibiotic resistance genes, and R3-T1, R3-T2 and R3-T3 (n=95, 30 and 45, respectively). To facilitate typing and the identification of plasmids in draft genomes using this framework, we established the Acinetobacter Typing database containing representative nucleotide and protein sequences of the type markers (https://github.com/MehradHamidian/AcinetobacterPlasmidTyping).IMPORTANCEThough they contribute to the dissemination of genes that confer resistance to clinically important carbapenem and aminoglycoside antibiotics used to treat life-threatening Acinetobacter baumannii infections, plasmids found in Acinetobacter species have not been well studied. As these plasmids do not resemble those found in other Gram-negative pathogens, available typing systems are unsuitable. The plasmid typing system developed for A. baumannii plasmids with an identifiable rep gene will facilitate the classification and tracking of sequenced plasmids. It will also enable the detection of plasmid-derived contigs present in draft genomes that are widely ignored currently. Hence, it will assist in the tracking of resistance genes and other genes that affect survival in the environment, as they spread through the population. As identical or similar plasmids have been found in other Acinetobacter species, the typing system will also be broadly applicable in identifying plasmids in other members of the genus.
Effects of interspecies interactions on marine community ecosystem function
Authors: Daniels Michael , Stubbusch Astrid K.M. , Held Noelle A. , Schubert Olga T. , Ackermann Martin 
Published: August 2022

AbstractMicrobial communities perform key ecosystem processes collectively. One such process is the degradation of carbohydrate polymers, which are the dominant pool of organic carbon in natural environments. Carbohydrate polymers are often degraded in a stepwise manner. Individual steps are performed by different microbial species, which form trophic cascades with carbon polymers at the bottom and fully oxidised carbon at the top. It is widely believed that these trophic cascades are hierarchically organised, where organisms at each level rely on organisms at the levels below. However, whether and how the higher-level organisms can also affect processes at the lower levels is not well understood. Here we studied how carbohydrate polymer degradation mediated by secreted enzymes is affected by species at higher trophic levels, i.e., species that cannot produce the enzymes for polymer degradation but can grow in presence of the polymer degraders. We used growth and enzyme assays in combination with transcriptomics to study how chitin degradation by a number of Vibrio strains is affected by the presence of different cross-feeders that consume metabolic by-products. We found that interactions between the degraders and cross-feeders influence the rate of chitin degradation by the community. Furthermore, we show that this is a result of changes in chitinase expression by degraders. Overall, our results demonstrate that interactions between species can influence key ecosystem functions performed by individuals within microbial communities. These results challenge the perspective that trophic cascades based on metabolically coupled microbial communities are unidirectional and provide mechanistic insights into these downstream interactions.
Structural analysis unravels the functional promiscuity of Quinolone synthase-mediated polyketide biosynthesis in Aegle marmelos Correa
Authors: Vijayanathan Mallika , Abhinav KV , Bandyopadhyay Debashree , Mahendran Kozhinjampara R , Sharaf Abdoallah , Pillai M Radhakrishna , Soniya EV 
Published: August 2022

AbstractQuinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Based on the high-resolution protein structure of AmQNS, this study provided a mechanistic explanation of the structure to synthetic selectivity. Additionally, it displays the comparatively wide active site entry that allows the catalytic pocket to accommodate bulky substrates, which affects the enzyme catalysis. We also develop a model framework for comprehending the structural constraints on ketide insertion, and postulate that AmQNS synthetic diversity is owing to its steric and electrostatic selectivity, which allows it to bind to a variety of core substrates. We further establish that AmQNS is structurally biased toward quinolone synthesis and only synthesizes acridone when malonyl-CoA concentrations are significantly high. In a nutshell, we anticipate that addressing the structural and molecular underpinnings of AmQNS–substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. Besides, the approaches can also be expanded to other potential enzymes, which will help the pharmaceutical sector by expanding the pool of potential medication leads.
Oligomeric polymorphism of HIV-1 Vpu protein in lipid environment and in solution
Authors: Majeed Saman , Adetuyi Oluwatosin , Islam Md Majharul , Zhao Bo , Georgieva Elka R. 
Published: August 2022

ABSTRACTThe HIV-1 encoded protein Vpu forms an oligomeric ion channel/pore in membranes and interacts with multiple host proteins to support virus lifecycle. However, Vpu molecular mechanisms are currently not well understood. The structures of full-length Vpu in its monomeric and oligomeric forms are unknown, although both the monomer and oligomer are deemed important. Here, we report on the diversity of Vpu oligomeric structures and how the environment affects the Vpu oligomer formation. We produced a uniquely designed MBP-Vpu chimera protein in E. coli in soluble form. We subjected this protein to analytical size exclusion chromatography (SEC) and negative staining electron microscopy (nsEM). Strikingly, we found that MBP-Vpu forms stable oligomers in solution, presumably driven by Vpu transmembrane domain self-association. Our coarse modeling suggests that these oligomers are pentamers, in agreement with the pentameric membrane-bound Vpu. To the best of our knowledge, this is the first observation of Vpu self-association out of lipid membrane environment. We further found that MBP-Vpu oligomer stability decreases when the protein was reconstituted in lipid membrane mimetics, such as β-DDM, and mixtures of lyso PC/PG or DHPC/DHPG—In these cases significant oligomer heterogeneity was observed with oligomeric order lesser than that of MBP-Vpu oligomer in solution, but larger oligomers were observed as well. Importantly, we found that in lyso PC/PG, above certain protein concentration, MBP-Vpu forms linear array-like structures, which is also novel. Thus, our studies provide unique information about Vpu protein quaternary organization by capturing multiple Vpu oligomeric structures, which we believe are physiologically relevant.
Critical factors in awakening the slumbering collections: a study based on XGBoost
Authors: Zhang Xiaoxiao , Shi Guoliang , Jin Qiupan 
Published: August 2022

PurposeThe purpose is to explore the essential reasons for the differences between book awakening phenomena, to develop the critical factors in awakening the slumbering collections and to provide a reliable basis for maximizing book value and optimizing collection allocation.Design/methodology/approachThe research employs the integrated learning algorithm XGBoost to measure driving factors. In the process of book circulation, the characteristics of collections and readers are worthy of attention. Therefore, this study also carries out feature selection and model construction from the two dimensions of books and readers.FindingsThe results show that reader features have a stronger impetus for the collection awakening phenomenon than collection features. Among reader features, education level, gender and major subject are the main factors, which are followed closely by the activity level; among collection features, publication date and price are the main driving factors. The indicators of book popularity are not significant, whose effect on the phenomenon of collection awakening is almost negligible.Originality/valueThis study aims to augment the theory of zero circulation from the theoretical level and, for the first time, seeks to define the phenomenon of collection awakening. This study attempts to present novel ideas for research in the field of libraries and to provide references for optimizing collection and maximizing the value of books.
Toward a better understanding of the attitude–behavior gap in organic food conative loyalty: a moderation and moderated mediation analysis
Authors: Anisimova Tatiana , Weiss Jan 
Published: August 2022

PurposePrevious research has found mixed evidence of an attitude–behavior gap in organic food consumption. However, the complex mechanisms underlying this gap warrant further investigation. The purpose of this study is to examine the role of word-of-mouth (WOM), trust, and involvement in the relationship between consumer organic food attitudes and conative loyalty. The Theory of Planned Behavior (TPB) was used as underlying framework for modeling our conceptualized arguments.Design/methodology/approachA moderation and moderated mediation analysis was performed on a cross-sectional sample of 1,011 Australian organic food consumers.FindingsThe results support the TPB-inspired moderated-mediation model. Specifically, the authors found moderated mediation effects of WOM, trust, and involvement on conative loyalty via attitudes toward organics.Research limitations/implicationsThe cross-sectional research design and the focus solely on Australian consumers constitute limitations of this study.Practical implicationsThe authors' findings imply that an analysis of the attitude–behavior gap should go beyond the testing of contingent consistency hypotheses and instead combine moderation and mediation mechanisms to better model consumer decision-making leading to conative loyalty. Practitioners would face a resource challenge when targeting low-trust, low-involvement, and low-WOM consumers as developing conative loyalty of these segments would require a longer-term approach through building favorable attitudes toward organic foods.Originality/valueThis study is one of the first to demonstrate the potential of examining the attitude–behavior gap in the organic food context through a moderated mediation lens in explaining the dynamics of conative loyalty.
Gender roles or gendered goals? Women's return to rural family business
Authors: Gashi Nulleshi Shqipe , Kalonaityte Viktorija 
Published: August 2022

PurposeThis paper aims to add to the theorization of the gender dynamic in rural areas by investigating the motives of women who join their family firm (or their spouse's family firm) and thereby defy the demographic trend of rural flight. The context of this study is the depopulation of rural areas with the closing of basic services and relocation of the younger population, and educated women in particular, to urban areas. Consequently, rural family businesses risk failing to find successors and suffering forced closure or relocation. The empirical site of the study is rural family firms in Sweden, a context characterized by a high level of gender equality in legislation and culture but gender-conservative business structures in rural regions.Design/methodology/approachThe empirical case in this paper builds on a qualitative study of nine (9) life course narratives of women entrepreneurs in a rural region of Southern Sweden who have returned to rural areas to join their family business. The authors follow the view established by gender scholars that women are active agents in navigating their lives, and their life story narratives offer insight into the considerations that inform their choice to stay or return to rural locations. In Sweden, the setting for the study, gender equality is widely supported by legislation, policy and institutional frameworks and popular understanding of gender relations. In contrast to the gender-progressive policies of Sweden at large, women's entrepreneurship in rural regions of Sweden tends to follow traditional gender hierarchies and face similar constraints as in rural areas of other countries. The juxtaposition of these competing sets of ideals makes Sweden an important and interesting place to study and draw insights from the experiences of women entrepreneurs.FindingsThe findings reveal that women who choose to join rural family firms view them primarily in a positive light and see this choice as aligned with their need for professional flexibility and assertiveness, rewarding relationships, and a calm, secure, well-balanced life. Theoretically, the study implies that women choosing to engage in rural family firms seek non-material benefits, such as work–life balance and social support, and may be driven in part by a sense of psychological ownership that extends to the rural community.Originality/valueThe findings provide novel insights on women as active agents in navigating their lives and the intrinsic (e.g. alignment of personal values) and extrinsic (e.g. community support) motives that inform their decisions. The study also raises questions regarding how women perceive themselves as “fitting in” to rural settings and to what extent the sense of security within these settings that the women describe may be contingent upon factors such as their families' embeddedness within the community as well as their conformity to the local social norms.
Would you share that? How the intensity of violent and sexual humor, gender and audience diversity affect sharing intentions for online advertisements
Authors: Freeman Richard , Marder Ben , Gorton Matthew , Angell Rob 
Published: August 2022

PurposeThe purpose of this study is to understand the effect of increasing the intensity of sexual or violent content on consumer responses to online video advertisements, with a particular emphasis on sharing intentions.Design/methodology/approachThe paper uses a between-subjects experimental design across two studies using new to the world online video advertisements as stimuli.FindingsStudy 1 finds that increasing the intensity of sexual and violent humor improves advertisement effectiveness amongst men but leads to significantly more negative attitudes toward the advertisement and brand amongst women. Study 2 identifies gender and humor type as moderators for sharing intentions in the presence of audience diversity. While men are more likely to publicly share sexual and violent humor advertisements, social anxiety mediates intentions to share sexual humor advertisements in the presence of greater audience diversity.Practical implicationsThe paper offers insights to practitioners regarding the use of risqué forms of humor as part of a digital marketing strategy.Originality/valueDrawing on and extending benign violation theory, the paper introduces and verifies a theoretical model for understanding consumer responses to the use of risqué forms of humor in online advertisements. It identifies how audience diversity affects sharing intentions for sexual and violent humor-based advertisements on social media.
Knowledge ecosystem of financial markets: a new perspective on alleviating the supply-demand contradiction of the rural finance in the post-COVID-19 era
Authors: Yang Yimin , Su Yuefeng , Yang Lulu , Zeng Xiongwang 
Published: August 2022

Purpose
This paper aims to establish a systematic cognition to alleviate the supply–demand contradiction in rural financial markets from an integrated perspective of knowledge management and proposes the concept of rural financial knowledge ecosystem (RFKE) to encourage multifaceted solutions.

Design/methodology/approach
The authors qualitatively describe the process that the knowledge management dilemmas cause the supply–demand contradiction in the rural finance and further summarize a systematic methodology from three dimensions: the knowledge subject, the knowledge environment and the knowledge ecology.

Findings
The authors list four types of knowledge management dilemmas leading to the supply–demand contradiction in the rural finance, i.e. the weak knowledge sharing, the poor knowledge flow, the slow knowledge updating and the imperfect knowledge environment. Meanwhile, the RFKE model consisting of the ecological subject, the ecological environment and the ecological regulation is also presented.

Research limitations/implications
The role of knowledge management in improving the allocation of financial resources to various rural financial market participants (government, rural financial institutions, farmers, agricultural enterprises, etc.).

Originality/value
The authors creatively give the RFKE model, which complements and enriches the theory of knowledge management. Meanwhile, relevant management practices are urgently needed under the macro circumstance of the COVID-19 pandemic and the rural revitalization in China.