bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal distributions of central-place foragers: honey bee foraging in a mass flowering crop
Authors: Robinson Samuel V J , Hoover Shelley E , Pernal Stephen F , Cartar Ralph V 
Published: November 2021

AbstractThe ideal-free distribution and central-place foraging are important ecological models that can explain the distribution of foraging organisms in their environment. However, this model ignores distance-based foraging costs from a central place (hive, nest), whereas central-place foraging ignores competition. Different foraging currencies and cooperation between foragers also create different optimal distributions of foragers, but are limited to a simple two-patch model. We present a hybrid model of the ideal-free distribution that uses realistic competitive effects although accounting for distance-based foraging, and test it using honey bees (Apis mellifera L.) foraging in canola fields (Brassica napus L.). Our simulations show that foragers maximizing efficiency (energy profits ÷losses) prioritize distance to their aggregation more than those maximizing net-rate (energy profits ÷time), and that social foragers move to more distant patches to maximize group benefits, meaning that social foragers do not approach an ideal-free distribution. Simulated efficiency-maximizers had a hump-shaped relationship of trip times with distance, spending shorter amounts of time in both nearby and far-away patches. Canola fields were far more attractive to simulated foragers than semi-natural areas, suggesting limited foraging on semi-natural lands during the bloom period of canola. Finally, we found that the observed distribution of honey bees in canola fields most closely resembled the optimal distribution of solitary efficiency-maximizers. Our model has both theoretical and practical uses, as it allows us to model central-place forager distributions in complex landscapes as well as providing information on appropriate hive stocking rates for agricultural pollination.
SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2–human mimicry and interactions
Authors: Ovek Damla , Taweel Ameer , Abali Zeynep , Tezsezen Ece , Koroglu Yunus Emre , Tsai Chung-Jung , Nussinov Ruth , Keskin Ozlem , Gursoy Attila 
Published: November 2021

Abstract

Summary
We present a web-based server for navigating and visualizing possible interactions between SARS-CoV-2 and human host proteins. The interactions are obtained from HMI_Pred which relies on the rationale that virus proteins mimic host proteins. The structural alignment of the viral protein with one side of the human protein–protein interface determines the mimicry. The mimicked human proteins and predicted interactions, and the binding sites are presented. The user can choose one of the 18 SARS-CoV-2 protein structures and visualize the potential 3D complexes it forms with human proteins. The mimicked interface is also provided. The user can superimpose two interacting human proteins in order to see whether they bind to the same site or different sites on the viral protein. The server also tabulates all available mimicked interactions together with their match scores and number of aligned residues. This is the first server listing and cataloging all interactions between SARS-CoV-2 and human protein structures, enabled by our innovative interface mimicry strategy.

Availability and implementation
The server is available at https://interactome.ku.edu.tr/sars/.
Remote service delivery during the COVID-19 pandemic: Questioning the impact of technology on relationship-based social work practice
Authors: Pascoe Katheryn Margaret 
Published: November 2021

Abstract
The coronavirus (COVID-19) pandemic caused widespread lockdowns, social distancing measures, restrictions to businesses and the closure of buildings. During this time social workers were required to adjust to remote practice, adopting technological adjuncts for continued engagement with service users. This article reports on qualitative interviews with fourteen front line social workers practicing during the pandemic in Northern Ireland, exploring the impact of remote delivery and technology on relationship-based practice. Findings highlight negative outcomes on relationship building and social worker self-care, alongside concerns that efficiency would be prioritised over future face-to-face contact with service users. The adoption of alternative methods of communication through technology has disrupted the core principles of relationship-based practice and has meant that, without proper planning or staff training, alternative models of delivery, which may have enabled some form of continuation and centralisation of relationship-based practice are under explored and require further investigation.
TBX1functions as a putative oncogene of breast cancer through promoting cell cycle progression
Authors: Huang Shuya , Shu Xiang , Ping Jie , Wu Jie , Wang Jifeng , Shidal Chris , Guo Xingyi , Bauer Joshua A , Long Jirong , Shu Xiao-Ou , Zheng Wei , Cai Qiuyin 
Published: November 2021

AbstractWe have previously identified a genetic variant, rs34331122 in the 22q11.21 locus, as being associated with breast cancer risk in a genome-wide association study. This novel variant is located in the intronic region of the T-box transcription factor 1 (TBX1) gene. Cis-expression quantitative trait loci analysis showed that expression of TBX1 was regulated by the rs34331122 variant. In the current study, we investigated biological functions and potential molecular mechanisms of TBX1 in breast cancer. We found that TBX1 expression was significantly higher in breast cancer tumor tissues than adjacent normal breast tissues and increased with tumor stage (P &lt; 0.05). We further knocked-down TBX1 gene expression in three breast cancer cell lines, MDA-MB-231, MCF-7 and T47D, using small interfering RNAs and examined consequential changes on cell oncogenicity and gene expression. TBX1 knock-down significantly inhibited breast cancer cell proliferation, colony formation, migration and invasion. RNA sequencing and flow cytometry analysis revealed that TBX1 knock-down in breast cancer cells induced cell cycle arrest in the G1 phase through disrupting expression of genes involved in the cell cycle pathway. Furthermore, survival analysis using the online Kaplan–Meier Plotter suggested that higher TBX1 expression was associated with worse outcomes in breast cancer patients, especially for estrogen receptor-positive breast cancer, with HRs (95% CIs) for overall survival (OS) and distant metastasis free survival (DMFS) of 1.5 (1.05–2.15) and 1.55 (1.10–2.18), respectively. In conclusion, our results suggest that the TBX1 gene may act as a putative oncogene of breast cancer through regulating expressions of cell cycle-related genes.
Transcription phenotype of circulating tumor cells in non-metastatic breast cancer
Authors: Shliakhtunou Yauheni A , Siamionau Valery M , Pobyarzhin Vyacheslau V 
Published: November 2021

AbstractThe presented research is relevant, as breast cancer is the most commonly diagnosed cancer in the female population worldwide, with the exception of skin cancer. The aim of this article is to study the transcription phenotype of circulating tumor cells in non-metastatic breast cancer. The transcriptional phenotype of circulating tumor cells (CTCs) was studied using real-time polymerase chain reaction (PCR). Three-year OS was 79.2, and 90.8 without the expression with p Log-Rank = 0.04. Independent prognostic factors for the recurrence of disease include the presence of CTCs expressing BIRC5 genes and ABC transporter genes in the peripheral blood before the start of special treatment for resectable breast cancer, as well as the preservation of CTCs per se after completion of special anticancer therapy. In patients with breast cancer stage I–IIIC, circulating tumor cells before special treatment have significant heterogeneity, manifested by a different transcriptional phenotype, including both actively growing and stem tumor cells, and cells at the epithelial-to-mesenchymal transition.
Endogenous sources of interbrain synchrony in duetting pianists
Authors: Gugnowska Katarzyna , Novembre Giacomo , Kohler Natalie , Villringer Arno , Keller Peter E , Sammler Daniela 
Published: November 2021

Abstract
When people interact with each other, their brains synchronize. However, it remains unclear whether interbrain synchrony (IBS) is functionally relevant for social interaction or stems from exposure of individual brains to identical sensorimotor information. To disentangle these views, the current dual-EEG study investigated amplitude-based IBS in pianists jointly performing duets containing a silent pause followed by a tempo change. First, we manipulated the similarity of the anticipated tempo change and measured IBS during the pause, hence, capturing the alignment of purely endogenous, temporal plans without sound or movement. Notably, right posterior gamma IBS was higher when partners planned similar tempi, it predicted whether partners’ tempi matched after the pause, and it was modulated only in real, not in surrogate pairs. Second, we manipulated the familiarity with the partner’s actions and measured IBS during joint performance with sound. Although sensorimotor information was similar across conditions, gamma IBS was higher when partners were unfamiliar with each other’s part and had to attend more closely to the sound of the performance. These combined findings demonstrate that IBS is not merely an epiphenomenon of shared sensorimotor information but can also hinge on endogenous, cognitive processes crucial for behavioral synchrony and successful social interaction.
Similar neural networks respond to coherence during comprehension and production of discourse
Authors: Morales Matías , Patel Tanvi , Tamm Andres , Pickering Martin J , Hoffman Paul 
Published: November 2021

Abstract
When comprehending discourse, listeners engage default-mode regions associated with integrative semantic processing to construct a situation model of its content. We investigated how similar networks are engaged when we produce, as well as comprehend, discourse. During functional magnetic resonance imaging, participants spoke about a series of specific topics and listened to discourse on other topics. We tested how activation was predicted by natural fluctuations in the global coherence of the discourse, that is, the degree to which utterances conformed to the expected topic. The neural correlates of coherence were similar across speaking and listening, particularly in default-mode regions. This network showed greater activation when less coherent speech was heard or produced, reflecting updating of mental representations when discourse did not conform to the expected topic. In contrast, regions that exert control over semantic activation showed task-specific effects, correlating negatively with coherence during listening but not during production. Participants who showed greater activation in left inferior prefrontal cortex also produced more coherent discourse, suggesting a specific role for this region in goal-directed regulation of speech content. Results suggest strong correspondence of discourse representations during speaking and listening. However, they indicate that the semantic control network plays different roles in comprehension and production.
Treatment and Outcome in Children With Tuberculous Meningitis: A Multicenter Pediatric Tuberculosis Network European Trials Group Study
Authors: Thee Stephanie , Basu Roy Robindra , Blázquez-Gamero Daniel , Falcón-Neyra Lola , Neth Olaf , Noguera-Julian Antoni , Lillo Cristina , Galli Luisa , Venturini Elisabetta , Buonsenso Danilo , Götzinger Florian , Martinez-Alier Nuria , Velizarova Svetlana , Brinkmann Folke , Welch Steven B , Tsolia Maria , Santiago-Garcia Begoña , Schilling Ralph , Tebruegge Marc , Krüger Renate ,   ptbnet TB Meningitis Study Group, Bogyi Matthias , Montagnani Carlotta , Lancella Laura , Salo Eeva , Syngelou Angeliki , Krivec Uros , Nalda Andrea Martín , Soriano-Arandes Antoni , Rivero Irene , Nieto Marta Benavides , Bueno Mercedes , del Rosal Teresa , Mayol Luis , Guarch Borja , Couceiro Jose Antonio , Laleona Carmelo Guerrero , Bennet Rutger , Kötz Karsten , Raffa Brittany , Shackley Fiona 
Published: November 2021

Abstract

Background
Currently, data on treatment, outcome, and prognostic factors in children with tuberculous meningitis (TBM) in Europe are limited. To date, most existing data on TBM originate from adult studies, or studies conducted in low-resource settings.

Methods
We designed a multicenter, retrospective study involving 27 pediatric healthcare institutions in 9 European countries via an established pediatric TB research network, before and after the 2014 revision of World Health Organization (WHO) dosing recommendations.

Results
Of 118 children, 39 (33.1%) had TBM grade 1, 68 (57.6%) grade 2, and 11 (9.3%) grade 3. Fifty-eight (49.1%) children received a standard 4-drug treatment regimen; other commonly used drugs included streptomycin, prothionamide, and amikacin. Almost half of the patients (48.3%; 56/116) were admitted to intensive care unit, with a median stay of 10 (interquartile range [IQR] 4.5–21.0) days. Of 104 children with complete outcome data, 9.6% (10/104) died, and only 47.1% (49/104) recovered fully. Main long-term sequelae included spasticity of 1 or more limbs and developmental delay both in 19.2% (20/104), and seizure disorder in 17.3% (18/104). Multivariate regression analyses identified microbiological confirmation of TBM, the need for neurosurgical intervention, and mechanical ventilation as risk factors for unfavorable outcome.

Conclusions
There was considerable heterogeneity in the use of TB drugs in this cohort. Despite few children presenting with advanced disease and the study being conducted in a high-resource setting, morbidity and mortality were high. Several risk factors for poor outcome were identified, which may aid prognostic predictions in children with TBM in the future.
Lack of Convincing Evidence That Borrelia burgdorferi Infection Causes Either Alzheimer Disease or Lewy Body Dementia
Authors: Wormser Gary P , Marques Adriana , Pavia Charles S , Schwartz Ira , Feder Henry M , Pachner Andrew R 
Published: November 2021

Abstract
The role that microorganisms might have in the development of Alzheimer disease is a topic of considerable interest. In this article, we discuss whether there is credible evidence that Lyme disease is a cause of Alzheimer disease and critically review a recent publication that claimed that Borrelia burgdorferi sensu stricto infection, the primary cause of Lyme disease in the United States, may cause Lewy body dementia. We conclude that no convincing evidence exists that Lyme disease is a cause of either Alzheimer disease or Lewy body dementia.
Complete Genome Sequencing of a NovelGloeobacterSpecies from a Waterfall Cave in Mexico
Authors: Saw Jimmy H , Cardona Tanai , Montejano Gustavo 
Published: November 2021

AbstractOnly two complete genomes of the cyanobacterial genus Gloeobacter from two very different regions of the world currently exist. Here, we present the complete genome sequence of a third member of the genus isolated from a waterfall cave in Mexico. Analysis of the average nucleotide identities (ANIs) between published Gloeobacter genomes revealed that the complete genome of this new member is only 92.7% similar to Gloeobacter violaceus and therefore we determined it to be a new species. We propose to name this new species Gloeobacter morelensis after the location in Mexico where it was isolated. The complete genome consists of one circular chromosome (4,921,229 bp), one linear plasmid (172,328 bp), and one circular plasmid (8,839 bp). Its genome is the largest of all completely sequenced genomes of Gloeobacter species. Pangenomic comparisons revealed that G. morelensis encodes 759 genes not shared with other Gloeobacter species. Despite being more closely related to G. violaceus, it features an extremely divergent psbA gene encoding an atypical D1 core subunit of Photosystem II previously only found within the genome of Gloeobacter kilaueensis. In addition, we detected evidence of concerted evolution of psbA genes encoding identical D1 in all three Gloeobacter genomes, a characteristic that seems widespread in cyanobacteria and may therefore be traced back to their last common ancestor.
On the L
p Brunn-Minkowski theory and the L
p Minkowski problem for C-coconvex sets
Authors: Yang Jin , Ye Deping , Zhu Baocheng 
Published: November 2021

Abstract
Let $C$ be a pointed closed convex cone in ${{\mathbb {R}}^n}$ with vertex at the origin $o$ and having nonempty interior. The set $A\subset C$ is $C$-coconvex if the volume of $A$ is finite and $A^{\bullet }=C\setminus A$ is a closed convex set. For $0&lt;p&lt;1$, the $p$-co-sum of $C$-coconvex sets is introduced and the corresponding $L_p$ Brunn–Minkowski inequality for $C$-coconvex sets is established. We also define the $L_p$ surface area measures, for $0\neq p\in {\mathbb {R}}$, of certain $C$-coconvex sets, which are critical in deriving a variational formula of the volume of the Wulff shape associated with a family of functions obtained from the $p$-co-sum. This motivates the $L_p$ Minkowski problem aiming to characterize the $L_p$ surface area measures of $C$-coconvex sets. The existence of solutions to the $L_p$ Minkowski problem for all $0\neq p\in {\mathbb {R}}$ is established. The $L_p$ Minkowski inequality for $0&lt;p&lt;1$ is proved and is used to obtain the uniqueness of the solutions to the $L_p$ Minkowski problem for $0&lt;p&lt;1$. For $p=0$, we introduce $(1-\tau )\diamond A_1\oplus _0\tau \diamond A_2$, the log-co-sum of two $C$-coconvex sets $A_{1}$ and $A_{2}$ with respect to $\tau \in (0, 1)$, and prove the log-Brunn–Minkowski inequality of $C$-coconvex sets. The log-Minkowski inequality is also obtained and is applied to prove the uniqueness of the solutions to the log-Minkowski problem that characterizes the cone-volume measures of $C$-coconvex sets. Our result solves an open problem raised by Schneider [41].
Elucidation of host diversity of the VanD-carrying genomic islands in enterococci and anaerobes
Authors: Hashimoto Yusuke , Hisatsune Junzo , Suzuki Masato , Kurushima Jun , Nomura Takahiro , Hirakawa Hidetada , Kojima Naoko , Ono Yuichi , Hasegawa Yutaka , Tanimoto Koichi , Sugai Motoyuki , Tomita Haruyoshi 
Published: November 2021

Abstract

Background
VanD is a rare type of vancomycin resistance worldwide. However, the host diversity of the vanD gene cluster and the structural similarity of their genomic islands are not well understood.

Methods
Three VanD-type Enterococcus faecium strains (AA620, AA622 and AA624) isolated from a Japanese patient who underwent vancomycin treatment in 2017 were analysed. This study utilized WGS analysis to characterize the three VanD-type E. faecium strains and describes the diversity of hosts possessing VanD-carrying genomic islands.

Results
The three isolates exhibited variable MICs of vancomycin. In the relatively vancomycin-resistant AA620, mutations were identified in vanSD and ddl. The strains AA622 and AA624 had intact ddl and harboured two vanD gene clusters. qRT-PCR results revealed the ddl mutation to be a factor affecting the high vancomycin resistance range of AA620. WGS data showed the 155 kb and 185 kb genomic islands harbouring the vanD gene cluster inserted in the coding region of the lysS gene, located in the chromosome in AA620 and AA622/624, respectively. Comparing the VanD-carrying genomic islands to available sequences of other enterococci and enteric anaerobes revealed how the genomic islands of these organisms isolated worldwide shared similar core genes and backbones. These anaerobes belonged to various genera within the order Eubacteriales. The phylogenetic cluster of the genomic island core genome alignment did not correlate with the host-species lineage, indicating horizontal gene transfer in the gut microbiota.

Conclusions
By horizontal gene transfer, various bacteria forming the gut microbiota maintain VanD-carrying genomic islands.
Deciphering the role of plant plasma membrane lipids in response to invasion patterns: how could biology and biophysics help?
Authors: Cordelier Sylvain , Crouzet Jérôme , Gilliard Guillaume , Dorey Stéphan , Deleu Magali , Dhondt-Cordelier Sandrine 
Published: November 2021

AbstractPlants have to constantly face pathogen attacks. To cope with diseases, they have to detect the invading pathogen as early as possible via the sensing of conserved motifs called invasion patterns. The first step of perception occurs at the plasma membrane. While many invasion patterns are perceived by specific proteinaceous immune receptors, several studies have highlighted the influence of the lipid composition and dynamics of the plasma membrane in the sensing of invasion patterns. In this review, we summarize current knowledge on how some microbial invasion patterns could interact with the lipids of the plasma membrane, leading to a plant immune response. Depending on the invasion pattern, different mechanisms are involved. This review outlines the potential of combining biological with biophysical approaches to decipher how plasma membrane lipids are involved in the perception of microbial invasion patterns.
Endomembrane mediated-trafficking of seed storage proteins: from Arabidopsis to cereal crops
Authors: Zheng Ping , Zheng Chunyan , Otegui Marisa S , Li Faqiang 
Published: November 2021

AbstractSeed storage proteins (SSPs) are of great importance in plant science and agriculture, particularly in cereal crops, due to their nutritional value and their impact on food properties. During seed maturation, massive amounts of SSPs are synthesized and deposited either within protein bodies derived from the endoplasmic reticulum, or into specialized protein storage vacuoles (PSVs). The processing and trafficking of SSPs vary among plant species, tissues, and even developmental stages, as well as being influenced by SSP composition. The different trafficking routes, which affect the amount of SSPs that seeds accumulate and their composition and modifications, rely on a highly dynamic and functionally specialized endomembrane system. Although the general steps in SSP trafficking have been studied in various plants, including cereals, the detailed underlying molecular and regulatory mechanisms are still elusive. In this review, we discuss the main endomembrane routes involved in SSP trafficking to the PSV in Arabidopsis and other eudicots, and compare and contrast the SSP trafficking pathways in major cereal crops, particularly in rice and maize. In addition, we explore the challenges and strategies for analyzing the endomembrane system in cereal crops.