bluuebunny/crossref_metadata_2025 huggingface dataset:
An Exploratory Analysis of Maternal Health Variables Increasing the Severity of Congenital Heart Disease in Infants
Authors: Butler Mary
Published: October 2022

Background:

Congenital heart defects (CHD) are the most prevalent birth anomaly and leading cause of infant morbidity and mortality worldwide. Heart defects are often attributed to chromosomal abnormality or environmental factors, but most causes remain unknown. The purpose of this analysis was to explore maternal health variables and the relationships to birth outcomes in infants with CHD.

Methods:

Secondary analysis of data from the Wisconsin Pediatric Cardiac Registry.

Results:

Maternal history of CHDs (odds ratio [OR] = 2.38; 95% confidence interval [CI], 1.42-3.98) and serious health conditions (OR = 1.537; 95%: CI, 1.08-2.17) increase infant risk and CHD severity. Maternal history of hypertension, serious health conditions, CHD, obesity, and income were predictors of birth weight (R² = 0.049, P < .05). Maternal history of hypertension, influenza, serious health conditions, and housing were predictors of gestational age (R
2 = 0.045, P < .05). Birth weight (BW) and gestational age (GA) did not correlate to the severity of CHD in this study (simple vs complex, BW = −0.014, GA = 0.011, r).

Discussion:

Maternal well-being influences the health of infants born with CHD. Positive maternal health contributes to near-normal birth weight and gestational age.

Conclusion:

Nurses must discuss optimal reproductive life planning strategies for decreasing risk of CHD and other infant disorders.
Fathers' Experiences in Alberta Family Integrated Care
Authors: Shafey Amy , Benzies Karen , Amin Reshma , Stelfox Henry T. , Shah Vibhuti
Published: October 2022

Background:

The Family Integrated Care (FICare) program adapted for Alberta (AB) level II neonatal intensive care units (NICUs) aims to increase parental involvement and support during their NICU stay. The experience of fathers of preterm infants in a FICare program is currently unknown.

Purpose:

To describe the experiences of fathers of preterm infants born at 320/7 to 346/7 weeks' gestational age with AB FICare.

Methods:

A qualitative substudy of a multicenter prospective cluster randomized controlled trial of FICare in 10 level II NICUs across Alberta. Fathers of preterm infants participated in a semistructured interview after discharge when their infants were at least 2 months' corrected gestational age. Journal entries written by fathers while in the NICU from the FICare intervention sites were also collected. Data were analyzed thematically and the interview and journal data were triangulated.

Findings:

Thirteen fathers (9 from the FICare intervention and 4 from standard care) participated in semistructured interviews and there were 24 journals collected. Seven themes emerged: fear of the unknown, mental preparation, identifying the father's role, parenting with supervision, effective communication, postneonatal intensive care transition, and family life. Fathers enrolled in AB FICare attributed their level of confidence and positive neonatal intensive care experience that continued postdischarge to the care and attention they received during hospitalization.

Conclusion:

AB FICare may improve experiences for fathers of preterm infants in the NICU with continuation postdischarge. Future research should include designing and evaluating father-specific NICU programs.
Nurse-Driven Interventions for Improving ELBW Neurodevelopmental Outcomes
Authors: Gomez Jessica , Wardell Diane
Published: October 2022

Survival rates for extremely low-birth-weight (ELBW) infants are improving as neurodevelopmental impairment (NDI) rates stay stable, thereby increasing the overall number of infants with NDI. Although there are many determinants of NDI in this population, nutritional factors are of interest because they are readily modifiable in the clinical setting. Nurses can influence nutritional factors such as improving access to human milk feeding, using growth monitoring, establishing feeding policies, implementing oral care with colostrum, facilitating kangaroo care, and providing lactation education for the mother. All of these measures assist in leading to a decrease in NDI rates among ELBW infants.
Recruitment Challenges of a Colorectal Cancer Screening Dissemination Study
Authors: Larkey Linda , Szalacha Laura A. , Bucho-Gonzalez Julie , Menon Usha
Published: October 2022

Background

Dissemination strategies to reach underserved and minority populations to promote screening for colorectal cancer (CRC) are key to reducing disparities. We conducted a study to examine a tailored messaging approach to navigate individuals from communities (i.e., lower income, less access to care, and underscreened) to clinics to receive CRC screening. We encountered several political, demographic, and secular trend issues that required reconsideration and redesign of implementation strategies.

Objectives

Through study implementation from 2012 to 2017, changes in medical reimbursement and immigration policies—at the state level and later at the national level—affected healthcare delivery systems that had initially committed to supporting the study and our recruitment methods. Although our selected zip codes and sites had previously yielded high rates of CRC screening nonadherence, within a few years, these sites showed substantially higher screening adherence rates—yielding limited numbers of eligible participants. In addition, state immigration policy trends created mistrust and fear, leading to lower participation rates than anticipated. This report documents and provides valuable insights on how we and the community network developed creative strategies to overcome these challenges.

Methods

New relationships with community partners were extended to tap advisory board input to meet the challenges. Criteria for clinic participation widened from originally selected Federally Qualified Health Centers (FQHCs) to various nonprofit, hybrid, and privately insured reimbursement types. Recruitment site options were creatively redefined to reach community participants where they live, work, and receive services.

Results

Strategies that engage community members in identifying alternative healthcare delivery structures and that link recruitment efforts to community-based service organizations were found to be critical to recapturing community trust in the face of unfavorable political environments. Widening the type of clinic partners from FQHCs to stand-alone nonprofits and private clinics and identifying unusual types of recruitment sites provided alternative solutions for successful study implementation.

Discussion

In prevention-based studies that face unplanned system and political barriers to recruitment, embedding the study in the community may aid in reestablishing trust levels to improve engagement and recruitment of clinic partners and eligible participants.
Scoring People With Spinal Muscular Atrophy on the Motor Function Measure Using the Microsoft Kinect
Authors: Vincent-Genod Dominique , Rippert Pascal , Coton Justine , Le Goff Laure , Barriere Aurélie , Berruyer Anne , Bernard Marjorie , Garde Camille , Gutierrez-Garcia Marta , Gilabert Stéphanie , Gomes-Lisboade-Souza Adriana , Daron Aurore , Servais Laurent , Thomann Guillaume , Vuillerot Carole
Published: October 2022

Purpose:

Assess the ability of the Kinect to capture movement and posture of people with spinal muscular atrophy (SMA) during completion of 14 items of the Motor Function Measure, a validated functional rating scale for people with neuromuscular diseases.

Methods:

Multicenter feasibility study in which Motor Function Measure items were scored as usual by the participant's therapist during the completion (Score-T) while another therapist scored items based only on the visualization of digital data collected using the Kinect (Score-D). Agreement and disagreement were investigated.

Results:

Twenty people with SMA type 2 or 3 were participants; 142 items were recorded and analyzed. There was 31.7% agreement between Score-T and Score-D for participants with SMA type 2, and 76.2% for those with SMA type 3.

Conclusions:

The results prevent us from considering the use of Kinect capture to deduce an automated scoring, but this device may be of interest to highlight potential compensations.
Distraction from pain depends on task demands and motivation
Authors: Vogel Todd A. , Falk Carl F. , Otto A. Ross , Roy Mathieu
Published: October 2022

Introduction:

Pain captures attention automatically, yet we can inhibit pain when we are motivated to perform other tasks. Previous studies show that engaging in a cognitively demanding task reduces pain compared with a task that is minimally demanding, yet the effects of motivation on this pain-reducing effect remain largely unexplored.

Objectives:

In this study, we hypothesized that motivating people to engage in a task with high demands would lead to more cognitive resources directed toward the task, thereby amplifying its pain-reducing effects.

Methods:

On different trials, participants performed an easy (left–right arrow discrimination) or demanding (2-back) cognitive task while receiving nonpainful or painful heat stimuli. In half of the trials, monetary rewards were offered to motivate participants to engage and perform well in the task.

Results:

Results showed an interaction between task demands and rewards, whereby offering rewards strengthened the pain-reducing effect of a distracting task when demands were high. This effect was reinforced by increased 2-back performance when rewards were offered, indicating that both task demands and motivation are necessary to inhibit pain.

Conclusions:

When task demands are low, motivation to engage in the task will have little impact on pain because performance cannot further increase. When motivation is low, participants will spend minimal effort to perform well in the task, thus hindering the pain-reducing effects of higher task demands. These findings suggest that the pain-reducing properties of distraction can be optimized by carefully calibrating the demands and motivational value of the task.
Spontaneous rhythm discrimination in a mammalian vocal learner
Authors: Verga Laura , Sroka Marlene G. U. , Varola Mila , Villanueva Stella , Ravignani Andrea
Published: October 2022

Rhythm and vocal production learning are building blocks of human music and speech. Vocal learning has been hypothesized as a prerequisite for rhythmic capacities. Yet, no mammalian vocal learner but humans have shown the capacity to flexibly and spontaneously discriminate rhythmic patterns. Here we tested untrained rhythm discrimination in a mammalian vocal learning species, the harbour seal (
Phoca vitulina
). Twenty wild-born seals were exposed to music-like playbacks of conspecific call sequences varying in basic rhythmic properties. These properties were called length, sequence regularity, and overall tempo. All three features significantly influenced seals' reaction (number of looks and their duration), demonstrating spontaneous rhythm discrimination in a vocal learning mammal. This finding supports the rhythm–vocal learning hypothesis and showcases pinnipeds as promising models for comparative research on rhythmic phylogenies.
Social buffering of the stress response: insights from fishes
Authors: Gilmour Kathleen M. , Bard Brittany
Published: October 2022

Social buffering of stress refers to the effect of a social partner in reducing the cortisol or corticosterone response to a stressor. It has been well studied in mammals, particularly those that form pair bonds. Recent studies on fishes suggest that social buffering of stress also occurs in solitary species, gregarious species that form loose aggregations and species with well-defined social structures and bonds. The diversity of social contexts in which stress buffering has been observed in fishes holds promise to shed light on the evolution of this phenomenon among vertebrates. Equally, the relative simplicity of the fish brain is advantageous for identifying the neural mechanisms responsible for social buffering. In particular, fishes have a relatively small and simple forebrain but the brain regions that are key to social buffering, including the social behaviour network, the amygdala and the hypothalamic–pituitary–adrenal/interrenal axis, are functionally conserved across vertebrates. Thus, we suggest that insight into the mechanistic and evolutionary underpinnings of stress buffering in vertebrates can be gained from the study of social buffering of stress in fishes.
Coupling computational vibrational models and experimental biotremology to develop a green pest control strategy against the greenhouse whiteflyTrialeurodes vaporariorum
Authors: Berardo Alice , Fattoruso Valeria , Mazzoni Valerio , Pugno Nicola M.
Published: October 2022

In applied biotremology, vibrational signals or cues are exploited to manipulate the target species behaviour. To develop an efficient pest control strategy, other than a detailed investigation into the pest biology and behaviour, the role of the substrate used to transmit the signal is an important feature to be considered, since it may affect vibrations spreading and effective signal transmission and perception. Therefore, we used a multi-disciplinary approach to develop a control technique against the greenhouse whitefly,Trialeurodes vaporariorum.First, anad hocvibrational disruptive noise has been developed, based on the acquired knowledge about the mating behaviour and vibrational communication of the mated species. Subsequently, we employed finite-element models to investigate a growing tomato plant response to the aforesaid noise. Modelling how vibrations spread along the plant allowed us to set up a greenhouse experiment to assess the efficacy in terms of insect population of the vibrational treatment, which was administrated through vibrational plates. The green methodology applied in this study represents an innovative, environmentally sound alternative to the usage of synthetic pesticides.
ATP-dependent polymerization dynamics of bacterial actin proteins involved in
Spiroplasma
swimming
Authors: Takahashi Daichi , Fujiwara Ikuko , Sasajima Yuya , Narita Akihiro , Imada Katsumi , Miyata Makoto
Published: October 2022

MreB is a bacterial protein belonging to the actin superfamily. This protein polymerizes into an antiparallel double-stranded filament that determines cell shape by maintaining cell wall synthesis.
Spiroplasma eriocheiris
, a helical wall-less bacterium, has five MreB homologous (SpeMreB1-5) that probably contribute to swimming motility. Here, we investigated the structure, ATPase activity and polymerization dynamics of SpeMreB3 and SpeMreB5. SpeMreB3 polymerized into a double-stranded filament with possible antiparallel polarity, while SpeMreB5 formed sheets which contained the antiparallel filament, upon nucleotide binding. SpeMreB3 showed slow P
i
release owing to the lack of an amino acid motif conserved in the catalytic centre of MreB family proteins. Our SpeMreB3 crystal structures and analyses of SpeMreB3 and SpeMreB5 variants showed that the amino acid motif probably plays a role in eliminating a nucleophilic water proton during ATP hydrolysis. Sedimentation assays suggest that SpeMreB3 has a lower polymerization activity than SpeMreB5, though their polymerization dynamics are qualitatively similar to those of other actin superfamily proteins, in which pre-ATP hydrolysis and post-P
i
release states are unfavourable for them to remain as filaments.
Lysosomal positioning diseases: beyond substrate storage
Authors: Scerra Gianluca , De Pasquale Valeria , Scarcella Melania , Caporaso Maria Gabriella , Pavone Luigi Michele , D'Agostino Massimo
Published: October 2022

Lysosomal storage diseases (LSDs) comprise a group of inherited monogenic disorders characterized by lysosomal dysfunctions due to undegraded substrate accumulation. They are caused by a deficiency in specific lysosomal hydrolases involved in cellular catabolism, or non-enzymatic proteins essential for normal lysosomal functions. In LSDs, the lack of degradation of the accumulated substrate and its lysosomal storage impairs lysosome functions resulting in the perturbation of cellular homeostasis and, in turn, the damage of multiple organ systems. A substantial number of studies on the pathogenesis of LSDs has highlighted how the accumulation of lysosomal substrates is only the first event of a cascade of processes including the accumulation of secondary metabolites and the impairment of cellular trafficking, cell signalling, autophagic flux, mitochondria functionality and calcium homeostasis, that significantly contribute to the onset and progression of these diseases. Emerging studies on lysosomal biology have described the fundamental roles of these organelles in a variety of physiological functions and pathological conditions beyond their canonical activity in cellular waste clearance. Here, we discuss recent advances in the knowledge of cellular and molecular mechanisms linking lysosomal positioning and trafficking to LSDs.
The voice of few, the opinions of many: evidence of social biases in Twitter COVID-19 fake news sharing
Authors: Castioni Piergiorgio , Andrighetto Giulia , Gallotti Riccardo , Polizzi Eugenia , De Domenico Manlio
Published: October 2022

Online platforms play a relevant role in the creation and diffusion of false or misleading news. Concerningly, the COVID-19 pandemic is shaping a communication network which reflects the emergence of collective attention towards a topic that rapidly gained universal interest. Here, we characterize the dynamics of this network on Twitter, analysing how unreliable content distributes among its users. We find that a minority of accounts is responsible for the majority of the misinformation circulating online, and identify two categories of users: a few active ones, playing the role of ‘creators’, and a majority playing the role of ‘consumers’. The relative proportion of these groups (approx. 14% creators—86% consumers) appears stable over time: consumers are mostly exposed to the opinions of a vocal minority of creators (which are the origin of 82% of fake content in our data), that could be mistakenly understood as representative of the majority of users. The corresponding pressure from a perceived majority is identified as a potential driver of the ongoing COVID-19 infodemic.
Modelling cosmic radiation events in the tree-ring radiocarbon record
Authors: Zhang Qingyuan , Sharma Utkarsh , Dennis Jordan A. , Scifo Andrea , Kuitems Margot , Büntgen Ulf , Owens Mathew J. , Dee Michael W. , Pope Benjamin J. S.
Published: October 2022

Annually resolved measurements of the radiocarbon content in tree-rings have revealed rare sharp rises in carbon-14 production. These ‘Miyake events’ are likely produced by rare increases in cosmic radiation from the Sun or other energetic astrophysical sources. The radiocarbon produced is not only circulated through the Earth’s atmosphere and oceans, but also absorbed by the biosphere and locked in the annual growth rings of trees. To interpret high-resolution tree-ring radiocarbon measurements therefore necessitates modelling the entire global carbon cycle. Here, we introduce ‘ticktack’ (https://github.com/SharmaLlama/ticktack/), the first open-source Python package that connects box models of the carbon cycle with modern Bayesian inference tools. We use this to analyse all public annual 14Ctree data, and infer posterior parameters for all six known Miyake events. They do not show a consistent relationship to the solar cycle, and several display extended durations that challenge either astrophysical or geophysical models.
The silkworm gustatory receptor BmGr63 is dedicated to the detection of isoquercetin in mulberry
Authors: Zhang Shaoyu , Tang Jiaqi , Li Yunfeng , Li Dong , Chen Guo , Chen Lin , Yang Zhen , He Ningjia
Published: October 2022

Gustatory systems in phytophagous insects are used to perceive feeding stimulants and deterrents, and are involved in insect decisions to feed on particular plants. During the process, gustatory receptors (Grs) can recognize diverse phytochemicals and provide a molecular basis for taste perception. The silkworm, as a representative Lepidoptera species, has developed a strong feeding preference for mulberry leaves. The mulberry-derived flavonoid glycoside, isoquercetin, is required to induce feeding behaviours. However, the corresponding Grs for isoquercetin and underlying molecular mechanisms remain unclear. In this study, we used molecular methods, voltage clamp recordings and feeding assays to identify silkworm BmGr63, which was tuned to isoquercetin. The use of qRT-PCR confirmed thatBmGr63was highly expressed in the mouthpart of fourth and fifth instar larvae. Functional analysis showed that oocytes expressingBmGr63from the ‘bitter’ clade responded to mulberry extracts. Among 20 test chemicals, BmGr63 specifically recognized isoquercetin. The preference for isoquercetin was not observed inBmGr63knock-down groups. The tuning between BmGr63 and isoquercetin has been demonstrated, which is meaningful to explain the silkworm-mulberry feeding mechanism from molecular levels and thus provides evidence for further feeding relationship studies between phytophagous insects and host plants.
Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae
Authors: Morinaga Kana , Kusada Hiroyuki , Sakamoto Sachiko , Murakami Takumi , Toyoda Atsushi , Mori Hiroshi , Meng Xian-Ying , Takashino Motoko , Murotomi Kazutoshi , Tamaki Hideyuki
Published: October 2022

Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18  :  1
cis 9 and C18  :  1
cis 9 dimethyl acetal, whereas those of TOC12T were C18  :  0 and C18  :  1
cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family

Atopobiaceae

, namely,

Olsenella phocaeensis

Marseille-P2936T (94.3 %) and

Olsenella umbonata

KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family

Atopobiaceae

. In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family

Atopobiaceae

, for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.
Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius
Authors: Sun Ya-Ping , Wang Bei-Bei , Zheng Xi-Wen , Wu Zhang-Ping , Hou Jing , Cui Heng-Lin
Published: October 2022

Three extremely halophilic archaeal strains (LT55T, SQT-29-1T and WLHS5T) were isolated from Gobi saline soil and a salt lake, China. These strains were most related to the genera

Natribaculum

and

Halovarius

(92.6–95.1 % similarities), and showed low similarities with other genera within the family

Natrialbaceae

based on 16S rRNA genes. Phylogenomic analysis confirmed that the three strains formed a distinct clade separated from the related genera

Halostagnicola

and

Natronococcus

, which indicated that they may represent a novel genus of the family

Natrialbaceae

. The average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and average amino acid identity (AAI) values among the three strains were no more than 87, 34 and 85 %, respectively, much lower than the threshold values for species demarcation. The major phospholipids of the three strains were phosphatidic acid (PA), phosphatidylglycerol (PG) and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid profiles of the three strains were diverse; sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD) were found in strains LT55T and WLHS5T, while mannosyl glucosyl diether (DGD-1) and S-DGD-1 in strain SQT-29-1T. The combination of phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strains WLHS5T (=CGMCC 1.13781T = JCM 33558T), SQT-29-1T (=CGMCC 1.16065T = JCM 33554T) and LT55T (=CGMCC 1.15188T = JCM 30838T) represent three novel species of a new genus within the family

Natrialbaceae

, for which the names, Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus gelatinilyticus sp. nov. and Halosolutus halophilus sp. nov., are proposed. Genome-based classification of genera

Natribaculum

and

Halovarius

revealed that

Halovarius luteus

should be transferred to the genus

Natribaculum

as Natribaculum luteum comb. nov. and

Natribaculum longum

as a heterotypic synonym of

Natribaculum breve

Liu et al. 2015.
Telomere-induced senescence increases aberrant intraneuronal amyloid-β accumulation by impairing autophagy in a mouse model of Alzheimer’s disease
Authors: Suelves Nuria , Saleki Shirine , Ibrahim Tasha , Palomares Debora , Vrancx Céline , Vadukul Devkee M , Papadopoulos Nicolas , Viceconte Nikenza , Claude Eloïse , Constantinescu Stefan N. , Decottignies Anabelle , Kienlen-Campard Pascal
Published: October 2022

Aging is a well-known risk factor for Alzheimer’s disease (AD) and other neurodegenerative pathologies, but the molecular and cellular changes occurring in the aging brain are poorly understood. AD pathology seems to correlate with the appearance of cells that become senescent due to the progressive accumulation of cellular insults causing DNA damage. In this study, we investigated the role of cellular senescence on AD pathology by crossing an amyloid-β (Aβ) mouse model of AD (5xFAD) with a mouse model of senescence that is genetically deficient for the RNA component of the telomerase (Terc-/-). Our results show that accelerated senescence reduces amyloid plaque formation and Aβ levels at an age when full-blown amyloid pathology is observed in 5xFAD mice. However, early and aberrant intraneuronal Aβ accumulation is observed in the subiculum and cortical layer V of senescent mice. Selective neurodegeneration linked to telomere attrition and early intraneuronal Aβ accumulation was observed in these particular regions. Finally, our results suggest that the effect of senescence on amyloid pathology might be mediated through an alteration in autophagy function. Altogether, these findings demonstrate the instrumental role of senescence in intraneuronal Aβ accumulation associated to AD pathophysiology, and further support future approaches targeting these processes for therapeutic intervention.
Hippocampal gamma oscillations form complex ensembles modulated by behavior and learning
Authors: Douchamps Vincent , di Volo Matteo , Torcini Alessandro , Battaglia Demian , Goutagny Romain
Published: October 2022

The hippocampus and the entorhinal cortex display a rich oscillatory activity, believed to support neural information processing in key cognitive functions1. In the hippocampal region CA1, a “slow gamma” rhythm (30-80 Hz) generated in CA3 would support memory retrieval whereas a “medium gamma” rhythm (60-120 Hz) generated in the entorhinal cortex would support memory encoding2,3. However, descriptions involving discrete gamma sub-bands can only partially account for the haphazard diversity of oscillatory behaviors observed in individual recordings during spatial navigation behavior. Here, we stress that transient gamma oscillatory episodes at any frequency or phase relative to the ongoing theta (4-12 Hz) rhythm can be recorded at any layer within CA1. Eventually, the commonly reported averages are dominated by a minority of very strong power events overshadowing gamma heterogeneity. Nevertheless, we show that such gamma diversity can be naturally explained by a simple mechanistic model, and that behavior-related information (position within a maze) can be decoded from most individual gamma events, despite their low power and erratic-like nature. Our results indicate that behavior specifically shapes ensembles of irregular hippocampal gamma oscillations, in a way which evolves with learning, depends on the hippocampal layer and is hard to reconcile with the hypothesis of rigid, narrowly tuned gamma sub-bands. Beyond randomness, the pervasive gamma diversity may thus reflect complexity at the “fringe-of-synchrony”4likely functional but invisible to classic average-based analyses.
Assessment of ethanol and nicotine interactions using a reinforcer demand modeling with grouped and individual levels of analyses in a long-access self-administration model using male rats
Authors: Robisona Christopher L. , Covab Nicole , Madoreb Victoria , Allenb Tyler , Barrettc Scott , Charntikov Sergios
Published: October 2022

Previous reports have indicated the reciprocal effects of nicotine and ethanol on their rewarding and reinforcing properties, but studies using methodological approaches resembling substance use in vulnerable populations are lacking. In our study, rats first self-administered ethanol, and their sensitivity to ethanol’s reinforcing effects was assessed using a reinforcer demand modeling approach. Subsequently, rats were equipped with intravenous catheters to self-administer nicotine, and their sensitivity to nicotine’s reinforcing effects was evaluated using the same approach. In the final phase, rats were allowed to self-administer ethanol and nicotine concurrently, investigating the influence of one substance on the rate of responding for the other substance. Group analyses revealed notable differences in demand among sucrose, sweetened ethanol, and ethanol-alone, with sucrose demonstrating the highest demand and ethanol-alone exhibiting greater sensitivity to changes in cost. At the individual level, our study finds significant correlations between rats’ demand for sucrose and sweetened ethanol, suggesting parallel efforts for both substances. Our individual data also suggest interconnections in the elasticity of demand for sweetened ethanol and ethanol-alone, as well as a potential relationship in price response patterns between ethanol and nicotine. Furthermore, concurrent self-administration of ethanol and nicotine at the group level displayed reciprocal effects, with reduced responding for nicotine in the presence of ethanol and increased responding for ethanol in the presence of nicotine. This study provides valuable insights into modeling the co-use of ethanol and nicotine and assessing their interaction effects using reinforcer demand modeling and concurrent self-administration or noncontingent administration tests. These findings contribute to our understanding of the complex interplay between ethanol and nicotine and have implications for elucidating the underlying mechanisms involved in polydrug use.
epitope1D: Accurate Taxonomy-Aware B-Cell Linear Epitope Prediction
Authors: da Silva Bruna Moreira , Ascher David B. , Pires Douglas E. V.
Published: October 2022

The ability to identify B-cell epitopes is an essential step in vaccine design, immunodiagnostic tests, and antibody production. Several computational approaches have been proposed to identify, from an antigen protein, which residues are likely to be part of an epitope, but have limited performance on relatively homogeneous data sets and lack interpretability, limiting biological insights that could be derived. To address these limitations, we have developed epitope1D, an explainable machine learning method capable of accurately identifying linear B-cell epitopes, leveraging two new descriptors: a graph-based signature representation of protein sequences, based on our well established CSM (Cutoff Scanning Matrix) algorithm and Organism Ontology information. Our model achieved Area Under the ROC curve of up to 0.935 on cross-validation and blind tests, demonstrating robust performance and outperforming state-of-the-art tools. epitope1D has been made available as a user-friendly web server interface and API athttp://biosig.lab.uq.edu.au/epitope1d.
Masked Minimizers: Unifying sequence sketching methods
Authors: Hoang Minh , Marçais Guillaume , Kingsford Carl
Published: October 2022

Minimizers and syncmers are sequence sketching methods that extract representative substrings from a long sequence. We show that both these sampling rules are different instantiations of a new unifying concept we call masked minimizers, which applies a sub-sampling binary mask on a minimizer sketch. This unification leads to the first formal procedure to meaningfully compare minimizers, syncmers and other comparable masked minimizers. We further demonstrate that existing sequence sketching metrics, such as density (which measures the sketch sparseness) and conservation (which measures the likelihood of the sketch being preserved under random mutations), should not be independently measured when evaluating masked minimizers. We propose a new metric that reflects the trade-off between these quantities called the generalized sketch score, or GSS. Finally, we introduce a sequence-specific and gradient-based learning objective that efficiently optimizes masked minimizer schemes with respect to the proposed GSS metric. We show that our method finds sketches with better overall density and conservation compared to existing expected and sequence-specific approaches, enabling more efficient and robust genomic analyses in the many settings where minimizers and syncmers are used.
Expected Distractor Context Biases the Attentional Template for Target Shapes
Authors: Lerebourg Maëlle , Lange Floris P. de , Peelen Marius V.
Published: October 2022

Visual search is supported by an internal representation of the target, the attentional template. However, which features are diagnostic of target presence critically depends on the distractors. Accordingly, previous research showed that consistent distractor context shapes the attentional template for simple targets, with the template emphasizing diagnostic dimensions (e.g., colour or orientation) in blocks of trials. Here, we investigated how distractor expectations bias attentional templates for complex shapes, and tested whether such biases reflect inter-trial priming or can be instantiated flexibly. Participants searched for novel shapes (cued by name) in two probabilistic distractor contexts: either the target’s orientation or rectilinearity was unique (80% validity). Across four experiments, performance was better when the distractor context was expected, indicating that target features in the expected diagnostic dimension were emphasized. Attentional templates were biased by distractor expectations when distractor context was blocked, also for participants reporting no awareness of the manipulation. Interestingly, attentional templates were also biased when distractor context was cued on a trial-by-trial basis, but only when the two contexts were consistently presented at distinct spatial locations. These results show that attentional templates can flexibly and adaptively incorporate expectations about target-distractor relations when looking for the same object in different contexts.

Public significance statement

When searching for an object (e.g., a green ball), the visual features that distinguish it from distractor objects depend on the features of these distractors (e.g., when searching among plants, its green colour is not useful to find the target). Here, we asked participants to search for novel shapes in contexts where different dimensions of the shapes were unique. We show that people learn which features are diagnostic in these distractor contexts and flexibly use expectations about the features that are diagnostic of the target to efficiently guide search.
Menopause, Brain Anatomy, Cognition and Alzheimer’s Disease
Authors: Costantino Manuela , Pigeau Grace , Parent Olivier , Ziolkowski Justine , Devenyi Gabriel A. , Gervais Nicole J. , Mallar Chakravarty M.
Published: October 2022

The menopause transition has been repeatedly associated with decreased cognitive performance and increased incidence of Alzheimer’s Disease (AD), particularly when it is induced surgically1,2or takes place at a younger age3,4. However, there are very few studies that use neuroimaging techniques to examine the effects of these variables in aggregate and in a large sample. Here, we use data from thousands of participants from the UK Biobank to assess the relationship between menopausal status, menopause type (surgical or natural), and age at menopause with cognition, AD, and neuroanatomical measures derived from magnetic resonance imaging. We find that for brain and cognitive measures, menopausal status, menopause type and age at surgical menopause do not impact the brain; but that there is a positive correlation between anatomy, cognition and age at non-surgical menopause. These results do not align with previous reports in the literature with smaller samples. However, we confirm that both early and surgical menopause are associated with a higher risk of developing AD, indicating that early and abrupt ovarian hormone deprivation might contribute to the development of the disorder.
Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
Authors: Zheng Andrew , Shaw Jim , Yu Yun William
Published: October 2022

Background

Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level has remained a challenging computational problem.

Results

We introduce Mora, a MetagenOmic read Re-Assignment algorithm capable of assigning short and long metagenomic reads with high precision, even at the strain level. Mora is able to accurately re-assign reads by first estimating abundances through an expectation-maximization algorithm and then utilizing abundance information to re-assign query reads. The key idea behind Mora is to maximize read re-assignment qualitieswhile simultaneouslyminimizing the difference from estimated abundance levels, allowing Mora to avoid over assigning reads to the same genomes. On simulated diverse reads, this allows Mora to achieve F1 scores comparable to other algorithms while having less runtime. However, Mora significantly outshines other algorithms on very similar reads. We show that the high penalty of over assigning reads to a common reference genome allows Mora to accurately infer correct strains for real data in the form of short E. coli reads and long Covid-19 reads.

Conclusions

Mora is a fast and accurate read re-assignment algorithm that is modularized, allowing it to be incorporated into general metagenomics and genomics workflows. It is freely available athttps://github.com/AfZheng126/MORA.
NEMETEX: a Python software for the visualisation of the network of metabolic exchanges
Authors: Palamin Michela , Frisinghelli Alice , Offer Elisabetta , Zampieri Guido , Basile Arianna , Campanaro Stefano
Published: October 2022

Motivation

Microorganisms have a pivotal role in ecology and human health and form complex networks where different species can interact and exchange a range of different compounds. Flux balance analysis can offer an insight into the production and the absorption of these metabolic compounds, but frequently results are difficult to visualise and interpret. Additionally, a clear understanding of the roles of microbial species in the community requires the integration of different information sources, including relative abundance, taxonomy and compounds exchange rate.

Results

To fill-in this gap the command-line tool NEMETEX (NEtwork for METabolic Exchanges) was developed to provide a graphical representation of the metabolites exchanged, joined with interactive visualisation of numerical data. This approach can undoubtedly represent an easy way to investigate high-throughput results obtained from metagenomics and flux balance analysis, providing a more direct interpretation of the data.

Availability and implementation

This program, accessory utilities, and their documentation are freely available athttps://github.com/palakela/NEMETEX
Neural Representation of The Self
Authors: Levorsen Marie , Aoki Ryuta , Matsumoto Kenji , Sedikides Constantine , Izuma Keise
Published: October 2022

Knowledge about one’s personality, the self-concept, shapes human experience. Social cognitive neuroscience has made strides addressing the question of where and how the self is represented in the brain. The answer, however, remains elusive. We conducted two functional magnetic resonance imaging experiments (with the second being preregistered) employing a self-reference task with a broad range of attributes and carrying out a searchlight representational similarity analysis. The importance of attributes to self-identity was represented in the medial prefrontal cortex (mPFC), whereas mPFC activation was unrelated both to self-descriptiveness of attributes (Experiments 1-2) and importance of attributes to a friend’s self-identity (Experiment 2). Our research provides a comprehensive answer to the abovementioned question: The self-concept is conceptualized in terms of self-importance and represented in the mPFC.
Novel Master Regulators of Microglial Phagocytosis and Repurposed FDA-approved Drug for Treatment of Alzheimer Disease
Authors: Zhu Kuixi , He Qianying , Tsai Sheng-Feng , Mudalige Dinusha Maheepala , Henrion Marc Y.R. , Zaidi Syed S.A. , Branden Lau , Tang Andrew , Cadiz Mika P. , Hodos-Nkhereanye Rachel , Moein Sara , Alamprese Melissa L. , Bennett David A. , De Jager Philip L. , Frye John D. , Ertekin-Taner Nilu□fer , Kuo Yu-Min , Ronaldson Patrick T. , Chang Rui
Published: October 2022

Microglia, the innate immune cells of the brain, are essential determinants of late-onset Alzheimer’s Disease (LOAD) neuropathology. Here, we developed an integrative computational systems biology approach to construct causal network models of genetic regulatory programs for microglia in Alzheimer’s Disease (AD). This model enabled us to identify novel key driver (KDs) genes for microglial functions that can be targeted for AD pharmacotherapy. We prioritizedFCER1G, HCK, LAPTM5, ITGB2, SLC1A2, PAPLN, GSAP, NTRK2, andCIRBPas KDs of microglial phagocytosis promoting neuroprotection and/or neural repair.In vitro, shRNA knockdown of each KD significantly reduced microglial phagocytosis. We repurposed riluzole, an FDA-approved ALS drug that upregulatesSLC1A2activity, and discovered that it stimulated phagocytosis of Aβ1-42 in human primary microglia and decreased hippocampal amyloid plaque burden/phosphorylated tau levels in the brain of aged 3xTg-AD mice. Taken together, these data emphasize the utlility of our integrative approach for repurposing drugs for AD therapy.
Deletion of carboxypeptidase E in beta cells disrupts proinsulin processing and alters beta cell identity in mice
Authors: Chen Yi-Chun , Taylor Austin J. , Fulcher James M. , Swensen Adam C. , Dai Xiao-Qing , Komba Mitsuhiro , Wrightson Kenzie L.C. , Fok Kenny , Patterson Annette E. , Klein-Geltink Ramon I. , MacDonald Patrick E. , Qian Wei-Jun , Verchere C. Bruce
Published: October 2022

Carboxypeptidase E (CPE) facilitates the conversion of prohormones into mature hormones and is highly expressed in multiple neuroendocrine tissues. Carriers ofCPEmutations have elevated plasma proinsulin and develop severe obesity and hyperglycemia. We aimed to determine whether loss ofCpein pancreatic beta cells disrupts proinsulin processing and accelerates development of diabetes and obesity in mice. Pancreatic beta cell-specific Cpe knockout mice (βCpeKO;Cpefl/flxIns1Cre/+) lack mature insulin granules and have elevated proinsulin in plasma; however, glucose-and KCl-stimulated insulin secretion in βCpeKO islets remained intact. High fat diet-fed βCpeKO mice showed comparable weight gain and glucose tolerance compared toWtlittermates. Notably, beta-cell area was increased in chow-fed βCpeKO mice and beta-cell replication was elevated in βCpeKO islets. Transcriptomic analysis of βCpeKO beta cells revealed elevated glycolysis andHif1α-target gene expression. Upon high glucose challenge, beta cells from βCpeKO mice showed reduced mitochondrial membrane potential, increased reactive oxygen species, reducedMafA, and elevatedAldh1a3transcript levels. Following multiple low-dose streptozotocin treatment, βCpeKO mice had accelerated hyperglycemia with reduced beta-cell insulin and Glut2 expression. These findings suggest thatCpeand proper proinsulin processing are critical in maintaining beta cell function during the development of diabetes.
Specific and non-uniform brain states during cold perception in mice
Authors: Koorliyil Haritha , Sitt Jacobo , Rivals Isabelle , Liu Yushan , Cazzanelli Silvia , Bertolo Adrien , Dizeux Alexandre , Deffieux Thomas , Tanter Mickael , Pezet Sophie
Published: October 2022

The quest to decode the complex supraspinal mechanisms that integrate cutaneous thermal information in the central system is still ongoing. The dorsal horn of the spinal cord is the first hub that encodes thermal input which is then transmitted to brain regions via the spinothalamic and thalamo-cortical pathways. So far, our knowledge about the strength of the interplay between the brain regions during thermal processing is limited. To address this question, we imaged the brains of awake and freely-moving mice using Functional Ultrasound imaging during plantar exposure to constant and varying temperatures. Our study, a synchronous large field investigation of mice brains reveals for the first time the brain states and the specific dynamic interplay between key regions involved in thermal processing. Our study reveals: i) a dichotomy in the response of the somato-motor-cingulate cortices and the hypothalamus, which was never described before, due to the lack of appropriate tools to study such regions with both good spatial and temporal resolutions. ii) We infer that cingulate areas may be involved in the affective responses to temperature changes. iii) Colder temperatures (ramped down) reinforces the disconnection between the somato-motor-cingulate and hypothalamus networks. iv) Finally, we also confirm the existence in the mouse brain of a dynamic brain mode characterized by low cognitive strength, described previously only in non-human primates and humans. The present study points towards the existence of a common hub between somato-motor and cingulate regions, whereas hypothalamus functions are related to a secondary network.