bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium Species on the Cutaneous Microbiome of Very Preterm Neonates
Authors: Shah Pritik A , Govindarajan Varun , Rangaiah Ambica , Diggikar Shivashankar , Devadas Sahana , Chunchanur Sneha K , Shankar Sathyanarayan Muthur , Das Subhadeep , Kariyappa Mallesh 
Published: February 2022

Abstract
The neonatal skin microbiome consists of all the genomes and genetic products of microorganisms harboring on an infant’s skin. Host and the microbiota develop a harmonious environment resulting in symbiosis. Any disruption of this environment could lead to pathological disease. This study was conducted to understand the neonatal skin microbiome of very preterm neonates (under 32 weeks) admitted to the Neonatal Intensive Care Unit(NICU) at a tertiary healthcare setting before and after kangaroo mother care (KMC), using next-generation sequencing (NGS). Skin swabs were collected on two different occasions and analyzed using the NGS technique after amplification via polymerase chain reaction. The results showed relative abundance for Mycobacterium tuberculosis in 83.33% and 66.67% (p = 0.29) and Mycobacteroides abscessus in 100% and 93.33% (p = 0.30) of the very preterm neonates on the skin microbiome before and after KMC, respectively as an incidental finding. The mere presence of these bacilli as commensals or as potential pathogens is alarming due to the risk of early exposure and incidence of tuberculosis from birth. These findings, in our view, are the first findings to be established in such a setting.
A Person-Centered Approach Understanding Stroke Survivor and Family Caregiver Emotional Health
Authors: Varughese Tina , Casameni Montiel Tahani , Engebretson Joan , Savitz Sean I. , Sharrief Anjail , Beauchamp Jennifer E. S. 
Published: February 2022

ABSTRACT

BACKGROUND: The purpose of this study was to incorporate a person-centered approach to understand the emotional health needs and perspectives of stroke survivors (SSs) and their caregivers. METHODS: In collaboration with 4 SSs and caregivers as research partners, quantitative data were collected to assess poststroke emotional health needs, and qualitative data were collected to gain insight into SS and caregiver emotional health perspectives after stroke. RESULTS: Forty surveys (n = 26 SSs, n = 14 caregivers) were collected. The predominate emotional health needs were frustration (65%), anxiety (54%), and stress (50%) for SSs and stress (71%), worry (57%), and frustration (57%) for caregivers. Two group interviews (n = 7 SSs, n = 3 caregivers) were completed. Four emerging themes were identified: receiving support from those in similar situations, poststroke emotional responses, situations experienced in healthcare settings, and a hypervigilance for sudden and unexpected events. CONCLUSION: Emotional healthcare services for SSs and their caregivers may consider providing reoccurring mental health education and multifaceted treatment approaches, including provision of peer support, and addressing the unique emotional stressors SSs and caregivers may be experiencing. The small sample size precludes generalizing the results into the broader stroke population. However, by leveraging the lived experience of SSs and their caregivers, the results may help find ways to support SSs' and caregivers' emotional health.
The Burden of Vaccine-preventable Diseases in Patients With Inflammatory Bowel Disease
Authors: Kröner Paul T. , Picco Michael F. , Cangemi John R. , Hayney Mary S. , Farraye Francis A. , Caldera Freddy 
Published: February 2022

Background:
Patients with inflammatory bowel disease (IBD) are at an increased risk of infections, including vaccine-preventable diseases (VPDs). The aim of this study was to explore the inpatient prevalence of VPD in patients with IBD, as well as inpatient outcomes.

Methods:
Retrospective study using the 2013-2017 Nationwide Inpatient Sample databases. All patients 18 years of age or older with International Classification of Diseases, Ninth and 10th Revisions, Clinical Modification (ICD-9/10 CM) codes for IBD were included, as well as patients with VPDs as a principal diagnostic code. The primary outcome was the occurrence and odds of VPD in patients with IBD compared with patients with no IBD. Secondary outcomes were inpatient mortality, morbidity, and economic burden compared with patients with IBD and non–vaccine-preventable infections (VPIs). Multivariate regression yielded adjusted odds ratios.

Results:
Of 1,622,245 (0.9%) patients with a diagnosis of IBD, 3560 (0.2%) had associated VPDs, while 131,150 patients had non-VPI (8.1%). The most common VPDs were influenza, herpes zoster (HZ), pneumococcal pneumonia, and varicella. Only HZ and varicella had increased odds of occurrence in patients with IBD of all ages. Patients with IBD 65 years of age or older had increased odds of VPD compared with patients under 65 years. Patients with IBD and associated VPD had higher odds of intensive care unit stay, systemic inflammatory response syndrome, and multiorgan failure compared with patients with IBD and non-VPI.

Conclusions:
VPDs represent a clinically relevant cause of infectious disease-related hospital admissions in patients with IBD. Patients with IBD are at increased risk for hospitalization due to HZ and varicella. Those hospitalized for VPD have higher morbidity compared with patients with IBD and non-VPI. These findings echo the importance of instituting optimal immunization schedules in patients with IBD, particularly in patients 65 years or older.
Effect of antiretroviral therapy care interruptions on mortality in children living with HIV
Authors: Davies Claire , Johnson Leigh , Sawry Shobna , Chimbetete Cleophas , Eley Brian , Vinikoor Michael , Technau Karl-Günter , Ehmer Jochen , Rabie Helena , Phiri Sam , Tanser Frank , Malisita Kennedy , Fatti Geoffrey , Osler Meg , Wood Robin , Newton Sam , Haas Andreas , Davies Mary-Ann 
Published: February 2022

Objective:
To evaluate the characteristics and outcomes of HIV-infected children that have care interruptions, during which the child's health status and use of medication is unknown.

Design:
We included data on children initiating ART between 2004 and 2016 at less than 16 years old at 16 International Epidemiologic Databases to Evaluate AIDS Southern Africa cohorts. Children were classified as loss to follow up (LTFU) if they had not attended clinic for more than 180 days. Children had a care interruption if they were classified as LTFU, and subsequently returned to care. Children who died within 180 days of ART start were excluded.

Methods:
The main outcome was all cause mortality. Two exposed groups were considered: those with a first care interruption within the first 6 months on ART, and those with a first care interruption after 6 months on ART. Adjusted hazard ratios were determined using a Cox regression model.

Results:
Among 53 674 children included, 23 437 (44%) had a care interruption, of which 10 629 (20%) had a first care interruption within 6 months on ART and 12 808 (24%) had a first care interruption after 6 months on ART. Increased mortality was associated with a care interruption within 6 months on ART [adjusted hazard ratio (AHR) = 1.52, 95% CI 1.12–2.04] but not with a care interruption after 6 months on ART (AHR = 1.05, 95% CI 0.77–1.44).

Conclusion:
The findings suggest that strengthening retention of children in care in the early period after ART initiation is critical to improving paediatric ART outcomes.
Posttreatment monitoring by ASCL1/LHX8 methylation analysis in women with HIV treated for cervical intraepithelial neoplasia grade 2/3
Authors: Vink Frederique J. , Steenbergen Renske D.M. , Kremer Wieke W. , Lissenberg-Witte Birgit I. , Heideman Daniëlle A.M. , Bleeker Maaike C.G. , van Zummeren Marjolein , Breytenbach Erika , Visser Cathy , Lukhwareni Azwidowi , Meijer Chris J.L.M. , Dreyer Greta 
Published: February 2022

Objective:
Women with HIV (WWH) have an increased risk to develop recurrent cervical intraepithelial neoplasia grade 2/3 (rCIN2/3) after treatment compared with HIV-negative women. Therefore, appropriate posttreatment monitoring of WWH is important. This study evaluates the performance of ASCL1 and LHX8 methylation analysis as posttreatment monitoring test in WWH treated for CIN2/3, as alternative to cytology or human papillomavirus (HPV) as follow-up test.

Design:
Prospective observational cohort study.

Methods:
WWH treated for CIN2/3 by large loop excision of the transformation zone (LLETZ) (n
= 61) were invited for follow-up study visits at 1, 2.5 and 4 years after baseline. Baseline and follow-up cervical scrapes were tested for cytology, HPV and DNA methylation of ASCL1 and LHX8 genes. The performance of these strategies for the detection of rCIN2/3 was evaluated in the first follow-up cervical scrape.

Results:
Thirteen (21.3%) rCIN2/3 lesions were detected within 4 years of follow-up. In women without rCIN2/3 in follow-up, methylation levels of ASCL1 and LHX8 decreased significantly after LLETZ treatment (P
= 0.02 and 0.007, respectively). In women with rCIN2/3, methylation levels remained high after LLETZ treatment. The 4-year rCIN2/3 risk was 4.9% (95% CI: 0.6–16.5) for ASCL1/LHX8-negative women, 8.1% (95% CI: 1.7–21.9) for HPV-negative women and 7.7% (95% CI: 2.1–18.5) for cytology-negative women.

Conclusion:
A negative ASCL1/LHX8 methylation test in follow-up is associated with a low rCIN2/3 risk and could serve as an objective test of cure and well tolerated alternative for HPV and/or cytology screening in the posttreatment monitoring of WWH.
Rescue therapies in epilepsy
Authors: Sharma Sonali , Detyniecki Kamil 
Published: February 2022

Purpose of review
The purpose of this review is to provide a succinct evaluation of the current rescue medications and action plans available to our patients with seizure clusters in the outpatient setting.

Recent findings
The main themes of the recent findings are that rescue medications and seizure action plans (SAPs) are underutilized, particularly in the adult population. The safety and efficacy of intranasal midazolam and intranasal diazepam is comparable with rectal diazepam for the treatment of seizure clusters. Additionally, this intranasal formulation has the benefit of a more socially acceptable route of administration and ease of use.

Summary
The implication of these findings is a greater variety and awareness in the rescue medications available to our patients suffering from seizure clusters.
An attempt of using public ambient temperature data in swine genetic evaluation for litter size traits at birth in Japan
Authors: Hara Hitomi , Ogawa Shinichiro , Ohnishi Chika , Ishii Kazuo , Uemoto Yoshinobu , Satoh Masahiro 
Published: February 2022

ABSTRACTTo obtain the fundamental information on using ambient temperature information in developing the model for routine swine genetic evaluation in Japan, we analyzed total number born (TNB), number born alive (NBA), and number stillborn (NSB) collected at a Japanese farm, together with off-farm ambient temperature measured at a nearest Automated Meteorological Data Acquisition System station. Five repeatability animal models were exploited, considering the effects of farrowing season (model 1), farrowing month (model 2), quadratic regressions of daily maximum ambient temperature of farrowing day (model 3), season and temperature (model 4), or month and temperature (model 5). Patterns of the effects of daily maximum temperature of farrowing day estimated using model 3 was similar to those of farrowing season by model 1 and those of farrowing month by model 2. Adding the effect of daily maximum temperature of farrowing day (models 4 and 5) could explain phenotypic variability greater than only considering either of farrowing season and month (models 1 and 2). Estimated heritability was stable among the models and the rank correlation of predicted breeding values between models was >0.98 for all traits. The results indicate the possibility that using public ambient temperature can capture a large part of the phenotypic variability in litter size traits at birth caused by the seasonality in Japan and do not harm, at least, the performance of genetic evaluation. This study could support the availability of public meteorological data in flexible developing operational models for future swine genetic evaluation in Japan.
Historical contingency drives compensatory evolution and rare reversal of phage resistance
Authors: Debray Reena , De Luna Nina , Koskella Britt 
Published: February 2022

ABSTRACTBacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, while others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each mutant lineage in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, while others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with resistance mutations in the same gene acquired more parallel sets of mutations than populations with resistance mutations in different genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria-phage coevolution, and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.
Conserved basal lamina proteins, laminin and nidogen, are repurposed to organize mechanosensory complexes responsible for touch sensation
Authors: Das Alakananda , Franco Joy A. , Mulcahy Ben , Wang Lingxin , Chapman Dail , Jaisinghani Chandni , Pruitt Beth L. , Zhen Mei , Goodman Miriam B. 
Published: February 2022

SummaryThe sense of touch is conferred by the conjoint function of somatosensory neurons and skin cells. These cells meet across a gap filled by a basal lamina, an ancient structure found in metazoans. UsingCaenorhabditis elegans, we show that membrane-matrix complexes containing laminin, nidogen, and the MEC-4 mechano-electrical transduction channel reside at this interface and are instrumental for proper touch sensation. These complexes fail to coalesce in touch-insensitive extracellular matrix mutants and in dissociated neurons. MEC-4, but not laminin or nidogen, is destabilized by point mutations in the C-terminal Kunitz domain of the extracellular matrix component, MEC-1. Thus, neuron-epithelial cell interfaces are instrumental in mechanosensory complex assembly and function. Loss of nidogen reduces the density of mechanoreceptor complexes and the amplitude of the touch-evoked currents they carry. These findings imply that somatosensory neurons secrete proteins that actively repurpose the basal lamina to generate special-purpose mechanosensory complexes responsible for vibrotactile sensing.
Polymorphic ribonucleoprotein folding as a basis for translational regulation
Authors: Dendooven Tom , Sonnleitner Elisabeth , Bläsi Udo , Luisi Ben F. 
Published: February 2022

AbstractThe widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes inPseudomonas aeruginosa. How this broadly acting protein can contribute to the regulation requirements of so many different genes remains puzzling. Here, we describe the structures of higher-order assemblies formed on control regions of differentP. aeruginosatarget mRNAs by Hfq and its partner protein Crc. Our results show that these assemblies have mRNA-specific quaternary architectures resulting from the combination of multivalent protein-protein interfaces and recognition of patterns in the RNA sequence. The structural polymorphism of the ribonucleoprotein assemblies enables selective translational repression of many different target mRNAs. This system suggests how highly complex regulatory pathways can evolve and be rewired with a simple economy of proteinogenic components.Graphical AbstractThe RNA chaperone Hfq, in conjunction with the co-repressor Crc, forms higher order assemblies on nascent mRNAs. These complexes impact on translation of hundreds of transcripts in the pathogenPseudomonas aeruginosa. Assemblies with different quaternary structures result from the interactions of the proteins with sequence motifs and structural elements in different mRNA targets, as well as from a repertoire of protein-to-protein interfaces. In this way, the combination of RNA sequence and two proteins can generate the diversity required to regulate many genes. It is proposed that the multi-step assembly process is highly cooperative and most likely competes kinetically with translation initiation to silence the targeted transcripts.
Fitness costs of pfhrp2 and pfhrp3 deletions underlying diagnostic evasion in malaria parasites
Authors: Nair Shalini , Li Xue , Nkhoma Standwell C. , Anderson Tim 
Published: February 2022

BackgroundRapid diagnostic tests based on detection of histidine rich proteins (HRP) are widely used for malaria diagnosis, but parasites carrying pfhrp deletions can evade detection and are increasing in frequency in some countries. Models aim to predict conditions under which pfhrp2 and/or pfhrp3 deletions will increase, but a key parameter – the fitness cost of deletions – is unknownMethodsWe removed pfhrp2 and/or pfhrp3 from a Malawian parasite clone using CRISPR/Cas9 and measured fitness costs by conducting pairwise competition experiments.ResultsWe observed significant fitness costs of 0.087 ± 0.008 (1 s.e.) per asexual cycle for pfhrp2 deletion and 0.113 ± 0.008 (1 s.e.) for the pfhrp2/3 double deletion, relative to the unedited progenitor parasite. The results demonstrate ∼10% reduced survival of parasites bearing deletions of these loci.ConclusionsPrior modelling suggested that diagnostic selection may drive increased frequency of pfhrp2 and pfhrp3 deletions when fitness costs are ≤10%. Our laboratory competition experiments are consistent with costs of pfhrp2/3 deletions lying at this critical tipping point. These results may inform future modelling efforts and help us to understand why pfhrp2/3 deletions are increasing in some locations (Ethiopia/Eritrea) but not in others (Mekong region).
Molecular Characterization in 3D Structure of MicroRNA Expressed in Leprosy
Authors: de Oliveira Andrade Luís Jesuino , Barreto de Jesus Humberto , Matos de Oliveira Luís , Farias de Oliveira Moema , Caricchio Santana Laura Farias , Matos de Oliveira Gabriela Correia 
Published: February 2022

ABSTRACTIntroductionHansen’s disease, or leprosy, is a major public health problem in developing countries, caused by Mycobacterium leprae, and affecting the skin and peripheral nerves. However, M. leprae can also affect bone tissue, mucous membranes, liver, eyes, and testicles, producing a variety of clinical phenotypes. MicroRNAs (miRNAs) have been expressed in the various clinical forms of leprosy and could potentially be used for its diagnosis.ObjectiveIn silico design of the molecular structure of miRNAs expressed in leprosy.MethodWe performed a nucleotide sequence search of 17 miRNAs expressed in leprosy, designing in silico the molecular structure of the following miRNAs: miRNA-26a, miRNA-27a, miRNA-27b, miRNA-29c, miRNA-34c, miRNA-92a-1, miRNA-99a-2, miRNA-101-1, miRNA-101-2, miRNA-125b-1, miRNA-196b, miRNA-425-5p, miRNA-452, miRNA-455, miRNA-502, miRNA-539, and miRNA-660. We extracted the nucleotides were from the GenBank of National Center for Biotechnology Information genetic sequence database. We aligned the extracted sequences with the RNA Folding Form, and the three-dimensional molecular structure design was performed with the RNAComposer.ResultsWe demonstrate the nucleotide sequences, and molecular structure projection of miRNAs expressed in leprosy, and produces a tutorial on the molecular model of the 17 miRNAs expressed in leprosy through in silico projection processing of their molecular structures.ConclusionWe demonstrate in silico design of selected molecular structures of 17 miRNAs expressed in leprosy through computational biology.
Ventral motor thalamic input to prelimbic cortex mediates cost-benefit decision-making in rats
Authors: Sieveritz Bianca , Duke Shannon Hayashi , Wickens Jeffery R. , Arbuthnott Gordon W. 
Published: February 2022

AbstractCorticostriatal neurons in prelimbic cortex contribute to decisions that require a trade-off between cost and benefit. The ventral motor thalamus sends dense projections to many cortical areas, including the prelimbic cortex. We investigated whether this input from the ventral motor thalamus to prelimbic cortex contributes to cost-benefit decision-making. Optogenetic inhibition of ventral motor thalamic axon terminals in prelimbic cortex biased rats towards a high cost-high benefit option and, in anesthetized rats, decreased neuronal activity in deep layers of prelimbic cortex. Stimulation of ventral motor thalamic nuclei induced a neuronal response in deep layers of prelimbic cortex and simultaneous optogenetic inhibition of layer 1 inhibitory interneurons similarly decreased neuronal activity. Our results indicate that ventral motor thalamic input to prelimbic cortex mediates cost-benefit decision-making.Significance StatementOur results indicate that ventral motor thalamic input to prelimbic cortex plays a critical role in decisions that require a trade-off between two conflicting reward values. Traditionally, ventral motor thalamic nuclei were primarily associated with motor control, but more recently these thalamic nuclei have been implicated in tasks that require animals to choose between two alternatives. Our results highlight the need to reevaluate the role of the ventral motor thalamic nuclei in cognition. Furthermore, prelimbic cortex and, more generally, prefrontal cortex have been associated with chronic stress and major depressive disorder, highlighting the possibility that ventral motor thalamic nuclei might be involved in these disorders.
Functional MRI reveals memories of mother in newborn chicks
Authors: Behroozi Mehdi , Lorenzi Elena , Tabrik Sepideh , Tegenthoff Martin , Gozzi Alessandro , Güntürkün Onur , Vallortigara Giorgio 
Published: February 2022

AbstractFilial imprinting has been used as a powerful ethological paradigm to investigate the neurobiology of early learning that affects lifelong behaviours. When a visually naïve chick is exposed to one of a wide range of conspicuous objects, it may learn its characteristics and subsequently recognises and selectively approaches this stimulus (usually the mother hen and siblings). While the initial phases of memory acquisition have been unravelled, the long-term storage and retrieval components of imprinting memories are still unknown. Here, we used functional MRI in awake newly hatched chicks to identify the long-term storage of imprinting memories in a wide network comprising the hippocampal formation, the medial striatum, the arcopallium, and the prefrontal-like nidopallium caudolaterale. These results provide the first example of non-invasive imaging of the brain in a newborn vertebrate.