Rhizobacterial community and growth-promotion trait characteristics of Zea mays L. inoculated with Pseudomonas fluorescens UM270 in three different soils.

There is an increasing demand for bioinoculants based on plant growth-promoting rhizobacteria (PGPR) for use in agricultural ecosystems. However, there are still concerns and limited data on their reproducibility in different soil types and their effects on endemic rhizosphere communities. Therefore, this study explored the effects of inoculating the PGPR, Pseudomonas fluorescens strain UM270, on maize growth (Zea mays L.) and its associated rhizosphere bacteriome by sequencing the 16S ribosomal genes under greenhouse conditions. The results showed that inoculation with PGPR P. fluorescens UM270 improved shoot and root dry weights, chlorophyll concentration, and total biomass in the three soil types evaluated (clay, sandy-loam, and loam) compared to those of the controls. Bacterial community analysis of the three soil types revealed that maize plants inoculated with the UM270 strain showed a significant increase in Proteobacteria and Acidobacteria populations, whereas Actinobacteria and Bacteroidetes decreased. Shannon, Pielou, and Faith alpha-biodiversity indices did not reveal significant differences between treatments. Beta diversity revealed a bacterial community differential structure in each soil type, with some variation among treatments. Finally, some bacterial groups were found to co-occur and co-exclude with respect to UM270 inoculation. Considered together, these results show that PGPR P. fluorescens UM270 increases maize plant growth and has an important effect on the resident rhizobacterial communities of each soil type, making it a potential agricultural biofertilizer.

High-precision frequency-controlled optical phase shifter with acousto-optic devices.

A fundamental parameter to determine how electromagnetic waves interfere is their relative phase, and achieving a fine control over it enables a wide range of interferometric applications. Existing phase control methods rely on modifying the optical path length either by changing the path followed by the light or by altering the thickness or index of refraction of an optical element in the setup. In this Letter, we present a novel, to the best of our knowledge, method, based on acousto-optic modulators (AOMs), which allows adjusting the phase by shifting the frequency of the light in a segment of its path. Since the amount of phase shift depends on the length of the segment, an optical fiber is used to realize a 2π shift. Two experimental implementations are described which deal with different sources of phase fluctuations. The first addresses fluctuations resulting from the optical fiber, while the second tackles unwanted variations originating from the AOMs.

gMCSpy: Efficient and accurate computation of genetic minimal cut sets in python.

MOTIVATION: The identification of minimal genetic interventions that modulate metabolic processes constitutes one of the most relevant applications of genome-scale metabolic models (GEMs). The concept of Minimal Cut Sets (MCSs) and its extension at the gene level, genetic Minimal Cut Sets (gMCSs), have attracted increasing interest in the field of Systems Biology to address this task. Different computational tools have been developed to calculate MCSs and gMCSs using both commercial and open-source software. RESULTS: Here, we present gMCSpy, an efficient Python package to calculate gMCSs in GEMs using both commercial and non-commercial optimization solvers. We show that gMCSpy substantially overperforms our previous computational tool GMCS, which exclusively relied on commercial software. Moreover, we compared gMCSpy with recently published competing algorithms in the literature, finding significant improvements in both accuracy and computation time. All these advances make gMCSpy an attractive tool for researchers in the field of Systems Biology for different applications in health and biotechnology. AVAILABILITY: The Python package gMCSpy can be accessed at: https://github.com/PlanesLab/gMCSpy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Current status and challenges in timely detection of cervical cancer in Mexico: expert consensus.

Cervical cancer is a significant public health problem in low- and middle-income countries, accounting for 85% of new cases worldwide. Due to poorly organized screening programs, cervical cancer is more likely to develop in vulnerable groups who do not initiate or rarely undergo screening. Cervical cytology and detecting high-risk human papillomavirus types are the recommended screening tools. Further, these strategies allow for accurately identifying women at a higher risk of cervical cancer and establishing screening times. New detection tools, such as novel biomarkers or automatic HPV detection in the vagina or urine, can improve screening coverage. This review aims to identify the challenges faced by detection programs and screening tools in Mexico to provide evidence-based recommendations to improve early detection programs for cervical cancer.

IgG4-related disease and B-cell malignancy due to an IKZF1 gain-of-function variant.

BACKGROUND: Monoallelic loss-of-function IKZF1 (IKAROS) variants cause B-cell deficiency or combined immunodeficiency, whereas monoallelic gain-of-function (GOF) IKZF1 variants have recently been reported to cause hypergammaglobulinemia, abnormal plasma cell differentiation, autoimmune and allergic manifestations, and infections. OBJECTIVE: We studied 7 relatives with autoimmune/inflammatory and lymphoproliferative manifestations to identify the immunologic disturbances and the genetic cause of their disease. METHODS: We analyzed biopsy results and performed whole-exome sequencing and immunologic studies. RESULTS: Disease onset occurred at a mean age of 25.2 years (range, 10-64, years). Six patients suffered from autoimmune/inflammatory diseases, 4 had confirmed IG4-related disease (IgG4-RD), and 5 developed B-cell malignancies: lymphoma in 4 and multiple myeloma in the remaining patient. Patients without immunosuppression were not particularly prone to infectious diseases. Three patients suffered from life-threatening coronavirus disease 2019 pneumonia, of whom 1 had autoantibodies neutralizing IFN-α. The recently described IKZF1 GOF p.R183H variant was found in the 5 affected relatives tested and in a 6-year-old asymptomatic girl. Immunologic analysis revealed hypergammaglobulinemia and high frequencies of certain lymphocyte subsets (exhausted B cells, effector memory CD4 T cells, effector memory CD4 T cells that have regained surface expression of CD45RA and CD28-CD57+ CD4+ and CD8+ T cells, TH2, and Tfh2 cells) attesting to immune dysregulation. Partial clinical responses to rituximab and corticosteroids were observed, and treatment with lenalidomide, which promotes IKAROS degradation, was initiated in 3 patients. CONCLUSIONS: Heterozygosity for GOF IKZF1 variants underlies autoimmunity/inflammatory diseases, IgG4-RD, and B-cell malignancies, the onset of which may occur in adulthood. Clinical and immunologic data are similar to those for patients with unexplained IgG4-RD. Patients may therefore benefit from treatments inhibiting pathways displaying IKAROS-mediated overactivity.

(-)-epicatechin treatment did not modify the thermogenic pathway in the gastrocnemius muscle of male rat offspring obeses by programming.

The aim of this study was to analyse the expression of genes related to the regulation of energy metabolism in skeletal muscle tissue by comparing male offspring in two age groups [at 110 and 245 postnatal days (pnd)] from a mother with obesity induced by a high-fat diet and (-)-epicatechin (Epi) administration. Four groups of six male offspring from different litters were randomly selected for the control groups [C and offspring of mothers with maternal obesity (MO)] or Epi intervention groups. We evaluated the effect of Epi on gastrocnemius tissue by analysing the mRNA and protein expression levels of Fndc5/irisin, Pgc-1α, Ucp3, and Sln. Epi significantly increased the Pgc-1α protein in the MO group of offspring at 110 pnd (p < 0.036, MO vs. MO+Epi), while at 245 pnd, Epi increased Fndc5/irisin mRNA expression in the MO+Epi group versus the MO group (p = 0.006).No differences were detected in Fndc5/irisin, Ucp3 or Sln mRNA or protein levels (including Pgc-1α mRNA) in the offspring at 110 pnd or in Pgc-1α, Ucp3, or Sln mRNA or protein levels (including Fndc5/irisin protein) at 245 pnd among the experimental groups. In conclusion, (-)-epicatechin treatment increased Fndc5/irisin mRNA expression and Pgc-α protein levels in the gastrocnemius muscle of offspring at postnatal days 110 and 245. Furthermore, it is suggested that the flavonoid effect in a model of obesity and its impact on thermogenesis in skeletal muscle are regulated by a different pathway than Fndc5/irisin.

Patient preferences in the treatment of stage III/IV classic Hodgkin lymphoma: Results from the CONNECT cross-sectional survey.

We explored patient front-line treatment preferences in newly diagnosed stage III/IV classic Hodgkin lymphoma (cHL). The CONNECT patient survey, administered online from 30 December 2020 to 1 March 2021, examined preferences overall and by age at diagnosis in 182 adult patients diagnosed with stage III/IV cHL within the past 10 years in the United States. At diagnosis, patients' median age was 36 years; 66% of patients were younger (aged 16-41 years) and 34% older (aged 42-85 years). When asked about initial treatment goals, 74% of patients ranked cure as their first or second goal (86% younger vs. 52% older patients; p < 0.001). At diagnosis, 72% of patients preferred aggressive treatment, and 85% were willing to accept more short-term risks in exchange for a better-working therapy long term. For long-term risks, younger versus older patients were significantly more concerned about second cancers (p < 0.001) and fertility issues (p = 0.007), whereas older patients were more concerned about lung damage (p = 0.028) and infections (p < 0.001). Most patients (94%) reported having a caregiver at some point, but 99% of these patients retained some control of treatment decisions. Collectively, these survey results highlight patient treatment preferences and differences in treatment goals and long-term side effect concerns based on patient age.

Genomic epidemiology of the primary methicillin-resistant Staphylococcus aureus clones causing invasive infections in Paraguayan children.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major human pathogens. It could carry numerous resistance genes and virulence factors in its genome, some of which are related to the severity of the infection. An observational, descriptive, cross-sectional study was designed to molecularly analyze MRSA isolates that cause invasive infections in Paraguayan children from 2009 to 2013. Ten representative MRSA isolates of the main clonal complex identified were analyzed with short-read paired-end sequencing and assessed for the virulome, resistome, and phylogenetic relationships. All the genetically linked MRSA isolates were recovered from diverse clinical sources, patients, and hospitals at broad gap periods. The pan-genomic analysis of these clones revealed three major and different clonal complexes (CC30, CC5, and CC8), each composed of clones closely related to each other. The CC30 genomes prove to be a successful clone, strongly installed and disseminated throughout our country, and closely related to other CC30 public genomes from the region and the world. The CC5 shows the highest genetic variability, and the CC8 carried the complete arginine catabolic mobile element (ACME), closely related to the USA300-NAE-ACME+, identified as the major cause of CA-MRSA infections in North America. Multiple virulence and resistance genes were identified for the first time in this study, highlighting the complex virulence profiles of MRSA circulating in the country. This study opens a wide range of new possibilities for future projects and trials to improve the existing knowledge on the epidemiology of MRSA circulating in Paraguay. IMPORTANCE: The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) is a public health problem worldwide. The most frequent MRSA clones identified in Paraguay in previous studies (including community and hospital acquired) were the Pediatric (CC5-ST5-IV), the Cordobes-Chilean (CC5-ST5-I), the SouthWest Pacific (CC30-ST30-IV), and the Brazilian (CC8-ST239-III) clones. In this study, the pan-genomic analysis of the most representative MRSA clones circulating in invasive infection in Paraguayan children over the years 2009-2013, such as the CC30-ST30-IV, CC5-ST5-IV, and CC8-ST8-IV, was carried out to evaluate their genetic diversity, their repertoire of virulence factors, and antimicrobial resistance determinants. This revealed multiple virulence and resistance genes, highlighting the complex virulence profiles of MRSA circulating in Paraguay. Our work is the first genomic study of MRSA in Paraguay and will contribute to the development of genomic surveillance in the region and our understanding of the global epidemiology of this pathogen.

Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis.

Introduction: Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF, and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Owing to the important role that the human leukocyte antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods: We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising 5159 cases and 27 459 controls, including a prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold of p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results: The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion: Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.

Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders.

Sleep and circadian rhythm disruptions are comorbid features of many pathologies and can negatively influence numerous health conditions, including degenerative diseases, metabolic illnesses, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. Thus, associations between sleep and/or circadian rhythm and alternative polyadenylation (APA), particularly in the context of other health challenges, are largely undescribed. APA is a process that generates various transcript isoforms from the same gene, resulting in effects on mRNA translation, stability, localization, and subsequent function. Here, we have identified unique APAs in rat brain that exhibit time-of-day-dependent oscillations in expression as well as APAs that are altered by sleep deprivation and the subsequent recovery period. Genes affected by APA usage include Mapt/Tau, Ntrk2, Homer1A, Sin3band Sorl. Sorl1 has two APAs which cycle with a 24 h period, one additional APA cycles with a 12 h period and one more that is reduced during recovery sleep. Finally, we compared sleep- or circadian-associated APAs with recently described APA-linked brain disorder susceptibility genes and found 46 genes in common.

The role of stimulus combinations in the repeated assessment of resurgence.

The current study examined the role of stimulus combinations on the repeated assessment of resurgence. Using a within-session resurgence procedure, rats were exposed to different conditions, each with distinct stimulus combinations (AAA, ABA, ABB, ABC and AAB). Two arrangements of stimulus changes were compared: Experiment 1 involved changes in stimulus combinations every five sessions, while Experiment 2 implemented changes every session. Resurgence was observed in both experiments; however, Experiment 2 demonstrated more consistent and repeated resurgence when stimulus combinations changed every session. Notably, the ABA, ABB and ABC conditions showed the highest percentage of sessions in which resurgence was observed. Lastly, the current study extends the application of the within-session resurgence procedure to rats and auditory stimuli, providing a reliable method for assessing resurgence in single subjects under different variable conditions.

The clinical presentation of major depressive disorder in youth with co-occurring obsessive-compulsive disorder.

BACKGROUND: Major depressive disorder (MDD) is common in youth and among the most frequent comorbid disorders in pediatric obsessive-compulsive disorder (OCD), but it is unclear whether the presence of OCD affects the symptom presentation of MDD in youth. METHODS: A sample of youth with OCD and MDD (n = 124) and a sample of youth with MDD but no OCD (n = 673) completed the Patient Health Questionnaire for Adolescents (PHQ-A). The overall and symptom-level presentation of MDD were examined using group comparisons and network analysis. RESULTS: Youth with MDD and OCD, compared to those with MDD and no OCD, had more severe MDD (Cohen's d = 0.39) and more reported moderate to severe depression (75 % vs 61 %). When accounting for demographic variables and the overall severity of MDD, those with comorbid OCD reported lower levels of anhedonia and more severe difficulties with psychomotor retardation/agitation. No significant differences in the interconnections among symptoms emerged. LIMITATIONS: Data were cross-sectional and self-reported, gold standard diagnostic tools were not used to assess OCD, and the sample size for the group with MDD and OCD was relatively small yielding low statistical power for network analysis. CONCLUSIONS: Youth with MDD and OCD have more severe MDD than those with MDD and no OCD and they experience more psychomotor issues and less anhedonia, which may relate to the behavioral activation characteristic of OCD.

Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis.

Background: Idiopathic pulmonary fibrosis (IPF) is a chronic lung condition that is more prevalent in males than females. The reasons for this are not fully understood, with differing environmental exposures due to historically sex-biased occupations, or diagnostic bias, being possible explanations. To date, over 20 independent genetic variants have been identified to be associated with IPF susceptibility, but these have been discovered when combining males and females. Our aim was to test for the presence of sex-specific associations with IPF susceptibility and assess whether there is a need to consider sex-specific effects when evaluating genetic risk in clinical prediction models for IPF. Methods: We performed genome-wide single nucleotide polymorphism (SNP)-by-sex interaction studies of IPF risk in six independent IPF case-control studies and combined them using inverse-variance weighted fixed effect meta-analysis. In total, 4,561 cases (1,280 females and 2,281 males) and 23,500 controls (8,360 females and 14,528 males) of European genetic ancestry were analysed. We used polygenic risk scores (PRS) to assess differences in genetic risk prediction between males and females. Findings: Three independent genetic association signals were identified. All showed a consistent direction of effect across all individual IPF studies and an opposite direction of effect in IPF susceptibility between females and males. None had been previously identified in IPF susceptibility genome-wide association studies (GWAS). The predictive accuracy of the PRSs were similar between males and females, regardless of whether using combined or sex-specific GWAS results. Interpretation: We prioritised three genetic variants whose effect on IPF risk may be modified by sex, however these require further study. We found no evidence that the predictive accuracy of common SNP-based PRSs varies significantly between males and females.

Physician frontline treatment preferences for stage III/IV classic Hodgkin lymphoma: the real-world US CONNECT study.

Aim: To understand US physicians' frontline (1L) treatment preferences/decision-making for stage III/IV classic Hodgkin lymphoma (cHL). Materials & methods: Medical oncologists and/or hematologists (≥2 years' practice experience) who treat adults with stage III/IV cHL were surveyed online (October-November 2020). Results: Participants (n = 301) most commonly considered trial efficacy/safety data and national guidelines when selecting 1L cHL treatments. Most physicians (91%) rated overall survival (OS) as the most essential attribute when selecting 1L treatment. Variability was seen among regimen selection for hypothetical newly diagnosed patients, with OS cited as the most common reason for regimen selection. Conclusion: While treatment selection varied based on patient characteristics, US physicians consistently cited OS as the top factor considered when selecting a 1L treatment for cHL.

Classic Hodgkin lymphoma (cHL) is a type of cancer that grows in lymph nodes. The researchers created a survey to assess how doctors in the USA choose medicine to treat patients who are newly diagnosed with an advanced stage of cHL (stage 3 or 4 out of 4 stages). We surveyed 301 doctors who treat patients with cHL. When choosing a medicine to treat cHL, most doctors said they consider results from research studies, how well the medicine works, information on the medicine's safety and recommendations in official guidelines. Most doctors said that overall survival (how long the patient survives after being diagnosed with cHL) is the most important outcome they consider when choosing a medicine to treat cHL. During the survey, doctors saw four unique patient profiles. These profiles differed in age, disease stage (how far along the cHL is) and other illnesses the patient has. While medicine choice was different across profiles, overall survival was still the reason for choosing each individual patient's medicine. These survey results show that doctors in the USA highly consider overall survival when choosing medicine for patients newly diagnosed with an advanced stage of cHL.

Wunderlich Syndrome in a Patient With Type 1 Diabetes Mellitus: Surgical Challenges and Management Strategies.

Wunderlich syndrome, a rare manifestation of spontaneous renal hemorrhage often attributed to renal angiomyolipomas, presents a complex clinical scenario demanding nuanced management. This article delves into the multifaceted dimensions of this syndrome, dissecting its clinical, diagnostic, and therapeutic intricacies. Illustrating this complexity is the case of a 26-year-old female with Wunderlich syndrome and comorbid type 1 diabetes mellitus, revealing challenges at the intersection of these conditions. While initial intervention via laparoscopic drainage and antibiotic therapy yielded symptomatic relief, the subsequent recurrence of a renal abscess prompted a re-evaluation of the treatment strategy, culminating in a second surgical intervention. The intricate interplay between Wunderlich syndrome and diabetes introduces unique challenges, with fluctuations in hemoglobin and recurrent leukocytosis mirroring the underlying complexities of this clinical dyad. This case underscores the indispensability of a multidisciplinary approach, seamlessly integrating medical and surgical modalities, coupled with vigilant postoperative monitoring. Swift identification of complications and adaptability of the treatment plan emerged as pivotal in addressing recurrent manifestations and averting long-term sequelae. The necessity for continuous surveillance and personalized management strategies becomes evident, emphasizing Wunderlich syndrome as a clinical entity requiring bespoke attention. In conclusion, this case serves as an example, highlighting the intricate nature of Wunderlich syndrome, accentuated by the presence of type 1 diabetes mellitus. The initial therapeutic success, followed by a recurrence, underscores the need for ongoing research, paving the way for refined diagnostic and treatment paradigms. The synthesis of clinical complexities in this scenario elucidates the imperative for a comprehensive understanding, guiding future endeavors aimed at optimizing the prognosis of patients affected by this uncommon syndrome.

The neurovascular unit of capillary blood vessels in the rat nervous system. A rapid-Golgi electron microscopy study.

We describe a pericapillary organ in the rat forebrain and cerebellar cortex. It consists of a series of tripartite synapses with synaptic extensions enveloped by astrocytic endfeet that are linked to the capillary wall by synaptic extensions. Reciprocal specializations of the pericyte-capillary blood vessel (CBV) with such specialized synapses suggest a mechanoreceptor role. In Golgi-impregnated and 3D reconstructions of the cerebral cortex and thalamus, a series of TSs appear to be sequentially ordered in a common dendrite, paralleled by synaptic outgrowths termed golf club synaptic extensions (GCE) opposed to a longitudinal crest (LC) from the capillary basal lamina (BL). Our results show that, in the cerebellar cortex, afferent fibers and interneurons display microanatomical structures that strongly suggest an interaction with the capillary wall. Afferent mossy fiber (MF) rosettes and ascending granule cell axons and their dendrites define the pericapillary passage interactions that are entangled by endfeet. The presence of mRNA of the mechanosensitive channel Piezo1 in the MF rosettes, together with the surrounding end-feet and the capillary wall form mechanosensory units. The ubiquity of such units to modulate synaptic transmission is also supported by Piezo1 mRNA expressing pyramidal isocortical and thalamic neurons. This scenario suggests that ascending impulses to the cerebellar and cortical targets are presynaptically modulated by the reciprocal interaction with the mechanosensory pericapillary organ that ultimately modulates the vasomotor response.