Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin.

The receptor-binding site of influenza A virus hemagglutinin partially overlaps with major antigenic sites and constantly evolves. In this study, we observe that mutations G186D and D190N in the hemagglutinin receptor-binding site have coevolved in two recent human H3N2 clades. X-ray crystallography results show that these mutations coordinately drive the evolution of the hemagglutinin receptor binding mode. Epistasis between G186D and D190N is further demonstrated by glycan binding and thermostability analyses. Immunization and neutralization experiments using mouse and human samples indicate that the evolution of receptor binding mode is accompanied by a change in antigenicity. Besides, combinatorial mutagenesis reveals that G186D and D190N, along with other natural mutations in recent H3N2 strains, alter the compatibility with a common egg-adaptive mutation in seasonal influenza vaccines. Overall, our findings elucidate the role of epistasis in shaping the recent evolution of human H3N2 hemagglutinin and substantiate the high evolvability of its receptor-binding mode.

Prevalence of co-existent COVID-19-associated pulmonary aspergillosis (CAPA) and its impact on early mortality in patients with COVID-19-associated pulmonary mucormycosis (CAPM).

BACKGROUND: Data on mixed mould infection with COVID-19-associated pulmonary aspergillosis (CAPA) and COVID-19-associated pulmonary mucormycosis (CAPM) are sparse. OBJECTIVES: To ascertain the prevalence of co-existent CAPA in CAPM (mixed mould infection) and whether mixed mould infection is associated with early mortality (≤7 days of diagnosis). METHODS: We retrospectively analysed the data collected from 25 centres across India on COVID-19-associated mucormycosis. We included only CAPM and excluded subjects with disseminated or rhino-orbital mucormycosis. We defined co-existent CAPA if a respiratory specimen showed septate hyphae on smear, histopathology or culture grew Aspergillus spp. We also compare the demography, predisposing factors, severity of COVID-19, and management of CAPM patients with and without CAPA. Using a case-control design, we assess whether mixed mould infection (primary exposure) were associated with early mortality in CAPM. RESULTS: We included 105 patients with CAPM. The prevalence of mixed mould infection was 20% (21/105). Patients with mixed mould infection experienced early mortality (9/21 [42.9%] vs. 15/84 [17.9%]; p = 0.02) and poorer survival at 6 weeks (7/21 [33.3] vs. 46/77 [59.7%]; p = 0.03) than CAPM alone. On imaging, consolidation was more commonly encountered with mixed mould infections than CAPM. Co-existent CAPA (odds ratio [95% confidence interval], 19.1 [2.62-139.1]) was independently associated with early mortality in CAPM after adjusting for hypoxemia during COVID-19 and other factors. CONCLUSION: Coinfection of CAPA and CAPM was not uncommon in our CAPM patients and portends a worse prognosis. Prospective studies from different countries are required to know the impact of mixed mould infection.

Gastrointestinal Bleeding in COVID-19 Infected Patients, and Management Outcomes.

Introduction: Gastrointestinal bleeding in COVID-19-infection poses unique challenges to patients owing to the high risk of concomitant respiratory failure. However, endoscopic care providers are prone to transmission. This study aimed to understand the risk and management outcomes of gastrointestinal bleeding in COVID-19-infected patients. Methods: Data were abstracted from electronic patient medical records, using ICD 10 codes, and demographic and clinical data were collected, for COVID-19-infected patients who developed gastrointestinal (GI) bleeding. Complications related to COVID-19 infection and management outcomes of GI bleeding were studied. Statistically, descriptive analysis was used because of the small sample size. Results: Eighteen COVID-19-infected patients developed episodes of GI bleeding, yielding a prevalence of 0.45%. Their mean age was 74.8 years, 55.5% were female, and 66.6% of patients (n=12) had upper GI bleeding symptoms, predominantly melena (55.5%), followed by coffee ground nasogastric aspirates (n=2). Only two patients (11.11%) had episodes of lower GI bleeding, and the remaining four patients (22.2%) had recurrent acute anemia requiring blood transfusion. The Glasgow-Blatchford score (GBS) at presentation ranged between 6 to 16 (mean 8.8) and seven patients (38.8%) underwent endoscopic evaluation for GI bleeding. The predominant comorbid conditions included hypertension (22.2%), diabetes mellitus (27.7%), chronic kidney disease (50%), ischemic heart disease (33%), atrial fibrillation (11.1%), and peripheral vascular disease (11.1%). The median hospitalization was 24.6 days (range: 3-54 days). The 30-day mortality rate in our cohort was 22.2%, (4/18) mainly noted in older patients aged> 60 years with comorbid conditions and severe COVID-19 infection. Conclusion: The prevalence of GI bleeding observed in our cohort was approximately 0.45%, significantly lower than the global prevalence observed, majority (66%) had upper GI bleeding. The exact reasons for the observed low prevalence of GI bleeding cannot be explained and will be the subject of future research.

Stomach bleeding in COVID-19-infected patients is a significant threat to the patients. This study aimed to understand the risk and management of stomach bleeding in patients infected with COVID-19. Medical records were retrospectively screened using appropriate disease codes to identify patients and collect information about their demographics and complications. Only 18 patients with stomach bleeding presented to the public hospitals in Al Ain from a total of 4000 COVID-19 patients during the peak of the pandemic. Majority of the patients had upper stomach bleeding (66%); the mean age of the patients was 78 years, majority of them being female (55.5%). The major comorbidity among the patients was chronic kidney disease (50%). The average duration of hospital stay was less than 25 days and the 30-day mortality was 22%. A higher mortality rate was observed in elderly patients with severe infections. The stomach bleeding observed in our patients was far less (0.45%) that in other COVID-19 patients globally, the reasons for which are not unknown.

Correction: The Development of a Clinical Research Model Complementing Medical Residency and the Assessment of Research Productivity.

[This corrects the article DOI: 10.7759/cureus.48684.].

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail.

Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.

Risk factors, mortality, and predictors of survival in COVID-19-associated pulmonary mucormycosis: a multicentre retrospective study from India.

OBJECTIVES: To compare COVID-19-associated pulmonary mucormycosis (CAPM) with COVID-19-associated rhino-orbital mucormycosis (CAROM), ascertain factors associated with CAPM among patients with COVID-19, and identify factors associated with 12-week mortality in CAPM. METHODS: We performed a retrospective multicentre cohort study. All study participants had COVID-19. We enrolled CAPM, CAROM, and COVID-19 subjects without mucormycosis (controls; age-matched). We collected information on demography, predisposing factors, and details of COVID-19 illness. Univariable analysis was used to compare CAPM and CAROM. We used multivariable logistic regression to evaluate factors associated with CAPM (with hypoxemia during COVID-19 as the primary exposure) and at 12-week mortality. RESULTS: We included 1724 cases (CAPM [n = 122], CAROM [n = 1602]) and 3911 controls. Male sex, renal transplantation, multimorbidity, neutrophil-lymphocyte ratio, intensive care admission, and cumulative glucocorticoid dose for COVID-19 were significantly higher in CAPM than in CAROM. On multivariable analysis, COVID-19-related hypoxemia (aOR, 2.384; 95% CI, 1.209-4.700), male sex, rural residence, diabetes mellitus, serum C-reactive protein, glucocorticoid, and zinc use during COVID-19 were independently associated with CAPM. CAPM reported a higher 12-week mortality than CAROM (56 of the 107 [52.3%] vs. 413 of the 1356 [30.5%]; p = 0.0001). Hypoxemia during COVID-19 (aOR [95% CI], 3.70 [1.34-10.25]) and Aspergillus co-infection (aOR [95% CI], 5.40 [1.23-23.64]) were independently associated with mortality in CAPM, whereas surgery was associated with better survival. DISCUSSION: CAPM is a distinct entity with a higher mortality than CAROM. Hypoxemia during COVID-19 illness is associated with CAPM. COVID-19 hypoxemia and Aspergillus co-infection were associated with higher mortality in CAPM.

A Novel Biophysical Model for the Generation of Sharp Wave Ripples in CA1 Hippocampus.

Synchronous activities among neurons in the brain generate emergent network oscillations such as the hippocampal Sharp-wave ripples (SPWRs) that facilitate information processing during memory formation. However, how neurons and circuits are functionally organized to generate oscillations remains unresolved. Biophysical models of neuronal networks can shed light on how thousands of neurons interact in intricate circuits to generate such emergent SPWR network events. Here we developed a large-scale biophysically realistic neural network model of CA1 hippocampus with functionally organized circuit modules containing distinct types of neurons. Model simulations reproduced synaptic, cellular and network aspects of physiological SPWRs. The model provided insights into the role of neuronal types and their microcircuit motifs in generating SPWRs in the CA1 region. The model also suggests experimentally testable predictions including the role of specific neuron types in the genesis of hippocampal SPWRs.

The Development of a Clinical Research Model Complementing Medical Residency and the Assessment of Research Productivity.

BACKGROUND AND OBJECTIVE: Despite modern healthcare infrastructure, there is a paucity of information about the clinical research framework supporting healthcare in the United Arab Emirates (UAE). Therefore, this study aimed to assess research performance productivity, and the clinical research framework, complementing medical residency, at the nation's hub for clinical research. METHODS: A cross-sectional retrospective review of records from the research database of the institution was conducted to assess productivity, and framework development, and data analyzed. RESULTS:  The migration of global healthcare providers, and the pharmaceutical industry offices, the adoption of the International Conference on Harmonization (ICH) guidelines, and electronic medical records established a research culture. Following the development of the governance framework, a total of 1,328 research projects were submitted to the ethics committee until 2023. Approximately 63% of the total studies were of minimal risk, followed by industry-sponsored clinical trials (4.9%, 58/1,163), and prospective interventional studies (3.5%, 39/1,163). Almost half (48.3%, 28/58) of the total industry-sponsored clinical trials were phase II and phase III. The number of peer-reviewed indexed publications, a measure of research productivity, indicated that the periods between 2011 and 2015, 2016 and 2020, and 2021 and 2023 witnessed a 3.8-, 9.3-, and 7.9-fold increase compared to the baseline period (1995-2005). The implementation of the Focus on International Research Strategy, Teaching, Evaluation, and Mentoring (FIRSTEM) strategy, to accommodate mandatory research activity requirements for residents by the physician licensing boards, observed substantial increases in output. The number of international peer-reviewed indexed publications/resident projects doubled from 10.8% (2010-2015) to 24% (2016-2020) and reached 40.1% in 2023. CONCLUSION: This is the first research governance model established in the UAE, a country with an increasing prevalence of diabetes, and cardiovascular and genetic diseases. The model indicates that the medical trainees differentiate the best research evidence in making decisions about the clinical care of patients. The study outcomes may potentially be useful for other countries in developing a clinical research framework.

Core-dependent post-translational modifications guide the biosynthesis of a new class of hypermodified peptides.

The ribosomally synthesized and post-translationally modified peptide (RiPPs) class of natural products has undergone significant expansion due to the rapid growth in genome sequencing data. Using a bioinformatics approach, we identify the dehydrazoles, a novel class of hypermodified RiPPs that contain both side chain dehydration of Ser residues, and backbone heterocyclization at Ser, Thr, and Cys residues to the corresponding azol(in)es. Structure elucidation of the hypermodified peptide carnazolamide, a representative class member, shows that 18 post-translational modifications are installed by just five enzymes. Complete biosynthetic reconstitution demonstrates that dehydration is carried out by an unusual DUF4135 dehydration domain fused to a zinc-independent cyclase domain (CcaM). We demonstrate that CcaM only modifies Ser residues that precede an azole in the core peptide. As heterocyclization removes the carbonyl following the Ser residue, CcaM likely catalyzes dehydration without generating an enolate intermediate. Additionally, CcaM does not require the leader peptide, and this core-dependence effectively sets the order for the biosynthetic reactions. Biophysical studies demonstrate direct binding of azoles to CcaM consistent with this azole moiety-dependent dehydration. Bioinformatic analysis reveals more than 50 related biosynthetic gene clusters that contain additional catalysts that may produce structurally diverse scaffolds.

Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase.

In bacteria, Ser/Thr protein kinase-like sequences are found as part of large multidomain polypeptides that biosynthesize lanthipeptides, a class of natural products distinguished by the presence of thioether cross-links. The kinase domain phosphorylates Ser or Thr residues in the peptide substrates. Subsequent ß-elimination by a lyase domain yields electrophilic dehydroamino acids, which can undergo cyclase domain-catalyzed cyclization to yield conformationally restricted, bioactive compounds. Here, we reconstitute the biosynthetic pathway for a class III lanthipeptide from Bacillus thuringiensis NRRL B-23139, including characterization of a two-component protease for leader peptide excision. We also describe the first crystal structures of a class III lanthipeptide synthetase, consisting of the lyase, kinase, and cyclase domains, in various states including complexes with its leader peptide and nucleotide. The structure shows interactions between all three domains that result in an active conformation of the kinase domain. Biochemical analysis demonstrates that the three domains undergo movement upon binding of the leader peptide to establish interdomain allosteric interactions that stabilize this active form. These studies inform on the regulatory mechanism of substrate recognition and provide a framework for engineering of variants of biotechnological interest.

Challenges in Assessing Blood Pressure in Adults Following Intravenous Paracetamol Infusion in the Emergency Room.

Background and objective The negligible side effects of paracetamol along with its ease of availability have catapulted paracetamol to be a widely used medication in emergency room management to reduce pain and subsequent elevations in blood pressure (BP). Our study aimed to address the challenges in informed clinical decision-making in the emergency room following paracetamol intravenous infusion. Methods This was a retrospective cross-sectional study involving the extraction of data from electronic medical records of patients who received intravenous paracetamol infusion between January 2022 and May 2022. Demographic information and BP-related data were collected for analysis. Results We initially considered a total of 162 patient records, with 132 of them eventually meeting the inclusion criteria. Among patients receiving paracetamol infusion for 15 minutes or less, 34% showed a drop of 1-5 mmHg in systolic BP (SBP), while 26% experienced a drop of 6-10 mmHg. However, infusion time longer than 16 minutes did not significantly reduce SBP. Diastolic BP (DBP) was not significantly affected by the duration of the paracetamol infusion. Analysis of the drop in SBP revealed no significant associations with age, gender, or ethnicity. Mean arterial pressure (MAP) was not significantly affected by the duration of paracetamol infusion. Conclusion Our findings suggest that intravenous paracetamol infusion does not significantly lower BP in adults in the emergency room, except for infusions of shorter durations. However, various factors, including infusion rate, patient characteristics, and concomitant medications, may influence BP measurements. The study emphasizes the need for establishing standardized criteria and conducting further research to assess intravenous paracetamol's hemodynamic effects accurately.

A biocatalytic platform for asymmetric alkylation of α-keto acids by mining and engineering of methyltransferases.

Catalytic asymmetric α-alkylation of carbonyl compounds represents a long-standing challenge in synthetic organic chemistry. Herein, we advance a dual biocatalytic platform for the efficient asymmetric alkylation of α-keto acids. First, guided by our recently obtained crystal structures, we develop SgvMVAV as a general biocatalyst for the enantioselective methylation, ethylation, allylation and propargylation of a range of α-keto acids with total turnover numbers (TTNs) up to 4,600. Second, we mine a family of bacterial HMTs from Pseudomonas species sharing less than 50% sequence identities with known HMTs and evaluated their activities in SAM regeneration. Our best performing HMT from P. aeruginosa, PaHMT, displays the highest SAM regeneration efficiencies (TTN up to 7,700) among HMTs characterized to date. Together, the synergistic use of SgvMVAV and PaHMT affords a fully biocatalytic protocol for asymmetric methylation featuring a record turnover efficiency, providing a solution to the notorious problem of asymmetric alkylation.

Inferring Pyramidal Neuron Morphology using EAP Data.

We report a computational algorithm that uses an inverse modeling scheme to infer neuron position and morphology of cortical pyramidal neurons using spatio-temporal extracellular action potential recordings.. We first develop a generic pyramidal neuron model with stylized morphology and active channels that could mimic the realistic electrophysiological dynamics of pyramidal cells from different cortical layers. The generic stylized single neuron model has adjustable parameters for soma location, and morphology and orientation of the dendrites. The ranges for the parameters were selected to include morphology of the pyramidal neuron types in the rodent primary motor cortex. We then developed a machine learning approach that uses the local field potential simulated from the stylized model for training a convolutional neural network that predicts the parameters of the stylized neuron model. Preliminary results suggest that the proposed methodology can reliably infer the key position and morphology parameters using the simulated spatio-temporal profile of EAP waveforms. We also provide partial support to validate the inference algorithm using in vivo data. Finally, we highlight the issues involved and ongoing work to develop a pipeline to automate the scheme.

Reverse engineering information processing in lateral amygdala during auditory tones.

Learning in the mammalian lateral amygdala (LA) during auditory fear conditioning (tone - foot shock pairing), one form of associative learning, requires N-methyl-D-aspartate (NMDA) receptor-dependent plasticity. Despite this fact being known for more than two decades, the biophysical details related to signal flow and the involvement of the coincidence detector, NMDAR, in this learning, remain unclear. Here we use a 4000-neuron computational model of the LA (containing two types of pyramidal cells, types A and C, and two types of interneurons, fast spiking FSI and low-threshold spiking LTS) to reverse engineer changes in information flow in the amygdala that underpin such learning; with a specific focus on the role of the coincidence detector NMDAR. The model also included a Ca2s based learning rule for synaptic plasticity. The physiologically constrained model provides insights into the underlying mechanisms that implement habituation to the tone, including the role of NMDARs in generating network activity which engenders synaptic plasticity in specific afferent synapses. Specifically, model runs revealed that NMDARs in tone-FSI synapses were more important during the spontaneous state, although LTS cells also played a role. Training trails with tone only also suggested long term depression in tone-PN as well as tone-FSI synapses, providing possible hypothesis related to underlying mechanisms that might implement the phenomenon of habituation.

Estimation of health literacy levels in patients with cardiovascular diseases in a Gulf country.

INTRODUCTION: Cardiovascular diseases (CVDs) are the leading cause of mortality worldwide. In the United Arab Emirates (UAE), the prevalence of deaths associated with CVD is higher than the global average, and the incidence of premature coronary heart disease is 10-15 years earlier than in Western nations. In patients with CVD, inadequate health literacy (HL) is significantly associated with poor health outcomes. The goal of this study is to assess HL levels among patients with CVD in the UAE to develop effective health system strategies for disease prevention and management. METHODS: A nationwide cross-sectional survey to assess HL levels in patients with CVD was conducted between January 2019 and May 2020 in the UAE. The association between health literacy level with patient age, gender, nationality, and education was determined using the Chi-Square test. The significant variables were further analyzed by ordinal regression. RESULTS: Of 336 participants (86.5% response rate), approximately half 51.5% (173/336) of the respondents were women, and 46% (146/336) of them attained high school level of education. More than 75% (268/336) of the participants were above the age of 50 years. Overall, 39.3% (132/336) of respondents possessed inadequate HL, and 46.4% (156/336) and 14.3% (48/336) demonstrated marginal and adequate HL, respectively. Inadequate health literacy was more prevalent among women, as compared to men. Age was significantly associated with HL levels. Participants under age 50 had higher adequate HL levels 45.6% (31/68), (95% CI (3.8-57.4), P < 0.001). There was no correlation between education and health literacy levels. CONCLUSION: The inadequate HL levels found in outpatients with CVD is a major health concern in the UAE. To improve population health outcomes, health system interventions, including targeted educational and behavioral programs for the older population are necessary.

Cog - A Radiological Indicator in Identifying Dysventilation Syndrome.

Background: Anterior epitympanic recess (AER) is a small anatomical space in the epitympanum anterior to level of the head of malleus. This space has received lot of attention because of its role in cholesteatoma. Dysventilation of AER can lead to retraction pockets and cholesteatomas. Due to the advent of endoscopic middle ear surgeries the visualization of the mucosal folds and spaces have been possible for the past 2 decades. Mucosal folds and spaces play an important role in middle ear ventilation and pathologies obstructing these ventilation pathways can lead to dysventilation resulting in retraction pockets / cholesteatoma. In our study we have analysed the importance of cog with respect to dysventilation syndrome. Materials and methods: This prospective radiological study was conducted at Apollo Hospitals, BG road, Bangalore for a study period of 1 year (January 2021-January 2022). All patients who underwent high resolution CT scan (HRCT) of temporal bone were included in this study. They were divided into 2 groups (Group I & II). For group I HRCT temporal bone of 200 normal scans were included and scans with chronic otitis media, congenital anomaly, temporal bone fractures and tumors were excluded from the study. 50 HRCT temporal bone scans of chronic otitis media with squamous disease were included in group II. Results: 200 HRCT scans were included in the normative data analysis of the temporal bone. Out of 200, 133 had complete cog, 54 had incomplete cog and 13 had absent cog (Table 2). We also calculated the mean diameters of the AER, AP diameter- 4.24 ± 1.3, TD - 3.36 ± 1.05 and VD - 5.3 ± 1.94 (Table 3). Similarly, we analyzed 50 HRCT temporal bone with squamous disease 32 out of 50 had absent cog (Table 4). We also calculated the dimension of AER in diseased temporal bones (Table 5). A paired T test was conducted in order to analyze these values. Conclusion: In our study we performed a radiological evaluation of AER and cog and found that incidence of absent cog is more among individuals with squamous disease than normal individuals. Hence we advocate that absent cog can lead to horizontally oriented tensor tympani that in turn results in dysventilation. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-023-03507-9.

Knowledge and Awareness Among Mothers Regarding Early Childhood Development: A Study From the United Arab Emirates.

Background and objective There is a dearth of studies on the knowledge and awareness among mothers on childhood development in the United Arab Emirates (UAE). Maternal knowledge of childhood development is a critical determinant of children's development and behavior. In light of this, we conducted this study to determine the level of maternal knowledge about childhood development. Methodology We employed a cross-sectional study design involving 200 mothers of all ages recruited using stratified random sampling. After obtaining informed consent, the participants were required to complete a questionnaire adapted from the "Ages and Stages" questionnaire, which covered demographics and items on developmental milestones. The questionnaire was validated and checked for reliability by using a focus group. Inferential statistics were used, and the association between the variables was analyzed using the Chi-squared test. Results Our findings indicated that the knowledge among mothers regarding child development is relatively low in the UAE. Two-thirds of the respondents were knowledgeable about gross motor skills (62% of the mothers knew the age at which a child could lift his/her head). Less than half of the mothers were well-informed about fine motor skills such as writing and drawing (44% of the mothers were aware of the age at which a child should be able to scribble on paper). The respondents demonstrated a lack of knowledge regarding children's speech and language skills. Regarding social skills, only 8% of the mothers were aware of the correct age at which a child should start to dress by himself/herself. Conclusion Although mothers in the UAE were knowledgeable about certain aspects of childhood development such as gross motor development, they were less knowledgeable regarding other aspects such as social and language skills. The gaps identified in our study highlight the need to implement effective health education programs so that mothers are better informed to help improve child development outcomes in the community.