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The Delta Smelt is a largely zooplank­tivorous, endangered fish endemic to the San Francisco Estuary (the estuary). High flows increase the availability of fresh and brackish water habitat for Delta Smelt, but also may mobilize contaminants, potentially increasing toxicological stress. Here, we examine the association between contaminants and Delta Smelt health across contrasting water year types and flow-related management actions. Our study spanned the fall season of three years: 1 dry year (2018) bracketed by 2 wet years (2017 and 2019) and coincided with several management actions meant to benefit Delta Smelt. We collected field water from six sites in the estuary that encompass the freshwater and low-salinity habitat of Delta Smelt and analyzed the water for contaminant concentrations. After a 96-hour exposure to the field water, we assessed cultured Delta Smelt survival and the histopathological condition of the gill and liver. Insecticides, particularly fipronil metabolites, were the most prevalent contaminants detected in 2017 and 2018, and a variety of contaminants associated with the rice harvest were detected in 2019. No acute toxicity was observed during any exposure, but we observed negative effects in the livers of Delta Smelt exposed to agricultural water from the Toe Drain and Cache Slough during a 2019 pulse flow action, which coincided with elevated detections and concentrations of organic pesticides. Other noteworthy sub-lethal effects, likely occurring in response to contaminant mixtures, included severe gill lesions in Delta Smelt exposed to Decker Island water in 2019. In the drier year of 2018, lesions were generally mild or absent. Thus, the trade-offs between increased habitat availability and contaminant loading may provide one explanation for why Delta Smelt abundance does not consistently respond positively to outflow.

During January and February 2022, a huge spike in the cases of COVID-19 was recorded in the Khyber Pakhtunkhwa (KP) province of Pakistan prompting the civil administration to institute new restrictions. To investigate the underlying causes of this surge, the regional Public Health Reference Lab (PHRL) launched a screening effort throughout the Province's remote and urban areas. Herein, we present our survey results during the peak months of the pandemic. The data indicated the prevalence of highly transmissible delta- and Omicron-like virus variants, which may explain the rise in positive cases. Phylogenetic analysis revealed the genetic association between the sequences from this study and those found in Pakistan as well as from geographically distant countries, suggesting a complex evolutionary history. For screening, we deployed an easy-to-use single primer-based polymerase chain reaction (PCR) assay to identify the circulation of SARS-CoV-2. The assay was validated using clinical swabs of COVID-19 patients and obtained consistent results with Sanger sequencing. Our survey identified a patient simultaneously infected with two variants of concern, indicating the presence of the Deltacron variant, although we cannot discount the possibility of sequencing errors. We recommend that SARS-CoV-2 be continuously monitored to detect single nucleotide polymorphisms (SNPs) that are causally linked to the emergence of new lineages. Our method provides a rapid and cost-effective detection assay for SARS-CoV-2 in a resource-constrained setting. [ABSTRACT FROM AUTHOR]

Basidiomata belonging to the genus Candolleomyces were collected from plains of Punjab, Pakistan, and characterized based on morpho-anatomical and phylogenetic analyses. In phylograms nrITS & nrLSU regions were used to ascertain exact positions of our new taxa in this genus. Three novel taxa, Candolleomyces granulosis, C. pabbiensis and C. umbonatus formed independent phylogenetic relationships within the genus Candolleomyces. With this addition, the taxa of Candolleomyces has become to 46. A key to the Asian Candolleomyces species is also given. [ABSTRACT FROM AUTHOR]

Rabbit viral haemorrhagic disease (RVHD) is a fatal threat to rabbits causing long-term problems and significant economic losses. In the current study, RVHD was identified and characterised in naturally infected rabbits in order to assess the genetic diversity of RHDV circulating in different Egyptian provinces from January 2019 to January 2022. Nineteen suspected samples were collected from outbreaks that occurred in nine provinces during 2019-2022. Ten liver samples out of nineteen were positive in the slide and plate haemagglutination (HA) test. HA titres ranged from 5 log2 to 12 log2. RHDV-positive liver homogenates were confirmed with RT-PCR and histopathology. Further characterisation of the selected four viral strains was performed by nucleotide sequencing of VP60 gene. Based on nucleotide sequence analysis, three isolates were identified as RHDV2 strains, while one isolate was assigned as RHDV1 strain. [ABSTRACT FROM AUTHOR]

Mangrove forests are critical coastal ecosystems that provide great socio‐ecological services, which are also highly vulnerable to climate change, particularly to sea level rise (SLR). Here we assess changes in mangrove forests in four distinct river/tide/wave‐dominant large deltas along the Indo‐Pacific coast based on 1,336 remote sensing images by machine learning techniques. We find that mangroves are migrating seaward at a rate of 18% ± 12% m/yr, which can offset landward mangroves loss, 67% of which caused by land use conversion. The fact that mangroves are expanding seaward with accretion rates exceeding SLR suggests that climate change has not yet triggered substantial loss in deltaic mangrove forests. Assuming that present environmental conditions do not change and that sediment and organic deposition in the deltaic topsets match SLR rates, we project that 90% of deltaic mangrove forests may start to retreat after 132–194 years. Early inundation of mangroves will occur in wave‐dominated delta. Plain Language Summary: Mangrove forests provide significant ecological and societal services, and mitigation global warming. However, large‐scale loss in mangroves could be induced by anthropogenic drivers and sea level rise (SLR). Our study based on deltas along the Indo‐Pacific coast, highlight that mangroves are expanding seaward at a rate of 18% ± 12% m/yr, indicating that there is little impacts from SLR and has not been substantial loss in mangrove forests in these deltas so far. Mangrove expansion here can efficiently offset 67% landward mangrove losses indicates that our new model project that 90% of mangrove shorelines will may start retreating within 132–194 years. We conclude that favoring mangroves expansion seaward would enhance coastal protection and reduce the need of landward mangrove restoration. Key Points: Mangroves along typical deltas are expanding seaward of about 18% ± 12% m/yr, indicating that there is little impacts from sea level riseMangrove expansion here can efficiently offset 67% landward mangrove lossesNew model project that 90% of mangrove fringes may start retreating within 132–194 years, and wave‐dominated delta present early inundation [ABSTRACT FROM AUTHOR]

River sediment supply (Qs) and longshore sediment transport (LST) are recognized as two paramount controls on river delta morphodynamics and stratigraphy. We employed the Delft3D model to simulate the evolution of deltas from fluvial to wave‐dominated conditions, revealing the interplay between river‐ and wave‐driven sediment quantities. Wave‐influenced deltas may show alternating accumulation and retreat patterns driven by avulsions and wave‐induced sediment diffusion, posing coastal management challenges. Deltas with higher wave energy evolve under a fine balance between river supply and intense wave‐mediated sediment redistribution and are highly vulnerable under conditions of sediment reduction. Reducing Qs by ∼40%–70%, common in modern dammed rivers, can rapidly shift bypass from ∼0 to 1 (no bypass to complete bypass). This leads to accelerated diffusion and potential sediment loss in modern deltas. The study highlights the importance of accurately computing sediment quantities in real‐world deltas for improved management, especially under increasing anthropogenic and climatic pressures. Plain Language Summary: Ocean waves, like proficient sculptors, shape the meeting points of rivers and seas—where deltas are created. Under the power of ocean waves, the sediments transported by rivers are organized into distinct patterns. Using an advanced computer model, our research unveils how this interplay affects the physical form of these deltas and their functioning. In certain conditions, the sediment carried by waves can jump over the river mouth and move further along the coastline, contributing to stretching the delta and inducing erosion. Currently, river sediments are getting blocked behind river dams, depriving deltas of their sediment nourishment. As sediment supply decreases, powerful waves at the sea erode deltas more easily, endangering ecosystems, human communities and infrastructure. Because deltas are facing challenges from climate change and increased human activities, informed and innovative management strategies based on better knowledge of natural processes are needed to preserve these valuable coastal regions. Key Points: Deltas transition from avulsion‐dominated with localized depocenters to more diffuse and alongshore‐deflected wave‐dominated depocentersBypass increases and trapping decreases abruptly when longshore transport (LST) at the river mouth equals river sediment transport (Qs)LST under large‐scale blocking due to mouth bar and shoreface adjustment feeds wave‐dominated updrift beach ridge plains (strandplains) [ABSTRACT FROM AUTHOR]

Background: Determination of SARS-CoV-2 variant is significant to prevent the spreads of COVID-19 disease. Methods: We aimed to evaluate the variants of SARS-CoV-2 rate in positive patients in Kanuni Sultan Suleyman Training and Research Hospital (KSS-TRH), Istanbul, Türkiye between 1st January and 30th November 2021 by using RT-PCR method. Results: Herein, 825,169 patients were evaluated (male:58.53% and female:41.47%) whether COVID-19 positive or not [(+):21.3% and (−):78.7%] and 175,367 patient was described as positive (53.2%-female and 46.8%-male) by RT-PCR. COVID-19 positive rate is observed highest in the 6–15- and 66–75-year age range. The frequencies were obtained as SARS-CoV-2 positive (without mutation of B.1.1.7 [B.1.1.7 (U.K), E484K, L452R, B.1.351 (S. Africa/Brazil) spike mutations] as 66.1% (n: 115,899), B.1.1.7 Variant as 23.2% (n:40,686), Delta mutation (L452R) variant as 9.8% (n:17,182), B.1.351 variant as 0.8% (n:1370) and E484K as 0.1% (n: 230). In April 2021, general SARS-CoV-2 and B.1.1.7 variant were dominantly observed. Up to July 2021, B.1.617.2 (Delta variant/ Indian variant) and E484K has been not observed. B.1.351 variant of SARS-CoV-2 has been started in February 2021 at the rarest ratio and March 2021 is the top point. September 2021 is the pick point of E484K. African/Brazil variant of SARS-CoV-2 has been started in February 2021 at the rarest ratio and March 2021 is the top point. September 2021 is the pick point of E484K. When the gender type is compared within the variants, women were found to be more prevalent in all varieties. Conclusions: The meaning of these mutations is very important to understand the transmission capacity of the COVID-19 disease, pandemic episode, and diagnosis of the virus with mutation types. Understanding the variant type is important for monitoring herd immunity and the spread of the disease. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), led to a global pandemic from 2020. In Thailand, five waves of outbreaks were recorded, with the fourth and fifth waves driven by the Delta and Omicron variants, resulting in over 20,000 new confirmed cases daily at their peaks. Methods: This cross-sectional study investigated the associations between clinical symptoms, vaccination status, antibody responses, and post-COVID-19 sequelae in COVID-19 patients. Plasma samples and clinical data were collected from participants admitted to hospitals in Thailand between July 2021 and August 2022, with follow-ups conducted for one year. The study included 110 participants infected with either the Delta (n = 46) or Omicron (n = 64) variants. Virus genotypes were confirmed by RT-PCR of nasal swab RNA and partial nucleotide sequencing of the S gene. IgG and IgA antibody levels against the receptor-binding domain (RBD) of SARS-CoV-2 Delta and Omicron variants were measured in plasma samples using ELISA. Results: Pneumonia was found to be associated with Delta variant infections, while sore throat, congestion or runny nose, and headache were linked to Omicron infections. Vaccination with fewer than two doses and diabetes mellitus were significantly associated with higher disease severity. Specific IgG and IgA antibodies against the RBD of the Delta variant generally rose by day 14 and were maintained for up to two months, whereas the pattern of antibody response to the Omicron variant was less clear. Antibody risings were found to be positively associated with pneumonia, certain underlying conditions (obesity, hypertension, dyslipidemia, and diabetes mellitus), and age ≥ 60 years. Delta variant infections were associated with forgetfulness, hair loss, and headache during the 1-year post-infection period. Females were more likely to experience hair loss, forgetfulness, and joint pain, while older age was associated with joint pain. Conclusions: This study enhances our understanding of SARS-CoV-2 infections in Thais, particularly concerning the Delta and Omicron variants. The findings can inform public health planning and response strategies for future outbreaks of SARS-CoV-2 or other emerging viral diseases. [ABSTRACT FROM AUTHOR]

Background: The global pandemic caused by SARS‐CoV‐2 has underlined the significance of strict genomic surveillance to track virus evolution and the possible emergence of new variants, particularly in densely populated countries like Bangladesh. This study outlines a strategic framework of genomic surveillance to track the evolution of the virus in Bangladesh between June 2021 and December 2022 through the National SARS‐CoV‐2 Variant Surveillance (NSVS) program involving collaboration across 4 major institutes and 13 hospitals nationwide. Methods: We aimed to capture the variants of SARS‐CoV‐2 throughout the country utilizing standardized procedures, modern sequencing technology, and stringent quality control, promoting data accuracy and the timely detection of new variants of concern. We sequenced over 2200 genomes, documenting the prevalence of the Delta variant initially, followed by the emergence of Omicron variants BA.1, BA.2, BA.5, and XBB, each affecting transmission rates and vaccine efficacy differently. Results: The clinical manifestations of the variants differed, with some symptoms occurring more frequently in Delta cases and vice versa. Vaccinated individuals were more affected by Omicron cases compared to Delta cases. These variants were responsible for two major COVID‐19 waves in the country, each with significant clinical effects. Phylogenetic analyses placed the local SARS‐CoV‐2 variants within a global context, indicating the Delta variant likely entered from India and Omicron from Europe. Conclusion: This research highlights the significance of collaborative surveillance strategies for guiding public health choices and the critical role of genomic analysis in monitoring virus evolution, shaping targeted pandemic responses. Bangladesh's contributions significantly enhance global insight into COVID‐19's genomic evolution. [ABSTRACT FROM AUTHOR]

Individuals with chronic lung disease (CLD) are more susceptible to respiratory viral infections; however, significant heterogeneity exists in the literature on CLD and COVID-19 outcomes. Data are lacking on outcomes with newer variants (eg, Omicron) and in vaccinated and boosted populations. What are the outcomes of SARS-CoV-2 infection in individuals with CLD during Delta and Omicron transmission in a highly vaccinated and boosted population-based cohort? Outcomes of Delta and Omicron SARS-CoV-2 infection in a highly vaccinated and boosted cohort of adult Singaporeans with CLD (including asthma, COPD, bronchiectasis, and pulmonary fibrosis) were contrasted against matched population control participants. Calendar time-scale Cox regressions were used to compare risk of infection, COVID-19-related hospitalizations, and severe COVID-19 disease, adjusting for sociodemographic factors and comorbidities. Overall, 68,782 individual patients with CLD and 534,364 matched population control participants were included. By the end of the Omicron wave, 92.7% of patients with CLD were boosted. Compared with control participants, patients with CLD showed higher risk of SARS-CoV-2 infection, COVID-19-related hospitalization, and severe COVID-19 during both the Delta wave (infection: adjusted hazards ratio [aHR], 1.22 [95% CI, 1.17-1.28]; hospitalization: aHR, 1.76 [95% CI, 1.61-1.92]; severe COVID-19: aHR, 1.75 [95% CI, 1.50-2.05]) and Omicron wave (infection: aHR, 1.15 [95% CI, 1.14-1.17]; hospitalization: aHR, 1.82 [95% CI, 1.74-1.91]; severe COVID-19: aHR, 2.39 [95% CI, 2.18-2.63]). During Omicron, significantly higher risk of infection, hospitalization, and severe COVID-19 was observed among patients with asthma (severe COVID-19: aHR, 1.31 [95% CI, 1.10-1.55]) and COPD (severe COVID-19: aHR, 1.36 [95% CI, 1.12-1.66]) compared with control participants. Severe exacerbation (requiring hospitalization) in the preceding year was associated with higher risk of poorer outcomes (Delta, severe COVID-19: aHR, 9.84 [95% CI, 6.33-15.28]; Omicron, severe COVID-19: aHR, 19.22 [95% CI, 15.35-24.06]). Risk was attenuated in the boosted group, with numerically lower HRs against hospitalization and severe COVID-19 in the four-dose group compared with the three-dose group. Increased risk of COVID-19-related hospitalization and severe COVID-19 was observed among patients with CLD compared with matched population control participants during Delta and Omicron predominance. Boosting attenuated serious COVID-19 outcomes. [ABSTRACT FROM AUTHOR]

Background: Oral candidiasis has been documented in patients with SARS-CoV-2 infection, with varying prevalence rates across geographic regions and patient demographics. This study aimed to ascertain the incidence, characteristics, and risk factors associated with the development of oral candidiasis in patients hospitalized for SARS-CoV-2 infection in a tertiary infectious diseases hospital in Romania. Methods: A retrospective analysis was conducted on adult patients hospitalized between March 2020 and December 2022 with moderate or severe forms of SARS-CoV-2 infection, for whom a culture of lingual scrapings for Candida spp. was performed. Results: A total of 294 patients were deemed eligible for inclusion in the analysis, with an incidence rate of oral candidiasis of 17.0%. The incidence of oral candidiasis was 4.2 times higher in patients with severe forms of SARS-CoV-2 infection compared to those with moderate forms. Patients with a diagnosis of COVID-19 and oral candidiasis were more likely to receive antibiotics (98.0% vs. 86.1%, p = 0.017) and corticosteroids (100% vs. 83.6%, p = 0.003) than those without oral candidiasis. These findings were associated with a 19% higher relative risk of developing oral candidiasis for patients who received corticosteroid therapy compared to those who did not, and a 13% higher relative risk for those who were administered antibiotics compared to those who were not. The presence of respiratory insufficiency increased the odds of oral candidiasis association 4.7-fold (88.0% vs. 61.1%, p < 0.001). Conclusions: Although the data have been analyzed retrospectively, we have shown that individuals with severe forms of COVID-19 exhibited an elevated risk of developing oral candidiasis. The administration of antibiotics and corticosteroids was identified as a positive predictor for the development of oral candidiasis. The data presented here suggest that a key aspect of the therapeutic management of patients with SARS-CoV-2 infection should include the implementation of preventive measures to minimize the risk of secondary fungal infections. [ABSTRACT FROM AUTHOR]

Rabbit viral haemorrhagic disease (RVHD) is a fatal threat to rabbits causing long-term problems and significant economic losses. In the current study, RVHD was identified and characterised in naturally infected rabbits in order to assess the genetic diversity of RHDV circulating in different Egyptian provinces from January 2019 to January 2022. Nineteen suspected samples were collected from out-breaks that occurred in nine provinces during 2019–2022. Ten liver samples out of nineteen were positive in the slide and plate haemagglutination (HA) test. HA titres ranged from 5 log2 to 12 log2. RHDV-positive liver homogenates were confirmed with RT-PCR and histopathology. Further characterisation of the selected four viral strains was performed by nucleotide sequencing of VP60 gene. Based on nucleotide sequence analysis, three isolates were identified as RHDV2 strains, while one isolate was assigned as RHDV1 strain.

Abstract The emergence of the SARS-CoV-2 virus led to a global pandemic, prompting extensive research efforts to understand its molecular biology, transmission dynamics, and pathogenesis. Recombination events have been increasingly recognized as significant contributor to the virus’s diversity and evolution, potentially leading to the emergence of novel strains with altered biological properties. Indeed, recombinant lineages such as the XBB variant and its descendants have subsequently dominated globally. Therefore, continued surveillance and monitoring of viral genome diversity are crucial to identify and understand the emergence and spread of novel strains. Through routine genomic surveillance of SARS-CoV-2 cases in Norway, we discovered a SARS-CoV-2 recombination event in a long-term infected immunocompromised COVID-19 (coronavirus disease) patient. A deeper investigation showed several recombination events between two distinct lineages of the virus, namely AY.98.1 and BA.5, that resulted in a single novel recombinant viral strain with a unique genetic signature. Our data is consistent with the presence of several concomitant recombinants in the patient, suggesting that these events occur frequently in vivo. This study underscores the importance of continued tracking of viral diversity and the potential impact of recombination events on the evolution of the SARS-CoV-2 virus.

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), led to a global pandemic from 2020. In Thailand, five waves of outbreaks were recorded, with the fourth and fifth waves driven by the Delta and Omicron variants, resulting in over 20,000 new confirmed cases daily at their peaks. Methods This cross-sectional study investigated the associations between clinical symptoms, vaccination status, antibody responses, and post-COVID-19 sequelae in COVID-19 patients. Plasma samples and clinical data were collected from participants admitted to hospitals in Thailand between July 2021 and August 2022, with follow-ups conducted for one year. The study included 110 participants infected with either the Delta (n = 46) or Omicron (n = 64) variants. Virus genotypes were confirmed by RT-PCR of nasal swab RNA and partial nucleotide sequencing of the S gene. IgG and IgA antibody levels against the receptor-binding domain (RBD) of SARS-CoV-2 Delta and Omicron variants were measured in plasma samples using ELISA. Results Pneumonia was found to be associated with Delta variant infections, while sore throat, congestion or runny nose, and headache were linked to Omicron infections. Vaccination with fewer than two doses and diabetes mellitus were significantly associated with higher disease severity. Specific IgG and IgA antibodies against the RBD of the Delta variant generally rose by day 14 and were maintained for up to two months, whereas the pattern of antibody response to the Omicron variant was less clear. Antibody risings were found to be positively associated with pneumonia, certain underlying conditions (obesity, hypertension, dyslipidemia, and diabetes mellitus), and age ≥ 60 years. Delta variant infections were associated with forgetfulness, hair loss, and headache during the 1-year post-infection period. Females were more likely to experience hair loss, forgetfulness, and joint pain, while older age was associated with joint pain. Conclusions This study enhances our understanding of SARS-CoV-2 infections in Thais, particularly concerning the Delta and Omicron variants. The findings can inform public health planning and response strategies for future outbreaks of SARS-CoV-2 or other emerging viral diseases.

Abstract Background Determination of SARS-CoV-2 variant is significant to prevent the spreads of COVID-19 disease. Methods We aimed to evaluate the variants of SARS-CoV-2 rate in positive patients in Kanuni Sultan Suleyman Training and Research Hospital (KSS-TRH), Istanbul, Türkiye between 1st January and 30th November 2021 by using RT-PCR method. Results Herein, 825,169 patients were evaluated (male:58.53% and female:41.47%) whether COVID-19 positive or not [( +):21.3% and (−):78.7%] and 175,367 patient was described as positive (53.2%-female and 46.8%-male) by RT-PCR. COVID-19 positive rate is observed highest in the 6–15- and 66–75-year age range. The frequencies were obtained as SARS-CoV-2 positive (without mutation of B.1.1.7 [B.1.1.7 (U.K), E484K, L452R, B.1.351 (S. Africa/Brazil) spike mutations] as 66.1% (n: 115,899), B.1.1.7 Variant as 23.2% (n:40,686), Delta mutation (L452R) variant as 9.8% (n:17,182), B.1.351 variant as 0.8% (n:1370) and E484K as 0.1% (n: 230). In April 2021, general SARS-CoV-2 and B.1.1.7 variant were dominantly observed. Up to July 2021, B.1.617.2 (Delta variant/ Indian variant) and E484K has been not observed. B.1.351 variant of SARS-CoV-2 has been started in February 2021 at the rarest ratio and March 2021 is the top point. September 2021 is the pick point of E484K. African/Brazil variant of SARS-CoV-2 has been started in February 2021 at the rarest ratio and March 2021 is the top point. September 2021 is the pick point of E484K. When the gender type is compared within the variants, women were found to be more prevalent in all varieties. Conclusions The meaning of these mutations is very important to understand the transmission capacity of the COVID-19 disease, pandemic episode, and diagnosis of the virus with mutation types. Understanding the variant type is important for monitoring herd immunity and the spread of the disease.

[Display omitted] • Delta variant showed higher viral RNA in multiple organs than omicron in hamsters. • Distinct metabolic responses in major organs of delta vs. omicron-infected hamsters. • Delta infection imprints dysregulated synaptic protein signature in hamsters brain. • Delta infection caused gut dysbiosis with increased inflammation-associated taxa. Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To shed light on the interaction between tissues and SARS-CoV-2 variants, we sought to characterize the complex relationship among acute multisystem manifestations, dysbiosis of the gut microbiota, and the resulting implications for SARS-CoV-2 variant-specific immunopathogenesis in the Golden Syrian Hamster (GSH) model using multi-omics approaches. Our investigation revealed the presence of increased SARS-CoV-2 genomic RNA in diverse tissues of delta-infected GSH compared to the omicron variant. Multi-omics analyses uncovered distinctive metabolic responses between the delta and omicron variants, with the former demonstrating dysregulation in synaptic transmission proteins associated with neurocognitive disorders. Additionally, delta-infected GSH exhibited an altered fecal microbiota composition, marked by increased inflammation-associated taxa and reduced commensal bacteria compared to the omicron variant. These findings underscore the SARS-CoV-2-mediated tissue insult, characterized by modified host metabolites, neurological protein dysregulation, and gut dysbiosis, highlighting the compromised gut-lung-brain axis during acute infection. [ABSTRACT FROM AUTHOR]

Aim: To study the manifestations of the COVID-19 epidemic and the clinical and epidemiological characteristics of adult patients with a new coronavirus infection during the dominance of the Delta SARS-COV-2 in the Russian Federation.Materials and Methods: Study included patients aged ≥18 years with a laboratory-confirmed diagnosis of COVID-19, detected in the period from 09/01/2021 to 11/30/2021 (n= 2 619 298) in 85 Russian regions.Results: There were 2 periods of rise and decline in the COVID-19 incidence and mortality during the spread of the Delta SARS-CoV-2 in Russia: June-September and OctoberDecember 2021 (Wald – Wolfowitz criterion, p

Abstract Naumure Multipurpose Project (NMP) featuring a 169 m high Concrete Face Rock Filled Dam (CFRD) is the proposed reservoir project in the West Rapti River with an installed capacity of 218.34 MW. Most of the rivers in Nepal carry significant sediment loads that will consequently catalyze reservoir sedimentation. This phenomenon prevails as the primary factor in reducing reservoirs useful life, making ineffective for both flood control and hydroelectricity generation. Ultimately, such process of sedimentation has adverse impacts on projects economic feasibility and long-term sustainability. Therefore, the objective of this research was to examine the expected sediment deposition pattern in the NMP reservoir throughout its operational period by employing 1D HEC-RAS model to simulate the sedimentation process. The model was simulated for 10, 20, 30, 40 and 50 years. Yang’s equation as a sediment transport function, Active layer as a bed sorting method and Toffaleti as a fall velocity method were best suited for the river reach. The delta deposition was formed between 11 km and 22 km upstream of the dam region in the Jhimruk river, with the sediment deposition depth reaching peaks of about 23 m, 38 m, 39 m, 41 m and 49 m in 10, 20, 30, 40 and 50 years, respectively. Similarly, the delta deposition was formed between 13 km and 33 km upstream of dam region in the Madi river, with the sediment deposition depth reaching peaks of about 47 m, 62 m, 60 m, 68 m and 75 m in 10, 20, 30, 40 and 50 years respectively. Headcutting of delta deposition occurred between 20 and 30 year due to high flood during low stage of reservoir. Furthermore, the study revealed that about 6.22%, 11.61%, 15.94%, 22.96% and 25.65% of the storage capacity of NMP reservoir will be depleted in 10, 20, 30, 40 and 50 years respectively.

Naumure Multipurpose Project (NMP) featuring a 169 m high Concrete Face Rock Filled Dam (CFRD) is the proposed reservoir project in the West Rapti River with an installed capacity of 218.34 MW. Most of the rivers in Nepal carry significant sediment loads that will consequently catalyze reservoir sedimentation. This phenomenon prevails as the primary factor in reducing reservoirs useful life, making ineffective for both flood control and hydroelectricity generation. Ultimately, such process of sedimentation has adverse impacts on projects economic feasibility and long-term sustainability. Therefore, the objective of this research was to examine the expected sediment deposition pattern in the NMP reservoir throughout its operational period by employing 1D HEC-RAS model to simulate the sedimentation process. The model was simulated for 10, 20, 30, 40 and 50 years. Yang's equation as a sediment transport function, Active layer as a bed sorting method and Toffaleti as a fall velocity method were best suited for the river reach. The delta deposition was formed between 11 km and 22 km upstream of the dam region in the Jhimruk river, with the sediment deposition depth reaching peaks of about 23 m, 38 m, 39 m, 41 m and 49 m in 10, 20, 30, 40 and 50 years, respectively. Similarly, the delta deposition was formed between 13 km and 33 km upstream of dam region in the Madi river, with the sediment deposition depth reaching peaks of about 47 m, 62 m, 60 m, 68 m and 75 m in 10, 20, 30, 40 and 50 years respectively. Headcutting of delta deposition occurred between 20 and 30 year due to high flood during low stage of reservoir. Furthermore, the study revealed that about 6.22%, 11.61%, 15.94%, 22.96% and 25.65% of the storage capacity of NMP reservoir will be depleted in 10, 20, 30, 40 and 50 years respectively. [ABSTRACT FROM AUTHOR]

In recent years, extensive exploration has contributed to significant advancements in the geological formations of the Kuqa Depression. In particular, the Paleogene Kumugeliemu Formation exhibits the development of expansive bedded evaporites. The combination of red sandstone, red mudstone, and gypsum-salt layers holds immense potential as a reservoir and cap association, thereby offering promising prospects for oil and gas exploration. However, our understanding of the sedimentary system and model governing this formation remains limited, impeding progress in the field of oil and gas exploration. To address this gap, this study delved into a detailed examination of the stratigraphy, depositional system, and model of the Kumugeliemu Formation through the application of core samples, logging data, and seismic analyses. The primary objective of this study was to establish a comprehensive theoretical foundation for future oil and gas exploration efforts targeting the Kumugeliemu Formation. The findings revealed a distinct division of the Kumugeliemu Formation into two 3rd order sequences, each characterized by a lowstand systems tract, transgressive systems tract, and highstand systems tract. Moreover, all systems tracts were further subdivided into 14 parasequence sets. During the depositional period of the Kumugeliemu Formation, alluvial fan, delta, and salt lake deposition systems developed from the periphery to the central region of the Kuqa Depression. The alluvial fan mainly exhibited braided channel sedimentary microfacies, whereas the delta region indicated plain distributary channels, submerged distributary channels, and interdistributary sedimentary microfacies. The salt lake area is characterized by shore-shallow lacustrine mud, beach-bar, salt mud flat, and salt flat sedimentary microfacies. Throughout the deposition of the Kumugeliemu Formation, the climate of the Kuqa Depression oscillated between arid and humid. During arid periods, the depression experienced diminished water body extent, heightened salinity levels, and extensive distribution of salt and salt mud flats within the basin, with alluvial fans and delta deposits primarily confined to the basin margins. Conversely, during the humid period, the depression experienced an expansion in the extent of the water bodies, leading to a decrease in salinity levels. The distribution of salt flat and salt mud flat deposits within the basin diminished, whereas alluvial fan and delta deposits advanced extensively across the basin. The establishment and spatial arrangement of the sedimentary system within the Kumugeliemu Formation were governed by a complex interplay of certain factors, such as the semi-closed paleotectonic pattern, paleoclimatic conditions of both dry and wet alternation, and the salt source supply brought by the transgression of the Paleo-Tethys Ocean. The findings of this study offer not only a valuable reference framework for the prospective exploration of hydrocarbon resources within the Kumugeliemu Formation of the Kuqa Depression but also potential insights into the evolution of similar depressions in other basins. [ABSTRACT FROM AUTHOR]

Background: In previous studies, there was an increase in mortality with secondary coinfections in all COVID-19 variants. However, no prior study has explored the association of coinfection with outcomes of hospitalized patients among the COVID-19 variants (Alpha, Delta, and Omicron). Methods: This observational cohort study involved 21,186 patients hospitalized with COVID-19 in 25 hospitals in Texas. Patients were divided into groups by surges of COVID-19: Alpha (November 1, 2020–February 10, 2021), Delta (July 10, 2021–October 14, 2021), and Omicron (December 21, 2021–March 3, 2022). Data were collected from electronic health records using methodology from the Viral Respiratory Illness Universal Study COVID-19 registry (NCT04323787) of COVID-19 hospitalizations. Multivariable Cox-proportional hazard regression model assessed the adjusted effect of different surge periods on mortality. Results: Bacterial coinfections varied among hospitalization surges associated with Alpha (8.5%), Delta (11.7%), and Omicron (11.9%) variants. Adjusted analyses showed a higher 30-day and 90-day mortality in all variants when coinfections were present compared with isolated COVID-19 infection. In particular, 30-day and 90-day mortality were significantly worse with Delta compared to Alpha and Omicron. Conclusions: All variants were associated with a higher mortality when bacterial coinfections were present. Delta was associated with a higher risk-adjusted mortality at 30 days and thereafter. [ABSTRACT FROM AUTHOR]

The northern inlet channel to Jezero crater (Sava Vallis) terminates in a fan‐shaped depositional feature, part of which blends into the separate well‐known western fan delta that is the field site for the Mars 2020 mission's Perseverance rover. Jezero's northern fan potentially represents either a second fan delta within the crater or a distal portion of the western fan. To constrain the fluvial and sedimentological history of Jezero and place the rover's in situ observations in proper geologic context, we photogeologically map the northern fan deposits at a larger mapping scale than previous studies, using ground‐based imaging from the Perseverance rover for context. Fifteen map units are identified using HiRISE‐based interpretations of geologic characteristics and inferred processes as well as crosscutting relative age relationships. Mapped units are also defined based on orbital data from CRISM and THEMIS to assess their compositional signatures. We interpret the northern fan deposits as older than the uppermost blocky unit in the western fan delta, suggesting that they were deposited contemporaneously with or prior to the deposition of the western fan, and under similar climate conditions. The eastern portion of the northern fan deposits shows evidence of fluvial deposition from Sava Vallis, while part of its western side could represent a distal part of the western fan delta. We synthesize our interpretations to present scenarios for the deposition of the northern and western fans, which can help constrain the history of both watersheds and place it into context within the broader Isidis basin region. Plain Language Summary: The Mars 2020 Perseverance rover has primarily focused on using its scientific instruments to study the delta along Jezero crater's western margin. But there are fan‐shaped features that appear to originate from both the crater's western and northern channels ‐ Neretva Vallis and Sava Vallis, respectively. In this project, we compile orbital images, spectroscopy data sets, and images taken by the rover's Mastcam‐Z instrument to investigate whether the northern fan originated from the northern channel or is an outlying part of the western delta. Based on these observations and the geologic map created using them, we show that the northern fan deposits are older than the uppermost unit mapped in the western delta. We also demonstrate how the western portion of the northern fan deposits could be an outer part of the western delta, while the eastern portion may preserve material from Sava Vallis. We show that some units across the northern and western fans are the same or similar, making this work useful as the rover's mission continues. Finally, we present scenarios that could lead to what we see in Jezero today, helping us to understand the potential history of this area and the relationship between the northern and western watersheds. Key Points: Deposition of Jezero crater's northern fan predates that of its western fan blocky material—the western delta's uppermost surficial unitThe northern fan shows evidence of deposition from Sava Vallis, but part of its western region could be a distal part of the western deltaThe stratigraphic and depositional hypotheses presented provide context for the Mars 2020 mission and help constrain the history of both watersheds [ABSTRACT FROM AUTHOR]

Background The emergence and rapid spread of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), poses a significant threat to human health and public safety. While next-generation sequencing (NGS) is capable of detecting and tracking new COVID-19 variants for disease diagnosis and prevention, its high cost and time-consuming nature limit its widespread use. In this study, our aim was to develop a highly adaptable and accurate RT-PCR method for identifying the Delta or BA.1 variants in inactivated COVID-19 vaccine. We devised three two-plex RT-PCR methods targeting specific mutation sites: S: Δ156–157, S: N211-, L212I, and S: Δ142–144, Y145D. The RT-PCR method targeting the S: Δ156–157 mutation site was able to distinguish the Delta variant from other COVID-19 virus strains, while the RT-PCR methods targeting the S: N211-, L212I or S: Δ142–144, Y145D mutation sites were able to distinguish the BA.1 variant from other COVID-19 virus strains. We separately validated these three two-plex RT-PCR methods, and the results demonstrated good linearity, repeatability, reproducibility, and specificity for each method. Moreover, all three methods can be applied in the production of SARS-CoV-2 variant inactivated vaccines, enabling the identification of Delta or BA.1 variants in virus cultures as well as in inactivated vaccine stocks. This study presents a systematic approach to identify COVID-19 variants using multiple RT-PCR methods. We successfully developed three two-plex RT-PCR methods that can identify Delta and BA.1 variants based on specific mutation sites, and we completed the validation of these three methods. [ABSTRACT FROM AUTHOR]

The future of the COVID pandemic and its public health and societal impact will be determined by the profile and spread of emerging variants and the timely identification and response to them. Wastewater surveillance of SARS-CoV-2 has been widely adopted in many countries across the globe and has played an important role in tracking infection levels and providing useful epidemiological information that cannot be adequately captured by clinical testing alone. However, novel variants can emerge rapidly, spread globally, and markedly alter the trajectory of the pandemic, as exemplified by the Delta and Omicron variants. Most mutations linked to the emergence of new SARS-CoV-2 variants are found within variable regions of the SARS-CoV-2 Spike protein. We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the Spike gene: the N-terminal domain and the receptor binding motif. Using this method in an operationalized public health program, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of variant incursion and spread. [ABSTRACT FROM AUTHOR]

The relationship between pangolin-CoV and SARS-CoV-2 has been a subject of debate. Further evidence of a special relationship between the two viruses can be found by the fact that all known COVID-19 viruses have an abnormally hard outer shell (low M disorder, i.e., low content of intrinsically disordered residues in the membrane (M) protein) that so far has been found in CoVs associated with burrowing animals, such as rabbits and pangolins, in which transmission involves virus remaining in buried feces for a long time. While a hard outer shell is necessary for viral survival, a harder inner shell could also help. For this reason, the N disorder range of pangolin-CoVs, not bat-CoVs, more closely matches that of SARS-CoV-2, especially when Omicron is included. The low N disorder (i.e., low content of intrinsically disordered residues in the nucleocapsid (N) protein), first observed in pangolin-CoV-2017 and later in Omicron, is associated with attenuation according to the Shell-Disorder Model. Our experimental study revealed that pangolin-CoV-2017 and SARS-CoV-2 Omicron (XBB.1.16 subvariant) show similar attenuations with respect to viral growth and plaque formation. Subtle differences have been observed that are consistent with disorder-centric computational analysis. [ABSTRACT FROM AUTHOR]

Long, J.H.; Hanebuth, T.J.J.; Durica, J.T., and Hawkes, A.D., 2024. Late Holocene stratigraphy and sedimentary facies distribution of an anthropogenically modified delta plain (Santee River Delta, South Carolina, U.S.A.). Journal of Coastal Research, 40(4), 623–646. Charlotte (North Carolina), ISSN 0749-0208. The Santee River of South Carolina has the second largest watershed in the eastern United States and forms the largest river-fed delta along the U.S. east coast. Anthropogenic modifications to the delta plain of the Santee River, and in many coastal environments within the region, have significantly altered the natural configurations of floodplains, channels, and shorelines. This study incorporated historic and modern state-of-the-art data sets and methods to evaluate the sediment distribution within the modern delta plain as well as the record of environmental change throughout the late Holocene as it is preserved within the subsurface stratigraphy. The study incorporated high-resolution seismo-acoustic and bathymetric data, detailed sediment core analysis, accelerator mass spectrometry 14C dating, micropaleontological analysis, and surface sediment samples to define geomorphic zones based on dominant depositional processes related to fluvial discharge, tides, and waves. Tidal- and wave-influenced conditions were established in the delta plain by around 3 kyr BP and continued into historic times, when the construction of rice fields across most of the delta plain fixed channel positions and isolated floodplains from flood-related sedimentation. Sediment distribution in the modern delta plain is significantly influenced by the maintained network of artificial canals and embankments associated with these historic fields. The influence of these modifications can also be seen within the stratigraphy beneath the delta plain, recording local changes in deposition and erosion that resulted from a modification in water circulation and sediment supply. [ABSTRACT FROM AUTHOR]

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Throughout the COVID-19 pandemic, the emergence of new viral variants has challenged public health efforts, often evading antibody responses generated by infections and vaccinations. This immune escape has led to waves of breakthrough infections, raising questions about the efficacy and durability of immune protection. Here we focus on the impact of SARS-CoV-2 Delta and Omicron spike mutations on ACE-2 receptor binding, protein stability, and immune response evasion. Delta and Omicron variants had 3–5 times higher binding affinities to ACE-2 than the ancestral strain (KDwt = 23.4 nM, KDDelta = 8.08 nM, KDBA.1 = 4.77 nM, KDBA.2 = 4.47 nM). The pattern recognition molecule mannose-binding lectin (MBL) has been shown to recognize the spike protein. Here we found that MBL binding remained largely unchanged across the variants, even after introducing mutations at single glycan sites. Although MBL binding decreased post-vaccination, it increased by 2.6-fold upon IgG depletion, suggesting a compensatory or redundant role in immune recognition. Notably, we identified two glycan sites (N717 and N801) as potentially essential for the structural integrity of the spike protein. We also evaluated the antibody and T cell responses. Neutralization by serum immunoglobulins was predominantly mediated by IgG rather than IgA and was markedly impaired against the Delta (5.8-fold decrease) and Omicron variants BA.1 (17.4-fold) and BA.2 (14.2-fold). T cell responses, initially conserved, waned rapidly within 3 months post-Omicron infection. Our data suggests that immune imprinting may have hindered antibody and T cell responses toward the variants. Overall, despite decreased antibody neutralization, MBL recognition and T cell responses were generally unaffected by the variants. These findings extend our understanding of the complex interplay between viral adaptation and immune response, underscoring the importance of considering MBL interactions, immune imprinting, and viral evolution dynamics in developing new vaccine and treatment strategies.

ObjectiveTo establish lactate and glucose differences between affected and non-affected limbs in cats with feline arterial thromboembolism (FATE). To evaluate the correlation between these values and survival to discharge as well as congestive heart failure (CHF).MethodsBlood glucose and lactate concentrations were prospectively obtained on admission from client-owned FATE cats and client-owned cats presented for other conditions. The glucose and lactate concentrations of the front limbs (or non-affected) and the hind limbs (or affected) were measured. Lactate (Δlactate) and glucose (Δglucose) differences between the two limbs were calculated.ResultsThe FATE group and control groups included 18 and 41 cats, respectively. The median age of the cats within the FATE group and control groups was 9.5 years and 5 years, respectively. The median Δlactate was significantly higher in the FATE group than in the control group (7.2 mmol/L versus 0.1 mmol/L, respectively; p ≤ 0.01). The median Δglucose was significantly higher in the FATE group than in the control group (155 mg/dL versus 3 mg/dL, respectively; p ≤ 0.01). A diagnosis of FATE was made using a ∆lactate cutoff of 2.2 mmol/L (100% sensitivity and 95% specificity) or a ∆glucose cutoff of 41 mg/dL (100% sensitivity and specificity). There was no correlation between Δlactate and Δglucose and survival to discharge. A higher ∆glucose was significantly associated with concurrent CHF (p = 0.01).ConclusionBoth Δlactate and Δglucose were accurate diagnostic tools for cats with FATE. Neither were correlated with survival to discharge. Higher Δglucose values were significantly associated with the presence of CHF.

Study region: The Minjiang River, located on the western side of the Taiwan Strait of East Asia, serves as a typical mountain river estuary system. Study focus: This research investigates the impact of reduced sediment discharge on the geomorphological changes in the Minjiang River estuary delta and its adjacent coasts. By integrating 45 years of shoreline data and nautical chart bathymetry, the study quantitatively delineates tempo-spatial change patterns and reveals the rapid response mechanisms to sediment discharge decrease. New hydrological insights for the region: The study demonstrates that the sandy shoreline near the Minjiang River estuary exhibits distinct tempo-spatial evolution patterns primarily due to decreased sediment discharge. The estuarine transition zone shows greater coastal resilience, with shoals providing essential sediment sources for development, while the shoreline south of the transition zone experiences progressively delayed erosion. The Minjiang River delta reacts swiftly to decreased sediment discharge, with a response time of significantly under ten years. Despite the temporary influence of extreme weather events such as typhoons on erosion states, continuous sediment discharge decrease remains the dominant factor. These insights highlight the heightened sensitivity and rapid adaptability of mountain rivers to environmental shifts, providing significant implications for understanding the repercussions of human activities on estuarine geomorphological alterations.

During January and February 2022, a huge spike in the cases of COVID-19 was recorded in the Khyber Pakhtunkhwa (KP) province of Pakistan prompting the civil administration to institute new restrictions. To investigate the underlying causes of this surge, the regional Public Health Reference Lab (PHRL) launched a screening effort throughout the Province’s remote and urban areas. Herein, we present our survey results during the peak months of the pandemic. The data indicated the prevalence of highly transmissible delta- and Omicron-like virus variants, which may explain the rise in positive cases. Phylogenetic analysis revealed the genetic association between the sequences from this study and those found in Pakistan as well as from geographically distant countries, suggesting a complex evolutionary history. For screening, we deployed an easy-to-use single primer-based polymerase chain reaction (PCR) assay to identify the circulation of SARS-CoV-2. The assay was validated using clinical swabs of COVID-19 patients and obtained consistent results with Sanger sequencing. Our survey identified a patient simultaneously infected with two variants of concern, indicating the presence of the Deltacron variant, although we cannot discount the possibility of sequencing errors. We recommend that SARS-CoV-2 be continuously monitored to detect single nucleotide polymorphisms (SNPs) that are causally linked to the emergence of new lineages. Our method provides a rapid and cost-effective detection assay for SARS-CoV-2 in a resource-constrained setting.

Since emerging in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has repeatedly crossed the species barrier with natural infections reported in various domestic and wild animal species. The emergence and global spread of SARS-CoV-2 variants of concern (VOCs) has expanded the range of susceptible host species. Previous experimental infection studies in cattle using Wuhan-like SARS-CoV-2 isolates suggested that cattle were not likely amplifying hosts for SARS-CoV-2. However, SARS-CoV-2 sero- and RNA-positive cattle have since been identified in Europe, India, and Africa. Here, we investigated the susceptibility and transmission of the Delta and Omicron SARS-CoV-2 VOCs in cattle. Eight Holstein calves were co-infected orally and intranasally with a mixed inoculum of SARS-CoV-2 VOCs Delta and Omicron BA.2. Twenty-four hours post-challenge, two sentinel calves were introduced to evaluate virus transmission. The co-infection resulted in a high proportion of calves shedding SARS-CoV-2 RNA at 1- and 2-days post-challenge (DPC). Extensive tissue distribution of SARS-CoV-2 RNA was observed at 3 and 7 DPC and infectious virus was recovered from two calves at 3 DPC. Next-generation sequencing revealed that only the SARS-CoV-2 Delta variant was detected in clinical samples and tissues. Similar to previous experimental infection studies in cattle, we observed only limited seroconversion and no clear evidence of transmission to sentinel calves. Together, our findings suggest that cattle are more permissive to infection with SARS-CoV-2 Delta than Omicron BA.2 and Wuhan-like isolates but, in the absence of horizontal transmission, are not likely to be reservoir hosts for currently circulating SARS-CoV-2 variants.

The southwestern region of Nigeria, primarily inhabited by the Yoruba people, has a significant Muslim population with a rich history dating back centuries. The establishment of mosques and the spread of Islam in the region was a gradual process that led to the formation of the League of Imams and Alfa in Yorubaland, Edo, and Delta (RābiTah) in 1962. This research examines the history, role, and challenges faced by the RābiTah in advance the interests of Muslims in the region. The research method used is a doctrinal approach with qualitative methods to collect and analyze information related to RābiTah. The study found that, over the years, RābiTah has achieved essential accomplishments such as becoming a respected regional Muslim league, holding annual meetings, resolving disputes, and providing awards to deserving individuals. However, the RābiTah also faced challenges, including encroachments on the Imam's authority, tribalism, political interference, and disputes among the ulama. Additionally, preferences for foreign religious rules and divisions among native clerics posed obstacles to RābiTah's goals. The implications of these findings suggest that to overcome these challenges and achieve its goals, RābiTah must prioritize unity among ulema, establish a governing body for Islamic teachings, learn from international Islamic organizations, advocate for the welfare of Imams, and increase public visibility through educational programs and outreach activities. Hopefully, these recommendations will help Rābitah strengthen its role and contribution to Muslims in the southwest region of Nigeria.

Many cell fate decisions are determined transcriptionally. Accordingly, some fate specification is prevented by Inhibitor of DNA-binding (Id) proteins that interfere with DNA binding by master regulatory transcription factors. We show that the Drosophila Id protein Extra macrochaetae (Emc) also affects developmental decisions by regulating caspase activity. Emc, which prevents proneural bHLH transcription factors from specifying neural cell fate, also prevents homodimerization of another bHLH protein, Daughterless (Da), and thereby maintains expression of the Death-Associated Inhibitor of Apoptosis (diap1) gene. Accordingly, we found that multiple effects of emc mutations on cell growth and on eye development were all caused by activation of caspases. These effects included acceleration of the morphogenetic furrow, failure of R7 photoreceptor cell specification, and delayed differentiation of non-neuronal cone cells. Within emc mutant clones, Notch signaling was elevated in the morphogenetic furrow, increasing morphogenetic furrow speed. This was associated with caspase-dependent increase in levels of Delta protein, the transmembrane ligand for Notch. Posterior to the morphogenetic furrow, elevated Delta cis-inhibited Notch signaling that was required for R7 specification and cone cell differentiation. Growth inhibition of emc mutant clones in wing imaginal discs also depended on caspases. Thus, emc mutations reveal the importance of restraining caspase activity even in non-apoptotic cells to prevent abnormal development, in the Drosophila eye through effects on Notch signaling.

El objetivo de este trabajo es actualizar y mejorar la cartografía existente sobre la distribución espacial de los bosques nativos de la provincia de Buenos Aires. Se desarrolló en el marco de un proyecto de transferencia ejecutado por investigadores del sistema científico tecnológico nacional para la Dirección de Bosques del Ministerio de Ambiente de la Provincia de Buenos Aires. El proyecto se enfocó en diseñar y llevar adelante una metodología para identificar y delimitar coberturas de bosque nativo uniformes para toda la provincia. Para actualizar la cartografía se usó una combinación de información relevada a campo con la interpretación visual de series multitemporales de imágenes ópticas de alta resolución, generalizada usando algoritmos de aprendizaje automático alimentados con información derivada de series de imágenes satelitales multiespectrales Sentinel-2. Los productos obtenidos se evaluaron por medio de la matriz de contingencia calculada a partir de datos etiquetados a campo. Se detalla la metodología utilizada para la clasificación automática, incluyendo la de etiquetado de puntos de entrenamiento, la información espectral empleada para alimentar los clasificadores, la selección de la metodología de clasificación en sí, los detalles del posprocesamiento para cada formación boscosa y la evaluación de los productos finales obtenidos. La delimitación obtenida excluye 235182 ha de las 968397 ha del mapeo vigente —que consideramos no correspondientes a bosque nativo— e incorpora 187512 ha de bosque nativo que no habían sido mapeadas antes. Así, la superficie total de bosque nativo mapeada en la provincia se redujo en 4.9%. La evaluación, realizada mediante 719 puntos etiquetados a campo, asigna una exactitud global de 0.89 y un índice kappa de 0.85 a la clasificación obtenida. Esto indica que la metodología propuesta es adecuada para delimitar bosques nativos en la provincia.

Abstract Mangrove forests are critical coastal ecosystems that provide great socio‐ecological services, which are also highly vulnerable to climate change, particularly to sea level rise (SLR). Here we assess changes in mangrove forests in four distinct river/tide/wave‐dominant large deltas along the Indo‐Pacific coast based on 1,336 remote sensing images by machine learning techniques. We find that mangroves are migrating seaward at a rate of 18% ± 12% m/yr, which can offset landward mangroves loss, 67% of which caused by land use conversion. The fact that mangroves are expanding seaward with accretion rates exceeding SLR suggests that climate change has not yet triggered substantial loss in deltaic mangrove forests. Assuming that present environmental conditions do not change and that sediment and organic deposition in the deltaic topsets match SLR rates, we project that 90% of deltaic mangrove forests may start to retreat after 132–194 years. Early inundation of mangroves will occur in wave‐dominated delta.

Abstract River sediment supply (Qs) and longshore sediment transport (LST) are recognized as two paramount controls on river delta morphodynamics and stratigraphy. We employed the Delft3D model to simulate the evolution of deltas from fluvial to wave‐dominated conditions, revealing the interplay between river‐ and wave‐driven sediment quantities. Wave‐influenced deltas may show alternating accumulation and retreat patterns driven by avulsions and wave‐induced sediment diffusion, posing coastal management challenges. Deltas with higher wave energy evolve under a fine balance between river supply and intense wave‐mediated sediment redistribution and are highly vulnerable under conditions of sediment reduction. Reducing Qs by ∼40%–70%, common in modern dammed rivers, can rapidly shift bypass from ∼0 to 1 (no bypass to complete bypass). This leads to accelerated diffusion and potential sediment loss in modern deltas. The study highlights the importance of accurately computing sediment quantities in real‐world deltas for improved management, especially under increasing anthropogenic and climatic pressures.

Summary: Background: Mouse models that recapitulate key features of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection are important tools for understanding complex interactions between host genetics, immune responses, and SARS-CoV-2 pathogenesis. Little is known about how predominantly cellular (Th1 type) versus humoral (Th2 type) immune responses influence SARS-CoV-2 dynamics, including infectivity and disease course. Methods: We generated knock-in (KI) mice expressing human ACE2 (hACE2) and/or human TMPRSS2 (hTMPRSS2) on Th1-biased (C57BL/6; B6) and Th2-biased (BALB/c) genetic backgrounds. Mice were infected intranasally with SARS-CoV-2 Delta (B.1.617.2) or Omicron BA.1 (B.1.1.529) variants, followed by assessment of disease course, respiratory tract infection, lung histopathology, and humoral and cellular immune responses. Findings: In both B6 and BALB/c mice, hACE2 expression was required for infection of the lungs with Delta, but not Omicron BA.1. Disease severity was greater in Omicron BA.1-infected hTMPRSS2-KI and double-KI BALB/c mice compared with B6 mice, and in Delta-infected double-KI B6 and BALB/c mice compared with hACE2-KI mice. hACE2-KI B6 mice developed more severe lung pathology and more robust SARS-CoV-2-specific splenic CD8 T cell responses compared with hACE2-KI BALB/c mice. There were no notable differences between the two genetic backgrounds in plasma cell, germinal center B cell, or antibody responses to SARS-CoV-2. Interpretation: SARS-CoV-2 Delta and Omicron BA.1 infection, disease course, and CD8 T cell response are influenced by the host genetic background. These humanized mice hold promise as important tools for investigating the mechanisms underlying the heterogeneity of SARS-CoV-2-induced pathogenesis and immune response. Funding: This work was funded by NIH U19 AI142790-02S1, the GHR Foundation, the Arvin Gottleib Foundation, and the Overton family (to SS and EOS); Prebys Foundation (to SS); NIH R44 AI157900 (to KJ); and by an American Association of Immunologists Career Reentry Fellowship (FASB).

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), rapidly spread across the globe in 2019. With the emergence of the Omicron variant, COVID-19 shifted into an endemic phase. Given the anticipated rise in cases during the fall and winter seasons, the strategy of implementing seasonal booster vaccines for COVID-19 is becoming increasingly valuable to protect public health. This practice already exists for seasonal influenza vaccines to combat annual influenza seasons. Our goal was to investigate an easily modifiable vaccine platform for seasonal use against SARS-CoV-2. In this study, we evaluated the genetically modified influenza virus ΔNA(RBD) as an intranasal vaccine candidate for COVID-19. This modified virus was engineered to replace the coding sequence for the neuraminidase (NA) protein with a membrane-anchored form of the receptor binding domain (RBD) protein of SARS-CoV-2. We designed experiments to assess the protection of ΔNA(RBD) in K18-hACE2 mice using lethal (Delta) and non-lethal (Omicron) challenge models. Controls of COVID-19 mRNA vaccine and our lab’s previously described intranasal virus like particle vaccine were used as comparisons. Immunization with ΔNA(RBD) expressing ancestral RBD elicited high anti-RBD IgG levels in the serum of mice, high anti-RBD IgA in lung tissue, and improved survival after Delta variant challenge. Modifying ΔNA(RBD) to express Omicron variant RBD shifted variant-specific antibody responses and limited viral burden in the lungs of mice after Omicron variant challenge. Overall, this data suggests that ΔNA(RBD) could be an effective intranasal vaccine platform that generates mucosal and systemic immunity towards SARS-CoV-2.

BackgroundMost research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants focuses on initial symptomatology with limited longer-term data. We characterized prevalences of prolonged symptoms 3 months post-SARS-CoV-2 infection across 3 variant time-periods (pre-Delta, Delta, and Omicron).MethodsThis multicenter prospective cohort study of adults with acute illness tested for SARS-CoV-2 compared fatigue severity, fatigue symptoms, organ system-based symptoms, and ≥3 symptoms across variants among participants with a positive ("COVID-positive") or negative SARS-CoV-2 test ("COVID-negative") at 3 months after SARS-CoV-2 testing. Variant periods were defined by dates with ≥50% dominant strain. We performed multivariable logistic regression modeling to estimate independent effects of variants adjusting for sociodemographics, baseline health, and vaccine status.ResultsThe study included 2402 COVID-positive and 821 COVID-negative participants. Among COVID-positives, 463 (19.3%) were pre-Delta, 1198 (49.9%) Delta, and 741 (30.8%) Omicron. The pre-Delta COVID-positive cohort exhibited more prolonged severe fatigue (16.7% vs 11.5% vs 12.3%; P = .017) and presence of ≥3 prolonged symptoms (28.4% vs 21.7% vs 16.0%; P < .001) compared with the Delta and Omicron cohorts. No differences were seen in the COVID-negatives across time-periods. In multivariable models adjusted for vaccination, severe fatigue and odds of having ≥3 symptoms were no longer significant across variants.ConclusionsProlonged symptoms following SARS-CoV-2 infection were more common among participants infected during pre-Delta than with Delta and Omicron; however, these differences were no longer significant after adjusting for vaccination status, suggesting a beneficial effect of vaccination on risk of long-term symptoms. Clinical Trials Registration. NCT04610515.

This study analyzed the role of electric charge in human viral infections. Examples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), dengue, Ebola, influenza A, and respiratory syncytial virus (RSV) are presented. Charge distribution in SARS-CoV-2 and electrostatic interactions of SARS-CoV-2 with its receptor, angiotensin-converting enzyme 2 (ACE2), were evaluated, and the mean time required for respired SARS-CoV-2 virus attachment was evaluated. The virus–cell attachment modality of all of the above viruses was calculated. The impact of electric charge on other viral-related processes, such as replication of virion material, release, and immune response, was also discussed. Special charge conditions in virus treatments were also indicated.

The article is devoted to the stylometric analysis of stories written by Jorge Luis Borges and Adolfo Bioy Casares under the common pseudonym Honorio Bustos Domecq. The work poses two questions: 1) Is Bustos Domecq’s style different from the writing style of Borges and Bioy Casares? 2) What is the share of influence of each of the co-authors on the formation of Bustos Domecq's style? To solve research problems, it is used Delta method, one of the most reliable stylometric tools to date; as well as the support vector machine, a common machine learning method that is used to solve classification problems. It turns out that Bustos Domecq's style differs from the style of the stories of Borges and Bioy Casares. However, in the texts of Bustos Domecq the authorial signal of Bioy Casares predominates, which is revealed on the basis of both stylometric and historical-literary analysis. The influence of Borges is more clearly manifested only in the first stories (1940s), when Bioy Caceres is a literary disciple of Borges, and in the second half of the 1960s, at a time of serious emotional upheavals for Borges, as well as his world recognition. Analysis of the topics of the stories, where Borges's authorial signal predominates, also confirms the results of stylometric experiments: the story “The Long Search for Tai An”, as well as the first texts of the collection The Chronicles of Bustos Domec “Tribute to Cesar Paladion”, “An Evening with Ramon Bonavena” and others really correspond to the poetics of Borges.

The estuarine delta is a densely populated and economically developed region, and its land use change research is of great significance for regional economic and social development. In this paper, the remote sensing images from 1987 to 2019 are classified, and the digital coastline system is used to analyze the change rate of coastline, and then explore the relationship between the two and the influencing factors. The results indicate that: From 1987 to 2019, the area of construction land, wetlands, and aquaculture ponds increased, with the area of construction land increasing by 57.34 km2, while the area of cultivated land, terrestrial vegetation, and water bodies decreased. From 1987 to 2019, the annual average rate of shoreline advancement was 33.90 m/a, and the direction of shoreline development was seaward extension, indicating that the shoreline was in a state of growth. The change of coastline is strongly associated with the change of land use type. This study provides reference for the protection and utilization of natural resources in the Qin River Delta.

Objectives: Studies have shown temporal changes in post-acute sequelae of COVID-19 (PASC) prevalence for early SARS-CoV-2 variants, although often lacking controls. This prospective study assesses the prevalence of symptoms in Delta- and Omicron-infected cases up to 12 months compared with population controls. Methods: Adult participants filled out surveys every 3 months (T0-T12) between July 2021 and August 2023. Cases were recruited with a positive SARS-CoV-2 test during the Delta or Omicron domination. Population controls were randomly invited from the Dutch Personal Records Database. Participants indicated the presence of 13 PASC-associated symptoms, and severity scores of fatigue, cognitive impairment, dyspnea, and pain. PASC prevalence was defined as the excess prevalence of havingat least one PASC-associated symptom in cases compared with population controls. Results: PASC prevalence was 34.3% at T3 and decreased to 21.7% at T12 for Delta and decreased from 18.7% at T3 to 16.7% at T12 for Omicron. At T12, the difference between Delta and Omicron was not significant. Delta cases generally had higher excess symptom scores for fatigue, dyspnea, and cognitive impairment than Omicron. Conclusions: In the first 9 months after infection, PASC prevalence was higher for Delta than Omicron, but the difference reduced over time and approximated after 12 months.

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.