bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences in the gut microbiome composition of Korean children and adult samples based on different DNA isolation kits
Authors: Baek Changyoon , Kim Woo Jin , Moon JaeWoo , Moon Seo Yoon , Kim Wonsub , Hu Hae-Jin , Min Junhong
Published: March 2022

Recent studies have revealed that the composition of human gut microbiota varies according to region, race, age, diet, living environment, and sampling and DNA extraction method. The purpose of this study was to broaden our understanding of the intestinal microbial composition of Koreans by conducting a 16S rRNA amplicon sequencing on 78 Korean samples composed of adults, children, normal and obese groups. We compared the microbiome composition and diversity of these groups at different levels including the phylum and genus level using two different stool DNA extraction kits of QIAamp® PowerFecal® DNA Kit (Qiagen, Hilden, Germany) and CT Max Fecal DNA Kit (Ct bio, Korea). We found that Ct bio (Ct) kit recovered higher DNA yields and OTUs than QIAamp® PowerFecal® DNA Kit (Qia). The Ct kit, which adopted more rigorous bead beating method, detected the most Gram-positive (G+) bacteria, Firmicutes, at the Phylum level, whereas the Qia kit, which used a less rigorous cell lysis method, found the most Gram-negative (G-) bacteria, Bacteroidetes. The Firmicutes-to-Bacteroidetes (F/B) ratio showed no significant difference between the obese and the normal groups of same kit; however, they were significantly different with two different kits. There was a difference in the intestinal flora between healthy Korean adults and children. The taxa that differed significantly between the adults and children were Bacteroides, Bifidobacterium, Prevotella, and Subdoligranulum. There was no significant difference in the intestinal flora between the normal weight group and the obese group in adults and children, respectively. This is probably because the difference in body mass index (BMI) between the sample groups collected in this study is statistically significant, but it is not large enough to show a clear difference in the flora. Therefore, these results should be interpreted with caution while considering the BMI values and Korean obesity criterion together.
Pandemic effects to autonomous vehicles test operations in California
Authors: Tan Adrian Chen Yang
Published: March 2022

Companies developing automated driving system (ADS) technologies have spent heavily in recent years to conduct live testing of autonomous vehicles operating in real world environments to ensure their reliable and safe operations. However, the unexpected onset and ongoing resurgent effects of the Covid-19 pandemic starting in March 2020 has serve to halt, change, or delay the achievement of these new product development test objectives. This study draws on data obtained from the California automated vehicle test program to determine the extent that testing trends, test resumptions, and test environments have been affected by the pandemic. The importance of government policies to support and enable autonomous vehicles development during pandemic conditions is highlighted.
Topical estrogen application promotes cutaneous wound healing in db/db female mice with type 2 diabetes
Authors: Mukai Kanae , Horike Shin-ichi , Meguro-Horike Makiko , Nakajima Yukari , Iswara Arya , Nakatani Toshio
Published: March 2022

Female sex hormones are beneficial effects for wound healing. However, till date, whether topical estrogen application can promote cutaneous wound healing in diabetes remains unclear. Therefore, the present study aimed to validate the effect of topical estrogen application on cutaneous wound healing in a type 2 diabetes db/db mice model. In total, 22 db/db female mice with type 2 diabetes and eight C57BL/6J female mice were subjected to two full-thickness wound injuries. The mice were divided into the db/db, db/db + estrogen, db/db + vehicle, and wild type (WT) groups. Wound healing was assessed until day 14. The db/db group had a significantly high wound area ratio (wound area/initial wound area) on days 3–14 and a significantly low re-epithelialization ratio on days 7 and 14. Moreover, their angiogenesis ratio was significantly low on day 7 and high on day 14. In contrast, compared with the db/db group, the db/db + estrogen group had a significantly lower wound area ratio on days 1–14 and angiogenesis ratio on day 14, thereby indicating early withdrawal of new blood vessels, as well as a significantly higher re-epithelialization ratio on days 7 and 14 and Ym1+ M2 macrophage/macrophage ratio on day 7. Moreover, microarray analysis showed that the top 10 upregulated or downregulated genes in the db/db group were reversed by estrogen treatment, particularly on day 14, in comparison with the WT group. Thus, topical estrogen application reduced the wound area, promoted re-epithelialization and angiogenesis, and increased the number of M2 macrophages in mice with type 2 diabetes. Furthermore, it improved the differential regulation of genes in db/db mice. Therefore, such treatment can enhance cutaneous wound healing in female mice with type 2 diabetes.
CD9 and folate receptor overexpression are not sufficient for VSV-G-independent lentiviral transduction
Authors: Bellotti Cristina , Stäuble Andreas , Steinfeld Robert
Published: March 2022

Extracellular vesicles have become a research focus for their potential as therapeutic vehicles that carry cargo substances. Extracellular vesicles may origin from the endosomal compartment and share several characteristics with the envelope of lentiviruses. A previous study reported that constitutive expression of the tetraspanin CD9, an extracellular vesicle marker, not only increases vesicle secretion from cells, but has also a positive effect on lentiviral transduction efficiency. Moreover, it was shown that expression of CD9 on the viral envelope in absence of viral glycoproteins was sufficient for the transduction of mammalian cells. In this study, we investigate the effect of CD9 and folate receptor alpha, a GPI-anchored protein, on biosynthesis and transduction efficiency of vesicles carrying lentiviral vectors. We demonstrate that neither CD9 nor FRα nor the combination of both were able to mediate a significant transduction of therapeutic vesicles carrying lentiviral RNA. Further studies are required to identify endogenous mammalian proteins that can be used for pseudotyping of viral envelopes to improve viral targeting without inducing immune responses.
Elevated levels of salivary α- amylase activity in saliva associated with reduced odds of obesity in adult Qatari citizens: A cross-sectional study
Authors: Al-Akl Neyla , Thompson Richard I. , Arredouani Abdelilah
Published: March 2022

The relationship between salivary α-amylase activity (ssAAa) and the risk of metabolic disorders remains equivocal. We aimed to assess this relationship in adults from Qatar, where obesity and type 2 diabetes are highly prevalent. We cross-sectionally quantified ssAAa in saliva and estimated AMY1 CN from whole-genome sequencing data from 1499 participants. Linear regression was used to assess the relationship between ssAAa and adiposity and glycemic markers. Logistic regression was used to examine the association between ssAAa and occurrence of obesity or diabetes. The mean and median ssAAa were significantly lower in obese individuals. There were significant inverse associations between ssAAa and BMI, and fat mass. We detected a marked effect of ssAAa on reduced odds of obesity after adjusting for age and sex, glucose, LDL, HLD, total cholesterol, and systolic and diastolic blood pressure (OR per ssAAa unit 0.998 [95% CI 0.996–0.999], p = 0.005), with ssAAa ranging between 6.8 and 422U/mL. The obesity odds were significantly lower in the upper half of the ssAAa distributional (OR 0.58 [95% CI 0.42–0.76], p<0.001) and lower in the top versus the bottom decile of the ssAAa distribution (OR 0.46 [95% CI 0.23–0.92], p = 0.03). Our findings suggest a potential beneficial relationship between high sAAa in saliva and low odds of obesity in Qatari adults.
Predictors of tuberculosis incidence and the effects of multiple deprivation indices on tuberculosis management in OR Tambo district over a 5-year period
Authors: Dlatu Ntandazo , Longo-Mbenza Benjamin , Apalata Teke
Published: March 2022

Background

This study investigated the associations between socio-economic deprivation and tuberculosis (TB) treatment outcomes, alongside well-known TB risk factors. The effects of healthcare expenditures and their growth on trends in TB incidence from 2009 to 2013 were also assessed.

Methods

Secondary data analysis was performed on data obtained from various sources including governmental, non-governmental and research institutions. Indicators for TB treatment outcomes included TB death rate, TB rate among the household contacts of the Index TB cases, TB treatment failure, HIV associated TB death rate, TB defaulter rate, and new TB smear positive cases. Analysis of variance (ANOVA) and Turkey’s tests for post-hoc analysis were used to compare means of variables of interest considering a type I error rate of 0.05. Regression models and canonical discriminant analysis (CDA) were used to explore the associations between trends in TB incidence and independent TB predictors. During CDA, Fischer’s linear functions, Eigen values, and Mahalanobis distances were determined with values of Wilk’s Lambda closer to zero being the evidence for well discriminated patient groups. Data analysis was performed using SPSS® statistical software version 23.0 (Chicago, IL).

Results

In total, 62 400 records of TB notification were analyzed for the period 2009–2013. The average TB incidence rate over a 5-year period was 298 cases per 100,000 inhabitants per year. The incidence of TB was reduced by 79.70% at the end of the evaluation as compared to the baseline data in 2009. Multiple linear regression analysis showed that the Expenditure per patient day equivalent (PDE) and PHC expenditure per capita were significantly and independently associated with the decline of TB incidence (adjusted R2= 60%; ρ = 0.002) following the equation:Y = (- 209× Expenditure per PDE) + (- 0.191 × PHC expenditure per capita). CDA showed that in the most socio-economically deprived communities (quintile 1), HIV associated TB death rates were significantly more likely to be higher as compared to the least socio-economically deprived group (quintile 5) [Eigen value (12.95), function coefficient (1.49) > (.77); Wilk’s Lambda = .019, p < .0001].

Conclusions

Although TB control programs in OR Tambo district have averted thousands of TB incident cases, their effects on HIV associated TB deaths among the most deprived communities remain insignificant. There is an urgent need for strengthening integration of TB/HIV services in most deprived settings.
Comparative statistical analysis of the release kinetics models for nanoprecipitated drug delivery systems based on poly(lactic-co-glycolic acid)
Authors: Heredia Nathaly S. , Vizuete Karla , Flores-Calero Marco , Pazmiño V. Katherine , Pilaquinga Fernanda , Kumar Brajesh , Debut Alexis
Published: March 2022

Poly(lactic-co-glycolic acid) is one of the most used polymers for drug delivery systems (DDSs). It shows excellent biocompatibility, biodegradability, and allows spatio-temporal control of the release of a drug by altering its chemistry. In spite of this, few formulations have reached the market. To characterize and optimize the drug release process, mathematical models offer a good alternative as they allow interpreting and predicting experimental findings, saving time and money. However, there is no general model that describes all types of drug release of polymeric DDSs. This study aims to perform a statistical comparison of several mathematical models commonly used in order to find which of them best describes the drug release profile from PLGA particles synthesized by nanoprecipitation method. For this purpose, 40 datasets extracted from scientific articles published since 2016 were collected. Each set was fitted by the models: order zero to fifth order polynomials, Korsmeyer-Peppas, Weibull and Hyperbolic Tangent Function. Some data sets had few observations that do not allow to apply statistic test, thus bootstrap resampling technique was performed. Statistic evidence showed that Hyperbolic Tangent Function model is the one that best fit most of the data.
Predicting mechanical ventilation effects on six human tissue transcriptomes
Authors: Somekh Judith , Lotan Nir , Sussman Ehud , Yehuda Gur Arye
Published: March 2022

Background

Mechanical ventilation (MV) is a lifesaving therapy used for patients with respiratory failure. Nevertheless, MV is associated with numerous complications and increased mortality. The aim of this study is to define the effects of MV on gene expression of direct and peripheral human tissues.

Methods

Classification models were applied to Genotype-Tissue Expression Project (GTEx) gene expression data of six representative tissues–liver, adipose, skin, nerve-tibial, muscle and lung, for performance comparison and feature analysis. We utilized 18 prediction models using the Random Forest (RF), XGBoost (eXtreme Gradient Boosting) decision tree and ANN (Artificial Neural Network) methods to classify ventilation and non-ventilation samples and to compare their prediction performance for the six tissues. In the model comparison, the AUC (area under receiver operating curve), accuracy, precision, recall, and F1 score were used to evaluate the predictive performance of each model. We then conducted feature analysis per each tissue to detect MV marker genes followed by pathway enrichment analysis for these genes.

Results

XGBoost outperformed the other methods and predicted samples had undergone MV with an average accuracy for the six tissues of 0.951 and average AUC of 0.945. The feature analysis detected a combination of MV marker genes per each tested tissue, some common across several tissues. MV marker genes were mainly related to inflammation and fibrosis as well as cell development and movement regulation. The MV marker genes were significantly enriched in inflammatory and viral pathways.

Conclusion

The XGBoost method demonstrated clear enhanced performance and feature analysis compared to the other models. XGBoost was helpful in detecting the tissue-specific marker genes for identifying transcriptomic changes related to MV. Our results show that MV is associated with reduced development and movement in the tissues and higher inflammation and injury not only in direct tissues such as the lungs but also in peripheral tissues and thus should be carefully considered before being implemented.
Risk factors for complicated grief among family members bereaved in intensive care unit settings: A systematic review
Authors: Sanderson Emma A. M. , Humphreys Sally , Walker Fiona , Harris Daniel , Carduff Emma , McPeake Joanne , Boyd Kirsty , Pattison Natalie , Lone Nazir I.
Published: March 2022

Background

Families of intensive care unit (ICU) decedents are at increased risk of experiencing complicated grief. However, factors associated with complicated grief in ICU and bereavement needs assessment are not available routinely. We aimed to conduct a systematic review identifying risk factors associated with complicated grief among family members of ICU decedents.

Materials and methods

MEDLINE, EMBASE, CINAHL, PsycINFO, the Cochrane Library and Web of Science were searched to identify relevant articles. Observational studies and randomised and non-randomised controlled trials were included. Studies were screened and quality appraised in duplicate. Risk of bias was assessed using Newcastle-Ottawa Scale. A narrative synthesis was undertaken.

Results

Seven studies conducted across three continents were eligible. Four studies were of high quality. 61 risk factors were investigated across the studies. Factors associated with a decreased risk of complicated grief included age, patient declining treatment and involvement in decision-making. Factors associated with increased risk included living alone, partner, dying while intubated, problematic communication, and not having the opportunity to say goodbye.

Conclusion

This systematic review has identified risk factors which may help identify family members at increased risk of complicated grief. Many of the studies has small sample sizes increasing the risk of erroneously reporting no effect due to type II error. Some factors are specific to the ICU setting and are potentially modifiable. Bereavement services tailored to the needs of bereaved family members in ICU settings are required. (PROSPERO registration ID 209503)
Modeling hepatitis C micro-elimination among people who inject drugs with direct-acting antivirals in metropolitan Chicago
Authors: Tatara Eric , Gutfraind Alexander , Collier Nicholson T. , Echevarria Desarae , Cotler Scott J. , Major Marian E. , Ozik Jonathan , Dahari Harel , Boodram Basmattee
Published: March 2022

Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease and mortality worldwide. Direct-acting antiviral (DAA) therapy leads to high cure rates. However, persons who inject drugs (PWID) are at risk for reinfection after cure and may require multiple DAA treatments to reach the World Health Organization’s (WHO) goal of HCV elimination by 2030. Using an agent-based model (ABM) that accounts for the complex interplay of demographic factors, risk behaviors, social networks, and geographic location for HCV transmission among PWID, we examined the combination(s) of DAA enrollment (2.5%, 5%, 7.5%, 10%), adherence (60%, 70%, 80%, 90%) and frequency of DAA treatment courses needed to achieve the WHO’s goal of reducing incident chronic infections by 90% by 2030 among a large population of PWID from Chicago, IL and surrounding suburbs. We also estimated the economic DAA costs associated with each scenario. Our results indicate that a DAA treatment rate of >7.5% per year with 90% adherence results in 75% of enrolled PWID requiring only a single DAA course; however 19% would require 2 courses, 5%, 3 courses and <2%, 4 courses, with an overall DAA cost of $325 million to achieve the WHO goal in metropolitan Chicago. We estimate a 28% increase in the overall DAA cost under low adherence (70%) compared to high adherence (90%). Our modeling results have important public health implications for HCV elimination among U.S. PWID. Using a range of feasible treatment enrollment and adherence rates, we report robust findings supporting the need to address re-exposure and reinfection among PWID to reduce HCV incidence.
Introduction to the PLOS ONE collection on ‘Understanding and preventing suicide: Towards novel and inclusive approaches’
Authors: Robinson Jo , Kolves Kairi , Sisask Merike
Published: March 2022

More than 700,000 people lose their lives to suicide each year and evidence suggests that the current COVID-19 pandemic is leading to increases in risk factors for suicide and suicide-related behaviour, in particular among young people. It is widely documented that some sectors of the population are over-represented in the suicide statistics. It is also well established that the pathways that lead someone to a suicidal crisis are complex and differ across regions and sectors of the population; as such a multi-faceted approach to prevention is required. Many of us would also argue that novel approaches, that combine broad population-based strategies with individual interventions, and approaches that capitalise on new technologies and methodologies are also required. For these reasons, when bringing together this collection, we deliberately sought studies that focused upon those groups who are over-represented in the suicide statistics yet under-represented in research. We also called for studies that reported on novel approaches to suicide prevention and for studies that reflected the voices of people with lived experience of suicide, also often unheard in research efforts.
TNF-α induces Claudin-1 expression in renal tubules in Alport mice
Authors: Iida Manami , Ohtomo Shuichi , Wada Naoko A. , Ueda Otoya , Tsuboi Yoshinori , Kurata Atsuo , Jishage Kou-ichi , Horiba Naoshi
Published: March 2022

Claudin-1 (CL-1) is responsible for the paracellular barrier function of glomerular parietal epithelial cells (PEC) in kidneys, but the role of CL-1 in proximal tubules remains to be elucidated. In this study, to evaluate CL-1 as a potential therapeutic drug target for chronic kidney disease, we investigated change of CL-1 expression in the proximal tubules of diseased kidney and elucidated the factors that induced this change. We established Alport mice as a kidney disease model and investigated the expression of CL-1 in diseased kidney using quantitative PCR and immunohistochemistry (IHC). Compared to wild type mice, Alport mice showed significant increases in plasma creatinine, urea nitrogen and urinary albumin excretion. CL-1 mRNA was increased significantly in the kidney cortex and CL-1 was localized on the adjacent cell surfaces of PECs and proximal tubular epithelial cells. The infiltration of inflammatory cells around proximal tubules and a significant increase in TNF-α mRNA were observed in diseased kidneys. To reveal factors that induce CL-1, we analyzed the induction of CL-1 by albumin or tumor necrosis factor (TNF)-α in human proximal tubular cells (RPTEC/TERT1) using quantitative PCR and Western blotting. TNF-α increased CL-1 expression dose-dependently, though albumin did not affect CL-1 expression in RPTEC/TERT1. In addition, both CL-1 and TNF-α expression were significantly increased in UUO mice, which are commonly used as a model of tubulointerstitial inflammation without albuminuria. These results indicate that CL-1 expression is induced by inflammation, not by albuminuria in diseased proximal tubules. Moreover, we examined the localization of CL-1 in the kidney of IgA nephropathy patients by IHC and found CL-1 expression was also elevated in the proximal tubular cells. Taken together, CL-1 expression is increased in the proximal tubular epithelial cells of diseased kidney. Inflammatory cells around the tubular epithelium may produce TNF-α which in turn induces CL-1 expression.
On heights and plains: How rodents from different habitats cope with three-dimensional environments?
Authors: Hagbi Zohar , Eilam David
Published: March 2022

Dwelling in a specific habitat requires adaptation to the habitat physical and biological properties in order to maximize fitness. Adaptations that are manifested in the organization of behavior in time and space reflect how the environment is perceived and utilized. Testing species from different habitats in the same laboratory environment can uncover the differences in their behavior and their adaptations to specific habitats. The question posed in this study is that of how two rodent species, one occupying flatlands (Tristram’s jird; Meriones tristrami) and the other occupying structured rocky habitats (common spiny mouse; Acomys dimidiatus), differ in the way that they explore the same three-dimensional laboratory environment. Individuals of these two species were introduced into an arena with a five-level ziggurat in the center, and their behavior was followed for 60 min. We found that both species preserved the typical spatiotemporal rodents’ behavior of establishing a home-base—a location that is a terminal from which they set out to explore the environment. However, the jirds, which live in flatlands, mainly travelled on the arena floor and the lower levels of the ziggurat; while, in contrast, the spiny mice, which live in rocky habitats and are used to climbing, mostly remained and travelled on the ziggurat, with some of them hardly descending to the arena floor. We suggest that the distinction in spatial behavior between the two species reflects their different motor abilities, different depth perception, and different umvelt (perceived world), in accordance with their different natural habitats.
High maternal BMI and low maternal blood BDNF may determine the limit of detection of amniotic fluid BDNF throughout gestation: Analysis of mother-fetus trios and literature review
Authors: Flöck Anne , Odainic Alexandru , Dolscheid-Pommerich Ramona , Jaskolski Michael Robert , Diedrich Anna Katharina , Puth Marie Therese , Schmidt Susanne , Stoffel-Wagner Birgit , Strizek Brigitte , Gembruch Ulrich , Merz Waltraut Maria
Published: March 2022

Objective

An increasing number of studies show the importance of brain-derived neurotrophic factor (BDNF) acting at the feto-placental interface, however, only a few studies describe BDNF levels in amniotic fluid (AF).

Methods

In this cross-sectional, prospective study, 109 maternal blood-amniotic fluid pairs (including 66 maternal blood-fetal-blood-amniotic fluid trios) were analyzed. BDNF concentrations were measured with a commercially available immunoassay.

Results

In 71 AF from 109 samples, AF-BDNF concentrations were below the lowest limit of Quantitation (LLoQ) of 1.19 pg/ml (group A), leaving 38 samples with measurable BDNF concentrations (group B). Patients in group A showed significantly higher maternal BMI before pregnancy (mean±SD 26.3± 6.7 (kg/m2) vs. 23.8 ±4.5 (kg/m2) p = 0.04) and lower maternal blood BDNF concentrations than the other group (mean±SD 510.6 ± 554.7 pg/ml vs. mean±SD 910.1± 690.1 pg/ml; p<0.0001). Spearman correlation showed a negative correlation between maternal BMI before pregnancy and maternal BDNF concentrations (r = -0.25, p = 0.01).

Conclusion

Our study is the first to correlate AF-BDNF samples with the corresponding maternal and fetal blood-BDNF samples. The significant negative correlation between maternal BMI before pregnancy and maternal BDNF and AF-BDNF concentrations below the limit of detection has to be evaluated in further studies.
The non-ELR CXC chemokine encoded by human cytomegalovirus UL146 genotype 5 contains a C-terminal β-hairpin and induces neutrophil migration as a selective CXCR2 agonist
Authors: Berg Christian , Wedemeyer Michael J. , Melynis Motiejus , Schlimgen Roman R. , Hansen Lasse H. , Våbenø Jon , Peterson Francis C. , Volkman Brian F. , Rosenkilde Mette M. , Lüttichau Hans R.
Published: March 2022

Human cytomegalovirus (HCMV) is a major pathogen in immunocompromised patients. The UL146 gene exists as 14 diverse genotypes among clinical isolates, which encode 14 different CXC chemokines. One genotype (vCXCL1GT1) is a known agonist for CXCR1 and CXCR2, while two others (vCXCL1GT5and vCXCL1GT6) lack the ELR motif considered crucial for CXCR1 and CXCR2 binding, thus suggesting another receptor targeting profile. To determine the receptor target for vCXCL1GT5, the chemokine was probed in a G protein signaling assay on all 18 classical human chemokine receptors, where CXCR2 was the only receptor being activated. In addition, vCXCL1GT5recruited β-arrestin in a BRET-based assay and induced migration in a chemotaxis assay through CXCR2, but not CXCR1. In contrast, vCXCL1GT1stimulated G protein signaling, recruited β-arrestin and induced migration through both CXCR1 and CXCR2. Both vCXCL1GT1and vCXCL1GT5induced equally potent and efficacious migration of neutrophils, and ELR vCXCL1GT4and non-ELR vCXCL1GT6activated only CXCR2. In contrast to most human chemokines, the 14 UL146 genotypes have remarkably long C-termini. Comparative modeling using Rosetta showed that each genotype could adopt the classic chemokine core structure, and predicted that the extended C-terminal tail of several genotypes (including vCXCL1GT1, vCXCL1GT4, vCXCL1GT5, and vCXCL1GT6) forms a novel β-hairpin not found in human chemokines. Secondary NMR shift and TALOS+ analysis of vCXCL1GT1supported the existence of two stable β-strands. C-terminal deletion of vCXCL1GT1resulted in a non-functional protein and in a shift to solvent exposure for tryptophan residues likely due to destabilization of the chemokine fold. The results demonstrate that non-ELR chemokines can activate CXCR2 and suggest that the UL146 chemokines have unique C-terminal structures that stabilize the chemokine fold. Increased knowledge of the structure and interaction partners of the chemokine variants encoded by UL146 is key to understanding why circulating HCMV strains sustain 14 stable genotypes.
Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates
Authors: Corry Jacqueline , Kettenburg Gwenddolen , Upadhyay Amit A. , Wallace Megan , Marti Michelle M. , Wonderlich Elizabeth R. , Bissel Stephanie J. , Goss Kyndal , Sturgeon Timothy J. , Watkins Simon C. , Reed Douglas S. , Bosinger Steven E. , Barratt-Boyes Simon M.
Published: March 2022

Severe influenza kills tens of thousands of individuals each year, yet the mechanisms driving lethality in humans are poorly understood. Here we used a unique translational model of lethal H5N1 influenza in cynomolgus macaques that utilizes inhalation of small-particle virus aerosols to define mechanisms driving lethal disease. RNA sequencing of lung tissue revealed an intense interferon response within two days of infection that resulted in widespread expression of interferon-stimulated genes, including inflammatory cytokines and chemokines. Macaques with lethal disease had rapid and profound loss of alveolar macrophages (AMs) and infiltration of activated CCR2+ CX3CR1+ interstitial macrophages (IMs) and neutrophils into lungs. Parallel changes of AMs and neutrophils in bronchoalveolar lavage (BAL) correlated with virus load when compared to macaques with mild influenza. Both AMs and IMs in lethal influenza were M1-type inflammatory macrophages which expressed neutrophil chemotactic factors, while neutrophils expressed genes associated with activation and generation of neutrophil extracellular traps (NETs). NETs were prominent in lung and were found in alveolar spaces as well as lung parenchyma. Genes associated with pyroptosis but not apoptosis were increased in lung, and activated inflammatory caspases, IL-1β and cleaved gasdermin D (GSDMD) were present in bronchoalveolar lavage fluid and lung homogenates. Cleaved GSDMD was expressed by lung macrophages and alveolar epithelial cells which were present in large numbers in alveolar spaces, consistent with loss of epithelial integrity. Cleaved GSDMD colocalized with viral NP-expressing cells in alveoli, reflecting pyroptosis of infected cells. These novel findings reveal that a potent interferon and inflammatory cascade in lung associated with infiltration of inflammatory macrophages and neutrophils, elaboration of NETs and cell death by pyroptosis mediates lethal H5N1 influenza in nonhuman primates, and by extension humans. These innate pathways represent promising therapeutic targets to prevent severe influenza and potentially other primary viral pneumonias in humans.
Spaces and Atmospheric Memories
Authors: Umbelino Luís António
Published: March 2022

Our starting point is the following hypothesis: the human constructions of architecture and urbanism are a destination of memory. Such a starting point calls for an investigation of the place that memory must occupy within the framework of a topological phenomenology. It is in the context of such a framework that our key argument is developed as follows: the alignment between memory and space reveals itself, in a particularly intense and illustrative way, in the immersive experiences of certain ambiences, or atmospheres.
Sited-Memory
Authors: Goffi Federica
Published: March 2022

This article narrates the encounter of the author with Angelo Rudella, the head of the construction site at the Castelvecchio Museum, Verona, during the period of Carlo Scarpa’s renovation (1957–1964, 1965–1975). Rudella visited the site on July 11, 2019, to identify the original place of Scarpa’s site office — an office that Rudella shared with Scarpa for the duration of the 1960s – 70s renovation work, and until Scarpa’s death. As one of the last storytellers, to be able to offer a first source account of Scarpa’s design process at Castelvecchio, he operated a sited re‑reading of architectural details, which he analysed in their present context. The visit began by identifying Scarpa’s site office and then walking throughout the Castelvecchio Museum so that recollections emerged on site through an instance of peripatetic storytelling. Relying on a historical mnemonic technique — the art of memory and storytelling — sited memories resurfaced along the museum path, triggering key recollections associated with the construction site and archival photographs. A few selected stories and details are presented, evidencing the role of Rudella as an essential collaborator.
Occurance, Toxicity, Impacts and Removal Technologies of Fluoride ions in Drinking Water
Authors: Laxmi V. , Singh S. , Hussain J. , Hussain I. , Kumar S.
Published: March 2022

One of the most prevalent pollutants of ground water is fluoride. India is among the 23 nations around
the globe where health problems occur due to excess ingestion of fluoride (> 1.5 mg/L) by drinking
water. The presence of fluoride in exceeding limits (> 1.5 mg/L) and its related problems of drinking
water prevailing in many parts of India is well documented. Consumption of fluoride couldn’t be
avoided because a large section of groundwater is contaminated from it, which results in fluorosis of
all the living forms. A number of defluoridation techniques are prevalent. Some of them could be used
in day-to-day life for fluoride removal in drinking water. The review article presents the current
information on fluoride in environment and its effects on human health and available methods of
defluoridation.
Microwave Assisted Synthesis of Benzoxazole-Triazole
Hybrid Derivatives as Antimicrobial Agents
Authors: Halwale Amool , Yadagiri B.
Published: March 2022

A series of new 1,3-benzoxazole based 1,2,3-triazoles compounds were synthesized using click reaction
under conventional and microwave irradiation methods. The microwave irradiation method gave higher
yields, shorter reaction time as compared to conventional method using green solvents, eco-friendly
reaction conditions. All the targeted compounds were characterized by IR, 1H, 13C NMR and mass
spectral analysis. Furthermore, the titled compounds were screened for their in vitro antimicrobial
activity against bacterial strains such as Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae
and Escherichia coli as well as fungi such as Aspergillus niger, Aspergillus flavus and Fusarium
oxysporum. Most of the compounds displayed good to excellent antimicrobial activity in comparison
to standard drugs.
Exfoliation of MoS2-RGO Hybrid 2D Sheets by Supercritical Fluid Process
Authors: Muniyappa Murthy , Shastri Mahesh , Shetty Manjunath , Gangaraju Vinay , Sriramoju Jagadeesh Babu , Muralidhar Sindhushree , Narayanaswamy Manikanta P. , Ravi Mudike , Marlingaiah Navyarani , Shivaramu Prasanna D. , C S Ananda Kumar , Rangappa Dinesh
Published: March 2022

Layered 2D transition metal dichalcogenides (TMD’s) have been considered as an important class of
materials in the field of energy and environmental applications. Therefore, it is desirable to fabricate
2D hybrid TMD’s materials in simple solution processing methods. In this study, MoS2-RGO hybrid
2D few layered sheets are produced by supercritical fluid process (SCF) by using ethanol as solvent at
250 ºC in a short duration of 0.5 h. Atomic force microscopy (AFM), transmission electron microscope
(TEM) and scanning electron microscope (SEM) images confirmed the formation of 2D hybrid few
layered sheets. The electrochemical impedance measurement indicates fivefold increase in conductivity
of bulk MoS2. This work presents rapid and one pot exfoliation of MoS2 and simultaneous reduction
of GO that can facilitate the production of 2D hybrid materials.
Barriers to physical assessment skills in nurses and nursing students: a comparative-descriptive cross-sectional study
Authors: Gülnar Emel , Bıyık Bayram Şüle , Özveren Hüsna
Published: March 2022

Research Problem/Aim: Physical assessment is an integral part of nursing interventions and an important learning outcome of nurse training programs. This paper investigated impediments preventing nurses and nursing students from putting physical assessment skills into practice.
Method: This was a comparative-descriptive and cross-sectional study. The sample consisted of 118 nurses and 95 nursing students. Data were gathered using a Demographic Characteristics Questionnaire, a Physical Assessment Knowledge and Practice Questionnaire, and the Barriers to Nurses’ Use of Physical Assessment Scale.
Findings: Nurses and students had a mean age of 30.53±7.14 and 21.80 ±0.77, respectively. Most nurses (82.3%) and students (95.8%) stated that they used physical assessment skills in clinical settings. Nurses had a mean Barriers to Nurses’ Use of Physical Assessment Scale “lack of time and interruptions,” “lack of influence on patient care,” subscale score of 3.30±0.69, 3.77±0.79, respectively. Students had a mean the Barriers to Nurses’ Use of Physical Assessment Scale “lack of time and interruptions” and “lack of influence on patient care,” subscale score of 3.36±0.65, and 3.96±0.75,  respectively. Students had a higher mean Barriers to Nurses’ Use of Physical Assessment Scale “ward culture” subscale score than nurses (p=0.001).
Conclusion: Students had a significantly higher Barriers to Nurses' Use of Physical Assessment Scale "ward culture" subscale score than nurses. The barriers preventing participants from using physical assessment skills mainly were the “lack of influence on patient care," "lack of time and interruptions," and "specialty area." Educators should encourage nursing students to develop physical assessment skills and put them into practice in laboratories. Hospital administrators should provide nurses with in-service training to execute their physical assessment skills in real-life clinical settings.
Pemetaan Luasan Hutan Mangrove Dengan Menggunakan Citra Satelit Di Pulau Mapur, Provinsi Kepulauan Riau
Authors: Putra Risandi Dwirama , Napitupulu Herlanto Sihar , Nugraha Aditya Hikmat , Suhana Mario Putra , Ritonga Abdul Rahman , Sari Tengku Ersti Yulika
Published: March 2022

Mapping can be used as an alternative solution to find out the distribution map of the mangrove ecosystem by utilizing remote sensing technology and can provide value to the mangrove ecosystem. The purpose of this study was to map the distribution of mangrove ecosystems on Mapur Island. Sentinel-2b image is one of the satellite imageries had performance used to analyze the distribution of mangrove ecosystems. The mapping of the distribution of mangroves on Mapur Island shows that the mangrove ecosystem is distributed from the east to the northwest of Mapur Island. The northern part of Mapur Island has a sandy substrate classification that does not allow the growth of mangroves in the area. The distribution of mangrove classification results using Sentinel Citra-2b has a high pixel value classified of 88%, the comparison the accuracy of in situ data classification of 80%. The largest mangrove density is on Mapur Island, with a value of density of 156,729 ha. Pemetaan dapat dijadikan salah satu solusi alternatif untuk mengetahui peta sebaran luasan ekosistem mangrove dengan memanfaatkan teknologi penginderaan jauh dan dapat memberikan nilai luasan ekosistem mangrove. Tujuan dari penelitian ini adalah melakukan pemetaan sebaran luasan ekosistem mangrove di Pulau Mapur. Citra Sentinel-2b merupakan salah satu citra yang dapat digunakan untuk menganalisis sebaran luasan ekosistem mangrove. Hasil dari pemetaan sebaran mangrove di Pulau Mapur dapat dilihat bahwa ekosistem mangrove tersebar di bagian timur hingga barat laut Pulau Mapur. Bagian utara Pulau Mapur mempunyai tipe substrat yang berpasir sehingga tidak memungkinkan tumbuhan mangrove dapat tumbuh di daerah tersebut. Sebaran mangrove hasil klasifikasi dengan menggunakan Citra Sentinel-2b memiliki nilai piksel terklasifikasi hamper sempurna adalah 88%, sedangkan akurasi klasifikasi terhadap lapangan 80%. Kerapatan mangrove di Pulau Mapur yang paling luas dengan tingkat kerapatan padat dengan luas 156.729 ha.
Penilaian Pencemaran Logam Berat Cd, Pb, Cu, dan Zn pada Sedimen Permukaan Perairan Matras, Sungailiat, Bangka
Authors: Nugraha Mohammad Agung , Pamungkas Aditya , Syari Indra Ambalika , Sari Suci Puspita , Umroh Umroh , Hudatwi Mu’alimah , Utami Eva , Akhrianti Irma , Priyambada Agung
Published: March 2022

Matras waters receive input of pollutants from tin mining activities. Heavy metals are toxic and carcinogenic to aquatic biota. Sediment is a carrier of heavy metal pollutants and can act as a “sink” and a “source”. Heavy metals in sediments can reflect the condition/quality of the aquatic system. The purpose of this study was to examine the contamination and ecological risk of heavy metals Cd, Pb, Cu, and Zn in the sediments of Matras waters, Sungailiat, Bangka Regency. Heavy metal test using atomic absorption spectrophotometer (AAS). The concentrations of heavy metals Cd, Pb, Cu, and Zn obtained ranged from 0.02-0.06 mg/kg (average 0.04 mg/kg), 0.12-0.18 mg/kg (mean- average 0.15 mg/kg), each station 0.01 mg/kg (mean 0.01 mg/kg), and 0.54-1.34 mg/kg (mean 0.92 mg/kg ). CF, I-Geo, PLI, and RI values for Cd, Pb, Cu, and Zn metals obtained in Matras water sediments showed low contamination levels (CF<1), not polluted (Igeo 0), not polluted (PLI < 1), and low ecological risk (RI < 150). The EF value obtained indicates the heavy metals Cd, Pb, Cu, and Zn in the Matras waters mainly receiving input from anthropogenic sources (EF value> 1.5). The low ecological risk status which is reinforced by the low values of CF, I-Geo, and PLI indicates that the negative potential of metals to biota is also low.  Perairan Matras menerima masukan bahan pencemar dari aktivitas penambangan timah. Logam berat bersifat toksik dan karsinogenik terhadap biota akuatik. Sedimen merupakan pembawa polutan logam berat dan dapat berperan sebagai “sink” and “source”. Logam berat pada sedimen dapat merefleksikan kondisi/ kualitas sistem akuatik. Tujuan penelitian ini untuk mengkaji kontaminasi dan resiko ekologi logam berat Cd, Pb, Cu, dan Zn pada sedimen Perairan Matras, Sungailiat, Kabupaten Bangka. Uji logam berat menggunakan metode spektrofotometer serapan atom (SSA). Konsentrasi logam berat Cd, Pb, Cu, dan Zn yang diperoleh berkisar antara 0,02-0,06 mg/kg (rata-rata 0,04 mg/kg), 0,12-0,18 mg/kg (rata-rata 0,15 mg/kg), setiap stasiun 0,01 mg/kg (rata-rata 0,01 mg/kg), dan 0,54-1,34 mg/kg (rata-rata 0,92 mg/kg). Nilai CF, I-Geo, PLI, dan RI untuk logam Cd, Pb, Cu, dan Zn yang diperoleh pada sedimen Perairan Matras menunjukkan tingkat kontaminasi rendah (CF<1), tidak tercemar (Igeo 0), tidak tercemar (PLI <1), dan resiko ekologi rendah (RI < 150). Nilai EF yang diperoleh mengindikasikan logam berat Cd, Pb, Cu, dan Zn perairan Matras utamanya mendapat masukan dari sumber antropogenik (nilai EF>1,5). Rendahnya status resiko ekologi yang diperkuat dengan rendahnya nilai CF, I-Geo, dan PLI menunjukkan potensi negatif logam terhadap biota juga rendah.
Kontaminasi Mikroplastik pada Perna viridis di Teluk Lampung
Authors: Rahim Zakiyah , Zamani Neviaty Putri , Ismet Meutia Samira
Published: March 2022

Fisheries activity in Lampung Bay which has been very active in recent years is the cultivation of green mussels (P. viridis) for consumption. Located in Teluk Betung Timur sub-district, this is considered appropriate because of the environmental parameters that support the life of P. viridis. The location of P. viridis cultivation is not far from coastal settlements (±500-600 m from settlements). Anthropogenic activities of coastal residents as well as the use of plastic materials in the cultivation are concerned to be the source of microplastic contamination that found in P. viridis. This study aims to determine the presence and characteristics of microplastics in P. viridis as well as to compare the abundance of microplastics in the gills and digestive organs. Taking 30 P. viridis by purposive sampling with homogeneous size. The samples were analyzed by microplastics in chemical oceanography and biology micro Laboratory, FPIK, IPB University. P. viridis tissue was destructed by using 10% KOH solution at a ratio of 1:3 (m/v) at 60 °C for 24 hours and then filtered using a 1.6 µm Whatman GF/A filter paper. Abundance of microplastics in whole soft tissue were 0.53±0.7 mgl/g. The gill organs were found to be more microplastic than the digestive organs (p<0.05). The fragments microplastic is most commonly found in intact tissues and digestive organs, while fiber is mostly found in the gills of P. viridis. Blue color and size <100 µm were most commonly found in intact tissues, gills and digestive organs of P. viridis.  Kegiatan perikanan di Teluk Lampung yang sangat aktif dalam beberapa tahun ini yaitu kultivasi kerang hijau (P. viridis) konsumsi. Berlokasi di kecamatan Teluk Betung Timur, hal ini dinilai tepat karena parameter lingkungan yang menunjang kehidupan P. viridis. Lokasi pembesaran P. viridis tidak jauh dari pemukiman penduduk pesisir (±500-600 m dari pemukiman). Kegiatan antropogenik penduduk pesisir juga penggunaan material plastik pada sistem pembesaran dikhawatirkan dapat menjadi sumber cemaran mikroplastik yang terdapat pada P. viridis. Penelitian ini bertujuan untuk mengetahui keberadaan dan karakteristik mikroplastik pada P. viridis juga membandingkan kelimpahan mikroplastik pada insang dan organ pencernaan. Pengambilan 30 P. viridis secara purposive sampling dengan ukuran homogen. Analisis mikroplastik dilakukan di laboratorium oseanografi kimia dan biologi mikro, FPIK, Universitas Pertanian Bogor. Destruksi jaringan P. viridis dengan menggunakan larutan KOH 10% perbandingan 1:3 (m/v) pada suhu 60 °C selama 24 jam lalu difiltrasi menggunakan filter paper whatman GF/A 1,6 µm. Mikroplastik tubuh kerang utuh yaitu 0,53±0,7 mgl/g. Organ insang lebih banyak ditemukan mikroplastik dibandingkan organ pencernaan (p<0,05). Bentuk fragmen paling banyak ditemukan di jaringan utuh dan organ pencernaan, sedangkan fiber banyak ditemukan di insang P. viridis. Warna biru dan ukuran <100 µm paling banyak ditemukan di jaringan utuh, insang maupun organ pencernaan P. viridis.
Ekplorasi Bakteri dari Air Laut yang Resisten Terhadap Pestisida Organofospat Khlorpirifos di Perairan Pantai Utara Jawa Tengah
Authors: Suryono Chrisna Adhi , Indarjo Agus , Rochaddi Baskoro , Setyati Wilis Ari
Published: March 2022

Chlorpyrifos from agricultural activities eventually will flow to marine waters through rivers. This research was conducted to determine the resistance of bacteria from seawater of 100ppm Chlorpyrifos.  Three of the five bacterial strains was isolated from seawater from Brebes and Pati, Central Java were selected because they were resistant to the pesticide chlorpyrifos. Analysis of 16S rRNA gene sequences showed that the isolates belonged to the genus Virgibacillus spp. (2 strains) and Bacillus sp (1 strains). This bacterial strain has great potential ability to bioremediation of coastal waters of Brebes and Pati, Central Java from chlorpyrifos pesticide residues.  Khlorpifos dari hasil kegiatan pertanian lama kelamaan akan menuju ke perairan laut melalui aliran sungai.  Penelitian dilakukan untuk mengetahui resistensi baktrei dari air laut yang tahan terhadap 100ppm Khlorpirifos.  Tiga dari lima strain bakteri yang diisolasi dari air laut dari Brebes dan Pati Jawa Tengah dipilih karena resisten terhadap pestisida khlorpirifos.  Analisis sekuens gen 16S rRNA menunjukkan bahwa isolat termasuk dalam genus Virgibacillus sp. (2 strain) dan Bacillus sp (1 strain). Strain bakteri ini memiliki potensi penggunaan yang besar untuk bioremediasi perairan pesisir Brebes dan Pati Jawa Tengah dari residu pestisida klorpirifos.