bluuebunny/crossref_metadata_2025 huggingface dataset:
Groundwater potential zones identification in Arba Minch town, Rift Valley, Ethiopia, using geospatial and AHP tools
Authors: Jothimani Muralitharan , Abebe Abel , Duraisamy Radhakrishnan
Published: August 2021

Groundwater is a vital natural resource that supports human needs, promotes industrial development, needs farming activities, and helps to maintain ecological balance. Geospatial technologies play an essential role in monitoring, assessing, and conserving groundwater resources. The present study was carried out at Arba Minch town, Rift Valley, southern Ethiopia. A total of eight important groundwater controlling parameters, such as lithology, geomorphology, lineament density, land-use/land cover, slope, precipitation, drainage density, and soil type, were considered to identify suitable groundwater potential zones. The analytical hierarchy process (AHP) technique was used to derive the standard weights for each parameter and its sub-parameters, emphasizing the relative importance of contributing parameters and sub-parameters for groundwater recharge. The present study’s potential groundwater zonation map was divided into three categories: poor, medium, and high. The output has shown about 36%, 24%, and 40% area falls under high, medium, and poor groundwater potential zones. Furthermore, the findings were validated using groundwater level data, which showed a strong correlation. The current study results showed the effect of geospatial techniques and the AHP method in groundwater potential mapping.
Analysis of Flat Slab Structures in Comparison with Conventional Slab Structures
Authors: Borkar Shital , Dabhekar Kuldeep , Khedikar Isha , Jaju Santosh
Published: August 2021

The main aim of this analysis is to study the seismic behaviour of different types of slab structures i.e. Flat slab structure, conventional slab structure, flat slab structure with drop under different earthquake zones. These buildings are multistory building. For our analysis, we have use G+5 storey building. The analysis used ETAB software. We also analyzed to make a comparison of behavior of flat bit of material building with old common 2 way bit of material system for different bands, parts like band, part zone-II, part zone-III, part zone-IV, part zone-V in respect with greatest point making bent moment.

Abbreviations-RCC (Reinforced Cement Concrete), ETAB (Extended Three-dimensional Analysis of Building Systems)
Behaviour of steel fibre reinforced concrete with wood ash as partial replacement
Authors: Kanmani S S , Umesha P K , Asha P
Published: August 2021

Nowadays in view of sustainable development it is very much important to reduce the usage of building materials that creates negative impact on environment. There is a necessity to reduce the production of cement content in order to reduce the CO2 content in the atmosphere and which may be achieved by introducing Mineral Admixtures in concrete. This also improves the quality of concrete. Wood ash is found to be one of the suitable mineral admixtures as it has got high pozzolanic activity. But strength of concrete decreases with increase in percentage of wood ash. The aim of this study is to enhance the strength of Steel Fibre Reinforced Concrete (SFRC) in which cement is partially replaced with wood ash. This research work presents the experimental investigation to evaluate the compressive strength and flexural strength with the addition of wood ash from 0 to 20% with increment of 5% in steel fibres reinforced concrete. From the experimental results, for the optimum 10% wood ash achieving considerable benefits in compressive strength and flexural strength.
Sustainable Bamboo Rooftop Tower for Communication
Authors: Umesha P K , Kanmani S S , Asha P.
Published: August 2021

In this paper, the feasibility of bamboo for a roof top telecommunication tower is analysed. For this, the bamboo of even shape, color and thickness is selected and tested for the physical and mechanical properties in the laboratory. The roof top towers of heights 6m, 9m and 12m erected on existing building (height 15m) are considered in the present study. The other parameter considered for the study are base widths and bracing patterns. The main loads acting on the tower self-weight, wind loads and antennae loads. The wind load values are calculated as per IS:875 (Part 3)-2015 The tower is modelled as truss elements in STAAD Pro software and analysed for different loads and load combinations. The governing tensile and compressive stresses are checked with the allowable stresses. The allowable stress in compression members depends on slenderness ratio. The allowable stress formulae are derived in line with IS:802(Part 1/Sec 2)-2016 and checked with actual stresses for the suitability of the tower members. The deflection is calculated for service load and checked with the allowable value as per TIA-222-G-2005 code. The strength and deflection of narrow 12 high towers are not within the permissible range hence they are not suitable.
Physical Activity Adoption and Maintenance Among Breast Cancer Survivors: A Randomized Trial of Peer Mentoring
Authors: Pinto Bernardine M , Dunsiger Shira I , Kindred Madison M , Mitchell Sheryl
Published: August 2021

Background

Peer support can extend the reach of physical activity (PA) interventions. In previous studies, peer support via weekly counseling calls increased PA at 3 and 6 months among breast cancer survivors, compared to contact control. However, effects were attenuated at 6 months. Interventions targeting PA maintenance among cancer survivors are limited. Hence, we extended prior work to identify effective PA maintenance interventions.

Purpose

Following a 3-month PA intervention, the study compared the effects of three 6-month interventions on PA at 12 months.

Methods

One hundred and sixty-one inactive breast cancer survivors participated in a 12-month randomized controlled trial. Intervention delivery was uniform for the first 3-months: all participants received a weekly call with their peer coach to encourage PA. Following month 3, participants self-monitored PA and received feedback reports (Reach Plus) or additionally received, a monthly phone call (Reach Plus Phone), or weekly text message (Reach Plus Message). Moderate-to-vigorous PA (MVPA) was measured using self-report (7 Day PAR) and accelerometry at baseline, 3, 6, 9, and 12 months.

Results

At 3 months, there were significant within group increases in self-reported and objectively measured MVPA with no between-group differences (ps > .05). At 6 months, adjusted longitudinal models showed that Reach Plus Message reported an additional 23.83 (SD = 6.33, f2 = .12) min/week of MVPA and Reach Plus Phone reported an additional 18.14 min/week (SD = 5.15, f2 =.16) versus Reach Plus. Results were similar at 9 months. At 12 months, Reach Plus Message and Reach Plus Phone both out-performed Reach Plus (ps = .04 and .05 respectively and effect sizes f2 = .11 and f2 = .21 respectively). Accelerometer data showed similar patterns: Reach Plus Message and Reach Plus Phone out-performed Reach Plus at 6 (f2 = .20) and 9 months (f2 = .09).

Conclusion

Phone calls from peer mentors and text messaging can support PA maintenance among breast cancer survivors.

Clinical Trial information

ClinicalTrials.Gov NCT02694640.
Evaluation of rates of virologic suppression in HIV-positive patients with varying numbers of comorbidities
Authors: Fischetti Briann , Sorbera Maria , Michael, Rebecca , Njeim Noor
Published: August 2021

Purpose

To evaluate the impact of the number of comorbidities on virologic suppression in HIV-positive patients.

Methods

This study included patients 18 years or older who were on antiretroviral therapy (ART) with at least 2 visits to an HIV primary care clinic in the past year. The primary outcome was the percentage of patients with an undetectable viral load (a blood HIV RNA level of <20 copies/mL) among groups of patients with 0, 1 or 2, 3 or 4, and 5 comorbidities, respectively. The secondary outcome was the percentage of patients with undetectable viral loads per each comorbidity, as listed above. The study was reviewed by an institutional review board and approved as exempt from full review.

Results

Among the 1,144 patients (median age of 52 years, 43% female, 74% Black) included in the study, 80% had an undetectable viral load, and the mean CD4 count was 638 cells/mm3. The majority of patients (48%) had 1 or 2 comorbidities, with only 2 patients having 5 comorbidities. For patients with 0, 1 or 2, 3 or 4, and 5 comorbidities, the percentages of patients with undetectable HIV viral loads were 76%, 81.7%, 87.9%, and 100%, respectively (P = 0.0009 in χ 2 test for trend). When looking at individual comorbidities, corresponding viral suppression rates were as follows: chronic kidney disease, 88.6%; hypertension, 85.8%; type 2 diabetes, 85.7%; clinical atherosclerotic cardiovascular disease, 83.1%; substance abuse, 76%; and psychiatric disorders, 75.2%.

Conclusion

Improved viral suppression was seen among HIV-positive patients with an increased number of comorbidities. Patients with psychiatric disorders had the lowest viral suppression rates amongst all of the comorbidity subgroups.
Computed Tomography Analysis of Nasal Anatomy in Dorsal Preservation Rhinoplasty
Authors: Eravci Fakih Cihat , Özer Halil , Arbağ Hamdi , Eryilmaz Mehmet Akif , Aricigil Mitat , Dündar Mehmet Akif
Published: August 2021

Background

Subdorsal septal resection and radix osteotomy are distinctive surgical steps in preservation rhinoplasty.

Objectives

The aim of this study was to evaluate the nasal bone thickness, the level of the septal bony-cartilaginous junction (K area), and the distances of the frontal sinus and skull base from the transverse osteotomy line in the Turkish population by means of conventional computed tomography (CT).

Methods

A retrospective evaluation was made of 203 consecutive preoperative paranasal CT scans of patients (classified in terms of age and gender) who had undergone rhinoplasty surgery between January 2020 and June 2021. The nasal bone thickness at the medial canthus level, and the distances between the transverse osteotomy line and the K area, the frontal sinus, and the cribriform plate were measured.

Results

The mean measurements were similar in terms of age groups (P = 0.402, P = 0.542, P = 0.134 and P = 0.276 for ages 18-30, 30-40, 40-50, and >50 years, respectively). The mean nasal bone thickness and the distance between the transverse osteotomy line and the K area showed statistical significance (P = 0.001 and P = 0.001, respectively). In both genders, the mean distances between the transverse osteotomy line and the frontal sinus and the cribriform plate were similar (P = 0.921 and P = 0.280, respectively). The nasal bone was thinner and the K area position more cephalic in females.

Conclusions

CT plays an important role in preoperative planning. The need for resection of the ethmoid perpendicular bone may be greater in males when lowering the dorsal hump, and hence they may be more prone to skull base complications. It is therefore necessary to be more careful in the surgical stage of subdorsal septal excision in males.
A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis
Authors: Schultz Darrin T , Francis Warren R , McBroome Jakob D , Christianson Lynne M , Haddock Steven H D , Green Richard E
Published: August 2021

Here, we present a karyotype, a chromosome-scale genome assembly, and a genome annotation from the ctenophore Hormiphora californensis (Ctenophora: Cydippida: Pleurobrachiidae). The assembly spans 110 Mb in 44 scaffolds and 99.47% of the bases are contained in 13 scaffolds. Chromosome micrographs and Hi-C heatmaps support a karyotype of 13 diploid chromosomes. Hi-C data reveal three large heterozygous inversions on chromosome 1, and one heterozygous inversion shares the same gene order found in the genome of the ctenophore Pleurobrachia bachei. We find evidence that H. californensis and P. bachei share thirteen homologous chromosomes, and the same karyotype of 1n = 13. The manually curated PacBio Iso-Seq-based genome annotation reveals complex gene structures, including nested genes and trans-spliced leader sequences. This chromosome-scale assembly is a useful resource for ctenophore biology and will aid future studies of metazoan evolution and phylogenetics.
Sirtuin 1 is involved in oleic acid-induced calf hepatocyte steatosis via alterations in lipid metabolism-related proteins
Authors: Ding Hongyan , Li Yu , Liu Leihong , Hao Ning , Zou Suping , Jiang Qianming , Liang Yusheng , Ma Nana , Feng Shibing , Wang Xichun , Wu Jinjie , Loor Juan J
Published: August 2021

Sirtuin 1 (SIRT1), an NAD-dependent protein deacetylase, plays a central role in the control of lipid metabolism in nonruminants. However, the role of SIRT1 in hepatic lipid metabolism in dairy cows with fatty liver is not well known. Thus, we used isolated primary bovine hepatocytes to determine the role of SIRT1 in protecting cells against oleic acid (OA)-induced steatosis. Recombinant adenoviruses to overexpress (AD-GFP-SIRT1-E) or knockdown (AD-GFP-SIRT1-N) SIRT1 were used for transduction of hepatocytes. Calf hepatocytes isolated from five female calves (1 d old, 30 to 40 kg) were used to determine both time required and the lowest dose of OA that could induce triacylglycerol (TAG) accumulation. Analyses indicated that 0.25 mM OA for 24 h was suitable to induce TAG accumulation. In addition, OA not only led to an increase in TAG, but also upregulated mRNA and protein abundance of sterol regulatory element-binding transcription factor 1 (SREBF1) and downregulated SIRT1 and peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PPARGC1A). Thus, these in vitro conditions were deemed optimal for subsequent experiments. Calf hepatocytes were cultured and incubated with OA (0.25 mM) for 24 h, followed by adenoviral AD-GFP-SIRT1-E or AD-GFP-SIRT1-N transduction for 48 h. Overexpression of SIRT1 led to greater protein and mRNA abundance of SIRT1 along with fatty acid oxidation-related genes including PPARGC1A, peroxisome proliferator-activated receptor alpha (PPARA), retinoid X receptor α (RXRA), and ratio of phospho-acetyl-CoA carboxylase alpha (p-ACACA)/total acetyl-CoA carboxylase alpha (ACACA). In contrast, it resulted in lower protein and mRNA abundance of genes related to lipid synthesis including SREBF1, fatty acid synthase (FASN), apolipoprotein E (APOE), and low-density lipoprotein receptor (LDLR). The concentration of TAG decreased due to SIRT1 overexpression. In contrast, silencing SIRT1 led to lower protein and mRNA abundance of SIRT1, PPARGC1A, PPARA, RXRA, and greater protein and mRNA abundance of SREBF1, FASN, APOE, and LDLR. Further, those responses were accompanied by greater content of cellular TAG and total cholesterol (TC). Overall, data from these in vitro studies indicated that SIRT1 is involved in the regulation of lipid metabolism in calf hepatocytes subjected to an increase in the supply of OA. Thus, it is possible that alterations in SIRT1 abundance and activity in vivo contribute to development of fatty liver in dairy cows.
Scientific aspirations of the Chinese Space Station program: an interview with Ming Gao
Authors: Zhao (赵维杰) Weijie
Published: August 2021

On 17 June 2021, China's spacecraft Shenzhou 12 took three Chinese astronauts into the Earth's orbit and docked with the assembly of Tianhe and Tianzhou, the core module and cargo ship of the Chinese Space Station (CSS), which had been launched and assembled in orbit earlier this year. The three astronauts became the first visitors of the CSS and would stay in orbit for about three months. In 2022, two laboratory cabin modules, Wentian and Mengtian, will be launched and assembled into Tianhe, completing the basic structure of the CSS. The CSS is designed to be used for at least 10 years, and will provide an outer space experimental platform for researchers from multiple disciplines.

On 23 July 2021, National Science Review (NSR) interviewed Professor Ming Gao (高铭), the Commander-in-Chief of the Space Utilizaiton System of the China Manned Space Program, Director General of the Technology and Engineering Center for Space Utilization (CSU) of the Chinese Academy of Sciences and an Academician of the International Academy of Astronautics. The Space Utilizaiton System is the scientific part of the CSS project, responsible for the design and organization of the onboard research programs. Gao has been involved in China's Manned Space Program since 1994, and has experienced the whole development process from the Shenzhou spacecraft to the CSS. In this interview, she introduces the scientific goals, plans and aspirations of the CSS.
Occidiofungin Is the Key Metabolite for Antifungal Activity of the Endophytic Bacterium Burkholderia sp. MS455 Against Aspergillus flavus
Authors: Jia Jiayuan , Ford Emerald , Hobbs Sarah M. , Baird Sonya M. , Lu Shi-En
Published: August 2021

Aflatoxin is a secondary metabolite produced by Aspergillus fungi and presents a major food safety concern globally. Among the available methods for prevention and control of aflatoxin, the application of antifungal bacteria has gained favor in recent years. An endophytic bacterium MS455, isolated from soybean, exhibited broad-spectrum antifungal activity against economically important pathogens, including Aspergillus flavus. MS455 was identified as a strain of Burkholderia based on genomic analysis. Random and site-specific mutations were used in discovery of the genes that share high homology to the ocf gene cluster of Burkholderia contaminans strain MS14, which is responsible for production of the antifungal compound occidiofungin. RNA sequencing analysis demonstrated that ORF1, a homolog to the ambR1 LuxR-type regulatory gene, regulates occidiofungin biosynthesis in MS455. Additionally, 284 differentially expressed genes, including 138 upregulated and 146 downregulated genes, suggesting that, in addition to its role in occidiofungin production, ORF1 is involved in expression of multiple genes, especially those involved in ornibactin biosynthesis. Plate bioassays showed the growth of A. flavus was significantly inhibited by the wild-type strain MS455 as compared with the ORF1 mutant. Similarly, corn kernel assays showed that growth of A. flavus and aflatoxin production were reduced significantly by MS455 as compared with buffer control and the ORF1 mutant. Collectively, the results demonstrated that production of occidiofungin is essential for antifungal activity of the endophytic bacterium MS455. This research has provided insights about antifungal mechanisms of MS455 and development of biological approaches to prevent aflatoxin contamination in plant production.
The Nursing Crisis in Acute Care
Authors: Kennedy Maureen Shawn
Published: August 2021

Who will ensure safe care if nurses leave hospitals?
Fetal Exposure to Antiseizure Medications
Authors: Rosenberg Karen
Published: August 2021

According to this study:

Cognitive outcomes at two years of age in the language domain of the Bayley Scales of Infant and Toddler Development, Third Edition, didn't differ between children of women with epilepsy and children of healthy women.

In adjusted analyses, however, higher blood levels of antiseizure medication in the third trimester were associated with lower scores for the motor and general adaptive domains.
My Pocket of Care
Authors: Wukovits Barbara
Published: August 2021

Meeting patients where they are in their loneliness and pain can help them heal.
Association between circulating CD39+CD8+ T cells pre-chemoradiotherapy and prognosis in patients with nasopharyngeal carcinoma
Authors: Dong Dan-Ning , Fan Pei-Wen , Feng Ya-Ning , Liu Gui-Hai , Peng Yan-Chun , Dong Tao , Wang Ruo-Zheng , Yu Jin-Ming
Published: August 2021

Background

The mortality rate among patients with nasopharyngeal carcinoma (NPC) has improved significantly with the advent of chemoradiotherapy strategies. However, distant metastasis remains problematic. Tumor-specific reactivity in cancer patients has been detected exclusively in CD39+ T cells, particularly in CD39+CD103+ T cells. Circulating cancer-specific T cells are important for protecting against metastasis. This study aimed to evaluate the predictive value of circulating CD39+CD8+ T cells for metastasis in patients with NPC.

Methods

We performed a cross-sectional, longitudinal study of 55 patients with newly diagnosed NPC of stage III–IVa. All patients were initially treated with standard combined chemoradiotherapy. Blood samples were obtained from 24 patients before and at 1 month and 6 months after treatment. T cell expression of CD39 and CD103, together with the markers of T cell exhaustion programmed death-1 (PD-1)/T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) and markers of cell differentiation CD27/CC-chemokine receptor 7/CD45RA, was examined by flow cytometry. The Wilcoxon rank-sum test analysis was used to analyze the differences between two groups. Kaplan-Meier analysis was used for analysis of progression-free survival (PFS).

Results

The expression of circulating CD39+CD8+ and CD39+CD103+ CD8+ T cells was significantly higher in patients without distant metastasis (CD39+CD8+: 6.52% [1.24%, 12.58%] vs. 2.41% [0.58%, 5.31%], Z=−2.073, P=0.038 and CD39+CD103+CD8+: 0.72% [0.26%, 2.05%] vs. 0.26% [0.12%, 0.64%], Z=−2.313, P = 0.021). Most CD39+ T cells did not express PD-1 or Tim-3. Patients with high expression of CD39+CD103+CD8+ T cells had better PFS than patients with low expression (log rank value = 4.854, P = 0.028). CD39+CD8+ T cells were significantly elevated at 1-month post-treatment (10.02% [0.98%, 17.42%] vs. 5.91% [0.61%, 10.23%], Z = −2.943, P = 0.003). The percentage of advanced differentiated CD8+ T cells also increased at 1-month post-treatment compared with pre-treatment (33.10% [21.60%, 43.05%] vs. 21.00% [11.65%, 43.00%], Z = −2.155, P = 0.031). There was a significant correlation between elevated CD39+CD8+ T cells and increased effector memory T cells (intermediate stage: r = 0.469, P = 0.031; advanced stage: r = 0.508, P = 0.019).

Conclusions

CD39+CD8+ circulating T cells have preserved effector function, contributing to an improved prognosis and a reduced risk of metastasis among NPC patients. These cells may thus be a useful predictive marker for a better prognosis in patients with NPC.
Delirium in Intensive Care Units
Authors: Salameh Basma , Al Razeeni Daifallah M. , Mansor Khulud , Abdallah Jihad M. , Ayed Ahmad , Salem Hiba
Published: August 2021

Delirium is an indicator of morbidity and mortality in intensive care unit (ICU) patients. It can lead to negative outcomes and longer hospital stays, thus increasing hospital costs. Despite national recommendations for daily assessment of delirium, it remains underdiagnosed. Many studies point to a lack of knowledge among health care professionals to accurately detect and manage ICU delirium. The aim of our study was to assess the knowledge, attitudes, and practices of Palestinian health care professionals regarding ICU delirium. The results of a cross-section observational study revealed that delirium appears to be often underrecognized or misdiagnosed in ICUs in Palestine. Therefore, it is critical to further educate the medical and nursing teams and to promote the use of validated tools that can aid in the assessment of this condition. In this way, the length of hospital stays and related health care costs can be reduced.
Assessing Language Delay in Twins
Authors: Foran Lori G. , Evans Kelli J. , Beverly Brenda L.
Published: August 2021

Identification of language disorders in children younger than 3 years remains challenging despite agreement that early intervention improves outcomes. This study of twin language and gesture development substantiated the twinning effect, an unexplained lag in expressive and receptive language seen in twins, for a group of 88, 16- to 18-month-old twins who did not present with extreme perinatal risk. A valid, parent-report measure revealed word production of 10th percentile and less for 15 twins. Pregnancy complications, but not a positive family history of speech, language, or learning disorders or other case history factors, significantly increased the odds of this early expressive delay. The twinning effect was more pronounced for gesture than for spoken vocabulary: 29 twins fell below gesture norms. This was unexpected. Because gesture signals early communicative intentionality, twins with early expressive delay who present with limited gestures, with or without additional risk factors, warrant priority consideration for early intervention.
Early Interventionists' Ratings of Family-Centered Practices in Natural Environments
Authors: Tomeny Kimberly R. , García-Grau Pau , McWilliam R. A.
Published: August 2021

Part C early intervention services should be family centered and occur in the context of families' natural environments and daily routines; yet research suggests that many early interventionists continue to work directly with the child and lack a full understanding of how they can implement best practices in the community. To help improve this implementation gap, discrepancy tools can be used to identify early interventionists' perspectives of their typical and ideal practices and gain knowledge of early interventionists' understanding of family-centered practices. The purpose of this study was to examine early interventionists' typical practices, ideal practices, and family consultation beliefs prior to one state's adoption of a family-centered early intervention model. Ninety-nine early interventionists completed a questionnaire examining their practices and beliefs. Results demonstrated that ratings of typical practices, ideal practices, and family consultation beliefs were relatively high overall, and early interventionists rated their typical practices only slightly lower than ideal practices. Item-level analysis, however, revealed a large discrepancy between typical and ideal ratings for the item related to working with the child versus the caregiver. Implications of our findings and recommended future directions are discussed.
A Geriatrics-Focused Hospitalist Trauma Comanagement Program Improves Quality of Care for Older Adults
Authors: Zhang Nasen J. , Sinvani Liron , Leung Tung Ming , Qiu Michael , Meyer Cristy L. , Sharma Ankita , Kurian Linda M. , Bank Matthew A. , Kast Charles L.
Published: August 2021

This study aimed to determine whether a geriatrics-focused hospitalist trauma comanagement program improves quality of care. A pre-/post-implementation study compared older adult trauma patients who were comanaged by a hospitalist with those prior to comanagement at a level 1 trauma center. One-to-one propensity score matching was performed based on age, gender, Injury Severity Score, comorbidity index, and critical illness on admission. Outcomes included orders for geriatrics-focused quality indicators, as well as hospital mortality and length of stay. Wilcoxon rank-sum test (continuous variables) and chi-square or Fisher exact test (categorical variables) were used to assess differences. Propensity score matching resulted in 290 matched pairs. The intervention group had decreased use of restraints (P = 0.04) and acetaminophen (P = 0.01), and earlier physical therapy (P = 0.01). Three patients died in the intervention group compared with 14 in the control (P = 0.0068). This study highlights that a geriatrics-focused hospitalist trauma comanagement program improves quality of care.
Paenibacillus agri sp. nov., isolated from soil
Authors: KIm Kyung Hyun , Seo Ye Lin , Baek Ju Hye , Jin Hyun Mi , Jeon Che Ok
Published: August 2021

A strict aerobic bacterium, strain JW14T was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14T was observed at 20–37 °C (optimum, 30 °C), pH 6.0–10.0 (optimum, pH 7.0) and in the presence of 0–2.0% NaCl (optimum, 0%). Strain JW14T contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C15:0, C16:0 and iso-C16 : 0 as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14T contained meso-diaminopimelic acid. The DNA G+C content of strain JW14T calculated from the whole genome sequence was 48.1 mol%. Strain JW14T was most closely related to

Paenibacillus graminis

DSM 15220T with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14T formed a distinct phyletic lineage from closely related type strains within the genus

Paenibacillus

. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14T represents a novel species of the genus

Paenibacillus

, for which the name Paenibacillus agri sp. nov. is proposed. The type strain is JW14T (=KACC 21840T=JCM 34279T).
Social contacts and other risk factors for respiratory infections among internally displaced people in Somaliland
Authors: van Zandvoort Kevin , Bobe Mohamed Omer , Hassan Abdirahman Ibrahim , Abdi Mohamed Ismail , Ahmed Mohammed Saed , Warsame Mohamed Yusuf , Wais Muna Awil , Diggle Emma , Satzke Catherine , Mulholland Kim , Egeh Mohamed Mohamoud , Hassan Mukhtar Muhumed , Hergeeye Mohamed Abdi , Eggo Rosalind M , Checchi Francesco , Flasche Stefan
Published: August 2021

Background

Populations affected by humanitarian crises experience high burdens of acute respiratory infections (ARI), potentially driven by risk factors for severe disease such as poor nutrition and underlying conditions, and risk factors that may increase transmission such as overcrowding and the possibility of high social mixing. However, little is known about social mixing patterns in these populations.

Methods

We conducted a cross-sectional social contact survey among internally displaced people (IDP) living in Digaale, a permanent IDP camp in Somaliland. We included questions on household demographics, shelter quality, crowding, travel frequency, health status, and recent diagnosis of pneumonia, and assessed anthropometric status in children. We calculated age-standardised social contact matrices to assess population mixing, and conducted regression analysis on risk factors for recent self-reported pneumonia.

Results

We found crowded households with high proportions of recent self-reported pneumonia (46% in children). 20% of children younger than five are stunted, and crude death rates are high in all age groups. ARI risk factors are common, but we did not find any significant associations with self-reported pneumonia. Participants reported around 10 direct contacts per day. Social contact patterns are assortative by age, and physical contact rates are very high (78%).

Conclusions

ARI risk factors are very common in this population, while the large degree of contacts that involve physical touch could further increase transmission. Such IDP settings potentially present a perfect storm of risk factors for ARIs and their transmission, and innovative approaches to address such risks are urgently needed.
Ergodic patterns of cell state transitions underlie the reproducibility of embryonic development
Authors: Genuth Miriam , Kojima Yasuhiro , Jülich Dörthe , Kiryu Hisanori , Holley Scott A.
Published: August 2021

The reproducibility of embryonic development is a remarkable feat of biological organization, but the underlying mechanisms are poorly understood. Clearly, gene regulatory networks are central to the orderly progression of development, but noisy molecular and cellular processes should reduce reproducibility. Here, we identify ergodicity, a type of dynamical stability, as underlying the reproducibility of development. In ergodic systems, a single timepoint measurement equals a time average. Focusing on the zebrafish tailbud, we define gene expression and cell motion states using a parallel statistical analyses of single cell RNA sequencing data and in vivo timelapse cell tracking data and a change point detection algorithm. Strikingly, the cell motion state transitions in each embryo exhibit the same patterns for both a single timepoint and a 2-3 hour time average. Both the cell motion and gene expression cell states exhibit balanced influx and outflux rates reflecting a spatiotemporal stability. Stated simply, these data indicate the pattern of changes in the tailbud doesn’t change. This ergodic pattern of cell state transitions may represent an emergent meta-state that links gene networks to the reproducible progression of embryogenesis.
Trade-off between stimulation focality and the number of coils in multi-locus transcranial magnetic stimulation
Authors: Nurmi Samuel , Karttunen Jere , Souza Victor H. , Ilmoniemi Risto J. , Nieminen Jaakko O.
Published: August 2021

Objective

Coils designed for transcranial magnetic stimulation (TMS) must incorporate trade-offs between the required electrical power or energy, focality and depth penetration of the induced electric field (E-field), coil size, and mechanical properties of the coil, as all of them cannot be optimally met at the same time. In multi-locus TMS (mTMS), a transducer consisting of several coils allows electronically targeted stimulation of the cortex without physically moving a coil. In this study, we aimed to investigate the relationship between the number of coils in an mTMS transducer, the focality of the induced E-field, and the extent of the cortical region within which the location and orientation of the maximum of the induced E-field can be controlled.

Approach

We applied convex optimization to design planar and spherically curved mTMS transducers of different E-field focalities and analyzed their properties. We characterized the trade-off between the focality of the induced E-field and the extent of the cortical region that can be stimulated with an mTMS transducer with a given number of coils.

Main results

At the expense of the E-field focality, one can, with the same number of coils, design an mTMS transducer that can control the location and orientation of the peak of the induced E-field within a wider cortical region.

Significance

With E-fields of moderate focality, the problem of electronically targeted TMS becomes considerably easier compared with highly focal E-fields; this may speed up the development of mTMS and the emergence of new clinical and research applications.
Teaching free energy calculations to learn from experimental data
Authors: Wieder Marcus , Fass Josh , Chodera John D.
Published: August 2021

Alchemical free energy calculations are an important tool in the computational chemistry toolbox, enabling the efficient calculation of quantities critical for drug discovery such as ligand binding affinities, selectivities, and partition coefficients. However, modern alchemical free energy calculations suffer from three significant limitations: (1) modern molecular mechanics force fields are limited in their ability to model complex molecular interactions, (2) classical force fields are unable to treat phenomena that involve rearrangements of chemical bonds, and (3) these calculations are unable to easily learn to improve their performance if readily-available experimental data is available. Here, we show how all three limitations can be overcome through the use of quantum machine learning (QML) potentials capable of accurately modeling quantum chemical energetics even when chemical bonds are made and broken. Because these potentials are based on mathematically convenient deep learning architectures instead of traditional quantum chemical formulations, QML simulations can be run at a fraction of the cost of quantum chemical simulations using modern graphics processing units (GPUs) and machine learning frameworks. We demonstrate that alchemical free energy calculations in explicit solvent are especially simple to implement using QML potentials because these potentials lack singularities and other pathologies typical of molecular mechanics potentials, and that alchemical free energy calculations are highly effective even when bonds are broken or made. Finally, we show how a limited number of experimental free energy measurements can be used to significantly improve the accuracy of computed free energies for unrelated compounds with no significant generalization gap. We illustrate these concepts on the prediction of aqueous tautomer free energies (related to tautomer ratios), which are highly relevant to drug discovery in that more than a quarter of all approved drugs exist as a mixture of tautomers.
Yeast-expressed Recombinant SARS-CoV-2 Receptor Binding Domain, RBD203-N1 as a COVID-19 Protein Vaccine Candidate
Authors: Chen Wen-Hsiang , Pollet Jeroen , Strych Ulrich , Lee Jungsoon , Liu Zhuyun , Kundu Rakhi Tyagi , Versteeg Leroy , Villar Maria Jose , Adhikari Rakesh , Wei Junfei , Poveda Cristina , Keegan Brian , Bailey Aaron Oakley , Chen Yi-Lin , Gillespie Portia M. , Kimata Jason T. , Zhan Bin , Hotez Peter J. , Bottazzi Maria Elena
Published: August 2021

Background

SARS-CoV-2 protein subunit vaccines are being evaluated by multiple manufacturers to fill the need for low-cost, easy to scale, safe, and effective COVID-19 vaccines for global access. Vaccine candidates relying on the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein have been the focus of our development program. In this paper, we report on the generation of the RBD203-N1 yeast expression construct, which produces a recombinant protein that when formulated with alum and the TLR-9 agonist, CpG1826 elicits a robust immune response and protection in mice.

Method

The RBD203-N1 antigen was expressed in the yeast Pichia pastoris X33. After fermentation at the 5 L scale, the protein was purified by hydrophobic interaction chromatography followed by anion exchange chromatography. The purified protein was characterized biophysically and biochemically, and after its formulation, the immunogenicity and efficacy were evaluated in mice.

Results, Conclusions, and Significance

The RBD203-N1 production process yielded 492.9 ± 3.0 mg/L of protein in the fermentation supernatant. A two-step purification process produced a >96% pure protein with a recovery rate of 55 ± 3% (total yield of purified protein: 270.5 ± 13.2 mg/L fermentation supernatant). The protein was characterized as a homogeneous monomer with well-defined secondary structure, thermally stable, antigenic, and when adjuvanted on alum and CpG, it was immunogenic and induced robust levels of neutralizing antibodies against SARS-CoV-2 pseudovirus. These characteristics show that this vaccine candidate is well suited for technology transfer with feasibility of its transition into the clinic to evaluate its immunogenicity and safety in humans.
Sensory Modality and Spoken Language Shape Reading Network in Blind Readers of Braille
Authors: Tian Mengyu , Saccone Elizabeth J. , Kim Judy S. , Kanjlia Shipra , Bedny Marina
Published: August 2021

The neural basis of reading is highly consistent across many languages and scripts. Are there alternative neural routes to reading? How does the sensory modality of symbols (tactile vs. visual) influence their neural representations? We examined these questions by comparing reading of visual print (sighted group, n=19) and tactile Braille (congenitally blind group, n=19). Blind and sighted readers were presented with written (words, consonant strings, non-letter shapes) and spoken stimuli (words, backward speech) that varied in word-likeness. Consistent with prior work, the ventral occipitotemporal cortex (vOTC) was active during Braille and visual reading. A posterior/anterior vOTC word-form gradient was observed only in sighted readers with more anterior regions preferring larger orthographic units (words). No such gradient was observed in blind readers. Consistent with connectivity predictions, in blind compared to sighted readers, posterior parietal cortices were recruited to a greater degree and contained word-preferring patches. Lateralization of Braille in blind readers was predicted by laterality of spoken language and reading hand. The effect of spoken language increased along a cortical hierarchy, whereas effect of reading-hand waned. These results suggested that the neural basis of reading is influenced by symbol modality and spoken language and support connectivity-based views of cortical function.
Circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, India
Authors: Argimón Silvia , Nagaraj Geetha , Shamanna Varun , Sravani Darmavaram , Vasanth Ashwini Kodlipet , Prasanna Akshatha , Poojary Aruna , Bari Anurag Kumar , Underwood Anthony , Kekre Mihir , Baker Stephen , Aanensen David M. , Lingegowda Ravikumar Kadahalli
Published: August 2021

We report the persistent circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, linked to the acquisition and maintenance of a previously characterized IncX3 plasmid carrying the ESBL gene blaSHV-12 and the fluoroquinolone resistance gene qnrB7 in the genetic context of a triple mutant also associated with fluoroquinolone resistance.
Prochlorococcus exudate stimulates heterotrophic bacterial competition with rival phytoplankton for available nitrogen
Authors: Calfee Benjamin C. , Glasgo Liz D. , Zinser Erik R.
Published: August 2021

The marine cyanobacterium Prochlorococcus numerically dominates the phytoplankton community of the nutrient-limited open ocean, establishing itself as the most abundant photosynthetic organism on Earth. This ecological success has been attributed to lower cell quotas for limiting nutrients, superior resource acquisition, and other advantages associated with cell size reduction and genome streamlining. In this study we tested the prediction that Prochlorococcus outcompetes its rivals for scarce nutrients, and that this advantage leads to its numerical success in nutrient-limited waters. Strains of Prochlorococcus and its sister genus Synechococcus grew well in both mono- and co-culture when nutrients were replete. However, in nitrogen-limited medium Prochlorococcus outgrew Synechococcus, but only when heterotrophic bacteria were also present. In the nitrogen-limited medium, the heterotroph Alteromonas macleodii outcompeted Synechococcus for nitrogen, but only if stimulated by exudate released by Prochlorococcus, or if a proxy organic carbon source was provided. Analysis of a nitrate reductase mutant Alteromonas suggested that Alteromonas outcompetes Synechococcus for nitrate, during which co-cultured Prochlorococcus grows on ammonia or other available nitrogen species. We propose that Prochlorococcus can stimulate antagonism between heterotrophic bacteria and potential phytoplankton competitors through a metabolic cross-feeding interaction, and this stimulation could contribute to the numerical success of Prochlorococcus in the nutrient-limited regions of the ocean.

Significance Statement

In nutrient-poor habitats, the competition for limited resources is thought to select for organisms with enhanced ability to scavenge nutrients and utilize them efficiently. Such adaptations characterize the cyanobacterium Prochlorococcus, the most abundant photosynthetic organism in the nutrient-limited open ocean. In this study the competitive superiority of Prochlorococcus over a rival cyanobacterium, Synechococcus, was captured in laboratory culture. Critically, this outcome was achieved only when key aspects of the open ocean were simulated: a limited supply of nitrogen, and the presence of heterotrophic bacteria. Results indicate that Prochlorococcus promotes its numerical dominance over Synechococcus by energizing the heterotroph’s ability to outcompete Synechococcus for available nitrogen. This study demonstrates how interactions between trophic groups can influence interactions within trophic groups.
A mechanistic switch from selective transporter to an ion channel impairs the filamentation signalling capability of ammonium transceptors in yeast
Authors: Williamson Gordon , Brito Ana Sofia , Bizior Adriana , Tamburrino Giulia , Mirandela Gaëtan Dias , Harris Thomas , Hoskisson Paul A. , Zachariae Ulrich , Marini Anna Maria , Boeckstaens Mélanie , Javelle Arnaud
Published: August 2021

Ammonium translocation through biological membranes by the ubiquitous Amt-Mep-Rh family of transporters plays a key role in all domains of life. Two highly conserved histidine residues protrude into the lumen of these transporters, forming the family’s characteristic Twin-His motif. It has been hypothesized that the motif is essential to confer the selectivity of the transport mechanism. Here, using a combination of in vitro electrophysiology, in vivo yeast functional complementation and in silico molecular dynamics simulations, we demonstrate that variations in the Twin-His motif trigger a mechanistic switch between a specific transporter, depending on ammonium deprotonation, to an unspecific ion channel activity. We therefore propose that there is no selective filter that governs the specificity in Amt-Mep transporters but the inherent mechanism of translocation, dependent on the fragmentation of the substrate, ensures the high specificity of the translocation. We further show that both mechanisms coexist in fungal Mep2 Twin-His variants, disrupting the transceptor function and so inhibiting the filamentation process. These data strongly support a transport mechanism-mediated signalling process in the long-standing debate on the sensory function of Mep2-like transporters.
Cytogenetic evidence supports Avena insularis being closely related to hexaploid oats
Authors: Fominaya Araceli , Loarce Yolanda , González Juan M. , Ferrer Esther
Published: August 2021

Cytogenetic observations, phylogenetic studies and genome analysis using high-density genetic markers have suggested a tetraploid Avena species carrying the C and D genomes (formerly C and A) to be the donor of all hexaploid oats (AACCDD). However, controversy surrounds which of the three extant CCDD tetraploid species - A. insularis, A. maroccana and A. murphyi - is most closely related to hexaploid oats. The present work describes a comparative karyotype analysis of these three CCDD tetraploid species and two hexaploid species, A. sativa and A. byzantina. This involved the use of FISH with six simple sequence repeats (SSRs) with the motifs CT, AAC, AAG, ACG, ATC and ACT, two repeated ribosomal sequences, and C genome-specific repetitive DNA. The hybridization pattern of A. insularis with oligonucleotide (AC)10 was also determined and compared with those previously published for A. sativa and A. byzantina. Significant differences in the 5S sites and SSR hybridization patterns of A. murphyi compared to the other CCDD species rule out its being directly involved in the origin of the hexaploids. In contrast, the repetitive and SSR hybridization patterns shown by the D genome chromosomes, and by most of the C genome chromosomes of A. maroccana and A. insularis, can be equated with the corresponding chromosomes of the hexaploids. Several chromosome hybridization signals seen for A. insularis, but not for A. maroccana, were shared with the hexaploid oats species, especially with A. byzantina. These diagnostic signals add weight to the idea that the extant A. insularis, or a direct ancestor of it, is the most closely related progenitor of hexaploid oats. The similarity of the chromosome hybridization patterns of the hexaploids and CCDD tetraploids was taken as being indicative of homology. A common chromosome nomenclature for CCDD species based on that of the hexaploid species is proposed.