bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Helicobacter pylori infection with coronary artery disease: is it an independent risk factor?
Authors: Riad Mohamed
Published: July 2021

Background

Coronary artery disease (CAD) is a dilemma and a serious cause of morbidity and mortality worldwide. Since CAD has been seen in people without the conventional risk factors like smoking, diabetes, and hypertension, the infectious theory being a risk factor has arisen.

Main body

Helicobacter pylori (HP) infection is the most common infection affecting the vast majority of the population worldwide. HP grows in the gastrointestinal tract (GIT) and responsible for chronic gastritis, peptic ulcer, gastric adenocarcinoma, and gastric lymphoma. A review of medical literature mainly PubMed has revealed several studies reporting that HP pathogenesis extends beyond the GIT to be a predisposing factor for atherosclerosis, dyslipidemia, thrombosis, and CAD. However, it remains a controversial issue that warrants extensive research.

Conclusion

This article gives insight into the diversity of opinions, evidence, and theories regarding the association between HP infection and CAD. The idea that CAD may be managed with antibiotics in certain patients seems to be creative and inspiring. More research is mandatory to either verify or reject this proposed correlation with strong scientific evidence and also to demonstrate the implications of the results on CAD management and outcome.
Balloon tracheoplasty for tracheal stenosis after prolonged intubation: a simple procedure, but is it effective?
Authors: Nosair Abdallah , Singer Mahmoud , Elkahely Mohamed , Abu-Gamila Rezk , Adel Waleed
Published: July 2021

Background

Tracheal stenosis following prolonged intubation is a relatively rare but serious problem. This condition is usually managed by surgical or endoscopic interventions. Bronchoscopic balloon dilatation for tracheal stenosis is considered a valuable tool used for the management of tracheal stenosis. In this article, we try to evaluate the role of balloon tracheoplasty in the management of tracheal stenosis and to assess the number of dilatation sessions usually needed as well as the short to midterm outcome.

Results

This study involved 40 patients with tracheal stenosis diagnosed by computed tomography (neck and chest) and bronchoscopy at the Security Force Hospital in Riyadh, KSA, between January 2013 and August 2018. Patients’ data were retrospectively reviewed and analyzed. Patients’ age ranged between 18 and 60 years. Thirty patients were males (75%); those patients underwent balloon tracheoplasty via dilatation of areas of narrowing using catheter balloon insufflation guided by fiber-optic bronchoscope. Ninety-five percent of the patients had initial success with acceptable dilatation of the stenotic area and improvement of the symptoms. There were no technical or major problems which resulted from the procedure, and no patient complained of severe pain or severe discomfort after the procedure. From the total of 81 BBD sessions, no in-hospital mortality is related to the procedure itself, and ICU stay ranged between 1 and 5 days post-procedure. Among those 40 patients, 16 patients (40%) needed one session, 10 patients (25%) needed two sessions, 8 patients (20%) needed three sessions, and 6 patients (15%) needed more than three sessions of balloon dilatation.

Conclusion

Balloon tracheoplasty is a simple, safe method and could be a promising and effective approach that offers immediate symptomatic relief for tracheal stenosis in cases with a history of prolonged intubation. It is worth mentioning that BBD is considered as a temporary measure, and most of the cases will need definitive or additional treatment either resection or stent placement.
Full thickness vs sliced mosaic cartilage graft in tympanoplasty: a comparative study
Authors: Elfouly Mahmoud S.
Published: July 2021

Background

Tympanoplasty is one of the most performed procedures in otorhinolaryngology—head and neck surgery. Reconstruction of hearing is one of its targeted goals (Jeffery et al., J Otolaryngol Head Neck Surg 46:48, 2017). Closure of tympanic membrane was accomplished by various grafts. Temporalis fascia is commonly used in tympanoplasty but it could not withstand pressure variations due to its low elasticity (Sözen et al., J Craniofac Surg 23:e280-e283, 2012). Cartilage was preferred in this condition owing to its rigidity (Zhang et al., Otol Neurotol 32:1234-1238, 2011). However, this rigid character is thought to hinder the acoustic transfer through the cartilage (Bozdemir et al., ORL J Otorhinolaryngol Relat Spec 74:28-32, 2012).

This study was conducted to determine the acoustic characteristics of sliced mosaic cartilage tympanoplasty.

Results

Comparable success rates were found among the 2 groups at 3 months postoperatively; 14 cases (88%) in group 1 and 20 cases (91%) in group 2. One year postoperatively, two cases with healed perforation in group 2 showed re-perforation; resulting in decreasing success rate to 81%, in contrast to constant success rate (88%) in the corresponding follow-up in group 1. However, the difference between the two groups remained insignificant (P = 1 in both follow ups).

Conclusion

Using split thickness cartilage slices arranged in mosaic pattern in type I tympanoplasty successfully overcame the hindering effect of cartilage on acoustic transfer, with no fear regarding take rate or complications.
Tracing the horizontal transport of microplastics on rough surfaces
Authors: Laermanns Hannes , Lehmann Moritz , Klee Marcel , J. Löder Martin G. , Gekle Stephan , Bogner Christina
Published: July 2021

Occurrence and distribution of microplastics in different ecosystems have recently become subjects of numerous studies. However, to date the research has focused mainly on marine and freshwater ecosystems and widely neglected terrestrial environments. Only recently, first studies investigated the microplastics contamination of soils. Therefore, we know little about the transport mechanisms of microplastics in soils and sediments and virtually nothing about their surface transport. In this study we investigate surface transport mechanisms by tracking fluorescent, irregularly shaped polymethyl methacrylate (PMMA) particles in real time in a laboratory setup. In 108 experimental runs, we vary the irrigation rates, inclinations and surface roughnesses. Additionally, we simulate the small-scale flow patterns to resolve the role of the roughness-induced microrelief. Our results suggest that microplastics are transported along preferential pathways resulting from the micro- and macrorelief, which can be correlated to the flow pattern observed in the computer simulation. Our model study facilitates a deeper insight into microplastic transport on different soil surfaces and serves as a pilot for investigating mechanisms of horizontal microplastic transport. However, microplastics are a diverse group of contaminants with varying shapes, densities and sizes. Therefore, for a full understanding of transport of microplastics in terrestrial environments, it is important to address these properties as well as more variable surfaces for horizontal migration and to include vertical transport mechanisms in future research.
Dispersion optimized operator for frequency-domain acoustic wave equation in an irregular grid
Authors: Kim Sihyung , Kim Young Seo , Shin Changsoo
Published: July 2021

A numerical technique is developed for dispersion optimization in frequency-domain acoustic wave modeling. The optimization is performed using the null space of the modeling operator, which reduces the dispersion error during modeling with a high wavenumber. Approximation of the modeling operator and optimization of the dispersion error can be applied to arbitrarily positioned nodes. To obtain an optimal wave operator, flexible approximation is used, and its degrees of freedom are fully functional with the basis for the nullspace of the operator. A dispersion-optimized operator based on this approach yields an improved reduction in the numerical dispersion error. Numerical examples are evaluated to demonstrate the effectiveness of the developed method, compared with those of the existing finite-difference and finite-element schemes. We have found that the developed approach can produce more accurate results for frequency-domain wave modeling with regular and irregular grids.
An iterative factored topography-dependent eikonal solver for anisotropic media
Authors: Zhou Xiaole , Lan Haiqiang , Chen Ling , Guo Gaoshan , Lei Yiming , Bin Waheed Umair , Pan Shulin
Published: July 2021

Accurate and efficient eikonal solvers for heterogeneous media play an important role in many areas of seismology, such as seismic tomography, migration, and earthquake localization. Incorporating seismic anisotropy and complex topography remain a computational challenge for finite-difference eikonal solvers. In recent years, the topography-dependent eikonal equation (TDEE) has been proposed as an effective way to calculate seismic traveltimes for isotropic and anisotropic media with irregular topography. However, the Lax-Friedrichs sweeping method used in previous studies to approximate the viscosity solution of TDEE for anisotropic media is more dissipative and needs a much higher number of iterations to converge. In addition, the TDEE solution for the initial point source has an upwind source singularity, which makes all TDEE solvers, even the high-order ones, exhibit polluted convergence and relatively large errors that propagate from the point source to the entire computational domain. To solve these problems, we have formulated the factored topography-dependent anisotropic eikonal (FTDAE) equation in tilted transversely isotropic (TTI) media using the factorization principle. Then, the resulting quartic equation can be numerically solved by using a fixed-point iteration technique based on the simpler elliptical anisotropic eikonal (EAE) equation with a high-order source term due to anelliptical anisotropy introduced by TTI media. At each iteration, the unknown traveltime in the EAE equation is factored into two functions: One of the functions is specified analytically to capture the source singularity, such that the unknown factor is differentiable in the source neighborhood and could be solved by the fast sweeping method. Numerical examples indicate that our FTDAE solver can treat source singularity successfully and achieve high accuracy after just a few iterations, independently of the mesh size, which could provide a more efficient and robust tool for traveltime calculation in the presence of seismic anisotropy and complex surfaces.
Combining single-station microtremor and gravity surveys for deep stratigraphic mapping
Authors: Sgattoni Giulia , Castellaro Silvia
Published: July 2021

Any stratigraphic reconstruction by means of surface geophysical methods is affected by the nonuniqueness of data inversion and by the resolution-depth trade-off. The combination of different geophysical techniques can reduce the number of degrees of freedom of the problem. We have focused on two low-impact single-station geophysical techniques: microtremor and gravity. These have been used by previous authors for stratigraphic mapping only by comparing the results independently. We suggest a procedure to combine microtremor and gravity data into a unique subsoil model and explore to what extent their combined use can overcome their individual weaknesses and constrain the final result. We apply the procedure to the Bolzano sedimentary basin, Northern Italy, to derive a 3D bedrock model of the basin. We use microtremor data to map the ground resonance frequencies and derive an initial 3D bedrock depth model by assuming a [Formula: see text] profile for the sediment fill. Then, we define a density model for rock and sediments and perform 3D gravity forward modeling. We then perturb the [Formula: see text] and density models and find the parameters that best fit the observed gravity anomalies. Data uncertainties are examined to explore the significance of the results. Joint use of the two techniques successfully helps interpret the stratigraphic model: Ground resonance frequencies guarantee the spatial resolution of the bedrock geometry model, whereas gravity data help constrain the frequency to depth conversion.
DNA Methylation Changes Associated With Type 2 Diabetes and Diabetic Kidney Disease in an East Asian Population
Authors: Kim Hakyung , Bae Jae Hyun , Park Kyong Soo , Sung Joohon , Kwak Soo Heon
Published: July 2021

Context

There is a growing body of evidence that epigenetic changes including DNA methylation influence the risk of type 2 diabetes (T2D) and its microvascular complications.

Objective

We conducted a methylome-wide association study (MWAS) to identify differentially methylated sites (DMSs) of T2D and diabetic kidney disease (DKD) in a Korean population.

Methods

We performed an MWAS in 232 participants with T2D and 197 nondiabetic controls with the Illumina EPIC bead chip using peripheral blood leukocytes. The T2D group was subdivided into 87 DKD patients and 80 non-DKD controls. An additional 819 individuals from 2 population-based cohorts were used to investigate the association of identified DMSs with quantitative metabolic phenotypes. A mendelian randomization (MR) approach was applied to evaluate the causal effect of metabolic phenotypes on identified DMSs.

Results

We identified 8 DMSs (each at BMP8A, NBPF20, STX18, ZNF365, CPT1A, and TRIM37, and 2 at TXNIP) that were significantly associated with the risk of T2D (P < 9.0 × 10–8), including 3 that were previously known (DMSs in TXNIP and CPT1A). We also identified 3 DMSs (in COMMD1, TMOD1, and FHOD1) associated with DKD. With our limited sample size, we were not able to observe a significant overlap between DMSs of T2D and DKD. DMSs in TXNIP and CTP1A were associated with fasting glucose and glycated hemoglobin A1c. In MR analysis, fasting glucose was causally associated with DMS in CPT1A.

Conclusion

In an East Asian population, we identified 8 DMSs, including 5 novel CpG loci, associated with T2D and 3 DMSs associated with DKD at methylome-wide statistical significance.
The Association of Gut Microbiota With Osteoporosis Is Mediated by Amino Acid Metabolism: Multiomics in a Large Cohort
Authors: Ling Chu-wen , Miao Zelei , Xiao Mian-li , Zhou Hongwei , Jiang Zengliang , Fu Yuanqing , Xiong Feng , Zuo Luo-shi-yuan , Liu Yu-ping , Wu Yan-yan , Jing Li-peng , Dong Hong-Li , Chen Geng-dong , Ding Ding , Wang Cheng , Zeng Fang-fang , Zhu Hui-lian , He Yan , Zheng Ju-Sheng , Chen Yu-ming
Published: July 2021

Context

Several small studies have suggested that the gut microbiome might influence osteoporosis, but there is little evidence from human metabolomics studies to explain this association.

Objective

This study examined the association of gut microbiome dysbiosis with osteoporosis and explored the potential pathways through which this association occurs using fecal and serum metabolomics.

Methods

We analyzed the composition of the gut microbiota by 16S rRNA profiling and bone mineral density using dual-energy X-ray absorptiometry in 1776 community-based adults. Targeted metabolomics in feces (15 categories) and serum (12 categories) were further analyzed in 971 participants using ultra-high-performance liquid chromatography coupled to tandem mass spectrometry.

Results

This study showed that osteoporosis was related to the beta diversity, taxonomy, and functional composition of the gut microbiota. The relative abundance of Actinobacillus, Blautia, Oscillospira, Bacteroides, and Phascolarctobacterium was positively associated with osteoporosis. However, Veillonellaceae other, Collinsella, and Ruminococcaceae other were inversely associated with the presence of osteoporosis. The association between microbiota biomarkers and osteoporosis was related to levels of peptidases and transcription machinery in microbial function. Fecal and serum metabolomics analyses suggested that tyrosine and tryptophan metabolism and valine, leucine, and isoleucine degradation were significantly linked to the identified microbiota biomarkers and to osteoporosis, respectively.

Conclusion

This large population-based study provided robust evidence connecting gut dysbiosis, fecal metabolomics, and serum metabolomics with osteoporosis. Our results suggest that gut dysbiosis and amino acid metabolism could be targets for intervention in osteoporosis.
The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection
Authors: Lau Ching-In , Rowell Jasmine , Yanez Diana C. , Solanki Anisha , Ross Susan , Ono Masahiro , Crompton Tessa
Published: July 2021

During positive selection at the transition from CD4+CD8+ double-positive (DP) to single-positive (SP) thymocyte, TCR signalling results in appropriate MHC restriction and signals for survival and progression. We show that the pioneer transcription factors Foxa1 and Foxa2 are required to regulate RNA splicing during positive selection of mouse T cells and that Foxa1 and Foxa2 have overlapping/compensatory roles. Conditional deletion of both Foxa1 and Foxa2 from DP thymocytes reduced positive selection and development of CD4SP, CD8SP and peripheral naïve CD4+ T cells. Foxa1 and Foxa2 regulated the expression of many genes encoding splicing factors and regulators, including Mbnl1, H1f0, Sf3b1, Hnrnpa1, Rnpc3, Prpf4b, Prpf40b and Snrpd3. Within the positively selecting CD69+DP cells, alternative RNA splicing was dysregulated in the double Foxa1/Foxa2 conditional knockout, leading to >850 differentially used exons. Many genes important for this stage of T-cell development (Ikzf1-3, Ptprc, Stat5a, Stat5b, Cd28, Tcf7) and splicing factors (Hnrnpab, Hnrnpa2b1, Hnrnpu, Hnrnpul1, Prpf8) showed multiple differentially used exons. Thus, Foxa1 and Foxa2 are required during positive selection to regulate alternative splicing of genes essential for T-cell development, and, by also regulating splicing of splicing factors, they exert widespread control of alternative splicing.
Demographic profile and clinical picture of patients presented with Paraphenylene Diamine (PPD)/ Kala Pathar poisoning at a District Teaching Hospital
Authors: Akbar Sheraz , Siddiqui Zahid Kamal , Diwan Rana Aamir , Rehm Muhammad Hassam
Published: July 2021

Objective: To document demographic profile, clinical features and management of patients presented with PPD/Kala Pathar poisoning at District Teaching Hospital Sahiwal, Pakistan.

Methods: This cross-sectional study utilized data for cases of PPD poisoning presented at study place from 1st July 2019 to 30th June 2020. Relevant information was recorded on a proforma.

Results: A total of 111 cases were included in study. Mean age was 23.01 ± 7.24 years. Majority of cases were observed in females (82%) and majority presented from rural areas (87.4%). Cervico-facial edema (78.4%) and respiratory distress (66.7%) were the most common findings. Evidence of some level of organ damage was recorded in following manner: kidneys (44.1%), musculoskeletal (50.5%) and cardiac (45.9%). Tracheostomy was carried out in 47.7% cases and dialysis in 11.7% cases. All cases ingested PPD in raw form. Mortality rate was 50.5%.

Conclusion: PPD poisoning is associated with high rate of morbidity and mortality. Effective clinical management requires multidisciplinary approach. Measures to restrict access to this means of suicide are urgently needed. We need to set up a surveillance system for cases of attempted suicide.

doi: https://doi.org/10.12669/pjms.37.5.4251

How to cite this:Akbar S, Siddiqui ZK, Diwan RA, Rehm MH. Demographic profile and clinical picture of patients presented with Paraphenylene Diamine (PPD)/ Kala Pathar poisoning at a District Teaching Hospital. Pak J Med Sci. 2021;37(5):1397-1401.  doi: https://doi.org/10.12669/pjms.37.5.4251

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Bilingual Aphasia Test in Urdu and its Clinical Implications
Authors: Ali Nadir , Rafi Muhammad Shaban
Published: July 2021

doi: https://doi.org/10.12669/pjms.37.5.4572

How to cite this:Ali N, Rafi MS. Bilingual Aphasia Test in Urdu and its Clinical Implications. Pak J Med Sci. 2021;37(5):1545-1546. doi: https://doi.org/10.12669/pjms.37.5.4572
Importance of respiratory syncytial virus as a predictor of hospital length of stay in bronchiolitis
Authors: Buendia Jefferson Antonio , Guerrero Patino Diana
Published: July 2021

Introduction: Bronchiolitis is the leading cause of hospitalization in children. Estimate potentially preventable variables that impact the length of hospital stay are a priority to reduce the costs associated with this disease. This study aims to identify clinical variables associated with length of hospital stay of bronchiolitis in children in a tropical middle-income country

Methods: We conducted a retrospective cohort study in 417 infants with bronchiolitis in tertiary centers in Colombia. All medical records of all patients admitted to the emergency department were reviewed. To identify factors independently associated we use negative binomial regression model, to estimate incidence rate ratios (IRR) and adjust for potential confounding variables

Results: The median of the length of hospital stay was 3.68 days, with a range of 0.74 days to 29 days, 138 (33.17%) of patients have a hospital stay of 5 or more days. After modeling and controlling for potential confounders age <6 months, comorbidities (CHD or neurological), BPD,  chest indrawing, RSV isolation, and C-reactive protein were independent predictors of LOS

Conclusions: Our results show that in infants with bronchiolitis, RSV isolation, age <6 months, comorbidities (CHD or neurological), BPD,  chest indrawing, and C-reactive protein were independent predictors of LOS. As a potentially modifiable risk factor, efforts to reduce the probability of RSV infection can reduce the high medical cost associates with prolonged LOS in bronchiolitis.
The genome sequence of the European robin, Erithacus rubecula Linnaeus 1758
Authors: Dunn Jenny C. , Liedvogel Miriam , Smith Michelle , Corton Craig , Oliver Karen , Skelton Jason , Betteridge Emma , Dolucan Jale , Quail Michael A. , Uliano-Silva Marcela , McCarthy Shane A. , Howe Kerstin , Torrance James , Wood Jonathan , Pelan Sarah , Sims Ying , Challis Richard , Threlfall Jonathan , Mead Daniel , Blaxter Mark
Published: July 2021

We present a genome assembly from an individual female Erithacus rubecula (the European robin; Chordata; Aves; Passeriformes; Turdidae). The genome sequence is 1.09 gigabases in span. The majority of the assembly is scaffolded into 36 chromosomal pseudomolecules, with both W and Z sex chromosomes assembled.
Sourcing Innovation: Integrated System or Individual Components?
Authors: Chen Zhi , Mihm Jürgen , Schlapp Jochen
Published: July 2021

Problem definition: Most industrial innovations consist of multiple interacting components that must be combined into a final product to form an integrated system. When procuring such complex innovations from their suppliers, buyers face a substantial challenge: Should they tender the integrated system as a whole or, instead, procure the system’s components individually from (possibly) different suppliers? Academic/practical relevance: Suppliers have become a major source of innovation for many firms, so buyers ponder how best to structure their procurement efforts. This paper offers guidance on how complex industrial products can be optimally sourced when the buyer’s primary goal is to identify and incentivize innovation. In contrast, most previous research on procurement has concentrated on cost-reduction efforts. Methodology: We use a game-theoretic model to design and compare different procurement mechanisms that allow a buying firm to tap into the innovation potential of its supplier base. Results: Three factors largely determine whether a buyer should procure an integrated system or individual components—namely, the novelty of the innovation to be sourced, the size of the supplier base, and the extent and distribution of component integration costs. We demonstrate how buyers can improve the effectiveness of procurement mechanisms via active supplier management. Managerial implications: Our study provides clear guidelines for managers seeking to source complex industrial innovation. The recommendations presented here reveal how the optimal procurement mechanism changes with the characteristics of the desired product and of the buyer’s supplier base.
The Effect of Scientific Reading Based Project Model in Empowering Creative Thinking Skills of Preservice Teacher in Elementary School
Authors: Suryandari Kartika Chrysti , Rokhmaniyah Rokhmaniyah , Wahyudi Wahyudi
Published: July 2021

Creative thinking skills are 21st century learning needs that can be applied through the Scientific Reading Based Project (SRBP) model. The purpose of this study is to empower creative thinking skills through SRBP models in science learning in elementary school teachers’ education students. This research is mixed research with qualitative and quantitative approaches. Qualitative research is used to explore students' creative thinking abilities. Quantitative research uses a quasi-experimental approach carried out for six months on the candidates of elementary school teachers’ education. Participants in this study were the candidate of elementary school teachers’ education of 75 people who took the Basic Concept of Science subject. Data collection in this study was through observation, documentation, pre-test, and post-test with essay questions to measure creative thinking skills. The final result of the project is the final product to measure creativity. The data analysis used was an ANOVA test to measure every aspect of creative thinking skill. Qualitative analysis was used to describe the learning process and the final project of creativity. The results showed that there was an increase in creative thinking skills from aspects of flexibility, elaboration, fluency and originality. The SRBP model has a positive effect on improving the ability to think creatively.
Phytochemical Screening and Nanosynthesis of Linum Usitassimum [Flax Seeds] Used in Hypothyroid Treatment
Authors: Bharadwaj Namita , siddiqui Naved
Published: July 2021

Medicinal plants are the richest biosource of drugs of traditional system of medicine. Flax seeds (Linum usitastassimum L) is a multipurpose crop and its consumption is beneficial for health. Flax seeds is a abundant spring of healthy fat, antioxidant and fibre. The nutrient in flax seeds may help under risk of diabetes, cancer, cardiac disease and thyroid. The present study deals with qualitatitive analysis of phytochemicals by the standard method of Harbone .followed by the extraction of seed oil by sohxlet apparatus using petroleum ether as solvent. Quantitative analysis were also done to determine the amount of such phytochemicals. Phytochemicals analysis of flax seeds showed the presence of glycosides, alkaloids and flavonoids in varying amounts which can be used in future for preparation of herbal drugs. Nanosynthesis of flax seeds were also done by using silver nitrate and silver nanoparticle were prepared. Characterisation of silver nanoparticle by U.V Spectroscopy,SEM and EDX Analysis And FTIR Analysis.
Watt-level blue light for precision spectroscopy, laser cooling and trapping of strontium and cadmium atoms
Authors: Tinsley Jonathan N. , Bandarupally Satvika , Penttinen Jussi-Pekka , Manzoor Shamaila , Ranta Sanna , Salvi Leonardo , Guina Mircea , Poli Nicola
Published: July 2021

High-power and narrow-linewidth laser light is a vital tool for atomic physics, being used for example in laser cooling and trapping and precision spectroscopy. Here we produce Watt-level laser radiation at 457.75 nm and 460.86 nm of respective relevance for the cooling transitions of cadmium and strontium atoms. This is achieved via the frequency doubling of a kHz-linewidth vertical-external-cavity surface-emitting laser (VECSEL), which is based on a novel gain chip design enabling lasing at > 2 W in the 915-928 nm region. Following an additional doubling stage, spectroscopy of the 1S0 → 1P1 cadmium transition at 228.87 nm is performed on an atomic beam, with all the transitions from all eight natural isotopes observed in a single continuous sweep of more than 4 GHz in the deep ultraviolet. The absolute value of the transition frequency of 114Cd and the isotope shifts relative to this transition are determined, with values for some of these shifts provided for the first time.
Real-time motion-induced error compensation for 4-step phase-shifting profilometry
Authors: Guo Wenbo , Wu Zhoujie , Zhang Qican , Wang Yajun
Published: July 2021

Phase-shifting profilometry has been widely used in high-accuracy three-dimensional (3D) shape measurement. However, for dynamic scenarios, the object motion will lead to extra phase shift and then motion-induced error. Convenient and efficient motion-induced error compensation is still challenging. Therefore, we proposed a real-time motion-induced error compensation method for 4-step phase-shifting profilometry. The four phase-shifting images are divided into two groups to calculate two corresponding wrapped phases, one from the first three fringes and the other from the last three fringes. As the motion-induced error doubles the frequency of the projected fringes, the average phase can effectively compensate the motion-induced error because there is a π/2 phase shift between the adjacent frames. Furthermore, we designed a time sequence by recycling the projection fringes in a proper order, and the efficiency of 3D reconstruction could be effectively improved. This method performs pixel-wise error compensation, based on which we realized 50 fps real-time 3D measurement by GPU acceleration. Experimental results demonstrate that the proposed method can effectively reduce the motion-induced error.
Low-threshold 1150  nm single-polarization single-frequency Yb-doped DFB fiber laser
Authors: Tao Yue , Jiang Man , Li Can , Zhou Pu , Jiang Zongfu
Published: July 2021

We demonstrate a stable single-polarization single-frequency distributed feedback Bragg (DFB) fiber laser at 1150 nm based on a 5 cm long Yb-doped fiber which, to the best of our knowledge, is the first demonstration of a Yb-doped fiber-based single-frequency laser with a wavelength longer than 1120 nm. The threshold is as low as 10 mW. The measured maximum output power is 10.6 mW, and the spectrum at the highest power shows an excellent optical signal-to-noise ratio of about 70 dB, considering the amplified spontaneous emission in a short wavelength. The polarization extinction ratio is 25 dB, and the spectral linewidth is 20 kHz. This fiber laser is suitable for seeding high-power 1150 nm narrow-linewidth laser amplifiers, which can be used as high brightness pump sources for rare-earth-doped fiber lasers and Raman fiber lasers, or to generate visible radiation in the yellow spectral range, facilitating medical and astronomic applications.
Effect of carbon-enriched digestate on the microbial soil activity
Authors: Holatko Jiri , Hammerschmiedt Tereza , Kintl Antonin , Danish Subhan , Skarpa Petr , Latal Oldrich , Baltazar Tivadar , Fahad Shah , Akça Hanife , Taban Suleyman , Kobzova Eliska , Datta Rahul , Malicek Ondrej , Hussain Ghulam Sabir , Brtnicky Martin
Published: July 2021

Objectives

As a liquid organic fertilizer used in agriculture, digestate is rich in many nutrients (i.e. nitrogen, phosphorus, sulfur, calcium, potassium); their utilization may be however less efficient in soils poor in organic carbon (due to low carbon:nitrogen ratio). In order to solve the disadvantages, digestate enrichment with carbon-rich amendments biochar or humic acids (Humac) was tested.

Methods

Soil variants amended with enriched digestate: digestate + biochar, digestate + Humac, and digestate + combined biochar and humic acids—were compared to control with untreated digestate in their effect on total soil carbon and nitrogen, microbial biomass carbon, soil respiration and soil enzymatic activities in a pot experiment. Yield of the test crop lettuce was also determined for all variants.

Results

Soil respiration was the most significantly increased property, positively affected by digestate + Humac. Both digestate + biochar and digestate + Humac significantly increased microbial biomass carbon. Significant negative effect of digestate + biochar (compared to the control digestate) on particular enzyme activities was alleviated by the addition of humic acids. No significant differences among the tested variants were found in the above-ground and root plant biomass.

Conclusions

The tested organic supplements improved the digestate effect on some determined soil properties. We deduced from the results (carbon:nitrogen ratio, microbial biomass and activity) that the assimilation of nutrients by plants increased; however, the most desired positive effect on the yield of crop biomass was not demonstrated. We assume that the digestate enrichment with organic amendments may be more beneficial in a long time-scaled trial.
A machine learning based exploration of COVID-19 mortality risk
Authors: Mahdavi Mahdi , Choubdar Hadi , Zabeh Erfan , Rieder Michael , Safavi-Naeini Safieddin , Jobbagy Zsolt , Ghorbani Amirata , Abedini Atefeh , Kiani Arda , Khanlarzadeh Vida , Lashgari Reza , Kamrani Ehsan
Published: July 2021

Early prediction of patient mortality risks during a pandemic can decrease mortality by assuring efficient resource allocation and treatment planning. This study aimed to develop and compare prognosis prediction machine learning models based on invasive laboratory and noninvasive clinical and demographic data from patients’ day of admission. Three Support Vector Machine (SVM) models were developed and compared using invasive, non-invasive, and both groups. The results suggested that non-invasive features could provide mortality predictions that are similar to the invasive and roughly on par with the joint model. Feature inspection results from SVM-RFE and sparsity analysis displayed that, compared with the invasive model, the non-invasive model can provide better performances with a fewer number of features, pointing to the presence of high predictive information contents in several non-invasive features, including SPO2, age, and cardiovascular disorders. Furthermore, while the invasive model was able to provide better mortality predictions for the imminent future, non-invasive features displayed better performance for more distant expiration intervals. Early mortality prediction using non-invasive models can give us insights as to where and with whom to intervene. Combined with novel technologies, such as wireless wearable devices, these models can create powerful frameworks for various medical assignments and patient triage.
Spatial disinfection potential of slightly acidic electrolyzed water
Authors: Kurahashi Midori , Ito Takaaki , Naka Angelica
Published: July 2021

Slightly acidic electrolyzed water (SAEW) was developed by Japanese companies over 20 years ago. SAEW has the advantage of potent sterilizing action while being relatively safe. This study evaluated the potential application of SAEW in spatial disinfection. Prior to experiments involving spatial spraying, the ability of SAEW to remove seven type of microorganisms that cause food poisoning was studied in vitro. Results indicated that free chlorine in SAEW, even at a low concentration (30 mg/L), was able to remove Cladosporium cladosporioides, a typical airborne fungus that degrades food, and spores such as Bacillus subtilis, a hardy bacterium. In an experiment involving spatial spraying, 3.43 log10 CFU/100 L of Staphylococcus epidermidis was sprayed in a room-sized space; the same space was then sprayed with SAEW. The number of settling microbes was measured and the sterilizing ability of SAEW was assessed. Results indicated that the concentration of S. epidermidis in the space was completely removed after 20 minutes of SAEW spraying. The above findings indicate that SAEW may be used to remove airborne microorganisms via spatial spraying.
This outcome feels right! subjective evaluations of coin flip outcomes reflect previously stated preferences
Authors: Jaffé Mariela E. , Greifeneder Rainer
Published: July 2021

When facing a difficult decision, individuals may rely on a coin flip to help them come to a conclusion. In some cases, however, individuals might not adhere to the coin’s outcome, but instead report liking or disliking the coin flip’s outcome, and may use this affective reaction to form their decision. In this manuscript we investigate the affective reaction towards the outcome of a coin flip and determine whether this affective reaction provides valid feedback in regards to individuals’ underlying preferences (Hypothesis 1). We further test whether flipping a coin results in a higher alignment between previous preferences and subsequent decisions (Hypothesis 2). We conducted three studies in the lab and with online samples. Throughout all studies we found support for the notion that the affective reactions regarding the coin flip’s outcome validly reflect previously indicated preferences or attractiveness ratings. Contrary to wide-spread expectations, however, we did not find reliable support for the notion that flipping a coin, compared to a control group, leads to decisions that are more in line with the previously stated preferences.
Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms
Authors: Martinez-Liu Luis , Hernandez-Guerrero Rafael , Rivera-Gomez Nancy , Martinez-Nuñez Mario Alberto , Escobar-Turriza Pedro , Peeters Eveline , Perez-Rueda Ernesto
Published: July 2021

Archaea represent a diverse phylogenetic group that includes free-living, extremophile, mesophile, symbiont, and opportunistic organisms. These prokaryotic organisms share a high significant similarity with the basal transcriptional machinery of Eukarya, and they share regulatory mechanisms with Bacteria, such as operonic organization and DNA-binding transcription factors (TFs). In this work, we identified the repertoire of TFs in 415 archaeal genomes and compared them with their counterparts in bacterial genomes. The comparisons of TFs, at a global level and per family, allowed us to identify similarities and differences between the repertoires of regulatory proteins of bacteria and archaea. For example, 11 of 62 families are more highly abundant in archaea than bacteria, and 13 families are abundant in bacteria but not in archaea and 38 families have similar abundances in the two groups. In addition, we found that archaeal TFs have a lower isoelectric point than bacterial proteins, i.e., they contain more acidic amino acids, and are smaller than bacterial TFs. Our findings suggest a divergence occurred for the regulatory proteins, even though they are common to archaea and bacteria. We consider that this analysis contributes to the comprehension of the structure and functionality of regulatory proteins of archaeal organisms.
Determination of the frequency, species distribution and antimicrobial resistance of staphylococci isolated from dogs and their owners in Trinidad
Authors: Suepaul Sharianne , Georges Karla , Unakal Chandrashekhar , Boyen Filip , Sookhoo Jamie , Ashraph Khalil , Yusuf Anisah , Butaye Patrick
Published: July 2021

The close contact between humans and their dogs can lead to the commingling of staphylococci and the exchange of mobile genetic elements encoding antimicrobial resistance. The objectives of this study were to determine the species distribution and antimicrobial resistance patterns of staphylococci colonizing canine pets and their owners in Trinidad. Staphylococci were isolated from canine pets and their owners and identified using MALDI-TOF mass spectrometry. Antimicrobial susceptibilities were determined using the Kirby-Bauer disc diffusion method against seven classes of antimicrobial agents. A total of 440 staphylococci were isolated from 112 canine pets and their owners, 53.4% were from canine pets and 46.6% were from owners. Twenty-four species were detected, of which, most isolates (32.5%) belonged to theStaphylococcus intermediusgroup (SIG).S.sciuriwas the most common species of coagulase-negative staphylococci (CoNS) comprising 22.3% of all isolates. Antimicrobial resistance was highest against commonly used antimicrobials, such as penicillin (51.4%), tetracycline (26.1%) and trimethoprim/sulfamethoxazole (18.6%). These antimicrobials also comprised the most common multidrug resistance (MDR) combination. Overall, 19.1% of isolates displayed multidrug resistance. No methicillin-resistantStaphylococcus aureus(MRSA) isolates were detected. However, methicillin resistance was detected in 13.3% and 15.1% of coagulase-positive staphylococci (CoPS) and the CoNS+CoVS (combined CoNS and coagulase-variable staphylococci) group respectively. The presence of methicillin-resistant staphylococci is worrisome because there is the potential for the transfer of these strains between dogs and humans. These strains may act as a reservoir of resistance genes.
Prognostic value of heart rate variability in patients with coronary artery disease in the current treatment era
Authors: Vuoti Antti O. , Tulppo Mikko P. , Ukkola Olavi H. , Junttila M. Juhani , Huikuri Heikki V. , Kiviniemi Antti M. , Perkiömäki Juha S.
Published: July 2021

Coronary artery disease (CAD) mortality has declined substantially over the past decades thanks to advancing medical and interventional/surgical treatments; therefore, the prognostic value of the heart rate variability in CAD in the current treatment era is not well established. We evaluated the prognostic significance of baseline heart rate variability in 1,757 ARTEMIS study patients with angiographically verified CAD. During an average follow-up time of 8.7 ± 2.2 years, a total of 285 (16.2%) patients died. Of the patients, 63 (3.6%) suffered sudden cardiac death or were resuscitated from sudden cardiac arrest (SCD/SCA), 60 (3.4%) experienced non-sudden cardiac death (NSCD), and death attributable to non-cardiac causes (NCD) occurred in 162 (9.2%) patients. For every 10 ms decrease in standard deviation of normal to normal intervals the risk for SCD/SCA, NSCD and NCD increased significantly: HR 1.153 (95% CI 1.075–1.236, p<0.001), HR 1.187 (95% CI 1.102–1.278, p<0.001) and HR 1.080 (95% CI 1.037–1.125, p<0.001), respectively. The natural logarithm of the low-frequency component of the power spectrum and the short-term scaling exponent of the detrended fluctuation analysis also had significant association with all modes of death (p<0.001). After relevant adjustment, standard deviation of normal-to-normal intervals retained its association with NSCD and NCD (p<0.01), the natural logarithm of the low-frequency component of the power spectrum with all modes of death (p from <0.05 to <0.01), and the short-term scaling exponent of the detrended fluctuation analysis with SCD/SCA (p<0.05) and NCD (p<0.001). In conclusion, impairment of many measures of heart rate variability predicts mortality but is not associated with any specific mode of death in patients with stable CAD during the current treatment era, limiting the clinical applicability of heart rate variability to targeting therapy.
Anchoring the T6SS to the cell wall: Crystal structure of the peptidoglycan binding domain of the TagL accessory protein
Authors: Nguyen Van Son , Spinelli Silvia , Cascales Éric , Roussel Alain , Cambillau Christian , Leone Philippe
Published: July 2021

The type VI secretion system (T6SS) is a widespread mechanism of protein delivery into target cells, present in more than a quarter of all sequenced Gram-negative bacteria. The T6SS constitutes an important virulence factor, as it is responsible for targeting effectors in both prokaryotic and eukaryotic cells. The T6SS comprises a tail structure tethered to the cell envelope via a trans-envelope complex. In most T6SS, the membrane complex is anchored to the cell wall by the TagL accessory protein. In this study, we report the first crystal structure of a peptidoglycan-binding domain of TagL. The fold is conserved with members of the OmpA/Pal/MotB family, and more importantly, the peptidoglycan binding site is conserved. This structure further exemplifies how proteins involved in anchoring to the cell wall for different cellular functions rely on an interaction network with peptidoglycan strictly conserved.
Modifying TIMER to generate a slow-folding DsRed derivative for optimal use in quickly-dividing bacteria
Authors: Patel Pavan , O’Hara Brendan J. , Aunins Emily , Davis Kimberly M.
Published: July 2021

It is now well appreciated that members of pathogenic bacterial populations exhibit heterogeneity in growth rates and metabolic activity, and it is known this can impact the ability to eliminate all members of the bacterial population during antibiotic treatment. It remains unclear which pathways promote slowed bacterial growth within host tissues, primarily because it has been difficult to identify and isolate slow growing bacteria from host tissues for downstream analyses. To overcome this limitation, we have developed a novel variant of TIMER, a slow-folding fluorescent protein, named DsRed42, to identify subsets of slowly dividing bacteria within host tissues. The original TIMER folds too slowly for fluorescence accumulation in quickly replicating bacterial species (Escherichia coli, Yersinia pseudotuberculosis), however DsRed42 accumulates red fluorescence in late stationary phase cultures of E. coli and Y. pseudotuberculosis. We show DsRed42 signal also accumulates during exposure to sources of nitric oxide (NO), suggesting DsRed42 signal detects growth-arrested bacterial cells. In a mouse model of Y. pseudotuberculosis deep tissue infection, DsRed42 signal was detected, and primarily accumulates in bacteria expressing markers of stationary phase growth. There was no significant overlap between DsRed42 signal and NO-exposed subpopulations of bacteria within host tissues, suggesting NO stress was transient, allowing bacteria to recover from this stress and resume replication. This novel DsRed42 variant represents a tool that will enable additional studies of slow-growing subpopulations of bacteria, specifically within bacterial species that quickly divide.
ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions
Authors: Rawle Daniel J. , Le Thuy T. , Dumenil Troy , Yan Kexin , Tang Bing , Nguyen Wilson , Watterson Daniel , Modhiran Naphak , Hobson-Peters Jody , Bishop Cameron , Suhrbier Andreas
Published: July 2021

SARS-CoV-2 uses the human ACE2 (hACE2) receptor for cell attachment and entry, with mouse ACE2 (mACE2) unable to support infection. Herein we describe an ACE2-lentivirus system and illustrate its utility forin vitroandin vivoSARS-CoV-2 infection models. Transduction of non-permissive cell lines with hACE2 imparted replication competence, and transduction with mACE2 containing N30D, N31K, F83Y and H353K substitutions, to match hACE2, rescued SARS-CoV-2 replication. Intrapulmonary hACE2-lentivirus transduction of C57BL/6J mice permitted significant virus replication in lung epithelium. RNA-Seq and histological analyses illustrated that this model involved an acute inflammatory disease followed by resolution and tissue repair, with a transcriptomic profile similar to that seen in COVID-19 patients. hACE2-lentivirus transduction of IFNAR-/-and IL-28RA-/-mouse lungs was used to illustrate that loss of type I or III interferon responses have no significant effect on virus replication. However, their importance in driving inflammatory responses was illustrated by RNA-Seq analyses. We also demonstrate the utility of the hACE2-lentivirus transduction system for vaccine evaluation in C57BL/6J mice. The ACE2-lentivirus system thus has broad application in SARS-CoV-2 research, providing a tool for both mutagenesis studies and mouse model development.