bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening of Aptamers That Bind to the Multivalent Aminoglycoside Amikacin
Authors: Alam AHM Khurshid , Miura Yoshiko , Tsukahara Toshifumi
Published: August 2021

Increased awareness of the multiple roles of RNA molecules has led to the realization that, in addition to their structural and functional roles, RNAs can be drug targets for small molecular therapy. The aim of this study was to identify multivalent amikacin specific RNA aptamers that can be a new target sites for aminoglycoside antibiotics, including amikacin using the systemic evolution of ligands by exponential enrichment (SELEX) method. Amikacin, a member of the aminoglycoside group of antibiotics, binds to specific sites in bacterial 16S ribosomal RNAs (rRNAs) and interferes with protein synthesis, leading to cell death. Here, we used the SELEX method to isolate high affinity RNA fragments (aptamers) that bind to amikacin. After five rounds of SELEX selection, in which a linear N25 DNA template was used for the first selection cycle, the resulting RNA was cloned and sequenced. Among the 38 clones generated, five groups of sequences (groups A through E) containing nine conserved motifs were identified. The sequences of groups A and B were almost identical, indicating that the selected RNA was enriched. Subsequently, the Basic Local Alignment Search Tool program was used to search for the conserved motifs in bacterial 16S rRNA sequences. Strikingly, no sequence homology was observed, suggesting that the conserved sequences (motifs) identified in this study may be novel target sites for amikacin.
Elucidating the Innate Immunological Effects of Mild Magnetic Hyperthermia on U87 Human Glioblastoma Cells: An in vitro Study
Authors: Persano Stefano , Vicini Francesco , Poggi Alessandro , Castrillo Fernandez Jordi Leonardo , Rizzo Giusy Maria Rita , Gavilan Helena , Silvestri Niccolo , Pellegrino Teresa
Published: August 2021

Cancer immunotherapies are gaining a large popularity and many of them have been approved as standard second-line or in some cases even as first-line treatment for a wide range of cancers. However, immunotherapy has not shown a clinically relevant success in glioblastoma (GBM), principally due to the brain’s “immune-privileged” status and the peculiar tumor microenvironment (TME) of GBM featured by lack of presence of tumor-infiltrating lymphocytes and the establishment of immunosuppressive mechanisms. Emerging evidence has highlighted the key role played by innate immune cells in immunosurveillance and in initiating and driving immune responses against GBM. Immunogenic cell death (ICD) is a promising approach to elicit direct activation of the innate immune system by inducing in target cancer cells the expression of molecular signatures recognized through a repertoire of innate immune cell pattern recognition receptors (PRRs) by effector innate immune cells. Herein, we explored local mild thermal treatment, generated by using ultrasmall (size ~ 17 nm) cubic-shaped iron oxide nanoparticles exposed to an external alternating magnetic field (AMF), to induce ICD in U87 glioblastoma cells. In accordance with what has been previously observed with other types of tumors, we found that mild hyperthermia modulates the immunological profile of U87 glioblastoma cells by inducing stress-associated signals leading to enhanced phagocytosis and killing of U87 cells by macrophages. Finally, we demonstrated that mild magnetic hyperthermia has a modulatory effect on the expression of inhibitory and activating NK cell ligands on target cells. Interestingly, alteration in the expression of NK ligands, caused by mild hyperthermia treatment, in U87 glioblastoma cells, increased their susceptibility to NK cell killing and NK cell functionality. The overall findings demonstrate that mild magnetic hyperthermia stimulates ICD and sensitizes GBM cells to NK-mediated killing by inducing the upregulation of specific stress ligands, providing a novel immunotherapeutic approach for GBM treatment, with potential to synergize with existing NK cell-based therapies thus improving their therapeutic outcomes.
Look at the Spatial Confining Effect on the Molecular Electrostatic Potential (Mep). A Case Study of the Hf and BrCN Molecules
Authors: Lipkowski Paweł , Kozłowska Justyna , Bartkowiak Wojciech
Published: August 2021

In this theoretical study we report on molecular electrostatic potential (MEP) of titled molecules confined by repulsive potentials of cylindrical symmetry mimicking a topology. Our calculations show that the spatial restriction significantly changes the picture of MEP of molecules in quantitative and qualitative sense. In particular, the drastic changes of MEP as a function of the strength of spatial confinement are observed for the BrCN molecule. This preliminary study is the first step in the investigations of the behavior of MEP of molecular systems under the orbital compression.
Kemampuan Komunikasi Matematis Siswa Terhadap Materi Persamaan Linear Satu Variabel
Authors: Sopia Nurapni
Published: August 2021

Penelitian ini bertujuan untuk mendeskripsikan kemampuan komunikasi matematis siswa SMP kelas VII B di SMP N 3 Sungai Tebelian, Sintang, Kalimantan Barat. Selain itu, untuk menelaah masalah-masalah komunikasi yang dihadapi siswa selama pembelajaran pada materi Persamaan Linear Satu Variabel. Adapun metode penelitian yang digunakan adalah metode deskripsi dengan subjek penelitian 25 siswa. Instrumen penelitian ini menggunakan angket respon untuk mengetahui kemampuan komunikasi matematis siswa dengan 12 butir pertanyaan yang disebarkan secara langsung melalui offline. Ada enam indikator kemampuan komunikasi matematis yang dianalisis namun hanya satu indikator yang dapat dicapai dengan presentase perolehan hasil angket siswa 3,5%.
Analisis Kesulitan Guru Matematika Kelas VII Dalam Menerapkan Pembelajaran Daring Selama Pandemi Covid-19 Di SMP Nusantara Indah
Authors: Hutagaol Anita Sri Rejeki
Published: August 2021

Tujuan penelitian untuk mengetahui kesulitan guru matematika kelas VII dalam menerapkan pembelajaran daring selama pandemi covid-19 di SMP Nusantara Indah. Penelitian ini merupakan penelitian kualitatif. Subjek penelitian guru matematika kelas VII SMP Nusantara Indah. Alat pengumpulan data yang digunakan adalah pedoman wawancara dan dokumen. Hasil penelitian ini menunjukkan pelaksanaan pembelajaran daring di masa pandemi covid-19 memiliki beragam problematika yang dialami oleh guru matematika, siswa, dan orangtua. Permasalahan dari guru matematika berupamenyampaikan materi pelajaran secara daring,beberapa siswa tidak aktif dalam mengikuti pembelajaran, kouta internet mahal,siswa berbohong kepada orang tua, susah mendapatkan jaringan internet. Beragam permasalahan tersebut dapat diatasi dengan membuat video pembelajaran,dipanggil kesekolah jika siswa mempunyai masalah atau kesulitan dalam mengikuti pembelajaran daring.
Tailored Mobile Messaging Intervention for Waterpipe Tobacco Cessation in Young Adults: A Randomized Trial
Authors: Mays Darren , Johnson Andrea C. , Phan Lilianna , Sanders Camilla , Shoben Abigail , Tercyak Kenneth P. , Wagener Theodore L. , Brinkman Marielle C. , Lipkus Isaac M.
Published: August 2021

Objectives. To test a tailored mobile health (i.e., mHealth) intervention for waterpipe tobacco cessation in young adults.

Methods. From 2018 to 2020 at 2 US sites, we conducted a randomized trial with 349 waterpipe tobacco smokers aged 18 to 30 years randomized to control (no intervention), untailored, or tailored intervention arms. Intervention arms received a 6-week mHealth intervention conveying risks of waterpipe tobacco through text and images and strategies to enhance motivation and support quitting. The tailored intervention was personalized to baseline measures and intervention text message responses. Risk appraisals, motivation to quit, waterpipe smoking frequency, and cessation were assessed at 6 weeks, 3 months, and 6 months.

Results. At 6 months, cessation was higher in the tailored (49%) than the control arm (29%; odds ratio = 2.4; 95% confidence interval = 1.3, 4.2) and smoking frequency was lower in the tailored (mean = 3.5 days) than the control arm (mean = 4.3 days; P = .006). At interim follow-ups, significant differences in other outcomes favored the tailored intervention.

Conclusions. Tailored mobile messaging can help young adult waterpipe tobacco smokers quit. This scalable intervention is poised for population implementation.
Orthopaedic Gene Therapy
Authors: Evans Christopher H. , Ghivizzani Steve C. , Robbins Paul D.
Published: August 2021

» Orthopaedics pioneered the expansion of gene therapy beyond its traditional scope of diseases that are caused by rare single-gene defects. Orthopaedic applications of gene therapy are most developed in the areas of arthritis and regenerative medicine, but several additional possibilities exist.

» Invossa, an ex vivo gene therapeutic for osteoarthritis, was approved in South Korea in 2017, but its approval was retracted in 2019 and remains under appeal; a Phase-III clinical trial of Invossa has restarted in the U.S.

» There are several additional clinical trials for osteoarthritis and rheumatoid arthritis that could lead to approved gene therapeutics for arthritis.

» Bone-healing and cartilage repair are additional areas that are attracting considerable research; intervertebral disc degeneration and the healing of ligaments, tendons, and menisci are other applications of interest. Orthopaedic tumors, genetic diseases, and aseptic loosening are additional potential targets.

» If successful, these endeavors will expand the scope of gene therapy from providing expensive medicines for a few patients to providing affordable medicines for many.
Comprehensive Studies of Formation Water for Achimov and Bazhenov Formations — Revitalizing Archived and Old Cores
Authors: Kazak Ekaterina Sergeevna , Kazak Andrey Vladimirovich
Published: August 2021

The sediments of Bazhenov (BF) and Achimov (ACh) formations have been studied for more than 50 years, and to date, a large amount of core material obtained during drilling at the stage of exploration is stored in the core stores of Russian industrial companies. The rise in the cost of the complex of geological exploration and the emergence of new research methods enabled studies of the old/dry core from previously drilled exploration wells. BF and ACh reservoir rocks have low permeability and initially low water saturation, and therefore, during storage, rock samples could partially retain pore water. To study its composition and quantitative content, we used the previously proposed integrated approach with proven effectiveness in fresh low-permeability BF rocks.

The studied materials include BF rock samples from 3 different fields stored for 2 years after sampling in the laboratory, and ACh rock samples from 12 fields, cored more than 10 years ago at the geologic exploration stage. The complex technique includes determining free and bound water contents by the evaporation method with isotopic analysis (δ18O and δD) of the released water. The modified water extraction method provides a range of pore water salinity, while the modified alcohol ammonium chloride method measures the cation exchange capacity (CEC). Auxilary methods include Rock-Eval pyrolysis to determine organic matter content, X-ray diffraction analysis (XRD) to assess the mineral composition of sediments. The verification of the results for the BF rock samples was carried out according to the data obtained for the new/fresh core, while for the ACh rock samples — according to the results of the direct chemical composition analysis of the formation water.

Despite the low permeability, we found that the BF and ACh rock samples during storage lost almost all (up to 90%) free water due to evaporation. At the same time, salts from formation water remained in the pore space, which made it possible to estimate the range of its NaCl salinity: 1.84–14.7 g/L for ACh rock samples and 4.49–20.19 g/L for BF rock samples. The obtained values set the lower limit of the possible pore water salinity of the studied ACh and BF rock samples. Moreover, the results match those from direct salinity measurements in the ACh depth intervals and the results of fresh BF core laboratory studies.

We showed that the old/dry BF and ACh core could be effectively used to assess the bound water content with subsequent determination of its genesis from isotopic composition data and CEC measurements. This opportunity relies on the high clay content in the studied BF and ACh rock samples.

The obtained results show the fundamental capability of informative laboratory studies of BF and ACh rock samples from public and private core storage facilities and give new life to archived and old/dry core.
Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis patient
Authors: Zheng Meiqin , Kang Yutong , Xu Yi , Xu Fangyi , Chen Yanjiong
Published: August 2021

Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the pathogenic agents. In this study, metagenomic sequencing was conducted to investigate the microbiome of the vitreous of an endophthalmitis patient whose disease progressed rapidly and was accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome. The main antibiotic resistance gene (ARG) types included beta-lactam, macrolide-lincosamide-streptogramin, and multidrug resistance genes. Additionally, the metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was isolated. The average nucleotide identities (ANI) and DNA–DNA hybridization (DDH) analysis between the genomes of Streptococcus sp. v1. nov and related species revealed that Streptococcus sp. v1. nov belongs to a new species. Pan/core genome analysis for Streptococcus sp. v1. nov. and tetra correlation search (TCS) top 25 hit strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to the ABC transporter system, which could indicate the unique virulence and pathogenic potential of Streptococcus sp. v1. nov. In addition, 7 virulence factors were identified in total, and most of them were classified as “offensive virulence factors”. The high pathogenicity of Streptococcus sp. v1. nov. could explain the patient's rapid disease progression. Our study first isolated an ocular pathogen with high virulence based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patients in the future.
Site Response Analysis of S2 Soil Deposits Focusing on the Effects of Liquefaction and Pore-Pressure Dissipation on the Ground Surface Response Spectrum
Authors: Anthi Maria , GEROLYMOS NIKOS
Published: August 2021

A numerical algorithm for executing non-linear ground response analysis of layered sites is developed, capable of reproducing liquefaction phenomena, considering the simultaneous dissipation of the excess pore water pressure through soil grains. Τhe wave propagation algorithm is based on the plasticity constitutive model for sand Ta-Ger expressed in a one dimensional p-q space form, which exhibits remarkable versatility in representing complex patterns of sand cyclic behavior, such as stiffness decay and decrease in strength due to build-up of pore-water pressure. Its calibration is based on shear modulus reduction and damping curves for drained loading conditions and liquefaction resistance curves for undrained conditions. A detailed presentation of the numerical model formulation is provided, indicating the numerical approach of the wave propagation and consolidation differential equations. The recorded seismic ground response of the Port Island array from Kobe 1995 earthquake is used as a benchmark for testing the validity of model predictions. The model is finally applied to estimate the elastic response spectra at the surface of soil profiles with liquefiable layers (ground type S2) as per EC8:2004. The investigation study involves the ground response analysis of diverse soil profiles, all including a liquefiable zone, excited with a suite of earthquake motions at their base. The acceleration time histories were extracted from the PEER Ground Motion Database having characteristics compatible with the NGA-estimated response spectrum at the bedrock and with key seismological parameters such as the earthquake magnitude Mw and horizontal distance from the fault RJB. Two different methods are applied regarding the selection of base excitations: Amplitude scaled records (to match a target response spectrum) and spectral matched records. From the results an idealized response spectrum is deduced in terms of the design spectrum parameters S, η, ΤΒ and TC. It is shown that the idealized ground surface response spectrum is marginally sensitive to method of base excitation selection.
Biomarker-based treatment stratification in ADHD: An out-of-sample validation
Authors: Voetterl Helena , Wingen Guido van , Michelini Giorgia , Griffiths Kristi , Gordon Evian , deBeus Roger , Korgaonkar Mayuresh , Loo Sandra , Palmer Donna , Breteler Rien , Denys Damiaan , Arnold Eugene , du Jour Paul , Ruth Rosalinde van , Jansen Jeanine , Dijk Hanneke van , Arns Martijn
Published: August 2021

Attention-deficit/hyperactivity disorder (ADHD) is characterized by neurobiological heterogeneity, possibly explaining why not all patients benefit from a given treatment. As a means to select the right treatment (stratification), biomarkers may aid in personalizing treatment prescription, thereby increasing remission rates.The present study introduces a clinically interpretable and actionable, age- and sex-standardized biomarker based on individual alpha peak frequency (iAPF) assessed during resting-state electroencephalography (EEG). The biomarker was developed in a heterogeneous sample (N=4249), and stratifies patients with a higher iAPF to Methylphenidate (MPH; N=336) and those with a lower iAPF to Neurofeedback (NFB; N=136), resulting in a predicted gain in normalized remission of 17-30%. Blinded out-of-sample validation studies for MPH (N=58) and NFB (N=96) corroborated these findings, yielding a predicted gain in stratified normalized remission of 36% and 29%, respectively.These findings suggest that acknowledging neurobiological heterogeneity can inform stratification of patients to their individual best treatment and enhance remission rates.
The Impact of Different Phases of the El Niño-Southern Oscillation Phenomenon on Goiás State Rainfalls and Temperature Characteristics Across Three Decades
Authors: Matta David Henriques  da , Coelho Caio Augusto dos Santos , Santos Leydson Lara dos , Stone Luis Fernando , Heinemann Alexandre Bryan
Published: August 2021

Rainfall and temperature are the two key parameters of crop development. Studying the characteristics of these parameters under El Niño-Southern Oscillation (ENSO) conditions is important to better understand the impacts of the different phases of this phenomenon (El Niño, Neutral, and La Niña conditions) on agriculture. This study analyzes 32 years (1980–2011) of climatic data from 128 weather stations across Goiás State in Brazil to determine the behavior of temperature and rainfall time series over three periods (1980–1989; 1990–1999 and 2000–2011) under El Niño, Neutral, and La Niña conditions. The analysis revealed no major impacts of ENSO conditions on accumulated rainfall characteristics, a feature particularly marked in the most recent period (2000–2011). ENSO impacting temperature was identified but presented considerable variability across the periods investigated. These impacts were marked in the first two periods as for maximum temperature and increased from the first to the last period as for minimum temperature. These features were noticed in both analyses in the entire Goiás State and most of the investigated mega-regions, except for the East and Northeast mega-regions as for minimum temperature. There were increases in maximum temperature values throughout the rainfed season (October to March) for all ENSO conditions and investigated periods. Minimum temperature also increased across the three investigated periods, and this was marked in the beginning of the rainfed season (October) under El Niño and Neutral conditions.
Rheumatic heart disease knowledge and associated factors among nurses working in cardiac centers at public and private hospitals of Addis Ababa: cross sectional study
Authors: Techane Tesfaye , Legesse Bethlehem , Ayalew Yohannes , Hailu Aklil
Published: August 2021

Back ground: It is proposed that the biggest gap in control of rheumatic heart disease is in implementing of ineffective primary and secondary preventive measures. These measures are supposed to be well addressed by nurses. For prevention and proper management, nurses are expected to have full knowledge about rheumatic heart disease. Therefor the main objective of the study was to assess the level of nurse’s knowledge and factors behind regarding RHD in the current study. Method: Institution based cross sectional study was conducted on nurses working in cardiac centers of public and private hospitals at Addis Ababa from April 1 to 30, 2021. Total sample size is 163 selected by purposive sampling method. Data was entered in to Epi-data version 4.5 and exported to SPSS version 25.0 and was checked for missing values. Data was cleaned. Descriptive statistics such as frequency, mean and percentages were calculated, described and displayed in tables, graphs and charts. Binary logistic regression was done to see the crude significant relation of each independent variable with nurse’s good knowledge score. Significant factors were identified based on multivariate logistics regression in 95% confidence level at P-value less than 0.05. Result: In the present study about 154 participants were participated. The mean correct answer response of the nurses for knowledge of RHD questions is 12.2 ± 5.2. Only 48.7% of the nurses have good knowledge towards RHD. Being male in gender, having history of sore throat, taking formal education in university or collage, taking in-service training on RHD, having higher wok experience, have found significantly associated with higher odds of nurses’ good knowledge towards RHD. Conclusion and recommendation: regular training regarding RHD management should be given to nurses who are working in cardiac centers. Rheumatic heart disease early treatment and prevention should be incorporated and reinforced in to nursing and other health related professions curriculums.
Improving CNN-Based Pest Recognition with a Post-Hoc Explanation of XAI
Authors: Chen Ching-Ju , Chen Ling-Wei , Yang Chun-Hao , Huang Ya-Yu , Huang Yueh-Min
Published: August 2021

Deep learning is currently quite prevalent and is often used in image classification or object detection. This article adds emerging research on the use of explainable AI (XAI) in Tessaratoma papillosa pest identification and investigates the connotation and importance of XAI, interpretability classification standards, and neural network interpretation methods and compares the quality of interpretations between different approaches and various trade-offs. The experimental results include the data processing in the research, the establishment of training models, a comparison of the results and feature visualization methods, and the consequences of improving the training models. First, we analyzed the data processing methods of the dataset, trained the VGG16 model, and finally added a visual interpretation method to the model to visualize and explain the model identification results. The experimental results indicated that the best visual discrimination effect was obtained through eXplanation with Ranked Area Integrals (XRAI). In this study, XAI was used to obtain the factors contributing to incorrect predictions based on post-hoc explanations. Based on the inferenced result, we proposed an adjustment method for improving the model accuracy as a basis for future research to subsequently adjust and improve the model. It is hoped that the experimental results of this study can provide researchers in artificial intelligence useful information so that they can use XAI to acquire appropriate interpretations to correct recognition accuracy and drive the development of XAI.
Factors Affecting Knowledge Regarding Unmet Need On Fertile Aged Women in Indonesia: Evaluation of 2012 and 2017 IDHS
Authors: Harzif Achmad Kemal , Maidarti Mila , Handayaning Fransisca Novi , Andyra Azizah Fitriayu
Published: August 2021

Background
The Family Planning (FP/KB) Program is a national method of controlling population growth rates while improving maternal and child health. Indonesia, as one of the largest countries, has abysmally low contraceptive coverage. One of its main issues is unmet contraceptive needs. This study aims to determine the factors that influence women's unmet need of childbearing age (WCA) in Indonesia.
Method:
An unpaired comparative analytic study with a cross-sectional method was conducted on secondary data obtained from 2012 and 2017 Indonesia Demographic and Health Survey (IDHS). The subjects in this study were all women of childbearing age (15–49 years). Subjects with incomplete data were excluded from the study. Unmet need was defined as WCA who did not use contraception but decline to have more children or wanted to delay their pregnancies. Chi-square analysis was performed on categorical data and Mann-Whitney U analysis on numerical data.
Result
A total of 45,607 WCA in the 2012 IDHS data and 29,627 WCA in the 2017 IDHS data were included in the study. In the 2012 IDHS data, factors influencing unmet needs were age (p = 0.023) and parity (p < 0.0001). In the 2017 IDHS data, factors influencing unmet needs were the residential area (p = 0.003), level of education (p = 0.008), level of spouse’s education (p < 0.0001), employment status (p = 0.03), possession of electricity (p = 0.001), and possession of television (p = 0.01)
Conclusion
Factors affecting unmet needs are age, parity, residential area, level of education, level of spouse's education, employment status, possession of television, and possession of electricity. There were no recurring factors on 2012 and 2017 IDHS data.
Clinicians’ Perceptions of The Health Status of Formerly Detained Immigrants
Authors: Hampton Kathryn , Mishori Ranit , Griffin Marsha , Hillier Claire , Pirrotta Elizabeth , Wang Nancy E.
Published: August 2021

Background

In the past decade, the U.S. immigration detention system regularly detained more than 30,000 people; in 2019 prior to the pandemic, the detention population exceeded 52,000 people. Inhumane detention conditions have been documented by internal government watchdogs, news media and human rights groups, finding over-crowding, poor hygiene and sanitation and poor and delayed medical care, as well as verbal, physical and sexual abuse.
Methods

This study surveyed health professionals across the United States who had provided care for immigrants who were recently released from immigration detention to assess clinician perceptions about the adverse health impact of immigration detention on migrant populations based on real-life clinical encounters. There were 150 survey responses, of which 85 clinicians observed medical conditions attributed to detention.
Results

These 85 clinicians reported seeing a combined 1300 patients with a medical issue related to their time in detention, including patients with delayed access to medical care or medicine in detention, patients with new or acute health conditions including infection and injury attributed to detention and patients with worsened chronic conditions or special needs conditions. Clinicians also provided details regarding sentinel cases, categorized into the following themes: Pregnant women, Children, Mentally Ill, COVID-19, and Other serious health issue.
Conclusions

This is the first survey, to our knowledge, of health care professionals treating individuals upon release from detention. Due to the lack of transparency by federal entities and limited access to detainees, this survey serves as a source of credible information about conditions experienced within immigration detention facilities and is a means of corroborating immigrant testimonials and media reports. These findings can help inform policy discussions regarding systematic changes to the delivery of healthcare in detention, quality assurance and transparent reporting.
Dogs (Canis Familiaris) Underestimate The Quantity of Connected Items: First Demonstration of Susceptibility To The Connectedness Illusion in Non-Human Animals
Authors: Lõoke Miina , Marinelli Lieta , Agrillo Christian , Guérineau Cécile , Mongillo Paolo
Published: August 2021

In humans, numerical estimation is affected by perceptual biases, such as those originating from the spatial arrangement of elements. Different animal species can also make relative quantity judgements. This includes dogs, who have been proposed as a good model for comparative neuroscience. However, dogs do not show the same perceptual biases observed in humans. Thus, the exact perceptual/cognitive mechanisms underlying quantity estimations in dogs and their degree of similarity with humans are still a matter of debate. Here we explored whether dogs are susceptible to the connectedness illusion, an illusion based on the tendency to underestimate the quantity of interconnected items. Dogs were first trained to choose the larger of two food arrays. Then, they were presented with two arrays containing the same quantity of food, of which one had items interconnected by lines. Dogs significantly selected the array with unconnected items, suggesting that, like in humans, connectedness determines underestimation biases, possibly disrupting the perceptual system’s ability to segment the display into discrete objects. The similarity in dogs’ and humans’ susceptibility to the connectedness, but not to other numerical illusions, suggests that different mechanisms are involved in the estimation of quantity of stimuli with different characteristics.
Differential Analysis of RNA Structure Probing Experiments at Nucleotide Resolution: Uncovering Regulatory Functions of RNA Structure
Authors: Yu Bo , Li Pan , Zhang Qiangfeng , Hou Lin
Published: August 2021

RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcriptome-wide analysis of RNA secondary structure in various cellular conditions. Differential analysis of structure probing data in different conditions can reveal the RNA structurally variable regions (SVRs), which is important for understanding RNA functions. Here, we propose DiffScan, a computational framework for normalization and differential analysis of structure probing data in high resolution. DiffScan preprocesses structure probing datasets to remove systematic bias, and then scans the transcripts to identify SVRs and adaptively determines their lengths and locations. The proposed approach is compatible with most structure probing platforms (e.g., icSHAPE, DMS-seq). When evaluated with simulated and benchmark datasets, DiffScan identifies structurally variable regions at nucleotide resolution, with substantial improvement in accuracy compared with existing SVR detection methods. Moreover, the improvement is robust when tested in multiple structure probing platforms. Application of DiffScan in a dataset of multi-subcellular RNA structurome identified multiple regions that form different structures in nucleus and cytoplasm, linking RNA structural variation to regulation of mRNAs encoding mitochondria-associated proteins. This work provides an effective tool for differential analysis of RNA secondary structure, reinforcing the power of structure probing experiments in deciphering the dynamic RNA structurome.
ADP-ribosylating adjuvant reveals plasticity in cDC1 cells that drive mucosal Th17 development and protection against influenza virus infection
Authors: Lycke Nils , Arabpour Mohammad , Lebrero-Fernández Cristina , Schön Karin , Stromberg Anneli , Börjesson Vanja , Lahl Katherina , Angeletti Davide , Agace William
Published: August 2021

Migratory dendritic cells carrying CD103 are the targets for mucosal vaccines. These belong to either of two lineage restricted subsets, cDC1 or cDC2 cells, which have been linked to priming of functionally distinct CD4 T cells. However, recent studies have identified plasticity in cDC2 cells with overlapping functions with cDC1 cells, while the converse has not been reported. We genetically engineered a vaccine adjuvant platform that targeted the cholera toxin A1 (CTA1) ADP-ribosylating enzyme to CD103+ cDC1 and cDC2 cells using a single chain antibody (scFv) to CD103. Unexpectedly, intranasal immunization with the CTA1-svFcCD103 adjuvant modified cDC1 cells to effectively prime Th17 cells, a function normally restricted to cDC2 cells. In fact, cDC2 cells were dispensible. Single cell RNAseq analysis revealed upregulation of Th17-promoting gene signatures in sorted cDC1 cells. Our finding represents a major shift of paradigm as we have documented functional plasticity in cDC1 cells.
Regionalization and Trend Analysis of Seasonal Precipitation (1970 - 2020) using Hierarchical Clustering and Wavelet Transform Approach in the Mahi River Basin, India
Authors: Sharma Aditya , Sharma Devesh , MS Shyam Sunder
Published: August 2021

Understanding the trend in seasonal precipitation in the context of climate change is crucial for the maintenance of regional water resources management. The present study examines the seasonal precipitation trend in the Mahi River basin, India by using the wavelet transform and clustering method. Very limited studies have been carried out over the basin using this approach. Daily gridded rainfall data (0.25°×0.25° spatial resolution) for 51 grids from 1970 to 2020 has been taken from India Meteorological Department (IMD) and the time series trend was tested by Mann-Kendall. The monthly, seasonal, and annual statistic has been analyzed for 51 years. We have also plotted the relationship of precipitation trend–elevation. After that, homogeneous precipitation regions are delineated with hierarchical clustering analysis. Results reveal that seasonal precipitation over the basin clusters into 4 subregions for monsoon (JJAS1 to JJAS4) and 3 subregions for winter, pre-monsoon, and post-monsoon seasons. After the regionalization of the subregions, the periodicity and the inter-seasonal relationship were analyzed using continuous wavelet transform (CWT). Findings revealed that the cross-correlation between pre-monsoon and monsoon seasons highly affect significantly in past over the basin. Further, the regional geography-altitude and moisture convergence perform a major role in the variability of seasonal precipitation. The output of the current study would be utilized in a better understanding of precipitation forecast, watershed, and agricultural planning which may give a better climate change indication at a regional-basin level. We also suggest future needs to more focus on the understanding of elevation-dependent wetting in hilly regions using a different type of datasets.
Mechanistic Insight of Biochar-layered Double Hydroxide Composite for Efficient Removal of Aqueous Pb(II) and Cu(II)
Authors: Su Xinyue , Chen Yan , Li Yanfei , Li Jing , Song Wen , Li Xuguang , Yan Liang-guo
Published: August 2021

To explore the heavy metal adsorption mechanisms by biochar-based materials, MgAl-layered double hydroxide (MgAl-LDH) was loaded on a commercial coconut shell biochar (BC) to obtain the composite (BC-LDH) for adsorptive decontamination of Pb(II) and Cu(II) in water. The removal capacities of BC-LDH (294 and 38.6 mg/g) was higher than BC (13.3 and 11.4 mg/g) and LDH (126 and 22.7 mg/g) for aqueous Pb(II) and Cu(II). The pseudo-second-order equation and the Langmuir model could better illustrate the adsorption process, respectively. The interaction mechanisms between BC-LDH and heavy metals were classified as mineral precipitation (Qpre), cation exchange and isomorphic replacement (Qexc), electrostatic attraction (Qele), and surface complexation (Qcom) according to the characterization results. The quantitative analysis indicated that the contributions of the above mechanisms of BC-LDH for Pb(II) and Cu(II) followed the order of Qpre > Qele > Qexc and Qpre > Qexc > Qele, respectively. Compared with BC, the Qpre increased and Qele decreased significantly, certified the combination of BC and LDH provided a kind of viable composite in heavy metal wastewater treatment.
Post-deposition Weathering of Pb-rich Particles From a Pb-Zn Smelting and Refining Factory Under Semiarid Conditions
Authors: Soto-Jiménez Martin Federico , Roos-Muñoz Sarahi , Soto-Morales Sarahi , Gómez-Lizarrága Laura Elena , Bucio-Galindo Lauro
Published: August 2021

In this study, urban dust samples were collected at 1 km radius surrounding one of the largest Ag-Cd-Pb-Zn smelting and refining complex in the world (Met-Mex Peñoles), which is in operation in Torreón (North México) since 1901. Metal-rich particles in urban dust were analyzed for elemental composition, and Pb-rich particles were identified, characterized, and analyzed for mineral identification by using conventional techniques such as scanning electron microscopy (SEM), Energy Dispersive X-Ray Spectroscopy (EDS), and X-ray powder diffraction (XRD). Pb-rich particles showed a variety of sizes and morphologies and different contents of Pb and other elements. Pb-rich particles were related to the fugitive and non-controlled emissions from Met-Mex Peñoles. Galena occurs in individual and metal-rich agglomerate particles. The presence of secondary Pb minerals (e.g., Pb carbonates, Pb sulfate, and Pb oxides) evidenced the weathering in Pb-rich particles and metal-rich agglomerates. Secondary Pb minerals are incorporated in finer particles than original sulfide minerals, and they are also more concentrated in Pb and chemically more available than galena for the environment and humans. Physical-chemical transformations on the weathered Pb-rich particles are increasing the availability and toxicity of lead in the urban dust and the potential impacts on the environment and human health.
Local Benefits Exceed Costs For Widespread Charging Infrastructure For On-Street Urban Parking
Authors: Schmutz Malenka , Vliet Oscar van , Patt Anthony
Published: August 2021

BackgroundLack of charging infrastructure is a critical barrier to the dissemination of electric cars and many cities have started installing charging stations in public parking spaces.We do a cost-benefit analyses of installing charging stations in public parking spaces, with different assumptions for uptake of electric cars, topology of charging stations, environmental benefits, and costs for infrastructure. We use the case study of Zurich, which is representative of dense European cities.ResultsWe find that building charging stations in residential areas has net positive benefits, as long as the charging stations are used at least one-third of the daytime. Net benefits remain positive if we remove noise or climate benefits.ConclusionsAiming to equip 40% of public residential parking spaces with charging points, and then accelerating or slowing down the deployment of charging stations based on their actual use appears to be a robust strategy that will result in positive net public benefits for city residents and stimulate uptake of electric cars.
Nanoselenium Transformation And Inhibition of Cadmium Accumulation By Regulating The Lignin Biosynthetic Pathway And Plant Hormone Signal Transduction In Pepper Plants
Authors: Li Dong , Zhou Chunran , Ma Jinling , Wu Yangliu , Kang Lu , An Quanshun , Zhang Jingbang , Deng Kailin , Li Jia-Qi , Pan Canping
Published: August 2021

Selenium (Se) can promote the growth and resistance of agricultural crops as fertilizers, while the role of nano-selenium (nano-Se) against Cd remains unclear in pepper plants (Capsicum annuum L.). Biofortification with nano-Se observably restored Cd stress by decreasing the level of Cd in plant tissues and boosting the accumulation in biomass. The Se compounds transformed by nano-Se were primarily in the form of SeMet and MeSeCys in pepper tissues. Differential metabolites and the genes of plant signal transduction and lignin biosynthesis were measured by employing transcriptomics and determining target metabolites. The number of lignin-related genes (PAL, CAD, 4CL, and COMT) and contents of metabolites (sinapyl alcohol, phenylalanine, p-coumaryl alcohol, caffeyl alcohol, and coniferaldehyde) were remarkably enhanced by treatment with Cd1Se0.2, thus, maintaining the integrity of cell walls in the roots. It also enhanced signal transduction by plant hormones and responsive resistance by inducing the biosynthesis of genes (BZR1, LOX3, and NCDE1) and metabolites (brassinolide, abscisic acid, and jasmonic acid) in the roots and leaves. In general, this study can enable a better understanding of the protective mechanism of nano-Se in improving the capacity of plants to resist environmental stress.
Temperature Distribution And Mechanical Properties of FSW Medium Thickness 2219 Aluminum Alloy
Authors: Lu Xiaohong , Luan Yihan , Meng Xiangyue , Zhou Yu , Zhao Ning , Liang Steven Y.
Published: August 2021

Friction stir welding (FSW) is a solid-state jointing technology, which has the advantages of high joint strength, low residual stress aXnd small deformation after welding. During the process of FSW, the welding temperature has an important effect on the quality of the weldment. Therefore, the heat generation model of FSW of medium thickness 2219 aluminum alloy is established based on the friction heat generation at the interface between the tool and the workpiece and the plastic deformation heat generation of the weldment material near the tool. The heat transfer model is set under the premise of considering heat conduction, thermal convection, and thermal radiation. Using JMatPro technology, the temperature-related material parameters of 2219 aluminum alloy are calculated based on the material composition, and the heat generation model is imported into the ABAQUS simulation software based on the DFLUX subroutine, and the establishment of the FSW thermodynamic model is realized. The effectiveness of the model is verified by FSW experiments. The thermodynamic model takes into account both heat generation (friction heat generation and plastic deformation heat generation) and heat transfer (heat conduction, thermal convection and thermal radiation), so it has a high prediction accuracy. Based on the FSW thermodynamic model, the influence of welding parameters on temperature distribution is explored, subsequently the influence of welding temperature on mechanical properties of welded joint are also studied. The research can provide guidance for predicting and characterizing the temperature distribution and the improvement of mechanical performance of FSW.
The Mutational Landscape of Upper Gastrointestinal Adenocarcinomas- A Study of Similarities and Differences
Authors: Krishnamurthy Kritika , Urioste Sophia Navajas , Cusnir Mike , Schwartz Michael , Alghamdi Sarah , Sriganes Vathany , Poppiti Robert
Published: August 2021

Purpose-The gastrointestinal tract is home to a wide variety of neoplasms. Gastrointestinal adenocarcinomas display distinct prognostic patterns. With the advent of next generation sequencing, attempts are being made to delineate distinct molecular characteristics of these adenocarcinomas from adjoining anatomical sites.Methods-Thirty-seven cases of upper gastrointestinal adenocarcinomas including those of the esophagus, gastroesophageal junction, stomach, small intestine and gallbladder were retrieved. Next generation sequencing data consisting of base substitutions, copy number variations, indels and rearrangements, in 324 genes, were analyzed for recurrent genetic abnormalities. Statistical analysis was performed using IBM SPSS25 and SAS software.Results-Genetic alterations were found in 181 genes. APC mutations were found in 50% of the esophageal adenocarcinomas, 5% of the gastric adenocarcinomas and 33.3% of the small intestinal adenocarcinomas (p=0.04). PIK3 gene family mutations were found in 10% of the gastric adenocarcinomas, 66% of the gall bladder adenocarcinomas and 66% of the small intestinal adenocarcinomas (p=0.002).The mutations were found exclusively in the PIK3 class 1 family.Conclusion-In this study, APC gene mutations were found to be more frequent in esophageal and small intestinal adenocarcinomas than previously reported. PIK3 class 1 gene family mutations were found to be more frequent in gallbladder and small intestinal adenocarcinomas.
Aptamer Selection Against Quinolones Antibiotics Using Immobilizing Free SELEX, and Studying Aptamer-Antibiotic Interaction By Spectroscopy and High-Resolution Mass Spectrometry
Authors: Kabiri Maryam , Rafati Hasan , Tohidfar Masoud , Aliahmadi Atousa , Ghassempour Alireza , Shahsavari Zeinab , Rezadoost Hassan
Published: August 2021

Over-consumption of antibiotics has led to antimicrobial resistance creating urgency to find fast and efficient techniques to monitor the level of antibiotics in the foods. The advantages of using aptamer for a variety of scientific challenges are becoming more abundant in different fields, making its applications more effective and cost-efficient. In this study, two aptamers against two quinolones antibiotics (Enrofloxacin and Ofloxacin) were isolated via GO-SELEX (graphene oxide assisted Systematic Evolution of Ligands by Exponential Enrichment). The interaction between the aptamer and its cognate antibiotic was investigated using spectroscopy and mass spectrometry. The obtained evidence from spectroscopy showed that the interaction of antibiotics with their aptamers resulted in a 41.98% and 22.45 % reduction in the extinction coefficient (ɛ) value of enrofloxacin and ofloxacin, respectively. This phenomenon could arise from the stacking interaction between the aromatic region of antibiotic and aptamer’s bases. The formation of the aptamer-antibiotic complex was studied by the high-resolution ESI-Q-TOF. In the obtained mass spectra, several peaks corresponding to the aptamer-antibiotic complexes with a wide range of charge distribution were identified, which could be explained by the fact that both aptamer-ENR and aptamer-OFLO complexes were stable in the gas phase and the intact complexes survived in the vacuum. This stability could be explained by the hydrogen bonding and electrostatic interactions between the aptamers and antibiotics. As both aptamers can distinguish quinolone from other antibiotic families, these aptamers may become great recognizing elements for apta-sensors.