bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trans-dimensional inversion of multimode seismic surface wave data from a trenched distributed acoustic sensing survey
Authors: Qu Luping , Dettmer Jan , Hall Kevin , Innanen Kristopher A , Macquet Marie , Lawton Donald C 
Published: March 2023

SUMMARYSeismic data acquired from surface-deployed distributed acoustic sensing (DAS) fibre are broad band and typically dense spatially sampled. Corresponding to these features, compared with geophone data, the low-frequency components in DAS data show higher signal-to-noise ratio and multimode dispersion curves by broad-band DAS data exhibit a higher resolution, which increases the investigation depth of near-surface structures and enhances identification and picking of dispersion curves, respectively. Therefore, DAS data are ideal for the estimates of reliable and highly resolved near-surface velocity profiles. As surface-wave dispersion inversion (SWD) is a natural scheme for near-surface investigation, in this study we have formulated a DAS-SWD inversion in which multiple SWD modes are extracted from the DAS data, and are used as input to a trans-dimensional (TD) inversion procedure, in which the number of subsurface layers is treated as an unknown. Vibroseis data with a minimum frequency of 1 Hz were sensed along a horizontal surface trench as part of a baseline seismic survey carried out by the University of Calgary at the Containment and Monitoring Institute Field Research Station in Newell County, Alberta, Canada. These surface DAS data readily permit the picking of multimode dispersion curves, which are observed to enhance velocity profile resolution in both shallow and deep regions of the near-surface simultaneously, with the TD algorithm adapting the model to reflect this improved resolution. To avoid collecting abnormal model samples with thin-interleaved high- and low-velocity layers based on the known geological information of the field site, we employed constraints that preclude the structures that have velocity drops over 100 m s−1 along depth. Data errors are estimated via a non-parametric iterative process in terms of covariance matrices that include off-diagonal elements. Synthetic examples show that SWD with higher-order modes provides additional constraints on the structure and accurate noise estimation. Inversion of the field data resulted in high-resolution estimates of shear wave velocity as a function of depth throughout the top 120 m of the subsurface. The inferred structure is consistent with existing estimates of the regional lithology but resolves additional layers between 1- and 50-m depth.
Cross-cancer pleiotropic analysis identifies three novel genetic risk loci for colorectal cancer
Authors: Sun Jing , Wang Lijuan , Zhou Xuan , Hu Lidan , Yuan Shuai , Bian Zilong , Chen Jie , Zhu Yingshuang , Farrington Susan M , Campbell Harry , Ding Kefeng , Zhang Dongfeng , Dunlop Malcolm G , Theodoratou Evropi , Li Xue 
Published: March 2023

AbstractBackgroundTo understand the shared genetic basis between colorectal cancer (CRC) and other cancers and identify potential pleiotropic loci for compensating the missing genetic heritability of CRC.MethodsWe conducted a systematic genome-wide pleiotropy scan to appraise associations between cancer-related genetic variants and CRC risk among European populations. Single nucleotide polymorphism (SNP)-set analysis was performed using data from the UK Biobank and the Study of Colorectal Cancer in Scotland (10 039 CRC cases and 30 277 controls) to evaluate the overlapped genetic regions for susceptibility of CRC and other cancers. The variant-level pleiotropic associations between CRC and other cancers were examined by CRC genome-wide association study meta-analysis and the pleiotropic analysis under composite null hypothesis (PLACO) pleiotropy test. Gene-based, co-expression and pathway enrichment analyses were performed to explore potential shared biological pathways. The interaction between novel genetic variants and common environmental factors was further examined for their effects on CRC.ResultsGenome-wide pleiotropic analysis identified three novel SNPs (rs2230469, rs9277378 and rs143190905) and three mapped genes (PIP4K2A, HLA-DPB1 and RTEL1) to be associated with CRC. These genetic variants were significant expressions quantitative trait loci in colon tissue, influencing the expression of their mapped genes. Significant interactions of PIP4K2A and HLA-DPB1 with environmental factors, including smoking and alcohol drinking, were observed. All mapped genes and their co-expressed genes were significantly enriched in pathways involved in carcinogenesis.ConclusionOur findings provide an important insight into the shared genetic basis between CRC and other cancers. We revealed several novel CRC susceptibility loci to help understand the genetic architecture of CRC.
The Office on Missing Persons in Sri Lanka: Why Truth Is a Radical Proposition
Authors: Kodikara Chulani 
Published: March 2023

ABSTRACT∞
In 2016, the Sri Lanka Parliament passed the Office on Missing Persons Act (OMP) ‘to search for and trace missing persons.’ At the time, Sinhala Buddhist nationalist leaders strongly objected to it. In this article, I read their resistance as resistance to a truth-seeking mechanism. Locating my analysis within a global paradigm of ‘dealing with the past’ through truth-seeking that assumes that ‘truth is easier than justice,’ I show that nationalist resistance to the OMP flies in the face of this assumption. In postwar Sri Lanka, truth is not just a second-best option to justice but an equally radical demand. However, I also show that those same resistors have maintained the OMP on returning to power for several different reasons. Finally, I explore the response of relatives of the disappeared to the OMP and their increasing demand for an international truth and justice mechanism.
Nirsevimab: review of pharmacology, antiviral activity and emerging clinical experience for respiratory syncytial virus infection in infants
Authors: Jorgensen Sarah C J 
Published: March 2023

AbstractRespiratory syncytial virus (RSV) is a leading cause of hospitalization and infant mortality worldwide. There are currently no approved vaccines against RSV, and immunoprophylaxis with the mAb palivizumab is limited to extremely vulnerable infants in resource-rich settings due to its high cost and the need for monthly injections throughout the RSV season. Nirsevimab (formerly MEDI8897) is a highly potent, long-acting, human, recombinant mAb that received approval for the prevention of RSV infection in newborns and infants during their first RSV season from the EMA and the UK’s Medicines and Healthcare products Regulatory Agency in November 2022 based on positive results in Phase 2b and 3 clinical trials. Nirsevimab targets the highly conserved site Ø of the prefusion conformation of the RSV fusion (F) protein and contains a triple amino acid substitution in the Fc domain that extends its half-life, allowing for a single dose to cover a typical RSV season in regions with temperate climates. In this article I review key attributes of nirsevimab with an emphasis on pharmacology, pharmacokinetics, antiviral activity, and the potential for resistance and escape variants. I also summarize current progress in clinical trials and consider future research priorities.
Association between antimicrobial consumption and resistance rate ofEscherichia coliin hospital settings
Authors: Abdullah Sabahat , Rahman Sajjad ur , Muhammad Faqir , Mohsin Mashkoor 
Published: March 2023

AbstractAimsThis study aims to quantify antimicrobial consumption (AMC) and antimicrobial resistance (AMR) in tertiary care hospitals in Pakistan.Methods and resultsThis observational study was conducted at two tertiary care hospitals of Pakistan over a 1-year period. The AMC and resistance patterns of Escherichia coli isolates collected from hospitals were observed and analysed using the pearson correlation coefficient. AMC in hospitals varied between 0.00186 and 0.72 (Mean = 0.12 ± 0.191) Defined Daily Dose (DDDs)/1000 patient-days. Fluoroquinolones were the most consumed antimicrobial followed by penicillins, cephalosporins, carbapenems, and aminoglycosides. Antimicrobial-resistant rates in hospitals varied between 92.2% and 34.6%. The highest resistance rate was observed for moxifloxacin, followed by ampicillin, cefotaxime, amoxicillin, ceftriaxone, ciprofloxacin, amoxiclav, and amikacin. Statistically significant association was found between AMC and resistance rate for ampicillin (r = 0.78, P = 0.032), cefotaxime (r = 0.87, P = 0.012), ceftriaxone (r = 0.67, P = 0.042), and ciprofloxacin (r = 0.63, P = 0.031). Additionally, there was a significant association between fluoroquinolone consumption and the resistance rate of third generation cephalosporins (r = 0.61, P = 0.032), and significance was also found when all antimicrobials were combined into 1 analysis (r = 0.721, P = 0.032).ConclusionThis data documented a significant association between AMC and resistant rates for multiple antimicrobial agents.
Transcriptome analysis ofAurantiochytrium limacinumunder low salt conditions
Authors: Kubo Yuki , Morimoto Daichi , Kato Shuri , Shiroi Mai , Ohara Kanta , Higashine Tokuhiro , Mori Yuki , Yoshimi Toru , Takeuchi Masato , Sawayama Shigeki 
Published: March 2023

AbstractAurantiochytrium limacinum can accumulate high amounts of omega-3 polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). Although salinity affects the DHA content, its impact on the metabolic pathway responsible for DHA production in A. limacinum is not completely understood. To address this issue, we investigated the transcriptional profile of A. limacinum under hypoosmotic stress. We first cultured A. limacinum under typical and low salinity for RNA sequencing, respectively. Transcriptome analyses revealed that 933 genes exhibited significant changes in expression under hypoosmotic conditions, of which 81.4% were downregulated. Strikingly, A. limacinum downregulated genes related to polyketide synthesis and fatty acid synthase pathways, while upregulating β-oxidation-related genes. In accordance with this, DHA production significantly decreased under hypoosmotic conditions, while antioxidant-related genes were significantly upregulated. Considering that β-oxidation of fatty acids generates energy and reactive oxygen species (ROS), our results suggest that A. limacinum utilizes fatty acids for energy to survive under hypoosmotic conditions and detoxifies ROS using antioxidant systems.
Determination of safety status and probiotic properties ofEnterococcusstrains isolated from traditional cheeses in Turkey
Authors: Kanak Eda Kiliç , Yilmaz Suzan Öztürk , Altindiş Mustafa , Tanriverdi Elif Seren , Otlu Barış 
Published: March 2023

AbstractAimsThis study aimed to evaluate the probiotic properties of Enterococcus strains isolated from Turkish traditional cheeses.Methods and resultsFifty-two Enterococcus spp. were taxonomically determined as follows: Enterococcus faecium (26), Enterococcus faecalis (18), Enterococcus durans (6), and Enterococcus italicus (2). The ability of isolates/strains to survive the harsh conditions (acidity and in-vitro gastric solution) of the gastrointestinal tract was established. They also showed auto-aggregation, hydrophobicity, and co-aggregation ability. Hydrophobicities of the strains were found between 0.8%–21%, 0.7%–56%, and 2%–63% for xylene, chloroform, and ethyl acetate, respectively. Autoaggregation values of the Enterococcus strains were 4%–20%, 7%–30%, and 36%–98% after 2, 4, and 24-h incubation, respectively. In this study, the Enterococcus strains tested showed co-aggregation ability with the Escherichia coli ATCC 25922, Salmonella Typhimurium ATCC 14028, and Staphylococcus aureus ATCC 25923. The results of PCR amplification revealed that only five strains possess virulence factor genes (gelE,asa1,cyl A,esp). We determined antibiotic resistance, biofilm forming abilities, and hemolytic activity for safety evaluation of strains.ConclusionsIn this large and comprehensive study, we found that only few of Enterococcus strains have promising probiotic potential, among which E. faecalis ES1 and E. faecium EM1 showed the best probiotic properties (are the most promising probiotic candidates).
Characterization ofl-fucose isomerase fromPaenibacillus rhizosphaeraeto producel-fuculose from hydrolyzed fucoidan and commercial fucose
Authors: Iqbal Muhammad Waheed , Riaz Tahreem , Mu Wanmeng , Mahmood Shahid , Qi Xianghui , Ni Dawei , Zhang Wenli 
Published: March 2023

AbstractAimsl-Fuculose is a valuable rare sugar that is used to treat a variety of ailments, including HIV, cancer, Hepatitis B, human lysosomal disease (fucosidosis), and cardio-protective medications. The enzymatic approach for the production of l-fuculose using l-fucose as a substrate would be an advantageous method with a wide range of industrial applications. The objective of this study is the characterization of recombinant l-fucose isomerase from Paenibacillus rhizosphaerae (Pa-LFI) for the production of l-fuculose from an inexpensive and natural source (fucoidan) as well as its comparison with commercial l-fucose (Sigma-Aldrich).Methods and resultsFucoidan, a fucose-containing polysaccharide (FPs), was isolated from Undaria pinnatifida, subsequently hydrolyzed, and characterized before the enzymatic production of l-fuculose. The results elaborate that FPs contain 35.9% of fucose along with other kinds of monosaccharides. The purified Pa-LFI exhibited a single band at 65 kDa and showed it as a hexamer with a native molecular mass of 396 kDa. The highest activity of 104.5 U mg−1 of Pa-LFI was perceived at a temperature of 50°C and pH 6.5 in the presence of 1 mM of Mn2+. The Pa-LFI revealed a melting temperature (Tm) of 75°C and a half-life of 12.6 h at 50°C. It exhibited that Pa-LFI with aldose substrate (l-fucose), has a stronger isomerizing activity, disclosing Km,kcat, and kcat/Km 86.2 mM, 32 831 min−1, and 335 min−1 mM−1, respectively. After reaching equilibrium, Pa-LFI efficiently catalyzed the reaction to convert l-fucose into l-fuculose and the conversion ratios of l-fuculose from 100 g L−1 of FPs and commercial fucose were around 6% (5.6 g L−1) and 30% (30.2 g L−1), respectively.ConclusionsAccording to the findings of the current study, the Pa-LFI will be useful in the manufacturing of l-fuculose using an effective and easy approach that produces no by-products.
Comparison of N2O-reducing abilities and genome features of twonosZ-containing denitrifying bacteria,Pseudomonas veroniiDM15 andPseudomonas frederiksbergensisDM22
Authors: Liu Chunmei , Sheng Rong , Chen Xing , Liu Yi , Wei Wenxue 
Published: March 2023

AbstractAimThe study systematically compared the N2O-reducing functional performances and the genomic features of two N2O-reducing isolates, aimed to screen out effective N2O-reducing bacteria with strong environmental adaption, and explore the possible regulation.Methods and ResultsTwo N2O reducers, namely, Pseudomonas veronii DM15 (DM15) and Pseudomonas frederiksbergensis DM22 (DM22), isolated from paddy soil were selected. Their N2O-reducing abilities, and nosZ gene transcript abundance were determined under different temperatures (20°C, 30°C, 40°C) and oxygen concentrations (0%, 10%, 21%), and the whole genomes were sequenced by Illumina sequencing. The results showed that both DM15 and DM22 exhibited the strongest N2O reducing activity at 30°C and under anaerobic conditions. In comparison, DM15 generally exhibited significantly higher N2O reducing abilities and nosZ gene expression than DM22 under all tested conditions. In addition, DM15 possessed obviously higher expression potentials (codon adaptation index (CAI) value) of nos genes than DM22, and the nos cluster of the former contained a transcriptional regulator gene of dnr, while the latter did not.ConclusionsThe results indicate that DM15 showed obviously stronger N2O-reducing abilities than DM22 under various conditions, which might be closely associated with its dnr transcriptional regulator, and thus promoting the higher transcriptional activities of nos genes. Although anaerobic conditions were the optimal conditions for N2O reduction in both strains, DM15 still reduced a certain amount of N2O even under aerobic conditions.
The use of phage display systems to combat infectious diseases in poultry: diagnostic, vaccine, and therapeutic approaches
Authors: Grabowski Łukasz , Pierzynowska Karolina , Gaffke Lidia , Cyske Zuzanna , Mincewicz Grzegorz , Węgrzyn Grzegorz 
Published: March 2023

AbstractDevelopment of molecular biology and understanding structures and functions of various biological molecules and entities allowed to construct various sophisticated tools for different biotechnological, medical, and veterinary applications. One of them is the phage display technology, based on the possibility to create specific bacteriophages bearing fusion genes, which code for fusion proteins consisting of a phage coat protein and a peptide of any amino acid sequence. Such proteins retain their biological functions as structural elements of phage virions while exposing foreign peptide sequences on their surfaces. Genetic manipulations allow to construct phage display libraries composed of billions of variants of exposed peptides; such libraries can be used to select peptides of desired features. Although the phage display technology has been widely used in biotechnology and medicine, its applications in veterinary and especially in poultry science were significantly less frequent. Nevertheless, many interesting discoveries have been reported also in the latter field, providing evidence for a possibility of effective applications of phage display-related methods in developing novel diagnostic tools, new vaccines, and innovative potential therapies dedicated to poultry. Especially, infectious diseases caused by avian viruses, bacteria, and unicellular eukaryotic parasites were investigated in this field. These studies are summarized and discussed in this review, with presentation of various possibilities provided by different phage display systems in development of useful and effective products facilitating management of the problem of infectious diseases of poultry.
Not just passengers, but co-pilots! Non-rhizobial nodule-associated bacteria promote cowpea growth and symbiosis with (brady)rhizobia
Authors: da Silva Thaíse Rosa , Rodrigues Ruth Terezinha , Jovino Raphael Silva , Carvalho Jackson Rafael de Sá , Leite Jakson , Hoffman Andreas , Fischer Doreen , Ribeiro Paula Rose de Almeida , Rouws Luc Felicianus Marie , Radl Viviane , Fernandes-Júnior Paulo Ivan 
Published: March 2023

AbstractAimsTo isolate and characterize non-rhizobial nodule-associated bacteria (NAB) from cowpea root-nodules regarding their performance of plant-growth-promoting mechanisms and their ability to enhance cowpea growth and symbiosis when co-inoculated with bradyrhizobia.Methods and ResultsSixteen NAB were isolated, identified, and in vitro evaluated for plant growth promotion traits. The ability to promote cowpea growth was analyzed when co-inoculated with Bradyrhizobium pachyrhizi BR 3262 in sterile and non-sterile substrates. The 16S rRNA gene sequences analysis revealed that NAB belonged to the genera Chryseobacterium (4), Bacillus (3), Microbacterium (3), Agrobacterium (1), Escherichia (1), Delftia (1), Pelomonas (1), Sphingomonas (1), and Staphylococcus (1). All strains produced different amounts of auxin siderophores and formed biofilms. Twelve out of the 16 strains carried the nifH, a gene associated with nitrogen fixation. Co-inoculation of NAB (ESA 424 and ESA 29) with Bradyrhizobium pachyrhizi BR 3262 significantly promoted cowpea growth, especially after simultaneous inoculation with the three strains.ConclusionsNAB are efficient cowpea growth promoters and can improve the efficiency of the symbiosis between cowpea and the N2-fixing microsymbiont B. pachyrhizi BR 3262, mainly under a specific triple microbial association.
The critical role of gut microbiota dysbiosis in skeletal muscle wasting: a systematic review
Authors: Nikkhah Amirabbas , Ejtahed Hanieh-Sadat , Ettehad Marvasti Fateme , Taghavi MinaSadat , Pakmehr Azin , Hajipour Firouzeh , Larijani Bagher 
Published: March 2023

AbstractAimsSkeletal muscle wasting is affected by the gut microbiota dysbiosis through multiple pathways, including inflammatory process, defected immune system, and anabolic resistance. We aimed to systematically review the studies investigating the gut microbiota composition in sarcopenic and cachexic humans and animals.MethodsWe carried out a comprehensively systematic search using relevant keywords on PubMed, Web of Science, and Scopus databases until July 2021. Original human observational research and animal studies related to our research topics published in English were selected.ResultsSeven human studies and five animal studies were included. Three human studies were case-control, whereas the other four were cross-sectional studies that investigated three different conditions, including age-related sarcopenia, as well as liver cirrhosis and cancer cachexia. The principal alteration in age-related sarcopenia and liver cirrhosis-induced sarcopenia was a reduction in short-chain fatty acids (SCFAs) -producing bacteria. Lachnospiraceae family, consisting of Lachnospira, Fusicatenibacter, Roseburia, and Lachnoclostridium, significantly decreased in age-related sarcopenia, while in liver cirrhosis-induced sarcopenia, the alpha diversity of gut microbiota decreased compared with the control group. Moreover, Enterobacteriaceae, which has a pro-inflammatory effect increased in muscle-wasted animals.ConclusionThis systematic review presents associations between the gut microbiota alterations and skeletal muscle wasting as a consequence of various pathologies, including aging sarcopenia, renal failure, and cancer cachexia in both human and animal studies.
Efficacy of chemical disinfectants against SARS-CoV-2 on high-touch surface materials
Authors: Hardison Rachael L , Nelson Sarah W , Limmer Rebecca , Marx Joel , Taylor Brian M , James Ryan R , Stewart Michael J , Lee Sang Don D , Calfee Michael Worth , Ryan Shawn P , Howard Megan W 
Published: March 2023

AbstractAimsThis study aimed to provide operationally relevant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface disinfection efficacy information.Methods and ResultsThree EPA-registered disinfectants (Vital Oxide, Peroxide, and Clorox Total 360) and one antimicrobial formulation (CDC bleach) were evaluated against SARS-CoV-2 on material coupons and were tested using Spray (no touch with contact time) and Spray & Wipe (wipe immediately post-application) methods immediately and 2 h post-contamination. Efficacy was evaluated for infectious virus, with a subset tested for viral RNA (vRNA) recovery. Efficacy varied by method, disinfectant, and material. CDC bleach solution showed low efficacy against SARS-CoV-2 (log reduction &lt; 1.7), unless applied via Spray & Wipe. Additionally, mechanical wiping increased the efficacy of treatments against SARS-CoV-2. The recovery of vRNA post-disinfection suggested that vRNA may overestimate infectious virus remaining.ConclusionsEfficacy depends on surface material, chemical, and disinfection procedure, and suggests that mechanical wiping alone has some efficacy at removing SARS-CoV-2 from surfaces. We observed that disinfectant treatment biased the recovery of vRNA over infectious virus.Significance and Impact of StudyThese data are useful for developing effective, real-world disinfection procedures, and inform public health experts on the utility of PCR-based surveillance approaches.