bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent progress in melting heat phenomenon for bioconvection transport of nanofluid through a lubricated surface with swimming microorganisms
Authors: Alqarni Marei Saeed , Yasmin Sumeira , Waqas Hassan , Khan Shan Ali
Published: May 2022

The cooling of numerous microelectronic devices has become a need in today's world. Nanofluids, a novel type of heat transport fluid containing nano-sized particles embedded in a host liquid, were developed a few years ago. Impact of ultra-fine nanoparticles with oil, water, or ethylene glycol produces these fluids. Nano-liquids have a variety of applications, including engine cooling, electronic devices, biomedicine, and the manufacture of thermal exchangers. The main objective of current research article is to scrutinizes theoretically, the effects of axisymmetric magnetohydrodynamic flow of bio-convective nanoliquid through a moving surface in the occurrence of swimming microorganisms. The idea of the envisaged model is improved by considering the consequence of thermal radiation, activation energy with generalized slip effects under convective boundaries. The present analysis is developed in the form of mathematical formulation and then solved numerically. The governing flow equations are transmuted into dimensionless nonlinear ODEs system by compatible similarity transformations and then integrated this so-formulated highly nonlinear problem numerically via bvp4c built-in scheme in MATLAB. The significance of influential parameters versus velocity field, temperature profile, concentration field and motile density of microorganism’s profile are examined with the aid of graphs and tabular data. The physical interpretation of outcomes highlight that the velocity receives increment for amplified mixed convection parameter. The thermal profile is found to be reducing with a greater Prandtl number. The concentration profile of nanoparticle boosts up for greater activation energy parameter. The microorganism’s profile is reduced via bioconvection Lewis number. This investigation contains the significance of bioconvection phenomenon, thermal radiation, slip effects and activation energy under convective boundary conditions. These impacts are used in axisymmetric, stagnation point flow of bioconvective magnetized nanofluid containing swimming gyrotactic motile microorganisms over a lubricated surface. The present analysis is not yet published.
Modified Meyerhof approach for forecasting reliable ultimate capacity of the large diameter bored piles
Authors: Al-Atroush M. E. , Hefny A. M. , Sorour T. M.
Published: May 2022

The static loading test is undoubtedly the most reliable method for forecasting the ultimate capacity of the large diameter bored piles (LDBP). However, in-situ loading of this class of piles until reaching failure is practically seldom due to the large amount of settlement required for shaft and base mobilization. Therefore, many international design standards recommend either capacity-based or settlement-based methods to estimate the LDBP ultimate capacity in case of the impossibility of performing loading tests during the design phase. However, those methods are invariably associated with various degrees of uncertainty resulting from several factors, as evidenced in several comparative analyses available in the literature. For instance, the settlement-based method of the Egyptian code of practice (ECP 202/4) usually underestimates the ultimate capacity of LDBP. In contrast, Meyerhof's capacity-based method often overestimates the LDBP’s ultimate capacity. In this paper, a modified approach has been proposed to forecast the ultimate capacity of the LDBP. This approach was modified from Meyerhof’s classical formula (1976) through three fundamental stages. First, an assessment study was performed to evaluate the reliability of the estimated LDBP ultimate capacity using Meyerhof’s classical method. For this purpose, results of full scale loaded to failure loading LDBP test and related twenty-eight parametric numerical models with various pile geometrical and soil geotechnical parameters have been used. Based on the assessment study findings, the essential modifications were suggested in the second stage to adapt Meyerhof’s classic method. In the third stage, the results of several numerical models and in-situ loading tests were employed to assess the accuracy of the developed modified method. This study showed that Meyerhof's classical method overestimated the ultimate capacity of LDBP with an error percentage ranging from 14 to 46%. On the other side, the proposed modified approach has succeeded in estimating the ultimate capacity of loaded to failure in-situ LDBP test and twenty numerical LDBP models with error percentages ranging from 0.267 to 7.75%.
Development and validation of a nomogram to predict the risk of death within 1 year in patients with non-ischemic dilated cardiomyopathy: a retrospective cohort study
Authors: Huang Yuan , Wang Hai-Yan , Jian Wen , Yang Zhi-Jie , Gui Chun
Published: May 2022

Predicting the chances mortality within 1 year in non-ischemic dilated cardiomyopathy patients can be very useful in clinical decision-making. This study has developed and validated a risk-prediction model for identifying factors contributing to mortality within 1 year in such patients. The predictive nomogram was constructed using a retrospective cohort study, with 615 of patients hospitalized in the First Affiliated Hospital of Guangxi Medical University between October 2012 and May 2020. A variety of factors, including presence of comorbidities, demographics, results of laboratory tests, echocardiography data, medication strategies, and instances of heart transplant or death were collected from electronic medical records and follow-up telephonic consultations. The least absolute shrinkage and selection operator and logistic regression analyses were used to identify the critical clinical factors for constructing the nomogram. Calibration, discrimination, and clinical usefulness of the predictive model were assessed using the calibration plot, C-index and decision curve analysis. Internal validation was assessed with bootstrapping validation. Among the patients from whom follow-up data were obtained, the incidence of an end event (deaths or heart transplantation within 1 year) was 171 cases per 1000 person-years (105 out of 615). The main predictors included in the nomogram were pulse pressure, red blood cell count, left ventricular end-diastolic dimension, levels of N-terminal pro b-type natriuretic peptide, medical history, in-hospital worsening heart failure, and use of angiotensin-converting enzyme inhibitors or angiotensin II receptor blockers. The model showed excellent discrimination with a C-index of 0.839 (95% CI 0.799–0.879), and the calibration curve demonstrated good agreement. The C-index of internal validation was 0.826, which demonstrated that the model was quite efficacious. A decision curve analysis confirmed that our nomogram was clinically useful. In this study, we have developed a nomogram that can predict the risk of death within 1 year in patients with non-ischemic dilated cardiomyopathy. This will be useful in the early identification of patients in the terminal stages for better individualized clinical decisions.
Attosecond stable dispersion-free delay line for easy ultrafast metrology
Authors: Tyagi Akansha , Sidhu Mehra S. , Mandal Ankur , Kapoor Sanjay , Dahiya Sunil , Rost Jan M. , Pfeifer Thomas , Singh Kamal P.
Published: May 2022

We demonstrate a dispersion-free wavefront splitting attosecond resolved interferometric delay line for easy ultrafast metrology of broadband femtosecond pulses. Using a pair of knife-edge prisms, we symmetrically split and later recombine the two wavefronts with a few tens of attosecond resolution and stability and employ a single-pixel analysis of interference fringes with good contrast using a phone camera without any iris or nonlinear detector. Our all-reflective delay line is theoretically analyzed and experimentally validated by measuring 1st and 2nd order autocorrelations and the SHG-FROG trace of a NIR femtosecond pulse. Our setup is compact, offers attosecond stability with flexibility for independent beam-shaping of the two arms. Furthermore, we suggest that our compact and in-line setup can be employed for attosecond resolved pump-probe experiments of matter with few-cycle pulses.
Machine learning phenomics (MLP) combining deep learning with time-lapse-microscopy for monitoring colorectal adenocarcinoma cells gene expression and drug-response
Authors: D’Orazio M. , Murdocca M. , Mencattini A. , Casti P. , Filippi J. , Antonelli G. , Di Giuseppe D. , Comes M. C. , Di Natale C. , Sangiuolo F. , Martinelli E.
Published: May 2022

High-throughput phenotyping is becoming increasingly available thanks to analytical and bioinformatics approaches that enable the use of very high-dimensional data and to the availability of dynamic models that link phenomena across levels: from genes to cells, from cells to organs, and through the whole organism. The combination of phenomics, deep learning, and machine learning represents a strong potential for the phenotypical investigation, leading the way to a more embracing approach, called machine learning phenomics (MLP). In particular, in this work we present a novel MLP platform for phenomics investigation of cancer-cells response to therapy, exploiting and combining the potential of time-lapse microscopy for cell behavior data acquisition and robust deep learning software architectures for the latent phenotypes extraction. A two-step proof of concepts is designed. First, we demonstrate a strict correlation among gene expression and cell phenotype with the aim to identify new biomarkers and targets for tailored therapy in human colorectal cancer onset and progression. Experiments were conducted on human colorectal adenocarcinoma cells (DLD-1) and their profile was compared with an isogenic line in which the expression of LOX-1 transcript was knocked down. In addition, we also evaluate the phenotypic impact of the administration of different doses of an antineoplastic drug over DLD-1 cells. Under the omics paradigm, proteomics results are used to confirm the findings of the experiments.
An image classification deep-learning algorithm for shrapnel detection from ultrasound images
Authors: Snider Eric J. , Hernandez-Torres Sofia I. , Boice Emily N.
Published: May 2022

Ultrasound imaging is essential for non-invasively diagnosing injuries where advanced diagnostics may not be possible. However, image interpretation remains a challenge as proper expertise may not be available. In response, artificial intelligence algorithms are being investigated to automate image analysis and diagnosis. Here, we highlight an image classification convolutional neural network for detecting shrapnel in ultrasound images. As an initial application, different shrapnel types and sizes were embedded first in a tissue mimicking phantom and then in swine thigh tissue. The algorithm architecture was optimized stepwise by minimizing validation loss and maximizing F1 score. The final algorithm design trained on tissue phantom image sets had an F1 score of 0.95 and an area under the ROC curve of 0.95. It maintained higher than a 90% accuracy for each of 8 shrapnel types. When trained only on swine image sets, the optimized algorithm format had even higher metrics: F1 and area under the ROC curve of 0.99. Overall, the algorithm developed resulted in strong classification accuracy for both the tissue phantom and animal tissue. This framework can be applied to other trauma relevant imaging applications such as internal bleeding to further simplify trauma medicine when resources and image interpretation are scarce.
Long-term prediction models for vision-threatening diabetic retinopathy using medical features from data warehouse
Authors: Jo Kwanhoon , Chang Dong Jin , Min Ji Won , Yoo Young-Sik , Lyu Byul , Kwon Jin Woo , Baek Jiwon
Published: May 2022

We sought to evaluate the performance of machine learning prediction models for identifying vision-threatening diabetic retinopathy (VTDR) in patients with type 2 diabetes mellitus using only medical data from data warehouse. This is a multicenter electronic medical records review study. Patients with type 2 diabetes screened for diabetic retinopathy and followed-up for 10 years were included from six referral hospitals sharing same electronic medical record system (n = 9,102). Patient demographics, laboratory results, visual acuities (VAs), and occurrence of VTDR were collected. Prediction models for VTDR were developed using machine learning models. F1 score, accuracy, specificity, and area under the receiver operating characteristic curve (AUC) were analyzed. Machine learning models revealed F1 score, accuracy, specificity, and AUC values of up 0.89, 0.89.0.95, and 0.96 during training. The trained models predicted the occurrence of VTDR at 10-year with F1 score, accuracy, and specificity up to 0.81, 0.70, and 0.66, respectively, on test set. Important predictors included baseline VA, duration of diabetes treatment, serum level of glycated hemoglobin and creatinine, estimated glomerular filtration rate and blood pressure. The models could predict the long-term occurrence of VTDR with fair performance. Although there might be limitation due to lack of funduscopic findings, prediction models trained using medical data can facilitate proper referral of subjects at high risk for VTDR to an ophthalmologist from primary care.
Tyrosine O-sulfation proteoforms affect HIV-1 monoclonal antibody potency
Authors: Cai Cindy X. , Doria-Rose Nicole A. , Schneck Nicole A. , Ivleva Vera B. , Tippett Brad , Shadrick William R. , O’Connell Sarah , Cooper Jonathan W. , Schneiderman Zachary , Zhang Baoshan , Gowetski Daniel B. , Blackstock Daniel , Demirji Jacob , Lin Bob C. , Gorman Jason , Liu Tracy , Li Yile , McDermott Adrian B. , Kwong Peter D. , Carlton Kevin , Gall Jason G. , Lei Q. Paula
Published: May 2022

CAP256V2LS, a broadly neutralizing monoclonal antibody (bNAb), is being pursued as a promising drug for HIV-1 prevention. The total level of tyrosine-O-sulfation, a post-translational modification, was known to play a key role for antibody biological activity. More importantly, here wedescribe for the first time the significance of the tyrosine-O-sulfation proteoforms. We developed a hydrophobic interaction chromatography (HIC) method to separate and quantify different sulfation proteoforms, which led to the direct functionality assessment of tyrosine-sulfated species. The fully sulfated (4-SO3) proteoform demonstrated the highest in vitro relative antigen binding potency and neutralization efficiency against a panel of HIV-1 viruses. Interestingly, highly variable levels of 4-SO3were produced by different clonal CHO cell lines, which helped the bNAb process development towards production of a highly potent CAP256V2LS clinical product with high 4-SO3proteoform. This study presents powerful insight for any biotherapeutic protein development where sulfation may play an important role in product efficacy.
HIV-associated vaginal microbiome and inflammation predict spontaneous preterm birth in Zambia
Authors: Price Joan T. , Vwalika Bellington , France Michael , Ravel Jacques , Ma Bing , Mwape Humphrey , Rittenhouse Katelyn J. , De Paris Kristina , Hobbs Marcia , Nelson Julie A. , Kasaro Margaret P. , Stringer Elizabeth M. , Stringer Jeffrey S. A.
Published: May 2022

A Lactobacillus-deficient, anaerobe-rich vaginal microbiome has been associated with local inflammation and spontaneous preterm birth (sPTB), but few studies have assessed this association in the setting of HIV. We performed metagenomic sequencing and inflammatory marker assays on vaginal swabs collected in pregnancy. We grouped samples into 7 metagenomic clusters (mgClust) using the non-redundant VIRGO catalogue, and derived inflammatory scores by factor analysis. Of 221 participants, median Shannon diversity index (SDI) was highest in HIV+ with detectable viral load (1.31, IQR: 0.85–1.66; p < 0.001) and HIV+ with undetectable virus (1.17, IQR: 0.51–1.66; p = 0.01) compared to HIV− (0.74, IQR: 0.35–1.26). Inflammatory scores positively correlated with SDI (+ 0.66, 95%CI 0.28, 1.03; p = 0.001), highest among anaerobe-rich mgClust2–mgClust6. HIV was associated with predominance of anaerobe-rich mgClust5 (17% vs. 6%; p = 0.02) and mgClust6 (27% vs. 11%; p = 0.002). Relative abundance of a novel Gardnerella metagenomic subspecies > 50% predicted sPTB (RR 2.6; 95%CI: 1.1, 6.4) and was higher in HIV+ (23% vs. 10%; p = 0.001). A novel Gardnerella metagenomic subspecies more abundant in women with HIV predicted sPTB. The risk of sPTB among women with HIV may be mediated by the vaginal microbiome and inflammation, suggesting potential targets for prevention.
Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance
Authors: Maiti Pulak Kumar , Mandal Sukhendu
Published: May 2022

The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.
In vitro and in ovo impact of the ionic dissolution products of boron-doped bioactive silicate glasses on cell viability, osteogenesis and angiogenesis
Authors: Decker Simon , Arango-Ospina Marcela , Rehder Felix , Moghaddam Arash , Simon Rolf , Merle Christian , Renkawitz Tobias , Boccaccini Aldo R. , Westhauser Fabian
Published: May 2022

Due to the pivotal role of angiogenesis in bone regeneration, the angiogenic properties of biomaterials are of high importance since they directly correlate with the biomaterials’ osteogenic potential via ‘angiogenic-osteogenic coupling’ mechanisms. The impact of bioactive glasses (BGs) on vascularization can be tailored by incorporation of biologically active ions such as boron (B). Based on the ICIE16-BG composition (in mol%: 49.5 SiO2, 36.3 CaO, 6.6 Na2O, 1.1 P2O5, 6.6 K2O), three B-doped BGs have been developed (compositions in mol%: 46.5/45.5/41.5 SiO2, 36.3 CaO, 6.6 Na2O, 1.1 P2O5, 6.6 K2O, 3/4/8 B2O3). The influence of B-doping on the viability, cellular osteogenic differentiation and expression of osteogenic and angiogenic marker genes of bone marrow-derived mesenchymal stromal cells (BMSCs) was analyzed by cultivating BMSCs in presence of the BGs’ ionic dissolution products (IDPs). Furthermore, the influence of the IDPs on angiogenesis was evaluated in ovo using a chorioallantoic membrane (CAM) assay. The influence of B-doped BGs on BMSC viability was dose-dependent, with higher B concentrations showing limited negative effects. B-doping led to a slight stimulation of osteogenesis and angiogenesis in vitro. In contrast to that, B-doping significantly enhanced vascularization in ovo, especially in higher concentrations. Differences between the results of the in vitro and in ovo part of this study might be explained via the different importance of vascularization in both settings. The implementation of new experimental models that cover the ‘angiogenic-osteogenic coupling’ mechanisms is highly relevant, for instance via extending the application of the CAM assay from solely angiogenic to angiogenic and osteogenic purposes.
Thigh muscle co-contraction patterns in individuals with anterior cruciate ligament reconstruction, athletes and controls during a novel double-hop test
Authors: Arumugam Ashokan , Häger Charlotte K.
Published: May 2022

Efficient neuromuscular coordination of the thigh muscles is crucial in maintaining dynamic knee stability and thus reducing anterior cruciate ligament (ACL) injury/re-injury risk. This cross-sectional study measured electromyographic (EMG) thigh muscle co-contraction patterns during a novel one-leg double-hop test among individuals with ACL reconstruction (ACLR;n = 34), elite athletes (n = 22) and controls (n = 24). Participants performed a forward hop followed by a 45° unanticipated diagonal hop either in a medial (UMDH) or lateral direction (ULDH). Medial and lateral quadriceps and hamstrings EMG were recorded for one leg (injured/non-dominant). Quadriceps-to-Hamstring (Q:H) ratio, lateral and medial Q:H co-contraction indices (CCIs), and medial-to-lateral Q:H co-contraction ratio (CCR; a ratio of CCIs) were calculated for three phases (100 ms prior to landing, initial contact [IC] and deceleration phases) of landing. We found greater activity of the quadriceps than the hamstrings during the IC and deceleration phases of UMDH/ULDH across groups. However, higher co-contraction of medial rather than lateral thigh muscles during the deceleration phase of landing was found; if such co-contraction patterns cause knee adduction, a putative mechanism to decrease ACL injury risk, during the deceleration phase of landing across groups warrants further investigation.
Gastric cancer biomarker analysis in patients treated with different adjuvant chemotherapy regimens within SAMIT, a phase III randomized controlled trial
Authors: Oshima Takashi , Tsuburaya Akira , Yoshida Kazuhiro , Yoshikawa Takaki , Miyagi Yohei , Rino Yasushi , Masuda Munetaka , Guan Jia , Tan Patrick , Grabsch Heike I. , Sakamoto Junichi , Tanaka Shiro
Published: May 2022

Biomarkers for selecting gastric cancer (GC) patients likely to benefit from sequential paclitaxel treatment followed by fluorinated-pyrimidine-based adjuvant chemotherapy (sequential paclitaxel) were investigated using tissue samples of patients recruited into SAMIT, a phase III randomized controlled trial. Total RNA was extracted from 556 GC resection samples. The expression of 105 genes was quantified using real-time PCR. Genes predicting the benefit of sequential paclitaxel on overall survival, disease-free survival, and cumulative incidence of relapse were identified based on the ranking of p-values associated with the interaction between the biomarker and sequential paclitaxel or monotherapy groups. Low VSNL1 and CD44 expression predicted the benefit of sequential paclitaxel treatment for all three endpoints. Patients with combined low expression of both genes benefitted most from sequential paclitaxel therapy (hazard ratio = 0.48 [95% confidence interval, 0.30–0.78]; p < 0.01; interaction p-value < 0.01). This is the first study to identify VSNL1 and CD44 RNA expression levels as biomarkers for selecting GC patients that are likely to benefit from sequential paclitaxel treatment followed by fluorinated-pyrimidine-based adjuvant chemotherapy. Our findings may facilitate clinical trials on biomarker-oriented postoperative adjuvant chemotherapy for patients with locally advanced GC.
Evaluation of cfDNA as an early detection assay for dense tissue breast cancer
Authors: Barbirou Mouadh , Miller Amanda A. , Gafni Erik , Mezlini Amel , Zidi Asma , Boley Nathan , Tonellato Peter J.
Published: May 2022

A cell-free DNA (cfDNA) assay would be a promising approach to early cancer diagnosis, especially for patients with dense tissues. Consistent cfDNA signatures have been observed for many carcinogens. Recently, investigations of cfDNA as a reliable early detection bioassay have presented a powerful opportunity for detecting dense tissue screening complications early. We performed a prospective study to evaluate the potential of characterizing cfDNA as a central element in the early detection of dense tissue breast cancer (BC). Plasma samples were collected from 32 consenting subjects with dense tissue and positive mammograms, 20 with positive biopsies and 12 with negative biopsies. After screening and before biopsy, cfDNA was extracted, and whole-genome next-generation sequencing (NGS) was performed on all samples. Copy number alteration (CNA) and single nucleotide polymorphism (SNP)/insertion/deletion (Indel) analyses were performed to characterize cfDNA. In the positive-positive subjects (cases), a total of 5 CNAs overlapped with 5 previously
reported BC-related oncogenes (KSR2, MAP2K4, MSI2, CANT1 and MSI2). In addition, 1 SNP was detected in KMT2C, a BC oncogene, and 9 others were detected in or near 10 genes (SERAC1, DAGLB, MACF1, NVL, FBXW4, FANK1, KCTD4, CAVIN1; ATP6V0A1 and ZBTB20-AS1) previously associated with non-BC cancers. For the positive–negative subjects (screening), 3 CNAs were detected in BC genes (ACVR2A, CUL3 and PIK3R1), and 5 SNPs were identified in 6 non-BC cancer genes (SNIP1, TBC1D10B, PANK1, PRKCA and RUNX2; SUPT3H). This study presents evidence of the potential of using cfDNA somatic variants as dense tissue BC biomarkers from a noninvasive liquid bioassay for early cancer detection.
Different clinical characteristics and impact of carbapenem-resistance on outcomes between Acinetobacter baumannii and Pseudomonas aeruginosa bacteraemia: a prospective observational study
Authors: Lee Chan Mi , Kim Young-Jun , Jung Sook-In , Kim Seong Eun , Park Wan Beom , Choe Pyoeng Gyun , Kim Eu Suk , Kim Chung-Jong , Choi Hee Jung , Lee Shinwon , Lee Sun Hee , Jung Younghee , Bang Ji Hwan , Cheon Shinhye , Kwak Yee Gyung , Kang Yu Min , Park Kyung-Hwa , Song Kyoung-Ho , Kim Hong Bin ,   The Korea INfectious Diseases (KIND) Study Group, Lee Chan Mi , Kim Young-Jun , Jung Sook-In , Kim Seong Eun , Park Wan Beom , Choe Pyoeng Gyun , Kim Eu Suk , Kim Chung-Jong , Choi Hee Jung , Lee Shinwon , Lee Sun Hee , Jung Younghee , Bang Ji Hwan , Cheon Shinhye , Kwak Yee Gyung , Kang Yu Min , Park Kyung-Hwa , Song Kyoung-Ho , Kim Hong Bin
Published: May 2022

This study aimed to evaluate the differences in clinical characteristics and impact of carbapenem resistance (CR) on outcomes between Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa) bacteraemia. We prospectively identified all patients with Ab and Pa bacteraemia in 10 hospitals over 1 year. Treatment failure was defined as all-cause 30-day mortality, persistent bacteraemia, or recurrent bacteraemia within 30 days. We included 304 Ab and 241 Pa bacteraemia cases. CR was detected in 216 patients (71%) with Ab bacteraemia and 55 patients (23%) with Pa bacteraemia. Treatment failure was significantly higher in CR-Ab than in CR-Pa (60.6% vs. 34.5%, P = 0.001). In Ab, severe sepsis or septic shock and high Pitt bacteraemia score were independent risk factors for treatment failure in the inappropriate empirical antibiotics group. In Pa, hospital-acquired infection and high Pitt bacteraemia score were independent risk factors for treatment failure in both groups. CR was an independent risk factor in Ab for treatment failure in both groups, but not in Pa bacteraemia. We demonstrated significant differences in clinical characteristics and impact of CR on clinical outcomes between Ab and Pa bacteraemia, suggesting that different treatment approaches may be needed.
Multi-dimensional quantitative model of communication network value
Authors: Wu Lijuan , Gan Chaoqin , Xu Zhongsen , Hui Jianqiang
Published: May 2022

In this paper, a multi-dimensional quantitative model is firstly founded for evaluating communication network value, and the quantification of the abstract concept of network value is realized. By analyzing various factors that influence the evaluation of network value from multiple perspectives, an index system of multi-dimensional network value evaluation is established. By adopting the analytic hierarchy process (AHP) method, not only the weight of each dimension is reasonably determined, but also the weight of different indicators in the second dimension is determined. By the characteristics of each dimension and its weight in the evaluation system, a multi-dimensional quantitative model for evaluating communication network value is constructed. By analyzing the value of Ethernet passive optical network (EPON), the rationality of the proposed quantitative model is demonstrated.
Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK
Authors: Waites William , Pearson Carl A. B. , Gaskell Katherine M. , House Thomas , Pellis Lorenzo , Johnson Marina , Gould Victoria , Hunt Adam , Stone Neil R. H. , Kasstan Ben , Chantler Tracey , Lal Sham , Roberts Chrissy H. , Goldblatt David ,   CMMID COVID-19 Working Group, Abbas Kaja , Abbott Sam , Atkins Katherine E. , Barnard Rosanna C. , Bosse Nikos I. , Brady Oliver , Chan Yung-Wai Desmond , Chapman Lloyd A. C. , Clifford Samuel , Davies Nicholas G. , Edmunds W. John , Eggo Rosalind M. , Endo Akira , Finch Emilie , Flasche Stefan , Foss Anna M. , Funk Sebastian , Gibbs Hamish P. , Gimma Amy , Hellewell Joel , Hodgson David , Hué Stéphane , Jafari Yalda , Jarvis Christopher I. , Jit Mark , Jombart Thibaut , Klepac Petra , Knight Gwenan M. , Koltai Mihaly , Krauer Fabienne , Kucharski Adam J. , Liu Yang , Lowe Rachel , McCarthy Ciara V. , Meakin Sophie R. , Medley Graham , Mee Paul , Munday James D. , Nightingale Emily S. , O’Reilly Kathleen , Pearson Carl A. B. , Prem Kiesha , Procter Simon R. , Pung Rachael , Quaife Matthew , Quilty Billy J. , Rosello Alicia , Russell Timothy W. , Sandmann Frank G. , Sun Fiona Yueqian , Tully Damien C. , Villabona-Arenas C. Julian , Waites William , Waterlow Naomi R. , Wong Kerry L. M. , van Zandvoort Kevin , Marks Michael , Eggo Rosalind M.
Published: May 2022

Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.
Corticotropin releasing hormone as an identifier of bronchiolitis obliterans syndrome
Authors: Niroomand Anna , Ghaidan Haider , Hallgren Oskar , Hansson Lennart , Larsson Hillevi , Wagner Darcy , Mackova Martina , Halloran Kieran , Hyllén Snejana , Lindstedt Sandra
Published: May 2022

Lung transplantion (LTx) recipients have low long-term survival and a high incidence of bronchiolitis obliterans syndrome (BOS), an inflammation of the small airways in chronic rejection of a lung allograft. There is great clinical need for a minimally invasive biomarker of BOS. Here, 644 different proteins were analyzed to detect biomarkers that distinguish BOS grade 0 from grades 1–3. The plasma of 46 double lung transplant patients was analyzed for proteins using a high-component, multiplex immunoassay that enables analysis of protein biomarkers. Proximity Extension Assay (PEA) consists of antibody probe pairs which bind to targets. The resulting polymerase chain reaction (PCR) reporter sequence can be quantified by real-time PCR. Samples were collected at baseline and 1-year post transplantation. Enzyme-linked immunosorbent assay (ELISA) was used to validate the findings of the PEA analysis across both time points and microarray datasets from other lung transplantation centers demonstrated the same findings. Significant decreases in the plasma protein levels of CRH, FERC2, IL-20RA, TNFB, and IGSF3 and an increase in MMP-9 and CTSL1 were seen in patients who developed BOS compared to those who did not. In this study, CRH is presented as a novel potential biomarker in the progression of disease because of its decreased levels in patients across all BOS grades. Additionally, biomarkers involving the remodeling of the extracellular matrix (ECM), such as MMP-9 and CTSL1, were increased in BOS patients.
Klotho expression in peripheral blood circulating cells is associated with vascular and systemic inflammation in atherosclerotic vascular disease
Authors: Martín-Núñez Ernesto , Pérez-Castro Atteneri , Tagua Víctor G. , Hernández-Carballo Carolina , Ferri Carla , Pérez-Delgado Nayra , Rodríguez-Ramos Sergio , Cerro-López Purificación , López-Castillo Ángel , Delgado-Molinos Alejandro , López-Tarruella Victoria Castro , Arévalo-Gómez Miguel A. , González-Luis Ainhoa , Martín-Olivera Alberto , Morales-Estévez Carmen Chaxiraxi , Mora-Fernández Carmen , Donate-Correa Javier , Navarro-González Juan F.
Published: May 2022

Cardiovascular disease is the leading cause of death worldwide. New therapeutic strategies are aimed to modulate the athero-inflammatory process that partially orchestrates underlying vascular damage. Peripheral blood circulating cells include different immune cells with a central role in the development of the atherogenic inflammatory response. The anti-aging protein α-Klotho has been related to protective effects against CVD. KL is expressed in monocytes, macrophages, and lymphocytes where it exerts anti-inflammatory effects. In this work, we analyse the relationships of the levels of inflammatory markers with the expression of the KL gene in PBCCs and with the serum levels of soluble KL in atherosclerotic vascular disease. For this, we conducted a cross-sectional single-center case–control study including a study group of 76 CVD patients and a control group of 16 cadaveric organ donors without medical antecedent or study indicating CVD. Vascular artery fragments and whole blood and serum samples were obtained during elective or organ retrieval surgery. Serum levels of sKL, TNFα and IL10, and gene expression levels of KL, TNF, IL10, NFKB1, DNMT1, and DNMT3A in PBCCs were measured. In these cells, we also determined KL promoter methylation percentage. Histological and immunohistochemical analyses were employed to visualize atherosclerotic lesions and to measure IL10 and TNFα levels in vascular fragments. Patients with CVD presented higher values of proinflammatory markers both at systemic and in the vasculature and in the PBCCs, compared to the control group. In PBCCs, CVD patients also presented lower gene expression levels of KL gene (56.4% difference, P < 0.001), higher gene expression levels of DNMT1 and DNMT3A (P < 0.0001, for both) and a higher methylation status of in the promoter region of KL (34.1 ± 4.1% vs. 14.6 ± 3.4%, P < 0.01). In PBCCs and vasculature, KL gene expression correlated inversely with pro-inflammatory markers and directly with anti-inflammatory markers. sKL serum levels presented similar associations with the expression levels of pro- and anti-inflammatory markers in PBCCs. The differences in KL expression levels in PBCCs and in serum sKL levels with respect to control group was even greater in those CVD patients with macroscopically observable atheromatous plaques. We conclude that promoter methylation-mediated downregulation of KL gene expression in PBCCs is associated with the pro-inflammatory status in atherosclerotic vascular disease.
Women in gig economy work less in the evenings
Authors: Dokuka Sofia , Kapuza Anastasia , Sverdlov Mikhail , Yalov Timofey
Published: May 2022

Women have been systematically disadvantaged in the labour market. This could be explained by a complex association of factors, such as the lower speed of women’s professional growth within companies, their under-representation in management positions, and the unequal distribution of caregiving and housework between men and women. The rise of the gig economy—a market system that is based on hiring independent contractors and freelance workers as opposed to creating full-time contracts—has brought researchers and policymakers into a discussion on the effects of online platforms and flexible work arrangements on labour market gender parity. In this study, we examine the case of the largest online English-language school in Eastern Europe, Skyeng. Data on 6,461,404 lessons given by 13,571 teachers demonstrate that women had fewer working hours than men in most age categories, but especially for ages 30–35. The workload deficit for the women could be partly attributed to the fact that they worked less often than the men did in the evenings (7–10 p.m.). We conclude that, despite the flexible work arrangements the gig economy has offered, the women taught fewer classes than the men (i.e., having fewer paid working hours), which in turn led to a gender pay gap. The rapid growth of the gig economy makes it important to monitor gender-gap dynamics as well as discuss potential mechanisms eliminating gender inequality in the labour market.
Pilot study of factors contributing to canine impaction after secondary alveolar bone grafting in unilateral cleft lip and palate patients
Authors: Tsurumi Yoko , Nishimura Kazuaki , Shimizu Megumi , Imai Yoshimichi , Igarashi Kaoru
Published: May 2022

Alveolar bone grafting (ABG) is broadly performed for cleft lip and palate patients. The rate of canine impaction post-ABG is much higher than the prevalence of canine impaction in non-cleft patients. This pilot study was designed to investigate factors involved in canine eruption failure after ABG and to predict the possibility of canine impaction in unilateral cleft lip and palate (UCLP) patients. This retrospective observational study examined 45 patients with UCLP (mean age 7.9 years) classified into an impacted group (n = 9) and a spontaneously erupted group (n = 36). From 3D images, we measured lateral incisor presence or absence, lateral incisor position on the cleft side, canine position, movement change, cleft volume, and canine and first premolar overlap-area. Multivariate logistic regression analysis using independent variables indicated significant differences in results, selecting highly relevant items. Multivariate analysis indicated a significant association between the overlap-area between the canine and the first premolar at pre-ABG (p = 0.038) and the distance between the cleft side cusp tips of canine and the lateral cleft margin of pre-ABG (p = 0.005). Results suggest that canine impaction is predictable at an early stage in pre-ABG and show the possibility of comprehensive diagnosis of canine impaction using computed tomography.
Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
Authors: Parteka-Tojek Zofia , Zhu Jacqueline Jufen , Lee Byoungkoo , Jodkowska Karolina , Wang Ping , Aaron Jesse , Chew Teng-Leong , Banecki Krzysztof , Plewczynski Dariusz , Ruan Yijun
Published: May 2022

The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
Prognostic modeling of predictive maintenance with survival analysis for mobile work equipment
Authors: Yang Zhen , Kanniainen Juho , Krogerus Tomi , Emmert-Streib Frank
Published: May 2022

In recent years there is a data surge of industrial and business data. This posses opportunities and challenges at the same time because the wealth of information is usually buried in complex and frequently disconnected data sets. Predictive maintenance utilizes such data for developing prognostic and diagnostic models that allow the optimization of the life cycle of machine components. In this paper, we address the modeling of the prognostics of machine components from mobile work equipment. Specifically, we are estimating survival curves and hazard rates using parametric and non-parametric models to characterize time dependent failure probabilities of machine components. As a result, we find the presence of different types of censoring masking the presence of different populations that can cause severe problems for statistical estimators and the interpretations of results. Furthermore, we show that the obtained hazard functions for different machine components are complex and versatile and are best modeled via non-parametric estimators. However, notable exceptions for individual machine components can be found amenable for a Generalized-gamma and Weibull model.
Design of highly perceptible dual-resonance all-dielectric metasurface colorimetric sensor via deep neural networks
Authors: Son Hyunwoo , Kim Sun-Je , Hong Jongwoo , Sung Jangwoon , Lee Byoungho
Published: May 2022

Colorimetric sensing, which provides effective detection of bio-molecular signals with one’s naked eye, is an exceptionally promising sensing technique in that it enables convenient detection and simplification of entire sensing system. Though colorimetric sensors based on all-dielectric nanostructures have potential to exhibit distinct color variations enabling manageable detection due to their trivial intrinsic loss, there is crucial limitation that the sensitivity to environmental changes lags behind their plasmonic counterparts because of relatively small region of near field-analyte interaction of the dielectric Mie-type resonator. To overcome this challenge, we proposed all-dielectric metasurface colorimetric sensor which exhibits dual-resonance in the visible region. Thereafter, we confirmed with simulation that, in the elaborately designed dual-Lorentzian-type spectra, highly perceptible variations of structural color were manifested even in minute change of peripheral refractive index. In addition to verifying physical effectiveness of the superior colorimetric sensing performance appearing in the dual-resonance type sensor, by combining advanced optimization technique utilizing deep neural networks, we attempted to maximize sensing performance while obtaining dramatic improvement of design efficiency. Through well-trained deep neural network that accurately simulates the input target spectrum, we numerically verified that designed colorimetric sensor shows a remarkable sensing resolution distinguishable up to change of refractive index of 0.0086.
Initial TK-deficient HSV-1 infection in the lip alters contralateral lip challenge immune dynamics
Authors: Rousseau Antoine , Haigh Oscar , Legrand Roger , Palgen Jean-Louis , Lemaitre Julien , Deback Claire , Oziol Noémie , Lomonte Patrick , Labetoulle Marc
Published: May 2022

Primary infection with herpes simplex type 1 (HSV-1) occurring around the mouth and nose switches rapidly to lifelong latent infection in sensitive trigeminal ganglia (TG) neurons. Sporadic reactivation of these latent reservoirs later in life is the cause of acute infections of the corneal epithelium, which can cause potentially blinding herpes simplex keratitis (HSK). There is no effective vaccine to protect against HSK, and antiviral drugs provide only partial protection against recurrences. We previously engendered an acute disease-free, non-reactivating latent state in mice when challenged with virulent HSV-1 in orofacial mucosa, by priming with non-neurovirulent HSV-1 (TKdel) before the challenge. Herein, we define the local immune infiltration and inflammatory chemokine production changes after virulent HSV-1 challenge, which were elicited by TKdelprime. Heightened immunosurveillance before virulent challenge, and early enhanced lymphocyte-enriched infiltration of the challenged lip were induced, which corresponded to attenuation of inflammation in the TG and enhanced viral control. Furthermore, classical latent-phase T cell persistence around latent HSV-1 reservoirs were severely reduced. These findings identify the immune processes that are likely to be responsible for establishing non-reactivating latent HSV-1 reservoirs. Stopping reactivation is essential for development of efficient vaccine strategies against HSV-1.
ILDR1 promotes influenza A virus replication through binding to PLSCR1
Authors: Liu Yueyue , Lin Shuqian , Xie Yunhui , Zhao Lu , Du Haibo , Yang Shifa , Yin Bin , Li Guiming , Zhao Zengcheng , Huang Zhongli , Xu Zhigang , Wu Jiaqiang
Published: May 2022

As a natural antiviral regulator, phospholipid scramblase 1 (PLSCR1) has been shown to inhibit influenza virus replication in infected cells through interacting with NP of influenza A virus (IAV). But its antiviral function as well as the underlying regulatory mechanism has not been examined in vivo. In the present work, we show that PLSCR1 expression is decreased in H1N1 SIV-infected mice, and Plscr1−/− mice are more susceptible to H1N1 SIV infection. By performing yeast two-hybrid screening, we identified immunoglobulin-like domain-containing receptor 1 (ILDR1) as a novel PLSCR1-binding partner. ILDR1 is highly expressed in the lungs, and its expression level is increased after virus infection. Interestingly, ILDR1 could not directly interact with virus NP protein, but could combine with PLSCR1 competitively. Our data indicates that there is a previously unidentified PLSCR1-ILDR1-NP regulatory pathway playing a vital role in limiting IAV infection, which provides novel insights into IAV-host interactions.