bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species
Authors: Overbeeke Annelieke , Hausmann Bela , Nikolov Georgi , Pereira Fatima C. , Herbold Craig W. , Berry David 
Published: November 2022

IntroductionGlycosaminoglycans (GAGs) present in the mucosal layer can be used as nutrients by certain intestinal bacteria, particularly members of the Bacteroides. GAG abundances are altered in some diseases such as inflammatory bowel diseases, which may affect microbial composition and activity, and it is therefore important to understand GAG utilization by members of the gut microbiota.MethodsWe used growth assays, transcriptomics, and comparative genomics to evaluate chondroitin sulfate (CS) and hyaluronan (HA) degradation ability by multiple gut Bacteroides species.Results and discussionWe found that not all Bacteroides species able to degrade CS could also degrade HA, despite having lyases which act on both compounds. We propose that in the model organism Bacteroides thetaiotaomicron, the lyase BT_3328 in combination with surface binding proteins BT_3329 and BT_3330 and potentially BT_4411 are involved in HA breakdown. Furthermore, degradation of both compounds provides public goods for other Bacteroides, including non-degraders, suggesting that cooperative degradation as well as cross-feeding may be widespread in the mucosal glycan utilization clade.
Seed endophytic ammonia oxidizing bacteria in Elymus nutans transmit to offspring plants and contribute to nitrification in the root zone
Authors: Liang Danni , Bowatte Saman 
Published: November 2022

BackgroundAmmonia oxidizing bacteria (AOB) in soil are of great biological importance as they regulate the cycling of N in agroecosystems. Plants are known to harbor AOB but how they occupy the plant is an unresolved question.MethodsMetabarcoding studies were carried out using Illumina MiSeq sequencing to test the potential of seed vectored AOB exchange between plants and soil.Results and discussionWe found 27 sequences associated with AOB strains belonging to the genera Nitrosospira, Nitrosovibrio, and Nitrosomonas inhabiting Elymus nutans seeds collected from four geographically distanced alpine meadows. Nitrosospira multiformis was the most dominant across the four locations. The AOB community in E. nutans seeds was compared with that of the leaves, roots and soil in one location. Soil and seeds harbored a rich but dissimilar AOB community, and Nitrosospira sp. PJA1, Nitrosospira sp. Nsp17 and Nitrosovibrio sp. RY3C were present in all plant parts and soils. When E. nutans seeds were germinated in sterilized growth medium under greenhouse conditions, the AOB in seeds later appeared in leaves, roots and growth medium, and contributed to nitrification. Testing the AOB community of the second-generation seeds confirmed vertical transmission, but low richness was observed.ConclusionThese results suggest seed vectored AOB may play a critical role in N cycle.
Predicting AT(N) pathologies in Alzheimer’s disease from blood-based proteomic data using neural networks
Authors: Zhang Yuting , Ghose Upamanyu , Buckley Noel J. , Engelborghs Sebastiaan , Sleegers Kristel , Frisoni Giovanni B. , Wallin Anders , Lleó Alberto , Popp Julius , Martinez-Lage Pablo , Legido-Quigley Cristina , Barkhof Frederik , Zetterberg Henrik , Visser Pieter Jelle , Bertram Lars , Lovestone Simon , Nevado-Holgado Alejo J. , Shi Liu 
Published: November 2022

Background and objectiveBlood-based biomarkers represent a promising approach to help identify early Alzheimer’s disease (AD). Previous research has applied traditional machine learning (ML) to analyze plasma omics data and search for potential biomarkers, but the most modern ML methods based on deep learning has however been scarcely explored. In the current study, we aim to harness the power of state-of-the-art deep learning neural networks (NNs) to identify plasma proteins that predict amyloid, tau, and neurodegeneration (AT[N]) pathologies in AD.MethodsWe measured 3,635 proteins using SOMAscan in 881 participants from the European Medical Information Framework for AD Multimodal Biomarker Discovery study (EMIF-AD MBD). Participants underwent measurements of brain amyloid β (Aβ) burden, phosphorylated tau (p-tau) burden, and total tau (t-tau) burden to determine their AT(N) statuses. We ranked proteins by their association with Aβ, p-tau, t-tau, and AT(N), and fed the top 100 proteins along with age and apolipoprotein E (APOE) status into NN classifiers as input features to predict these four outcomes relevant to AD. We compared NN performance of using proteins, age, and APOE genotype with performance of using age and APOE status alone to identify protein panels that optimally improved the prediction over these main risk factors. Proteins that improved the prediction for each outcome were aggregated and nominated for pathway enrichment and protein–protein interaction enrichment analysis.ResultsAge and APOE alone predicted Aβ, p-tau, t-tau, and AT(N) burden with area under the curve (AUC) scores of 0.748, 0.662, 0.710, and 0.795. The addition of proteins significantly improved AUCs to 0.782, 0.674, 0.734, and 0.831, respectively. The identified proteins were enriched in five clusters of AD-associated pathways including human immunodeficiency virus 1 infection, p53 signaling pathway, and phosphoinositide-3-kinase–protein kinase B/Akt signaling pathway.ConclusionCombined with age and APOE genotype, the proteins identified have the potential to serve as blood-based biomarkers for AD and await validation in future studies. While the NNs did not achieve better scores than the support vector machine model used in our previous study, their performances were likely limited by small sample size.
Disrupted visual input unveils the computational details of artificial neural networks for face perception
Authors: Li Yi-Fan , Ying Haojiang 
Published: November 2022

BackgroundConvolutional Neural Network (DCNN), with its great performance, has attracted attention of researchers from many disciplines. The studies of the DCNN and that of biological neural systems have inspired each other reciprocally. The brain-inspired neural networks not only achieve great performance but also serve as a computational model of biological neural systems.MethodsHere in this study, we trained and tested several typical DCNNs (AlexNet, VGG11, VGG13, VGG16, DenseNet, MobileNet, and EfficientNet) with a face ethnicity categorization task for experiment 1, and an emotion categorization task for experiment 2. We measured the performance of DCNNs by testing them with original and lossy visual inputs (various kinds of image occlusion) and compared their performance with human participants. Moreover, the class activation map (CAM) method allowed us to visualize the foci of the “attention” of these DCNNs.ResultsThe results suggested that the VGG13 performed the best: Its performance closely resembled human participants in terms of psychophysics measurements, it utilized similar areas of visual inputs as humans, and it had the most consistent performance with inputs having various kinds of impairments.DiscussionIn general, we examined the processing mechanism of DCNNs using a new paradigm and found that VGG13 might be the most human-like DCNN in this task. This study also highlighted a possible paradigm to study and develop DCNNs using human perception as a benchmark.
Face masks have a limited effect on the feeling of being looked at
Authors: Lobmaier Janek S. , Knoch Daria 
Published: November 2022

IntroductionWearing face masks has been promoted as an effective measure to reduce the spread of COVID-19. Because face masks cover a major part of the face, they have detrimental effects on various aspects of social cognition. Yet, a highly important feature of the face is not occluded by face masks: the eyes. The eyes play an important role in social interactions: knowing where another person is looking is of central importance when interacting with others. Recent research has reported an attentional shift toward the eye region as a consequence of the widespread exposure to face masks. However, no study has yet investigated the influence of face masks on the perception of eye gaze direction. Here we investigated whether face masks have an effect on the feeling of being looked at. Assuming an attentional shift toward the eyes, we might expect more accurate gaze perception in faces wearing face masks.MethodsSixty-five participants decided for a series of realistic avatar faces whether each face was making eye contact or not. Half of the faces wore face masks, the other half did not. For each participant and separately for each condition (mask vs. no mask), we calculated the cone of direct gaze (CoDG), a commonly used measure to quantify the range of gaze angles within which an observer assumes mutual gaze.ResultsContrary to our expectations, results show that mutual gaze is not recognized more accurately in masked faces. Rather, the CoDG was, on average, slightly wider for faces wearing masks compared to faces without masks.DiscussionNotwithstanding the relatively small effect of face mask, these findings potentially have implications on our social interactions. If we inadvertently feel looked at by an onlooker, we may react inappropriately by reciprocating the alleged approach orientation.
Mutations matter: An observational study of the prognostic and predictive value of KRAS mutations in metastatic colorectal cancer
Authors: Lavacchi Daniele , Fancelli Sara , Roviello Giandomenico , Castiglione Francesca , Caliman Enrico , Rossi Gemma , Venturini Jacopo , Pellegrini Elisa , Brugia Marco , Vannini Agnese , Bartoli Caterina , Cianchi Fabio , Pillozzi Serena , Antonuzzo Lorenzo 
Published: November 2022

BackgroundAbout half of metastatic colorectal cancers (CRCs) harbor Rat Sarcoma (RAS) activating mutations as oncogenic driver, but the prognostic role of RAS mutations is not fully elucidated. Interestingly, specific hotspot mutations have been identified as potential candidates for novel targeted therapies in several malignancies as per G12C. This study aims at evaluating the association between KRAS hotspot mutations and patient characteristics, prognosis and response to antiangiogenic drugs.MethodsData from RAS-mutated CRC patients referred to Careggi University Hospital, between January 2017 and April 2022 were retrospectively and prospectively collected. Tumor samples were assessed for RAS mutation status using MALDI-TOF Mass Spectrometry, Myriapod NGS-56G Onco Panel, or Myriapod NGS Cancer Panel DNA.ResultsAmong 1047 patients with available RAS mutational status, 183 KRAS-mutated patients with advanced CRC had adequate data for clinicopathological and survival analysis. KRAS mutations occurred at codon 12 in 67.2% of cases, codon 13 in 23.5%, codon 61 in 2.2%, and other codons in 8.2%. G12C mutation was identified in 7.1% of patients and exon 4 mutations in 7.1%. KRAS G12D mutation, as compared to other mutations, was significantly associated with liver metastases (1-sided p=0.005) and male sex (1-sided p=0.039), KRAS G12C mutation with peritoneal metastases (1-sided p=0.035), KRAS G12V mutation with female sex (1-sided p=0.025) and no surgery for primary tumor (1-sided p=0.005). No associations were observed between specific KRAS variants and age, ECOG PS, site of primary tumor, pattern of recurrence for resected patients, and lung, distant lymph node, bone, or brain metastases.Overall survival (OS) was significantly longer in patients with KRAS exon 4 mutations than in those with other KRAS mutations (mOS 43.6 months vs 20.6 months; HR 0.45 [0.21-0.99], p=0.04). No difference in survival was observed for mutations at codon 12/13/61 (p=0.1). Treatment with bevacizumab (BV) increased significatively mPFS (p=0.036) and mOS (p=0.019) of the entire population with a substantial benefit in mOS for G12V mutation (p=0.031).ConclusionsPatterns of presentation and prognosis among patients with specific RAS hotspot mutations deserve to be extensively studied in large datasets, with a specific attention to the uncommon isoforms and the role of anti-angiogenic drugs.
The use of carbon monoxide breath test to detect the effect of iron overload on erythrocyte lifespan in MDS
Authors: Zhang Yao , Qian Yan , Song Lu-xi , Xiao Chao , Chang Chun-kang 
Published: November 2022

ObjectiveTo investigate the effect of iron overload (IO) on red blood cell (RBC) lifespan in MDS patients with the use of carbon monoxide breath testMethodsThe red blood cell lifespan of 93 patients with myelodysplastic syndrome (MDS) and 22 healthy volunteers in the control group were measured by alveolar gas carbon monoxide (CO) assay, with the detection of liver iron concentration, iron metabolism index, erythropoietin (EPO) concentration, peripheral blood inflammatory cytokines, etc. The MDS patients were divided into the severe IO group, mild IO group and non IO group according to liver iron concentration. The effect of IO on RBC lifespan was analyzed in MDS patients.ResultsThe RBC lifespan of MDS patients in the severe IO group was significantly lower than that in the mild IO group (p&lt;0.05), while the RBC life span in the mild IO group was significantly lower than that in the non IO group (p&lt;0.05). The expression of inflammatory cytokines in the severe IO group was significantly higher than that of the mild and non IO groups. After receiving iron removal treatment(ICT), the expression of inflammatory cytokines was decreased significantly, and the RBC lifespan was significantly prolonged (p&lt;0.05).Besides, liver iron concentration was significantly positively correlated with EPO concentration, while EPO concentration was significantly negatively correlated with RBC lifespan, especially in the MDS-RS subgroup. The RBC lifespan in the EPO&gt;1000 group was significantly lower than that in the EPO&lt;1000 group.ConclusionIO can shorten RBC lifespan in MDS patients, which may be result from the increase of endogenous EPO and the over-expression of inflammatory cytokines. After ICT, the ineffective hematopoiesis caused by increased EPO may reduced and the decrease of inflammatory cytokine may significantly prolong the RBC lifespan in MDS patients.
Thermal ablation in pancreatic cancer: A scoping review of clinical studies
Authors: Farmer William , Hannon Gary , Ghosh Shubhrima , Prina-Mello Adriele 
Published: November 2022

BackgroundPancreatic cancer is a deadly cancer with a 5-year survival rate less than 10%. Only 20% of patients are eligible to receive surgery at diagnosis. Hence, new therapies are needed to improve outcomes for non-surgical candidates. Thermal ablation techniques can offer a non-invasive alternative to surgery.AimThe aim of this review is to map the literature for the use of thermal ablative techniques: Radiofrequency ablation (RFA), High-intensity focused ultrasound (HIFU), Microwave ablation (MWA), and Laser ablation (LA) in the management of patients with PC.MethodsA search strategy was applied to PUBMED and EMBASE using keywords concerning pancreatic cancer, radiofrequency ablation, ultrasound ablation, laser ablation, and microwave ablation. The studies that fit this inclusion criteria were summarized in table format and results reviewed for interpretation.Results72 clinical studies were included. Most of the included studies related to RFA (n=35) and HIFU (n=27). The most common study design was retrospective (n=33). Only 3 randomized control trials (RCT) were included, all of which related to RFA. Safety outcomes were reported in 53 of the 72 studies, and survival outcomes were reported in 39. Statistically significant survival benefits were demonstrated in 11 studies.ConclusionThe evidence for the benefit of MWA and LA in PC patients is limited. RFA and HIFU are safe and feasible therapies to be used in PC patients. Further RCTs where thermal techniques are standardized and reported are necessary in the future to elucidate thermal ablation’s clinical utility, and before an evidence-based decision on its routine use in PC management can be considered.
Development of a novel nomogram for predicting clinically significant prostate cancer with the prostate health index and multiparametric MRI
Authors: Mo Li-Cai , Zhang Xian-Jun , Zheng Hai-Hong , Huang Xiao-peng , Zheng Lin , Zhou Zhi-Rui , Wang Jia-Jia 
Published: November 2022

IntroductionOn prostate biopsy, multiparametric magnetic resonance imaging (mpMRI) and the Prostate Health Index (PHI) have allowed prediction of clinically significant prostate cancer (csPCa).MethodsTo predict the likelihood of csPCa, we created a nomogram based on a multivariate model that included PHI and mpMRI. We assessed 315 males who were scheduled for prostate biopsies.ResultsWe used the Prostate Imaging Reporting and Data System version 2 (PI-RADS V2) to assess mpMRI and optimize PHI testing prior to biopsy. Univariate analysis showed that csPCa may be identified by PHI with a cut-off value of 77.77, PHID with 2.36, and PI-RADS with 3 as the best threshold. Multivariable logistic models for predicting csPCa were developed using PI-RADS, free PSA (fPSA), PHI, and prostate volume. A multivariate model that included PI-RADS, fPSA, PHI, and prostate volume had the best accuracy (AUC: 0.882). Decision curve analysis (DCA), which was carried out to verify the nomogram’s clinical applicability, showed an ideal advantage (13.35% higher than the model that include PI-RADS only).DiscussionIn conclusion, the nomogram based on PHI and mpMRI is a valuable tool for predicting csPCa while avoiding unnecessary biopsy as much as possible.
Added survival benefit of whole brain radiotherapy in brain metastatic non-small cell lung cancer: Development and external validation of an individual prediction model
Authors: Trikhirhisthit Kyrhatii , Setakornnukul Jiraporn , Thephamongkhol Kullathorn 
Published: November 2022

BackgroundThe heterogeneous survival benefit of whole brain radiotherapy (WBRT) in brain metastatic non-small cell lung cancer (NSCLC) was prospectively evidenced in the Quality of Life after Treatment for Brain Metastases (QUARTZ) trial, resulting in inconsistent guideline recommendations and diverse clinical practices for giving WBRT. The objective of this study was to develop and externally validate an individual prediction model to demonstrate the added survival benefit of WBRT to assist decision making when giving WBRT is undetermined.MethodsFor model development, we collected 479 brain metastatic NSCLC patients unfit for surgery or stereotactic radiotherapy techniques at Siriraj Hospital. Potential predictors were age, sex, performance status, histology, genetic mutation, neurological symptoms, extracranial disease, previous systemic treatment, measurable lesions, further systemic treatment, and WBRT. Cox proportional hazard regression was used for survival analysis. We used multiple imputations to handle missing data and a backward selection method for predictor selection. Bootstrapping was used for internal validation, while model performance was assessed with discrimination (c-index) and calibration prediction accuracy. The final model was transformed into a nomogram and a web-based calculator. An independent cohort from Sawanpracharak Hospital was used for external validation.ResultsIn total, 452 patients in the development cohort died. The median survival time was 4.4 (95% CI, 3.8–4.9) months, with 5.1 months for patients who received WBRT and 2.3 months for those treated with optimal supportive care (OSC). The final model contained favorable predictors: female sex, KPS &gt; 70, receiving additional systemic treatment, and WBRT. Having active extracranial disease, experiencing neurological symptoms, and receiving previous systemic treatment were adverse predictors. After optimism correction, the apparent c-index dropped from 0.71 (95% CI, 0.69–0.74) to 0.70 (95% CI, 0.69–0.73). The predicted and observed values agreed well in all risk groups. Our model performed well in the external validation cohort, with a c-index of 0.66 (95% CI, 0.59–0.73) and an acceptable calibration.ConclusionsThis model (https://siriraj-brainmetscore.netlify.app/) predicted the added survival benefit of WBRT for individual brain metastatic NSCLC patients, with satisfactory performance in the development and validation cohorts. The results certify its value in aiding treatment decision-making when the administration of WBRT is unclear.
Socio-economic and ethnocultural influences on geographical disparities in breast cancer screening participation in Victoria, Australia
Authors: Stuart Geoffrey W. , Chamberlain James A. , Milne Roger L. 
Published: November 2022

ObjectiveTo examine the socio-economic and ethnocultural characteristics of geographical areas that may influence variation in breast cancer screening participation.MethodsIn a cross-sectional analysis breast cancer screening participation for statistical areas in Victoria, Australia (2015-2017) was linked with data from the 2016 Australian Census. We selected four commonly used area-level measures of socio-economic status from the Australian Census (i) income (ii) educational level (iii) occupational status and (iv) employment profile. To assess the ethnocultural characteristics of statistical areas we used the Census measures (i) country of birth (ii) language spoken at home (iii) fluency in English (iv) religion and (v) the proportion of immigrants in an area, together with their recency of migration.ResultsAll the selected measures were related to screening participation. There was a high degree of association both within and between socio-economic and ethnocultural characteristics of areas as they relate to screening. Ethnocultural characteristics alone accounted for most of the explained geographical disparity in screening participation.ConclusionsGeographical disparities in breast cancer screening participation may be due to ethnocultural factors that are confounded with socio-economic factors.
Visual Acuity alterations in heavily impaired Congenital Zika Syndrome (CZS) children
Authors: Baran Luiz C. P. , Lima Diego da S. , Silva Leonardo A. , Tabares Heydi S. , Dias Sarah L. , Zin Andrea Araújo , Moreira Maria E. L. , da Costa Marcelo F. , Ventura Dora F. 
Published: November 2022

IntroductionThis study aimed to assess visual acuity (VA) in Congenital Zika Syndrome (CZS)-children to evaluate visual loss. To that end we evaluated 41 CZS - children, from Rio de Janeiro using Teller Acuity Cards.MethodsTo asses VA, we evaluated 41 CZS - children, from Rio de Janeiro using Teller Acuity Cards. The children had Zika virus-infection confirmed by reverse transcription–polymerase chain reaction (RT-PCR) or clinical evaluation.ResultsIn 39 out of 41 (95%) children, the VA scores were below normative values, while in 10 cases, VA was only marginally below normal; in the remaining 29 cases, VA was more than 0.15 logMAR below the lower limit. There was no correlation between VA and the cognitive domain tasks, although there was a correlation between VA and motor domain tasks. Thirty-seven children performed at least one task in the cognitive set, while fourteen children did not perform any task in the motor set. Children with VA above the lower limit performed better in the cognitive and motor tasks.DiscussionWe concluded that ZIKV- infected children with CZS were highly VA impaired which correlated with motor performance, but not with cognitive performance. Part of the children had VA within the normal limits and displayed better performance in the cognitive and motor sets. Therefore, even if heavily impaired, most children had some degree of VA and visual function.